@article {19691, title = {Discovering Pronoun Categories using Discourse Information}, journal = {Proceedings of the 35th Annual Conference of the Cognitive Science Society}, year = {Submitted}, abstract = {Abstract Interpretation of a pronoun is driven by properties of syntactic distribution. Consequently, acquiring the meaning and the distribution are intertwined. In order to learn that a pronoun is reflexive, learners need to know which entity the pronoun refers to in a ...}, url = {http://ling.umd.edu/~naho/orita_cogsci2013.pdf}, author = {McKeown, R and Feldman, N H and Lidz, J and Jordan Boyd-Graber} } @article {19692, title = {Evaluating Regularized Anchor Words}, journal = {mimno.infosci.cornell.edu}, year = {Submitted}, abstract = {Abstract We perform a comprehensive examination of the recently proposed anchor method for topic model inference using topic interpretability and held-out likelihood measures. After measuring the sensitivity to the anchor selection process, we incorporate L2 and Beta ...}, url = {http://mimno.infosci.cornell.edu/nips2013ws/nips2013tm_submission_27.pdf}, author = {Nguyen, T and Hu, Y and Jordan Boyd-Graber} } @article {19690, title = {Topic Models for Translation Domain Adaptation}, journal = {mimno.infosci.cornell.edu}, year = {Submitted}, abstract = {Abstract Topic models have been successfully applied in domain adaptation for translation models. However, previous works applied topic models only on source side and ignored the relations between source and target languages in machine translation. This paper ...}, url = {http://mimno.infosci.cornell.edu/nips2013ws/nips2013tm_submission_19.pdf}, author = {Hu, Y and Zhai, K and Edelman, V and Jordan Boyd-Graber} } @article {19693, title = {Tree-based Label Dependency Topic Models}, journal = {cs.umd.edu}, year = {Submitted}, abstract = {Abstract Multi-labeled corpora, where each document is tagged with a set of labels, are ubiquitous. When the number of unique labels in the dataset is large, there are naturally some dependencies among the labels. In this paper, we propose TREELAD{\textemdash}a ...}, url = {http://www.cs.umd.edu/~vietan/2013_l2h.pdf}, author = {Nguyen, V A and Jordan Boyd-Graber and Chang, J and Resnik, P} } @article {20548, title = {Rapid, quantitative therapeutic screening for Alzheimer{\textquoteright}s enzymes enabled by optimal signal transduction with transistors}, journal = {The Analyst}, volume = {145}, year = {2020}, month = {Feb-04-2021}, pages = {2925 - 2936}, issn = {0003-2654}, doi = {10.1039/C9AN01804B}, url = {http://xlink.rsc.org/?DOI=C9AN01804Bhttp://pubs.rsc.org/en/content/articlepdf/2020/AN/C9AN01804Bhttp://pubs.rsc.org/en/content/articlepdf/2020/AN/C9AN01804B}, author = {Le, Son T. and Morris, Michelle A. and Cardone, Antonio and Guros, Nicholas B. and Klauda, Jeffery B. and Sperling, Brent A. and Richter, Curt A. and Pant, Harish C. and Balijepalli, Arvind} } @article {20391, title = {Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children}, journal = {Journal of Oral Microbiology}, year = {2019}, month = {12/2018}, pages = {1557986}, abstract = {Studies of the microbiome associated with dental caries have largely relied on 16S rRNA sequence analysis, which is associated with PCR biases, low taxonomic resolution, and inability to accurately study functions. Here, we employed whole metagenome shotgun sequencing, coupled with high-resolution analysis algorithm, to analyze supragingival microbiomes from 30 children with or without dental caries. A total of 726 bacterial strains belonging to 406 species, in addition to 34 bacteriophages were identified. A core bacteriome was identified at the species and strain levels. Species of Prevotella, Veillonella, as yet unnamed Actinomyces, and Atopobium showed strongest association with caries; Streptococcus sp. AS14 and Leptotrichia sp. Oral taxon 225, among others, were overabundant in caries-free. For several species, the association was strain-specific. Furthermore, for some species, e.g. Streptococcus mitis and Streptococcus sanguinis, sister strains showed differential associations. Noteworthy, associations were also identified for phages: Streptococcus phage M102 with caries and Haemophilus phage HP1 with caries-free. Functionally, potentially relevant features were identified including urate, vitamin K2, and polyamine biosynthesis in association with caries; and three deiminases and lactate dehydrogenase with health. The results demonstrate new associations between the microbiome and dental caries at the strain and functional levels that need further investigation.}, doi = {10.1080/20002297.2018.1557986}, url = {https://www.tandfonline.com/doi/full/10.1080/20002297.2018.1557986}, author = {Al-Hebshi, Nezar Noor and Baraniya, Divyashri and Chen, Tsute and Hill, Jennifer and Puri, Sumant and Tellez, Marisol and Hassan, Nur A. and Rita R Colwell and Ismail, Amid} } @article {20449, title = {Quantum Capacitance-Limited MoS2 Biosensors Enable Remote Label-Free Enzyme Measurements}, journal = {Nanoscale}, year = {2019}, month = {Jan-01-2019}, issn = {2040-3364}, doi = {10.1039/C9NR03171E}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2019/NR/C9NR03171Ehttp://pubs.rsc.org/en/content/articlepdf/2019/NR/C9NR03171E}, author = {Le, Son T and Guros, Nicholas B and Bruce, Robert C and Cardone, Antonio and Amin, Niranjana D and Zhang, Siyuan and Klauda, Jeffery and Pant, Harish C and Richter, Curt A and Balijepalli, Arvind} } @article {20293, title = {Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments}, journal = {Frontiers in Microbiology}, year = {2018}, month = {Jan-06-2020}, doi = {10.3389/fmicb.2018.01361}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.01361/full}, author = {Hourigan, Suchitra K. and Subramanian, Poorani and Hasan, Nur A. and Ta, Allison and Klein, Elisabeth and Chettout, Nassim and Huddleston, Kathi and Deopujari, Varsha and Levy, Shira and Baveja, R and Clemency, Nicole C. and Baker, Robin L. and Niederhuber, John E. and Rita R Colwell} } @conference {20251, title = {Interpolation-Based Gray-Level Co-Occurrence Matrix Computation for Texture Directionality Estimation}, booktitle = {IEEE 22nd Signal Processing Algorithms, Architectures, Arrangements, and Applications Conference}, year = {2018}, month = {12/06/2018}, publisher = {IEEE}, organization = {IEEE}, address = {Poznan, Poland}, abstract = {A novel interpolation-based model for the computation of the Gray Level Co-occurrence Matrix (GLCM) is presented. The model enables GLCM computation for any real valued angles and offsets, as opposed to the traditional, lattice-based model. A texture directionality estimation algorithm is defined using the GLCM-derived correlation feature. The robustness of the algorithm with respect to image blur and additive Gaussian noise is evaluated. It is concluded that directionality estimation is robust to image blur and low noise levels. For high noise levels, the mean error increases but remains bounded. The performance of the directionality estimation algorithm is illustrated on fluorescence microscopy images of fibroblast cells. The algorithm was implemented in C++ and the source code is available in an openly accessible repository.}, isbn = { 978-8-3620-6533-2}, doi = {10.23919/SPA.2018.8563413 }, url = {https://ieeexplore.ieee.org/document/8563413}, author = {Marcin Kociolek and Mary Brady and Peter Bajcsy and Cardone, Antonio} } @article {20299, title = {Occurrence of Vibrio cholerae in water reservoirs of Burkina Faso}, journal = {Research in Microbiology}, volume = {169}, year = {2018}, month = {Jan-01-2018}, pages = {1 - 10}, abstract = {Africa is currently an important region in which cholera epidemics occur. Little is known about the presence of Vibrio cholerae in freshwater bodies in Africa. There are ca. 1700 lakes and reservoirs in Burkina Faso, most of which have been built within recent decades to secure water resources. The purpose of this study was to investigate the presence of V. cholerae in the water of reservoirs, using the most-probable-number polymerase chain reaction. Results showed that V. cholerae could be detected in water samples collected from 14 of 39 sampled reservoirs. The concentrations varied from 0 MPN/l to more than 1100 MPN/l. Fifty strains of V. cholerae isolated on CHROMagar{\texttrademark} vibrio were identified as V. cholerae non-O1/non-O139, none of which carried the ctxA gene. A significant positive correlation was found between the presence of V. cholerae in the reservoirs and both alkaline pH and phytoplankton biomass. V. cholerae was present in significantly higher numbers in reservoirs of urban areas than in rural areas. Since V. cholerae non-O1/non-O139 has been shown to be a causative agent of endemic diarrheal outbreaks, their presence in Burkina Faso reservoirs suggests they may play a role in gastroenteritis in that country.}, issn = {09232508}, doi = {10.1016/j.resmic.2017.08.004}, url = {https://www.sciencedirect.com/science/article/pii/S092325081730147X?via\%3Dihub}, author = {Kabor{\'e}, Saidou and Cecchi, Philippe and Mosser, Thomas and Toubiana, Myl{\`e}ne and Traor{\'e}, Oumar and Ouattara, Aboubakar S. and Traor{\'e}, Alfred S. and Barro, Nicolas and Rita R Colwell and Monfort, Patrick} } @article {20290, title = {Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)}, journal = {Biological Reviews}, year = {2018}, month = {Jan-11-2018}, pages = {1813 - 1831}, abstract = {Environmentally transmitted diseases are comparatively poorly understood and managed, and their ecology is particularly understudied. Here we identify challenges of studying environmental transmission and persistence with a six-sided interdisciplinary review of the biology of anthrax (Bacillus anthracis). Anthrax is a zoonotic disease capable of maintaining infectious spore banks in soil for decades (or even potentially centuries), and the mechanisms of its environmental persistence have been the topic of significant research and controversy. Where anthrax is endemic, it plays an important ecological role, shaping the dynamics of entire herbivore communities. The complex eco-epidemiology of anthrax, and the mysterious biology of Bacillus anthracis during its environmental stage, have necessitated an interdisciplinary approach to pathogen research. Here, we illustrate different disciplinary perspectives through key advances made by researchers working in Etosha National Park, a long-term ecological research site in Namibia that has exemplified the complexities of the enzootic process of anthrax over decades of surveillance. In Etosha, the role of scavengers and alternative routes (waterborne transmission and flies) has proved unimportant relative to the long-term persistence of anthrax spores in soil and their infection of herbivore hosts. Carcass deposition facilitates green-ups of vegetation to attract herbivores, potentially facilitated by the role of anthrax spores in the rhizosphere. The underlying seasonal pattern of vegetation, and herbivores{\textquoteright} immune and behavioural responses to anthrax risk, interact to produce regular {\textquoteleft}anthrax seasons{\textquoteright} that appear to be a stable feature of the Etosha ecosystem. Through the lens of microbiologists, geneticists, immunologists, ecologists, epidemiologists, and clinicians, we discuss how anthrax dynamics are shaped at the smallest scale by population genetics and interactions within the bacterial communities up to the broadest scales of ecosystem structure. We illustrate the benefits and challenges of this interdisciplinary approach to disease ecology, and suggest ways anthrax might offer insights into the biology of other important pathogens. Bacillus anthracis, and the more recently emerged Bacillus cereus biovar anthracis, share key features with other environmentally transmitted pathogens, including several zoonoses and panzootics of special interest for global health and conservation efforts. Understanding the dynamics of anthrax, and developing interdisciplinary research programs that explore environmental persistence, is a critical step forward for understanding these emerging threats. }, doi = {10.1111/brv.12420}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12420}, author = {Carlson, Colin J. and Getz, Wayne M. and Kausrud, Kyrre L. and Cizauskas, Carrie A. and Blackburn, Jason K. and Bustos Carrillo, Fausto A. and Rita R Colwell and Easterday, W. Ryan and Ganz, Holly H. and Kamath, Pauline L. and {\O}kstad, Ole A. and Turner, Wendy C. and Kolsto, Anne-Brit and Stenseth, Nils C.} } @article {20320, title = {Application of a paper based device containing a new culture medium to detect Vibrio cholerae in water samples collected in Haiti}, journal = {Journal of Microbiological Methods}, volume = {133}, year = {2017}, month = {Jan-02-2017}, pages = {23 - 31}, issn = {01677012}, doi = {10.1016/j.mimet.2016.12.014}, url = {https://www.sciencedirect.com/science/article/pii/S0167701216303578?via\%3Dihub}, author = {Briquaire, Romain and Rita R Colwell and Boncy, Jacques and Rossignol, Emmanuel and Dardy, Aline and Pandini, Isabelle and Villeval, Fran{\c c}ois and Machuron, Jean-Louis and Huq, Anwar and Rashed, Shah and Vandevelde, Thierry and Rozand, Christine} } @article {20448, title = {A Bioinformatics 3D Cellular Morphotyping Strategy for Assessing Biomaterial Scaffold Niches}, journal = {ACS Biomaterials Science \& Engineering}, volume = {3}, year = {2017}, month = {Sep-10-2017}, pages = {2302 - 2313}, issn = {2373-9878}, doi = {10.1021/acsbiomaterials.7b00473}, url = {http://pubs.acs.org/doi/10.1021/acsbiomaterials.7b00473http://pubs.acs.org/doi/pdf/10.1021/acsbiomaterials.7b00473}, author = {Florczyk, Stephen J. and Simon, Mylene and Juba, Derek and Pine, P. Scott and Sarkar, Sumona and Chen, Desu and Baker, Paula J. and Bodhak, Subhadip and Cardone, Antonio and Brady, Mary C. and Bajcsy, Peter and Simon, Carl G.} } @article {20306, title = {Characterization of Pathogenic Vibrio parahaemolyticus from the Chesapeake Bay, Maryland}, journal = {Frontiers in Microbiology}, year = {2017}, month = {Mar-12-2018}, doi = {10.3389/fmicb.2017.02460}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02460}, author = {Chen, Arlene J. and Hasan, Nur A. and Haley, Bradd J. and Taviani, Elisa and Tarnowski, Mitch and Brohawn, Kathy and Johnson, Crystal N. and Rita R Colwell and Huq, Anwar} } @article {20318, title = {CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules}, journal = {Journal of Bacteriology}, year = {2017}, month = {Mar-05-2018}, abstract = {Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs.}, issn = {0021-9193}, doi = {10.1128/JB.00842-16}, url = {http://jb.asm.org/lookup/doi/10.1128/JB.00842-16}, author = {Carpenter, Megan R. and Kalburge, Sai S. and Borowski, Joseph D. and Peters, Molly C. and Rita R Colwell and Boyd, E. Fidelma}, editor = {DiRita, Victor J.} } @article {20313, title = {Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP)}, journal = {Journal of Biomolecular Techniques : JBT}, volume = {28}, year = {2017}, month = {Jan-04-2017}, pages = {31 - 39}, abstract = {The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the {\textquotedblleft}Door to Hell{\textquotedblright} crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.}, issn = {1524-0215}, doi = {10.7171/jbt.17-2801-004}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345951/}, author = {Tighe, Scott and Afshinnekoo, Ebrahim and Rock, Tara M. and McGrath, Ken and Alexander, Noah and McIntyre, Alexa and Ahsanuddin, Sofia and Bezdan, Daniela and Green, Stefan J. and Joye, Samantha and Stewart Johnson, Sarah and Baldwin, Don A. and Bivens, Nathan and Ajami, Nadim and Carmical, Joseph R. and Herriott, Ian Charold and Rita R Colwell and Donia, Mohamed and Foox, Jonathan and Greenfield, Nick and Hunter, Tim and Hoffman, Jessica and Hyman, Joshua and Jorgensen, Ellen and Krawczyk, Diana and Lee, Jodie and Levy, Shawn and Garcia-Reyero, {\`a}lia and Settles, Matthew and Thomas, Kelley and {\'o}mez, Felipe and Schriml, Lynn and Kyrpides, Nikos and Zaikova, Elena and Penterman, Jon and Mason, Christopher E.} } @article {20309, title = {The microbiomes of blowflies and houseflies as bacterial transmission reservoirs}, journal = {Scientific Reports}, year = {2017}, month = {Jan-12-2017}, abstract = {Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.}, doi = {10.1038/s41598-017-16353-x}, url = {http://www.nature.com/articles/s41598-017-16353-x}, author = {Junqueira, AC and Ratan, Aakrosh and Acerbi, Enzo and Drautz-Moses, Daniela I. and Premkrishnan, BNV and Costea, PI and Linz, Bodo and Purbojati, Rikky W. and Paulo, Daniel F. and Gaultier, Nicolas E. and Subramanian, Poorani and Hasan, Nur A. and Rita R Colwell and Bork, Peer and Azeredo-Espin, Ana Maria L. and Bryant, Donald A. and Schuster, Stephan C.} } @article {20316, title = {SYN-004 (ribaxamase), an oral beta-lactamase, mitigates antibiotic-mediated dysbiosis in a porcine gut microbiome model}, journal = {Journal of Applied Microbiology}, year = {2017}, month = {Jan-07-2017}, pages = {66 - 79}, abstract = { Aim To evaluate an antibiotic inactivation strategy to protect the gut microbiome from antibiotic-mediated damage. Methods and Results SYN-004 (ribaxamase) is an orally delivered beta-lactamase intended to degrade penicillins and cephalosporins within the gastrointestinal tract to protect the microbiome. Pigs (20 kg, n = 10) were treated with ceftriaxone (CRO) (IV, 50 mg kg-1, SID) for 7 days and a cohort (n = 5) received ribaxamase (PO, 75 mg, QID) for 9 days beginning the day before antibiotic administration. Ceftriaxone serum levels were not statistically different in the antibiotic-alone and antibiotic + ribaxamase groups, indicating ribaxamase did not alter systemic antibiotic levels. Whole-genome metagenomic analyses of pig faecal DNA revealed that CRO caused significant changes to the gut microbiome and an increased frequency of antibiotic resistance genes. With ribaxamase, the gut microbiomes were not significantly different from pretreatment and antibiotic resistance gene frequency was not increased. Conclusion Ribaxamase mitigated CRO-mediated gut microbiome dysbiosis and attenuated propagation of the antibiotic resistance genes in pigs. Significance and Impact of the Study Damage of the microbiome can lead to overgrowth of pathogenic organisms and antibiotic exposure can promote selection for antibiotic-resistant micro-organisms. Ribaxamase has the potential to become the first therapy designed to protect the gut microbiome from antibiotic-mediated dysbiosis and reduce emergence of antibiotic resistance. }, doi = {10.1111/jam.13432}, url = {https://onlinelibrary.wiley.com/doi/10.1111/jam.13432}, author = {Connelly, S. and Bristol, J.A. and Hubert, S. and Subramanian, P. and Hasan, N.A. and Rita R Colwell and Kaleko, M.} } @conference {20065, title = {3D Cellular Morphotyping of Scaffold Niches}, booktitle = {2016 32nd Southern Biomedical Engineering Conference (SBEC)}, year = {2016}, publisher = {IEEE}, organization = {IEEE}, author = {Florczyk, Stephen J and Simon, Mylene and Juba, Derek and Pine, P Scott and Sarkar, Sumona and Chen, Desu and Baker, Paula J and Bodhak, Subhadip and Cardone, Antonio and Brady, Mary and others} } @article {20324, title = {Chitin promotes Mycobacterium ulcerans growth}, journal = {FEMS Microbiology Ecology}, volume = {928565871}, year = {2016}, month = {Jun-06-2017}, pages = {fiw067}, abstract = {Mycobacterium ulcerans (MU) is the causative agent of Buruli ulcer, an emerging human infectious disease. However, both the ecology and life cycle of MU are poorly understood. The occurrence of MU has been linked to the aquatic environment, notably water bodies affected by human activities. It has been hypothesized that one or a combination of environmental factor(s) connected to human activities could favour growth of MU in aquatic systems. Here, we tested in vitro the growth effect of two ubiquitous polysaccharides and five chemical components on MU at concentration ranges shown to occur in endemic regions. Real-time PCR showed that chitin increased MU growth significantly providing a nutrient source or environmental support for the bacillus, thereby, providing a focus on the association between MU and aquatic arthropods. Aquatic environments with elevated population of arthropods provide increased chitin availability and, thereby, enhanced multiplication of MU. If calcium very slightly enhanced MU growth, iron, zinc, sulphate and phosphate did not stimulate MU growth, and at the concentration ranges of this study would limit MU population in natural ecosystems.}, doi = {10.1093/femsec/fiw067}, url = {https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw067}, author = {Sanhueza, Daniel and Chevillon, Christine and Rita R Colwell and Babonneau, J{\'e}r{\'e}mie and Marion, Estelle and Marsollier, Laurent and {\'e}gan, {\c c}ois}, editor = {Sobecky, Patricia} } @article {20329, title = {Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic}, journal = {Proceedings of the National Academy of Sciences}, year = {2016}, month = {Nov-08-2017}, pages = {E5062 - E5071}, abstract = {Climate change is having a dramatic impact on marine animal and plant communities but little is known of its influence on marine prokaryotes, which represent the largest living biomass in the world oceans and play a fundamental role in maintaining life on our planet. In this study, for the first time to our knowledge, experimental evidence is provided on the link between multidecadal climatic variability in the temperate North Atlantic and the presence and spread of an important group of marine prokaryotes, the vibrios, which are responsible for several infections in both humans and animals. Using archived formalin-preserved plankton samples collected by the Continuous Plankton Recorder survey over the past half-century (1958{\textendash}2011), we assessed retrospectively the relative abundance of vibrios, including human pathogens, in nine areas of the North Atlantic and North Sea and showed correlation with climate and plankton changes. Generalized additive models revealed that long-term increase in Vibrio abundance is promoted by increasing sea surface temperatures (up to \~{}1.5 {\textdegree}C over the past 54 y) and is positively correlated with the Northern Hemisphere Temperature (NHT) and Atlantic Multidecadal Oscillation (AMO) climatic indices (P < 0.001). Such increases are associated with an unprecedented occurrence of environmentally acquired Vibrio infections in the human population of Northern Europe and the Atlantic coast of the United States in recent years.}, issn = {0027-8424}, doi = {10.1073/pnas.1609157113}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1609157113}, author = {Vezzulli, Luigi and Grande, Chiara and Reid, Philip C. and {\'e}laou{\"e}t, Pierre and Edwards, Martin and {\"o}fle, Manfred G. and Brettar, Ingrid and Rita R Colwell and Pruzzo, Carla} } @article {20060, title = {Computational study of the inhibitory mechanism of~the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore}, journal = {Journal of Computer-Aided Molecular Design}, volume = {30}, year = {2016}, month = {Jan-06-2016}, pages = {513 - 521}, issn = {0920-654X}, doi = {10.1007/s10822-016-9922-3}, url = {http://link.springer.com/10.1007/s10822-016-9922-3http://link.springer.com/content/pdf/10.1007/s10822-016-9922-3http://link.springer.com/content/pdf/10.1007/s10822-016-9922-3.pdfhttp://link.springer.com/article/10.1007/s10822-016-9922-3/fulltext.html}, author = {Cardone, Antonio and Brady, M. and Sriram, R. and Pant, H. C. and Hassan, S. A.} } @article {20325, title = {Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak}, journal = {BMC Microbiology}, year = {2016}, month = {Jan-12-2016}, doi = {10.1186/s12866-016-0894-1}, url = {http://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0894-1}, author = {Ottesen, Andrea and Ramachandran, Padmini and Reed, Elizabeth and White, James R. and Hasan, Nur and Subramanian, Poorani and Ryan, Gina and Jarvis, Karen and Grim, Christopher and Daquiqan, Ninalynn and Hanes, Darcy and Allard, Marc and Rita R Colwell and Brown, Eric and Chen, Yi} } @article {20330, title = {IncA/C Conjugative Plasmids Mobilize a New Family of Multidrug Resistance Islands in Clinical Vibrio cholerae Non-O1/Non-O139 Isolates from Haiti}, journal = {mBio}, year = {2016}, month = {Jul-09-2016}, abstract = {Mobile genetic elements play a pivotal role in the adaptation of bacterial populations, allowing them to rapidly cope with hostile conditions, including the presence of antimicrobial compounds. IncA/C conjugative plasmids (ACPs) are efficient vehicles for dissemination of multidrug resistance genes in a broad range of pathogenic species of Enterobacteriaceae. ACPs have sporadically been reported in Vibrio cholerae, the infectious agent of the diarrheal disease cholera. The regulatory network that controls ACP mobility ultimately depends on the transcriptional activation of multiple ACP-borne operons by the master activator AcaCD. Beyond ACP conjugation, AcaCD has also recently been shown to activate the expression of genes located in the Salmonella genomic island 1 (SGI1). Here, we describe MGIVchHai6, a novel and unrelated mobilizable genomic island (MGI) integrated into the 3' end of trmE in chromosome I of V. cholerae HC-36A1, a non-O1/non-O139 multidrug-resistant clinical isolate recovered from Haiti in 2010. MGIVchHai6 contains a mercury resistance transposon and an integron In104-like multidrug resistance element similar to the one of SGI1. We show that MGIVchHai6 excises from the chromosome in an AcaCD-dependent manner and is mobilized by ACPs. Acquisition of MGIVchHai6 confers resistance to β-lactams, sulfamethoxazole, tetracycline, chloramphenicol, trimethoprim, and streptomycin/spectinomycin. In silico analyses revealed that MGIVchHai6-like elements are carried by several environmental and clinical V. cholerae strains recovered from the Indian subcontinent, as well as from North and South America, including all non-O1/non-O139 clinical isolates from Haiti.}, doi = {10.1128/mBio.00509-16}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00509-16}, author = {Carraro, Nicolas and Rivard, Nicolas and Ceccarelli, Daniela and Rita R Colwell and Burrus, Vincent} } @article {20321, title = {Modeling Sustainability: Population, Inequality, Consumption, and Bidirectional Coupling of the Earth and Human Systems}, journal = {National Science Review}, year = {2016}, month = {Nov-12-2016}, pages = {nww081}, abstract = {Over the last two centuries, the impact of the Human System has grown dramatically, becoming strongly dominant within the Earth System in many different ways. Consumption, inequality, and population have increased extremely fast, especially since about 1950, threatening to overwhelm the many critical functions and ecosystems of the Earth System. Changes in the Earth System, in turn, have important feedback effects on the Human System, with costly and potentially serious consequences. However, current models do not incorporate these critical feedbacks. We argue that in order to understand the dynamics of either system, Earth System Models must be coupled with Human System Models through bidirectional couplings representing the positive, negative, and delayed feedbacks that exist in the real systems. In particular, key Human System variables, such as demographics, inequality, economic growth, and migration, are not coupled with the Earth System but are instead driven by exogenous estimates, such as United Nations population projections. This makes current models likely to miss important feedbacks in the real Earth{\textendash}Human system, especially those that may result in unexpected or counterintuitive outcomes, and thus requiring different policy interventions from current models. The importance and imminence of sustainability challenges, the dominant role of the Human System in the Earth System, and the essential roles the Earth System plays for the Human System, all call for collaboration of natural scientists, social scientists, and engineers in multidisciplinary research and modeling to develop coupled Earth{\textendash}Human system models for devising effective science-based policies and measures to benefit current and future generations.}, issn = {2095-5138}, doi = {10.1093/nsr/nww081}, url = {https://academic.oup.com/nsr/article-lookup/doi/10.1093/nsr/nww081}, author = {Motesharrei, Safa and Rivas, Jorge and Kalnay, Eugenia and Asrar, Ghassem R. and Busalacchi, Antonio J. and Cahalan, Robert F. and Cane, Mark A. and Rita R Colwell and Feng, Kuishuang and Franklin, Rachel S. and Hubacek, Klaus and Miralles-Wilhelm, Fernando and Miyoshi, Takemasa and Ruth, Matthias and Sagdeev, Roald and Shirmohammadi, Adel and Shukla, Jagadish and Srebric, Jelena and Yakovenko, Victor M. and Zeng, Ning} } @article {20341, title = {Building Infectious Disease Research Programs to Promote Security and Enhance Collaborations with Countries of the Former Soviet Union}, journal = {Frontiers in Public Health}, volume = {35361632}, year = {2015}, month = {Feb-11-2017}, doi = {10.3389/fpubh.2015.00271}, url = {http://journal.frontiersin.org/Article/10.3389/fpubh.2015.00271/abstract}, author = {Bartholomew, James C. and Pearson, Andrew D. and Stenseth, Nils C. and LeDuc, James W. and Hirschberg, David L. and Rita R Colwell} } @article {20348, title = {Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species}, journal = {Proceedings of the National Academy of Sciences}, year = {2015}, month = {Feb-05-2017}, pages = {E2813 - E2819}, abstract = {Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea.}, issn = {0027-8424}, doi = {10.1073/pnas.1503928112}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1503928112}, author = {Hasan, Nur A. and Grim, Christopher J. and Lipp, Erin K. and Rivera, Irma N. G. and Chun, Jongsik and Haley, Bradd J. and Taviani, Elisa and Choi, Seon Young and Hoq, Mozammel and Munk, A. Christine and Brettin, Thomas S. and Bruce, David and Challacombe, Jean F. and Detter, J. Chris and Han, Cliff S. and Eisen, Jonathan A. and Huq, Anwar and Rita R Colwell} } @article {19903, title = {Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation.}, journal = {J Comput Chem}, year = {2015}, month = {2015 Mar 18}, abstract = {

A method is proposed to study protein-ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. {\textcopyright} 2015 Wiley Periodicals, Inc.

}, issn = {1096-987X}, doi = {10.1002/jcc.23883}, author = {Cardone, Antonio and Bornstein, Aaron and Pant, Harish C and Brady, Mary and Sriram, Ram and Hassan, Sergio A} } @article {20337, title = {Environmental Surveillance for Toxigenic Vibrio cholerae in Surface Waters of Haiti}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {92}, year = {2015}, month = {Jul-01-2015}, pages = {118 - 125}, abstract = {Epidemic cholera was reported in Haiti in 2010, with no information available on the occurrence or geographic distribution of toxigenic Vibrio cholerae in Haitian waters. In a series of field visits conducted in Haiti between 2011 and 2013, water and plankton samples were collected at 19 sites. Vibrio cholerae was detected using culture, polymerase chain reaction, and direct viable count methods (DFA-DVC). Cholera toxin genes were detected by polymerase chain reaction in broth enrichments of samples collected in all visits except March 2012. Toxigenic V. cholerae was isolated from river water in 2011 and 2013. Whole genome sequencing revealed that these isolates were a match to the outbreak strain. The DFA-DVC tests were positive for V. cholerae O1 in plankton samples collected from multiple sites. Results of this survey show that toxigenic V. cholerae could be recovered from surface waters in Haiti more than 2 years after the onset of the epidemic.}, issn = {0002-9637}, doi = {10.4269/ajtmh.13-0601}, url = {http://www.ajtmh.org/content/journals/10.4269/ajtmh.13-0601}, author = {Hill, Vincent R. and Humphrys, Michael S. and Kahler, Amy M. and Boncy, Jacques and Tarr, Cheryl L. and Huq, Anwar and Chen, Arlene and Katz, Lee S. and Mull, Bonnie J. and Derado, Gordana and Haley, Bradd J. and Freeman, Nicole and Rita R Colwell and Turnsek, Maryann} } @conference {20066, title = {Estimating Actin Fiber Orientation using Interpolation-Based Grey-Level Co-Occurrence Matrix Computation}, booktitle = {BioImage Informatics Conference }, year = {2015}, month = {10/2015}, author = {Cardone, Antonio and Brady, Mary and Kociolek, Marcin and Bajcsy, Peter} } @article {20338, title = {Nontoxigenic Vibrio cholerae Non-O1/O139 Isolate from a Case of Human Gastroenteritis in the U.S. Gulf Coast}, journal = {Journal of Clinical Microbiology}, year = {2015}, month = {Jun-01-2016}, pages = {9 - 14}, abstract = {An occurrence of Vibrio cholerae non-O1/O139 gastroenteritis in the U.S. Gulf Coast is reported here. Genomic analysis revealed that the isolate lacked known virulence factors associated with the clinical outcome of a V. cholerae infection but did contain putative genomic islands and other accessory virulence factors. Many of these factors are widespread among environmental strains of V. cholerae, suggesting that there might be additional virulence factors in non-O1/O139 V. cholerae yet to be determined. Phylogenetic analysis revealed that the isolate belonged to a phyletic lineage of environmental V. cholerae isolates associated with sporadic cases of gastroenteritis in the Western Hemisphere, suggesting a need to monitor non-O1/O139 V. cholerae in the interest of public health.}, issn = {0095-1137}, doi = {10.1128/JCM.02187-14}, url = {http://jcm.asm.org/lookup/doi/10.1128/JCM.02187-14}, author = {Hasan, Nur A. and Rezayat, Talayeh and Blatz, Peter J. and Choi, Seon Young and Griffitt, Kimberly J. and Rashed, Shah M. and Huq, Anwar and Conger, Nicholas G. and Rita R Colwell and Grimes, D. Jay}, editor = {Munson, E.} } @article {20342, title = {Satellite Based Assessment of Hydroclimatic Conditions Related to Cholera in Zimbabwe}, journal = {PLOS ONE}, year = {2015}, month = {May-09-2017}, pages = {e0137828}, abstract = {Introduction Cholera, an infectious diarrheal disease, has been shown to be associated with large scale hydroclimatic processes. The sudden and sporadic occurrence of epidemic cholera is linked with high mortality rates, in part, due to uncertainty in timing and location of outbreaks. Improved understanding of the relationship between pathogenic abundance and climatic processes allows prediction of disease outbreak to be an achievable goal. In this study, we show association of large scale hydroclimatic processes with the cholera epidemic in Zimbabwe reported to have begun in Chitungwiza, a city in Mashonaland East province, in August, 2008. Principal Findings Climatic factors in the region were found to be associated with triggering cholera outbreak and are shown to be related to anomalies of temperature and precipitation, validating the hypothesis that poor conditions of sanitation, coupled with elevated temperatures, and followed by heavy rainfall can initiate outbreaks of cholera. Spatial estimation by satellite of precipitation and global gridded air temperature captured sensitivities in hydroclimatic conditions that permitted identification of the location in the region where the disease outbreak began. Discussion Satellite derived hydroclimatic processes can be used to capture environmental conditions related to epidemic cholera, as occurred in Zimbabwe, thereby providing an early warning system. Since cholera cannot be eradicated because the causative agent, Vibrio cholerae, is autochthonous to the aquatic environment, prediction of conditions favorable for its growth and estimation of risks of triggering the disease in a given population can be used to alert responders, potentially decreasing infection and saving lives. }, doi = {10.1371/journal.pone.0137828}, url = {https://dx.plos.org/10.1371/journal.pone.0137828}, author = {Jutla, Antarpreet and Aldaach, Haidar and Billian, Hannah and Akanda, Ali and Huq, Anwar and Rita R Colwell}, editor = {Schumann, Guy J-P.} } @conference {20067, title = {Segmentation and sub-cellular feature-based analysis of microscopy images}, booktitle = {BioImage Informatics Conference }, year = {2015}, month = {10/2015}, author = {Cardone, Antonio and Chalfoun, Joe and Peskin, Adele and Bajcsy, Peter and Kociolek, Marcin and Bhadriraju, Kiran and Brady, Mary} } @article {20062, title = {Survey statistics of automated segmentations applied to optical imaging of mammalian cells}, journal = {BMC bioinformatics}, volume = {16}, year = {2015}, pages = {1}, author = {Bajcsy, Peter and Cardone, Antonio and Chalfoun, Joe and Halter, Michael and Juba, Derek and Kociolek, Marcin and Majurski, Michael and Peskin, Adele and Simon, Carl and Simon, Mylene and others} } @article {20340, title = {A unified initiative to harness Earth{\textquoteright}s microbiomes}, journal = {Science}, year = {2015}, month = {Jun-10-2017}, pages = {507 - 508}, issn = {0036-8075}, doi = {10.1126/science.aac8480}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aac8480}, author = {Alivisatos, A. P. and Blaser, M. J. and Brodie, E. L. and Chun, M. and Dangl, J. L. and Donohue, T. J. and Dorrestein, P. C. and Gilbert, J. A. and Green, J. L. and Jansson, J. K. and Knight, R. and Maxon, M. E. and McFall-Ngai, M. J. and Miller, J. F. and Pollard, K. S. and Ruby, E. G. and Taha, S. A. and Rita R Colwell} } @article {20346, title = {Use of Environmental Parameters to Model Pathogenic Vibrios in Chesapeake Bay}, journal = {Journal of Environmental Informatics}, year = {2015}, month = {Jan-01-2015}, abstract = {Although the transportation sector is a major contributor to urban air pollution and global climate change due to its substantial energy consumptions, previous studies for evacuation practices in this sector seldom took environmental consequences into account. As an attempt in event-related evacuation planning under uncertainty, this study proposed an emission-mitigation-oriented fuzzy evacuation management (emoFEM) model. Comprehensive considerations over system efficiency, environmental protection, economic cost and resource availability were incorporated within a general modeling formulation to facilitate evacuation management in a systematic and compromise manner. Vague and ambiguous information embedded within evacuation problems could be quantified and directly communicated into the optimization process, greatly improving conventional tools for evacuation management under uncertainty. The proposed emoFEM model was then applied to a hypothetic but representative case. Useful solutions were generated, which could help identify timely, safe and cost-effective evacuation schemes without significant disturbances over normal municipal traffic and environmental quality. The advantages of emoFEM were further revealed through comparing its solutions with those from its deterministic counterpart. }, issn = {17262135}, doi = {10.3808/jei.201500307}, url = {http://www.iseis.org/jei/abstract.asp?no=201500307}, author = {Zaitchik, B. F. and Guikema, S. D. and Haley, B. J. and Taviani, E. and Chen, A. and Brown, M.E. and Huq, A. and Rita R Colwell} } @article {20359, title = {Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens}, journal = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY}, year = {2014}, month = {Jan-09-2014}, pages = {3208 - 3214}, issn = {1466-5026}, doi = {10.1099/ijs.0.060145-0}, url = {http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.060145-0}, author = {Kirchberger, P. C. and Turnsek, M. and Hunt, D. E. and Haley, B. J. and Rita R Colwell and Polz, M. F. and Tarr, C. L. and Boucher, Y.} } @article {20361, title = {Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing}, journal = {PLoS ONE}, year = {2014}, month = {Aug-05-2015}, pages = {e97699}, abstract = {Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90\% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.}, doi = {10.1371/journal.pone.0097699}, url = {https://dx.plos.org/10.1371/journal.pone.0097699}, author = {Hasan, Nur A. and Young, Brian A. and Minard-Smith, Angela T. and Saeed, Kelly and Li, Huai and Heizer, Esley M. and McMillan, Nancy J. and Isom, Richard and Abdullah, Abdul Shakur and Bornman, Daniel M. and Faith, Seth A. and Choi, Seon Young and Dickens, Michael L. and Cebula, Thomas A. and Rita R Colwell}, editor = {Ahmed, Niyaz} } @article {20334, title = {Occurrence in Mexico, 1998{\textendash}2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage}, journal = {Proceedings of the National Academy of Sciences}, volume = {111}, year = {2014}, month = {Aug-07-2014}, pages = {9917 - 9922}, issn = {0027-8424}, doi = {10.1073/pnas.1323408111}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1323408111}, author = {Alam, Munirul and Rashed, Shah M and Mannan, Shahnewaj Bin and Islam, Tarequl and Lizarraga-Partida, Marcial L. and Delgado, Gabriela and Morales-Espinosa, Rosario and Mendez, Jose Luis and Navarro, Armando and Watanabe, Haruo and Ohnishi, Makoto and Hasan, Nur A. and Huq, Anwar and Sack, R. Bradley and Rita R Colwell and Cravioto, Alejandro} } @article {20360, title = {Validation of high throughput sequencing and microbial forensics applications}, journal = {Investigative Genetics}, volume = {5}, year = {2014}, month = {Jan-01-2014}, pages = {9}, abstract = {High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.}, issn = {2041-2223}, doi = {10.1186/2041-2223-5-9}, url = {http://investigativegenetics.biomedcentral.com/articles/10.1186/2041-2223-5-9}, author = {Budowle, Bruce and Connell, Nancy D and Bielecka-Oder, Anna and Rita R Colwell and Corbett, Cindi R and Fletcher, Jacqueline and Forsman, Mats and Kadavy, Dana R and Markotic, Alemka and Morse, Stephen A and Murch, Randall S and Sajantila, Antti and Schmedes, Sarah E and Ternus, Krista L and Turner, Stephen D and Minot, Samuel} } @article {20366, title = {Viewing Marine Bacteria, Their Activity and Response to Environmental Drivers from Orbit}, journal = {Microbial Ecology}, year = {2014}, month = {Jan-04-2014}, pages = {489 - 500}, abstract = {Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.}, issn = {0095-3628}, doi = {10.1007/s00248-013-0363-4}, url = {http://link.springer.com/10.1007/s00248-013-0363-4}, author = {Grimes, D. Jay and Ford, Tim E. and Rita R Colwell and Baker-Austin, Craig and Martinez-Urtaza, Jaime and Subramaniam, Ajit and Capone, Douglas G.} } @article {19684, title = {Argviz: Interactive Visualization of Topic Dynamics in Multi-party Conversations}, journal = {Human Language Technologies: The 2013 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, year = {2013}, month = {2013/00/01}, abstract = {Abstract We introduce an efficient, interactive framework{\textemdash}Argviz{\textemdash}for experts to analyze the dynamic topical structure of multi-party conversations. Users inject their needs, expertise, and insights into models via iterative topic refinement. The refined topics feed into a ...}, url = {https://www.aclweb.org/anthology-new/N/N13/N13-3.pdf$\#$page=42}, author = {Nguyen, V A and Hu, Y and Jordan Boyd-Graber} } @article {19685, title = {Binary to Bushy: Bayesian Hierarchical Clustering with the Beta Coalescent}, year = {2013}, month = {2013/00/01}, pages = {1079 - 1087}, abstract = {Abstract Discovering hierarchical regularities in data is a key problem in interacting with large datasets, modeling cognition, and encoding knowledge. A previous Bayesian solution-- -Kingman{\textquoteright}s coalescent---provides a convenient probabilistic model for data represented ...}, url = {http://papers.nips.cc/paper/5161-binary-to-bushy-bayesian-hierarchical-clustering-with-the-beta-coalescent}, author = {Hu, Yuening and Jordan Boyd-Graber and Daume III, Hal and Ying, Z Irene} } @article {19160, title = {Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space}, journal = {Journal of Computational Biology}, volume = {20}, number = {1}, year = {2013}, abstract = {The Dirichlet process is used to model probability distributions that are mixtures of an unknown number of components. Amino acid frequencies at homologous positions within related proteins have been fruitfully modeled by Dirichlet mixtures, and we use the Dirichlet process to derive such mixtures with an unbounded number of components. This application of the method requires several technical innovations to sample an unbounded number of Dirichlet-mixture components. The resulting Dirichlet mixtures model multiple-alignment data substantially better than do previously derived ones. They consist of over 500 components, in contrast to fewer than 40 previously, and provide a novel perspective on the structure of proteins. Individual protein positions should be seen not as falling into one of several categories, but rather as arrayed near probability ridges winding through amino acid multinomial space.}, keywords = {ALIGNMENT, computational molecular biology, dynamic programming, multiple alignment, sequence analysis}, doi = {10.1089/cmb.2012.0244}, author = {Nguyen,Viet-An and Jordan Boyd-Graber and Altschul, Stephen F.} } @article {20363, title = {Engaging Actively with Issues in the Responsible Conduct of Science: Lessons from International Efforts Are Relevant for Undergraduate Education in the United States}, journal = {CBE{\textemdash}Life Sciences Education}, year = {2013}, month = {Jan-12-2013}, pages = {596 - 603}, abstract = {Numerous studies are demonstrating that engaging undergraduate students in original research can improve their achievement in the science, technology, engineering, and mathematics (STEM) fields and increase the likelihood that some of them will decide to pursue careers in these disciplines. Associated with this increased prominence of research in the undergraduate curriculum are greater expectations from funders, colleges, and universities that faculty mentors will help those students, along with their graduate students and postdoctoral fellows, develop an understanding and sense of personal and collective obligation for responsible conduct of science (RCS). This Feature describes an ongoing National Research Council (NRC) project and a recent report about educating faculty members in culturally diverse settings (Middle East/North Africa and Asia) to employ active-learning strategies to engage their students and colleagues deeply in issues related to RCS. The NRC report describes the first phase of this project, which took place in Aqaba and Amman, Jordan, in September 2012 and April 2013, respectively. Here we highlight the findings from that report and our subsequent experience with a similar interactive institute in Kuala Lumpur, Malaysia. Our work provides insights and perspectives for faculty members in the United States as they engage undergraduate and graduate students, as well as postdoctoral fellows, to help them better understand the intricacies of and connections among various components of RCS. Further, our experiences can provide insights for those who may wish to establish {\textquotedblleft}train-the-trainer{\textquotedblright} programs at their home institutions.}, doi = {10.1187/cbe.13-09-0184}, url = {https://www.lifescied.org/doi/10.1187/cbe.13-09-0184}, author = {Clements, John D. and Connell, Nancy D. and Dirks, Clarissa and El-Faham, Mohamed and Hay, Alastair and Heitman, Elizabeth and Stith, James H. and Bond, Enriqueta C. and Rita R Colwell and Anestidou, Lida and Husbands, Jo L. and Labov, Jay B.} } @article {20364, title = {Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments}, journal = {Aquatic Biosystems}, volume = {9}, year = {2013}, month = {Jan-01-2013}, pages = {17}, abstract = {Background The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10{\textdegree}30' N, 64{\textdegree}40' W), B (10{\textdegree}40' N, 64{\textdegree}45' W) and D (10{\textdegree}43{\textquoteright}N, 64{\textdegree}32{\textquoteright}W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands. Results DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability. Conclusions In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.}, issn = {2046-9063}, doi = {10.1186/2046-9063-9-17}, url = {http://aquaticbiosystems.biomedcentral.com/articles/10.1186/2046-9063-9-17}, author = {Bozo-Hurtado, Lorelei and Garc{\'\i}a-Amado, M and Chistoserdov, Andrei and Varela, Ramon and Narvaez, J and Rita R Colwell and Su{\'a}rez, Paula} } @article {19700, title = {Improving public transit accessibility for blind riders by crowdsourcing bus stop landmark locations with Google street view}, journal = {The 15th International ACM SIGACCESS Conference}, year = {2013}, month = {2013/00/21}, pages = {16 - 8}, publisher = {SIGACCESS, ACM Special Interest Group on Accessible ComputingACM}, address = {New York, New York, USA}, abstract = {Abstract Low-vision and blind bus riders often rely on known physical landmarks to help locate and verify bus stop locations (eg., by searching for a shelter, bench, newspaper bin). However, there are currently few, if any, methods to determine this information a priori via ...}, isbn = {9781450324052}, doi = {10.1145/2513383.2513448}, url = {http://dl.acm.org/citation.cfm?doid=2513383.2513448}, author = {Hara, Kotaro and Azenkot, Shiri and Campbell, Megan and Bennett, Cynthia L and Le, Vicki and Pannella, Sean and Moore, Robert and Minckler, Kelly and Ng, Rochelle H and Jon Froehlich} } @article {19687, title = {Lexical and Hierarchical Topic Regression}, year = {2013}, month = {2013/00/01}, pages = {1106 - 1114}, abstract = {Abstract Inspired by a two-level theory that unifies agenda setting and ideological framing, we propose supervised hierarchical latent Dirichlet allocation (SHLDA) which jointly captures documents{\textquoteright} multi-level topic structure and their polar response variables. Our ...}, url = {http://papers.nips.cc/paper/5163-lexical-and-hierarchical-topic-regression}, author = {Nguyen, Viet-An and Jordan Boyd-Graber and Resnik, Philip} } @conference {19213, title = {Mind the Theoretical Gap: Interpreting, Using, and Developing Behavioral Theory in HCI Research}, booktitle = {CHI 2013 To Appear}, year = {2013}, month = {2013}, author = {Hekler, E. B. and Klasnja,P. and Jon Froehlich and Buman, M. P.} } @article {19686, title = {Modeling topic control to detect influence in conversations using nonparametric topic models}, journal = {Machine Learning}, year = {2013}, month = {2013/00/01}, pages = {1 - 41}, publisher = {Springer US}, abstract = {Abstract Identifying influential speakers in multi-party conversations has been the focus of research in communication, sociology, and psychology for decades. It has been long acknowledged qualitatively that controlling the topic of a conversation is a sign of ...}, doi = {10.1007/s10994-013-5417-9/fulltext.html}, url = {http://link.springer.com/article/10.1007/s10994-013-5417-9/fulltext.html}, author = {Nguyen, Viet-An and Jordan Boyd-Graber and Resnik, Philip and Cai, Deborah A and Midberry, Jennifer E and Wang, Yuanxin} } @conference {19159, title = {Online Latent Dirichlet Allocation with Infinite Vocabulary}, booktitle = {International Conference on Machine Learning}, year = {2013}, type = {Conference Paper}, abstract = {Topic models based on latent Dirichlet allocation (LDA) assume a predefined vocabulary. This is reasonable in batch settings but not reasonable for streaming and online settings. To address this lacuna, we extend LDA by drawing topics from a Dirichlet process whose base distribution is a distribution over all strings rather than from a finite Dirichlet. We develop inference using online variational inference and{\textemdash}to only consider a finite number of words for each topic{\textemdash}propose heuristics to dynamically order, expand, and contract the set of words we consider in our vocabulary. We show our model can successfully incorporate new words and that it performs better than topic models with finite vocabularies in evaluations of topic quality and classification performance.}, author = {Zhai,Ke and Jordan Boyd-Graber} } @article {19372, title = {Parallel geometric classification of stem cells by their three-dimensional morphology}, journal = {Computational Science \& Discovery}, volume = {6}, year = {2013}, month = {01/2013}, pages = {015007}, doi = {10.1088/1749-4699/6/1/015007}, author = {Juba,Derek and Cardone, Antonio and Ip, Cheuk Yiu and Simon Jr, Carl G and K Tison, Christopher and Kumar, Girish and Brady,Mary and Varshney, Amitabh} } @article {19371, title = {Segmenting time-lapse phase contrast images of adjacent NIH 3T3 cells.}, journal = {Journal of microscopy}, volume = {249}, year = {2013}, month = {2013 Jan}, pages = {41-52}, abstract = {We present a new method for segmenting phase contrast images of NIH 3T3 fibroblast cells that is accurate even when cells are physically in contact with each other. The problem of segmentation, when cells are in contact, poses a challenge to the accurate automation of cell counting, tracking and lineage modelling in cell biology. The segmentation method presented in this paper consists of (1) background reconstruction to obtain noise-free foreground pixels and (2) incorporation of biological insight about dividing and nondividing cells into the segmentation process to achieve reliable separation of foreground pixels defined as pixels associated with individual cells. The segmentation results for a time-lapse image stack were compared against 238 manually segmented images (8219 cells) provided by experts, which we consider as reference data. We chose two metrics to measure the accuracy of segmentation: the {\textquoteright}Adjusted Rand Index{\textquoteright} which compares similarities at a pixel level between masks resulting from manual and automated segmentation, and the {\textquoteright}Number of Cells per Field{\textquoteright} (NCF) which compares the number of cells identified in the field by manual versus automated analysis. Our results show that the automated segmentation compared to manual segmentation has an average adjusted rand index of 0.96 (1 being a perfect match), with a standard deviation of 0.03, and an average difference of the two numbers of cells per field equal to 5.39\% with a standard deviation of 4.6\%.}, keywords = {Animals, Cell Adhesion, Cell Count, Cell Division, Cell Shape, Computational Biology, Fibroblasts, Image Processing, Computer-Assisted, Mice, Microscopy, Phase-Contrast, NIH 3T3 Cells, Reproducibility of results, Sensitivity and Specificity, Time-Lapse Imaging}, issn = {1365-2818}, doi = {10.1111/j.1365-2818.2012.03678.x}, author = {Chalfoun, J and Kociolek, M and Dima, A and Halter, M and Cardone, Antonio and Peskin, A and Bajcsy, P and Brady, M.} } @article {19688, title = {Spoiler Alert: Machine Learning Approaches to Detect Social Media Posts with Revelatory Information}, year = {2013}, month = {2013/00/01}, abstract = {ABSTRACT Spoilers{\textemdash}critical plot information about works of fiction that {\textquotedblleft}spoil{\textquotedblright} a viewer{\textquoteright}s enjoyment{\textemdash}have prompted elaborate conventions on social media to allow readers to insulate themselves from spoilers. However, these solutions depend on the ...}, url = {http://www.umiacs.umd.edu/~jbg/docs/2013_spoiler.pdf}, author = {Jordan Boyd-Graber and Glasgow, K and Zajac, J S} } @article {19716, title = {TIGRFAMs and Genome Properties in 2013.}, journal = {Nucleic Acids Res}, volume = {41}, year = {2013}, month = {2013 Jan}, pages = {D387-95}, abstract = {

TIGRFAMs, available online at http://www.jcvi.org/tigrfams is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations. The Genome Properties database, available at http://www.jcvi.org/genome-properties, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature.

}, keywords = {Databases, Protein, Genome, Archaeal, Genome, Bacterial, Genomics, Internet, Markov chains, Molecular Sequence Annotation, Proteins, sequence alignment}, issn = {1362-4962}, doi = {10.1093/nar/gks1234}, author = {Haft, Daniel H and Jeremy D Selengut and Richter, Roland A and Harkins, Derek and Basu, Malay K and Beck, Erin} } @article {20064, title = {Understanding the impact of image quality on segmentation accuracy}, journal = {SPIE Newsroom}, year = {2013}, month = {2013}, author = {Li-Baboud, Ya-Shian and Cardone, Antonio and Chalfoun, Joe and Bajcsy, Peter and Elliott, John} } @inbook {19646, title = {Why {\textquotedblleft}Fiat-Shamir for Proofs{\textquotedblright} Lacks a Proof}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2013}, month = {2013/01/01/}, pages = {182 - 201}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {The Fiat-Shamir heuristic [CRYPTO {\textquoteright}86] is used to convert any 3-message public-coin proof or argument system into a non-interactive argument, by hashing the prover{\textquoteright}s first message to select the verifier{\textquoteright}s challenge. It is known that this heuristic is sound when the hash function is modeled as a random oracle. On the other hand, the surprising result of Goldwasser and Kalai [FOCS {\textquoteright}03] shows that there exists a computationally sound argument on which the Fiat-Shamir heuristic is never sound, when instantiated with any actual efficient hash function. This leaves us with the following interesting possibility: perhaps we can securely instantiates the Fiat-Shamir heuristic for all 3-message public-coin statistically sound proofs, even if we must fail for some computationally sound arguments. Indeed, this has been conjectured to be the case by Barak, Lindell and Vadhan [FOCS {\textquoteright}03], but we do not have any provably secure instantiation under any {\textquotedblleft}standard assumption{\textquotedblright}. In this work, we give a broad black-box separation result showing that the security of the Fiat-Shamir heuristic for statistically sound proofs cannot be proved under virtually any standard assumption via a black-box reduction. More precisely: {\textendash}If we want to have a {\textquotedblleft}universal{\textquotedblright} instantiation of the Fiat-Shamir heuristic that works for all 3-message public-coin proofs, then we cannot prove its security via a black-box reduction from any assumption that has the format of a {\textquotedblleft}cryptographic game{\textquotedblright}. {\textendash}For many concrete proof systems, if we want to have a {\textquotedblleft}specific{\textquotedblright} instantiation of the Fiat-Shamir heuristic for that proof system, then we cannot prove its security via a black box reduction from any {\textquotedblleft}falsifiable assumption{\textquotedblright} that has the format of a cryptographic game with an efficient challenger.}, keywords = {Algorithm Analysis and Problem Complexity, Computation by Abstract Devices, Data Encryption, Systems and Data Security}, isbn = {978-3-642-36593-5, 978-3-642-36594-2}, url = {http://link.springer.com/chapter/10.1007/978-3-642-36594-2_11}, author = {Bitansky, Nir and Dana Dachman-Soled and Garg, Sanjam and Jain, Abhishek and Kalai, Yael Tauman and L{\'o}pez-Alt, Adriana and Wichs, Daniel}, editor = {Sahai, Amit} } @article {12980, title = {BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics}, journal = {Systematic BiologySyst Biol}, volume = {61}, year = {2012}, month = {2012/01/01/}, pages = {170 - 173}, abstract = {Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.}, keywords = {Bayesian phylogenetics, gpu, maximum likelihood, parallel computing}, isbn = {1063-5157, 1076-836X}, doi = {10.1093/sysbio/syr100}, url = {http://sysbio.oxfordjournals.org/content/61/1/170}, author = {Ayres,Daniel L and Darling,Aaron and Zwickl,Derrick J and Beerli,Peter and Holder,Mark T and Lewis,Paul O and Huelsenbeck,John P and Ronquist,Fredrik and Swofford,David L and Cummings, Michael P. and Rambaut,Andrew and Suchard,Marc A} } @conference {19488, title = {Before We Knew It: An Empirical Study of Zero-day Attacks in the Real World}, booktitle = {CCS {\textquoteright}12 Proceedings of the 2012 ACM conference on Computer and Communications Security}, series = {CCS {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {833 - 844}, publisher = {ACM}, organization = {ACM}, abstract = {Little is known about the duration and prevalence of zero-day attacks, which exploit vulnerabilities that have not been disclosed publicly. Knowledge of new vulnerabilities gives cyber criminals a free pass to attack any target of their choosing, while remaining undetected. Unfortunately, these serious threats are difficult to analyze, because, in general, data is not available until after an attack is discovered. Moreover, zero-day attacks are rare events that are unlikely to be observed in honeypots or in lab experiments. In this paper, we describe a method for automatically identifying zero-day attacks from field-gathered data that records when benign and malicious binaries are downloaded on 11 million real hosts around the world. Searching this data set for malicious files that exploit known vulnerabilities indicates which files appeared on the Internet before the corresponding vulnerabilities were disclosed. We identify 18 vulnerabilities exploited before disclosure, of which 11 were not previously known to have been employed in zero-day attacks. We also find that a typical zero-day attack lasts 312 days on average and that, after vulnerabilities are disclosed publicly, the volume of attacks exploiting them increases by up to 5 orders of magnitude.}, keywords = {full disclosure, vulnerabilities, zero-day attacks}, isbn = {978-1-4503-1651-4}, url = {http://doi.acm.org/10.1145/2382196.2382284}, author = {Bilge, Leyla and Tudor Dumitras} } @article {12424, title = {Besting the Quiz Master: Crowdsourcing Incremental Classification Games}, journal = {Empirical Methods in Natural Language Processing}, year = {2012}, month = {2012///}, abstract = {Cost-sensitive classification, where the features used in machine learning tasks have a cost, has been explored as a means of balancing knowl- edge against the expense of obtaining new fea- tures. We introduce a setting where humans engage in classification with incrementally re- vealed features: the collegiate trivia circuit. By providing the community with a web-based system to practice, we collected tens of thou- sands of implicit word-by-word ratings of how useful features are for eliciting correct answers. Observing humans{\textquoteright} classification process, we improve the performance of a state-of-the art classifier. We also use the dataset to evaluate a system to compete in the incremental classifica- tion task through a reduction of reinforcement learning to classification. Our system learns when to answer a question, performing better than baselines and most human players.}, author = {Satinoff,Brianna and Jordan Boyd-Graber} } @article {20063, title = {Biases from model assumptions in texture sub-cellular image segmentation}, journal = {SPIE Newsroom}, volume = {13}, year = {2012}, author = {Cardone, Antonio and Amelot, Julien and Li-Baboud, Ya-Shian and Brady, Mary and Bajcsy, Peter} } @inbook {12400, title = {Collecting Semantic Similarity Ratings to Connect Concepts in Assistive Communication Tools}, booktitle = {Modeling, Learning, and Processing of Text Technological Data StructuresModeling, Learning, and Processing of Text Technological Data Structures}, series = {Studies in Computational Intelligence}, volume = {370}, year = {2012}, month = {2012///}, pages = {81 - 93}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {To compensate for the common inability of people with lexical production impairments to access and express intended concepts, we make use of models of human semantic memory that build on the notion of semantic similarity and relatedness. Such models, constructed on evidence gained from psycholinguistic experiments, form the basis of a large lexical database, WordNet . We augment WordNet with many additional links among words and concepts that are semantically related. Making this densely connected semantic network available to people with anomic aphasia through assistive technologies should enable them to navigate among related words and concepts and retrieve the words that they intend to express.}, isbn = {978-3-642-22612-0}, url = {http://dx.doi.org/10.1007/978-3-642-22613-7_5}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Fellbaum,Christiane}, editor = {Mehler,Alexander and K{\"u}hnberger,Kai-Uwe and Lobin,Henning and L{\"u}ngen,Harald and Storrer,Angelika and Witt,Andreas} } @conference {19218, title = {The design and evaluation of prototype eco-feedback displays for fixture-level water usage data}, year = {2012}, month = {2012}, pages = {2367 - 2376}, publisher = {ACM}, organization = {ACM}, isbn = {145031015X}, author = {Jon Froehlich and Findlater,L. and Ostergren, M. and Ramanathan, S. and Peterson,J. and Wragg, I. and Larson,E. and Fu, F. and Bai, M. and Patel,S.} } @article {19253, title = {Design and Synthesis for Multimedia Systems Using the Targeted Dataflow Interchange Format}, journal = {IEEE Transactions on Multimedia}, volume = {14}, year = {2012}, month = {2012}, pages = {630 - 640}, abstract = {Development of multimedia systems that can be targeted to different platforms is challenging due to the need for rigorous integration between high-level abstract modeling, and low-level synthesis and optimization. In this paper, a new dataflow-based design tool called the targeted dataflow interchange format is introduced for retargetable design, analysis, and implementation of embedded software for multimedia systems. Our approach provides novel capabilities, based on principles of task-level dataflow analysis, for exploring and optimizing interactions across design components; object-oriented data structures for encapsulating contextual information for components; a novel model for representing parameterized schedules that are derived from repetitive graph structures; and automated code generation for programming interfaces and low-level customizations that are geared toward high-performance embedded-processing architectures. We demonstrate our design tool for cross-platform application design, parameterized schedule representation, and associated dataflow graph-code generation using a case study centered around an image registration application.}, keywords = {associated dataflow graph-code generation, Computational modeling, contextual information encapsulation, cross-platform application design, data flow graphs, Data models, Data structures, Dataflow graphs, design components, design tools, Digital signal processing, electronic data interchange, embedded signal processing, Embedded software, high-level abstract modeling, high-performance embedded-processing architectures, Image coding, image registration application, image representation, low-level customizations, low-level optimization, low-level synthesis, Multimedia communication, multimedia systems, multimedia systems development, object-oriented data structures, object-oriented methods, parameterized schedule representation, programming interfaces, repetitive graph structures, retargetable design, Schedules, scheduling, software synthesis, Streaming media, targeted dataflow interchange format, task-level dataflow analysis}, isbn = {1520-9210}, author = {Chung-Ching Shen and Wu, Shenpei and Sane, N. and Wu, Hsiang-Huang and Plishker,W. and Bhattacharyya, Shuvra S.} } @inbook {18698, title = {Determining Protein Dynamics from 15N Relaxation Data by Using DYNAMICS}, booktitle = {Protein NMR Techniques}, series = {Methods in Molecular Biology}, volume = {831}, year = {2012}, month = {2012///}, pages = {485 - 511}, publisher = {Humana Press}, organization = {Humana Press}, abstract = {Motions are essential for protein function, and knowledge of protein dynamics is a key to our understanding the mechanisms underlying protein folding and stability, ligand recognition, allostery, and catalysis. In the last two decades, NMR relaxation measurements have become a powerful tool for characterizing backbone and side chain dynamics in complex biological macromolecules such as proteins and nucleic acids. Accurate analysis of the experimental data in terms of motional parameters is an essential prerequisite for developing physical models of motions to paint an adequate picture of protein dynamics. Here, I describe in detail how to use the software package DYNAMICS that was developed for accurate characterization of the overall tumbling and local dynamics in a protein from nuclear spin-relaxation rates measured by NMR. Step-by-step instructions are provided and illustrated through an analysis of 15 N relaxation data for protein G.}, keywords = {Biomedical and Life Sciences}, isbn = {978-1-61779-480-3}, url = {http://www.springerlink.com/content/q667p0k138058103/abstract/}, author = {Fushman, David}, editor = {Shekhtman,Alexander and Burz,David S. and Walker,John M.} } @article {12432, title = {Dictionary-based Face Recognition Under Variable Lighting and Pose}, journal = {IEEE Transactions on Information Forensics and Security}, volume = {PP}, year = {2012}, month = {2012/02/27/}, pages = {1 - 1}, abstract = {We present a face recognition algorithm based on simultaneous sparse approximations under varying illumination and pose. A dictionary is learned for each class based on given training examples which minimizes the representation error with a sparseness constraint. A novel test image is projected onto the span of the atoms in each learned dictionary. The resulting residual vectors are then used for classification. To handle variations in lighting conditions and pose, an image relighting technique based on pose-robust albedo estimation is used to generate multiple frontal images of the same person with variable lighting. As a result, the proposed algorithm has the ability to recognize human faces with high accuracy even when only a single or a very few images per person are provided for training. The efficiency of the proposed method is demonstrated using publicly available databases and it is shown that this method is efficient and can perform significantly better than many competitive face recognition algorithms.}, keywords = {Biometrics, dictionary learning, face recognition, illumination variation,, outlier rejection}, isbn = {1556-6013}, doi = {10.1109/TIFS.2012.2189205}, author = {Patel, Vishal M. and Wu,T. and Biswas,S. and Phillips,P. and Chellapa, Rama} } @article {19658, title = {Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size}, journal = {Nature Cell Biology}, volume = {14}, year = {2012}, month = {2012/05//}, pages = {518 - 525}, abstract = {Networks of epithelial and endothelial tubes are essential for the function of organs such as the lung, kidney and vascular system. The sizes and shapes of these tubes are highly regulated to match their individual functions. Defects in tube size can cause debilitating diseases such as polycystic kidney disease and ischaemia. It is therefore critical to understand how tube dimensions are regulated. Here we identify the tyrosine kinase Src as an instructive regulator of epithelial-tube length in the Drosophila tracheal system. Loss-of-function Src42 mutations shorten tracheal tubes, whereas Src42 overexpression elongates them. Surprisingly, Src42 acts distinctly from known tube-size pathways and regulates both the amount of apical surface growth and, with the conserved formin dDaam, the direction of growth. Quantitative three-dimensional image analysis reveals that Src42- and dDaam-mutant tracheal cells expand more in the circumferential than the axial dimension, resulting in tubes that are shorter in length{\textemdash}but larger in diameter{\textemdash}than wild-type tubes. Thus, Src42 and dDaam control tube dimensions by regulating the direction of anisotropic growth, a mechanism that has not previously been described.}, isbn = {1465-7392}, url = {http://www.nature.com/ncb/journal/v14/n5/abs/ncb2467.html}, author = {Nelson, Kevin S. and Zia Khan and Moln{\'a}r, Imre and Mih{\'a}ly, J{\'o}zsef and Kaschube, Matthias and Beitel, Greg J.} } @article {20387, title = {Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)}, journal = {Applied and Environmental Microbiology}, year = {2012}, month = {Mar-10-2013}, pages = {7249 - 7257}, abstract = {Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.}, issn = {0099-2240}, doi = {10.1128/AEM.01296-12}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01296-12}, author = {Johnson, Crystal N. and Bowers, John C. and Griffitt, Kimberly J. and Molina, Vanessa and Clostio, Rachel W. and Pei, Shaofeng and Laws, Edward and Paranjpye, Rohinee N. and Strom, Mark S. and Chen, Arlene and Hasan, Nur A. and Huq, Anwar and Noriea, Nicholas F. and Grimes, D. Jay and Rita R Colwell} } @inbook {19634, title = {Efficient Password Authenticated Key Exchange via Oblivious Transfer}, booktitle = {Public Key Cryptography {\textendash} PKC 2012}, series = {Lecture Notes in Computer Science}, year = {2012}, month = {2012/01/01/}, pages = {449 - 466}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a new framework for constructing efficient password authenticated key exchange (PAKE) protocols based on oblivious transfer (OT). Using this framework, we obtain: an efficient and simple UC-secure PAKE protocol that is secure against adaptive corruptions without erasures. efficient and simple PAKE protocols under the Computational Diffie-Hellman (CDH) assumption and the hardness of factoring. (Previous efficient constructions rely on hash proof systems, which appears to be inherently limited to decisional assumptions.) All of our constructions assume a common reference string (CRS) but do not rely on random oracles.}, keywords = {adaptive security, Algorithm Analysis and Problem Complexity, Computer Communication Networks, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, oblivious transfer, Password Authenticated Key Exchange, search assumptions, Systems and Data Security, UC security}, isbn = {978-3-642-30056-1, 978-3-642-30057-8}, url = {http://link.springer.com/chapter/10.1007/978-3-642-30057-8_27}, author = {Canetti, Ran and Dana Dachman-Soled and Vaikuntanathan, Vinod and Wee, Hoeteck}, editor = {Fischlin, Marc and Buchmann, Johannes and Manulis, Mark} } @article {12422, title = {Efficient Tree-Based Topic Modeling}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {Topic modeling with a tree-based prior has been used for a variety of applications be- cause it can encode correlations between words that traditional topic modeling cannot. How- ever, its expressive power comes at the cost of more complicated inference. We extend the SPARSELDA (Yao et al., 2009) inference scheme for latent Dirichlet allocation (LDA) to tree-based topic models. This sampling scheme computes the exact conditional distri- bution for Gibbs sampling much more quickly than enumerating all possible latent variable assignments. We further improve performance by iteratively refining the sampling distribution only when needed. Experiments show that the proposed techniques dramatically improve the computation time.}, author = {Hu,Yuening and Jordan Boyd-Graber} } @article {14484, title = {The first international workshop on entity-oriented search (EOS)}, journal = {SIGIR Forum}, volume = {45}, year = {2012}, month = {2012/01//}, pages = {43 - 50}, abstract = {The First International Workshop on Entity-Oriented Search (EOS) workshop was held on July 28, 2011 in Beijing, China, in conjunction with the 34th Annual International ACM SIGIR Conference (SIGIR 2011). The objective for the workshop was to bring together academic researchers and industry practitioners working on entity-oriented search to discuss tasks and challenges, and to uncover the next frontiers for academic research on the topic. The workshop program accommodated two invited talks, eleven refereed papers divided into three technical paper sessions, and a group discussion.}, isbn = {0163-5840}, doi = {10.1145/2093346.2093353}, url = {http://doi.acm.org/10.1145/2093346.2093353}, author = {Balog,Krisztian and de Vries,Arjen P. and Serdyukov,Pavel and Wen,Ji-Rong} } @article {19131, title = {A framework for human microbiome research}, journal = {Nature}, volume = {486}, year = {2012}, month = {2012}, pages = {215 - 221}, abstract = {A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.}, author = {Meth{\'e}, B.A. and Nelson,K. E and Pop, Mihai and Creasy, H.H. and Giglio, M.G. and Huttenhower, C. and Gevers, D. and Petrosino, J.F. and Abubucker, S. and Badger, J.H.} } @article {19660, title = {Global secretome analysis identifies novel mediators of bone metastasis}, journal = {Cell Research}, volume = {22}, year = {2012}, month = {2012/09//}, pages = {1339 - 1355}, abstract = {Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis. Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1, CST2, and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1. Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.}, keywords = {bone, cancer, metastasis, proteomics, secretome}, isbn = {1001-0602}, url = {http://www.nature.com/cr/journal/v22/n9/abs/cr201289a.html}, author = {Blanco, Mario Andres and LeRoy, Gary and Zia Khan and Ale{\v c}kovi{\'c}, Ma{\v s}a and Zee, Barry M. and Garcia, Benjamin A. and Kang, Yibin} } @article {12419, title = {Grammatical structures for word-level sentiment detection}, journal = {North American Association of Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {Existing work in fine-grained sentiment anal- ysis focuses on sentences and phrases but ig- nores the contribution of individual words and their grammatical connections. This is because of a lack of both (1) annotated data at the word level and (2) algorithms that can leverage syn- tactic information in a principled way. We ad- dress the first need by annotating articles from the information technology business press via crowdsourcing to provide training and testing data. To address the second need, we propose a suffix-tree data structure to represent syntac- tic relationships between opinion targets and words in a sentence that are opinion-bearing. We show that a factor graph derived from this data structure acquires these relationships with a small number of word-level features. We demonstrate that our supervised model per- forms better than baselines that ignore syntac- tic features and constraints.}, author = {Jordan Boyd-Graber and Sayeed,Asad B. and Rusk,Bryan and Weinberg, Amy} } @article {15427, title = {Grey-box GUI Testing: Efficient Generation of Event Sequences}, journal = {arXiv:1205.4928}, year = {2012}, month = {2012/05/22/}, abstract = {Graphical user interfaces (GUIs), due to their event driven nature, present a potentially unbounded space of all possible ways to interact with software. During testing it becomes necessary to effectively sample this space. In this paper we develop algorithms that sample the GUI{\textquoteright}s input space by only generating sequences that (1) are allowed by the GUI{\textquoteright}s structure, and (2) chain together only those events that have data dependencies between their event handlers. We create a new abstraction, called an event-dependency graph (EDG) of the GUI, that captures data dependencies between event handler code. We develop a mapping between EDGs and an existing black-box user-level model of the GUI{\textquoteright}s workflow, called an event-flow graph (EFG). We have implemented automated EDG construction in a tool that analyzes the bytecode of each event handler. We evaluate our "grey-box" approach using four open-source applications and compare it with the current state-of-the-art EFG approach. Our results show that using the EDG reduces the number of test cases while still achieving at least the same coverage. Furthermore, we were able to detect 2 new bugs in the subject applications.}, keywords = {68N30, Computer Science - Software Engineering}, url = {http://arxiv.org/abs/1205.4928}, author = {Arlt,Stephan and Banerjee,Ishan and Bertolini,Cristiano and Memon, Atif M. and Sch{\"a}f,Martin} } @article {19315, title = {A Hybrid System for Error Detection in Electronic Dictionaries}, number = {CASL-1308-2}, year = {2012}, abstract = {A progress report on CASL{\textquoteright}s research on error detection in electronic dictionaries, including a hybrid system, application and evaluation on a second dictionary and a graphical user interface. }, author = {Zajic, David and David Doermann and Bloodgood,Michael and Rodrigues,Paul and Ye,Peng and Zotkina,Elena} } @article {19129, title = {Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli}, journal = {Infection and immunity}, volume = {80}, year = {2012}, month = {2012}, pages = {2791 - 2801}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea, mainly in developing countries. Although there are 25 different ETEC adhesins described in strains affecting humans, between 15\% and 50\% of the clinical isolates from different geographical regions are negative for these adhesins, suggesting that additional unidentified adhesion determinants might be present. Here, we report the discovery of Coli Surface Antigen 23 (CS23), a novel adhesin expressed by an ETEC serogroup O4 strain (ETEC 1766a), which was negative for the previously known ETEC adhesins, albeit it has the ability to adhere to Caco-2 cells. CS23 is encoded by an 8.8-kb locus which contains 9 open reading frames (ORFs), 7 of them sharing significant identity with genes required for assembly of K88-related fimbriae. This gene locus, named aal (adhesion-associated locus), is required for the adhesion ability of ETEC 1766a and was able to confer this adhesive phenotype to a nonadherent E. coli HB101 strain. The CS23 major structural subunit, AalE, shares limited identity with known pilin proteins, and it is more closely related to the CS13 pilin protein CshE, carried by human ETEC strains. Our data indicate that CS23 is a new member of the diverse adhesin repertoire used by ETEC strains.}, author = {Del Canto, F. and Botkin, D.J. and Valenzuela, P. and Popov, V. and Ruiz-Perez, F. and Nataro, J.P. and Levine, M.M. and Stine, O.C. and Pop, Mihai and Torres, A.G. and others} } @article {19721, title = {InterPro in 2011: new developments in the family and domain prediction database.}, journal = {Nucleic Acids Res}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D306-12}, abstract = {

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

}, keywords = {Databases, Protein, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, software, Terminology as Topic, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkr948}, author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F and Rivoire, Catherine and Sangrador-Vegas, Amaia and Jeremy D Selengut and Sigrist, Christian J A and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D and Wu, Cathy H and Yeats, Corin and Yong, Siew-Yit} } @article {12854, title = {Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico}, journal = {Journal of Clinical Microbiology}, year = {2012}, month = {04/2012}, abstract = {Vibrio cholerae O1 Classical (CL) biotype caused the 5th and 6th, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the 7th pandemic in Asia in the 1970{\textquoteright}s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia, and it had never been reported from Latin America, V. cholerae CL and ET biotypes, including hybrid ET were found associated with endemic cholera in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from endemic cholera in Mexico, between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits, and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and bio-typing data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim/sulfamethoxazole, furazolidone, ampicillin, and gentamycin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all the CL biotype strains, although the Mexican strains differed with the Bangladeshi strains in 1-2 DNA bands. The difference may be subtle, but consistent, as confirmed by the sub-clustering patterns in the PFGE-based dendrogram, and can serve as regional signature, suggesting pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from that of Asia.}, isbn = {0095-1137, 1098-660X}, doi = {10.1128/JCM.00189-12}, url = {http://jcm.asm.org/content/early/2012/04/12/JCM.00189-12}, author = {Alam,Munirul and Islam,M. Tarequl and Rashed,Shah Manzur and Johura,Fatema-Tuz and Bhuiyan,Nurul A. and Delgado,Gabriela and Morales,Rosario and Mendez,Jose Luis and Navarro,Armando and Watanabe,Haruo and Hasan,Nur-A. and Rita R Colwell and Cravioto,Alejandro} } @article {20382, title = {Vibrio cholerae in a historically cholera-free country}, journal = {Environmental Microbiology Reports}, year = {2012}, month = {Jan-08-2012}, pages = {381 - 389}, abstract = {We report the autochthonous existence of Vibrio cholerae in coastal waters of Iceland, a geothermally active country where cholera is absent and has never been reported. Seawater, mussel and macroalgae samples were collected close to, and distant from, sites where geothermal activity causes a significant increase in water temperature during low tides. Vibrio cholerae was detected only at geothermal-influenced sites during low-tides. None of the V. cholerae isolates encoded cholera toxin (ctxAB) and all were non-O1/non-O139 serogroups. However, all isolates encoded other virulence factors that are associated with cholera as well as extra-intestinal V. cholerae infections. The virulence factors were functional at temperatures of coastal waters of Iceland, suggesting an ecological role. It is noteworthy that V. cholerae was isolated from samples collected at sites distant from anthropogenic influence, supporting the conclusion that V. cholerae is autochthonous to the aquatic environment of Iceland.}, doi = {10.1111/j.1758-2229.2012.00332.x}, url = {http://doi.wiley.com/10.1111/j.1758-2229.2012.00332.x}, author = {Haley, Bradd J. and Chen, Arlene and Grim, Christopher J. and Clark, Philip and Diaz, Celia M and Taviani, Elisa and Hasan, Nur A. and Sancomb, Elizabeth and Elnemr, Wessam M and Islam, Muhammad A. and Huq, Anwar and Rita R Colwell and Benediktsd{\'o}ttir, Eva} } @article {18540, title = {Lithium: Event-Driven Network Control}, volume = {GT-CS-12-03}, year = {2012}, month = {2012///}, institution = {Georgia Institute of Technology}, abstract = {This paper introduces event-driven network control, a network control framework that makes networks easier to manage by automating many tasks that must currently be performed by manually modifying low-level, distributed, and complex device configuration. We identify four policy domains that inherently capture many events: time, user, history, and traffic flow. We then present Lithium, an event-driven network control framework that can implement policies expressed using these domains. Lithium can support policies that automatically react to a wide range of events, from fluctuations in traffic volumes to changes in the time of day. Lithium allows network operators to specify networkwide policies in terms of a high-level, event-driven policy model, as opposed to configuring individual network devices with low-level commands. To show that Lithium is practical, general, and applicable in different types of network scenarios, we have deployed Lithium in both a campus network and a home network and used it to implement more flexible and dynamic network policies. We also perform evaluations to show that Lithium introduces negligible overhead beyond a conventional OpenFlow-based control framework.}, url = {http://hdl.handle.net/1853/43377}, author = {Kim,H. and Voellmy,A. and Burnett,S. and Feamster, Nick and Clark,R.} } @article {20381, title = {Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios}, journal = {The ISME Journal}, volume = {6111114882511}, year = {2012}, month = {Jan-01-2012}, pages = {21 - 30}, abstract = {The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45\% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.}, issn = {1751-7362}, doi = {10.1038/ismej.2011.89}, url = {http://www.nature.com/articles/ismej201189}, author = {Vezzulli, Luigi and Brettar, Ingrid and Pezzati, Elisabetta and Reid, Philip C and Rita R Colwell and H{\"o}fle, Manfred G and Pruzzo, Carla} } @article {19275, title = {Mapping Parameterized Cyclo-static Dataflow Graphs onto Configurable Hardware}, journal = {Journal of Signal Processing Systems}, volume = {66}, year = {2012}, month = {2012}, pages = {285 - 301}, abstract = {In recent years, parameterized dataflow has evolved as a useful framework for modeling synchronous and cyclo-static graphs in which arbitrary parameters can be changed dynamically. Parameterized dataflow has proven to have significant expressive power for managing dynamics of DSP applications in important ways. However, efficient hardware synthesis techniques for parameterized dataflow representations are lacking. This paper addresses this void; specifically, the paper investigates efficient field programmable gate array (FPGA)-based implementation of parameterized cyclo-static dataflow (PCSDF) graphs. We develop a scheduling technique for throughput-constrained minimization of dataflow buffering requirements when mapping PCSDF representations of DSP applications onto FPGAs. The proposed scheduling technique is integrated with an existing formal schedule model, called the generalized schedule tree, to reduce schedule cost. To demonstrate our new, hardware-oriented PCSDF scheduling technique, we have designed a real-time base station emulator prototype based on a subset of long-term evolution (LTE), which is a key cellular standard.}, keywords = {4G communication systems, Circuits and Systems, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow modeling, Electrical Engineering, FPGA implementation, Image Processing and Computer Vision, Parameterized dataflow, pattern recognition, scheduling, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-011-0599-5}, author = {Kee, Hojin and Chung-Ching Shen and Bhattacharyya, Shuvra S. and Wong, Ian and Yong Rao and Kornerup, Jacob} } @article {13829, title = {Modality and Negation in SIMT Use of Modality and Negation in Semantically-Informed Syntactic MT}, journal = {Computational Linguistics}, year = {2012}, month = {2012///}, pages = {1 - 48}, abstract = {This paper describes the resource- and system-building efforts of an eight-week Johns Hopkins University Human Language Technology Center of Excellence Summer Camp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation (SIMT). We describe a new modality/negation (MN) annotation scheme, the creation of a (publicly available) MN lexicon, and two automated MN taggers that we built using the annotation scheme and lexicon. Our annotation scheme isolates three components of modality and negation: a trigger (a word that conveys modality or negation), a target (an action associated with modality or negation) and a holder (an experiencer of modality). We describe how our MN lexicon was semi-automatically produced and we demonstrate that a structure-based MN tagger results in precision around 86\% (depending on genre) for tagging of a standard LDC data set.}, isbn = {0891-2017}, doi = {10.1162/COLI_a_00099}, url = {http://dx.doi.org/10.1162/COLI_a_00099}, author = {Baker,Kathryn and Bloodgood,Michael and Dorr, Bonnie J and Callison-Burch,Chris and Filardo,Nathaniel W. and Piatko,Christine and Levin,Lori and Miller,Scott} } @conference {12423, title = {Modeling Images using Transformed Indian Buffet Processes}, booktitle = {International Conference of Machine Learning}, year = {2012}, month = {2012///}, abstract = {Latent feature models are attractive for image modeling, since images generally contain mul- tiple objects. However, many latent feature models ignore that objects can appear at dif- ferent locations or require pre-segmentation of images. While the transformed Indian buffet process (tIBP) provides a method for modeling transformation-invariant features in unsegmented binary images, its current form is inappropriate for real images because of its computational cost and modeling assumptions. We combine the tIBP with likelihoods appropriate for real images and develop an efficient inference, using the cross- correlation between images and features, that is theoretically and empirically faster than existing inference techniques. Our method discovers rea- sonable components and achieve effective image reconstruction in natural images.}, author = {Zhai,Ke and Hu,Yuening and Williamson,Sinead and Jordan Boyd-Graber} } @conference {12418, title = {Mr. LDA: A Flexible Large Scale Topic Modeling Package using Variational Inference in MapReduce}, booktitle = {Proceedings of ACM International Conference on World Wide Web, 2012}, year = {2012}, month = {2012///}, abstract = {Latent Dirichlet Allocation (LDA) is a popular topic modeling tech- nique for exploring document collections. Because of the increasing prevalence of large datasets, there is a need to improve the scal- ability of inference for LDA. In this paper, we introduce a novel and flexible large scale topic modeling package in MapReduce (Mr. LDA). As opposed to other techniques which use Gibbs sampling, our proposed framework uses variational inference, which easily fits into a distributed environment. More importantly, this variational implementation, unlike highly tuned and specialized implementa- tions based on Gibbs sampling, is easily extensible. We demonstrate two extensions of the models possible with this scalable framework: informed priors to guide topic discovery and extracting topics from a multilingual corpus. We compare the scalability of Mr. LDA against Mahout, an existing large scale topic modeling package. Mr. LDA out-performs Mahout both in execution speed and held-out likelihood.}, author = {Zhai,Ke and Jordan Boyd-Graber and Asadi,Nima and Alkhouja,Mohamad} } @article {12857, title = {Occurrence of protozoans \& their limnological relationships in some ponds of Mathbaria, Bangladesh}, journal = {University Journal of Zoology, Rajshahi University}, volume = {29}, year = {2012}, month = {2012///}, pages = {69 - 71}, isbn = {1023-6104}, url = {http://journals.sfu.ca/bd/index.php/UJZRU}, author = {Mozumder,P. K. and Banu,M. A. and Naser,M. N. and Ali,M. S. and Alam,M. and Sack,R. B. and Rita R Colwell and Huq,A.} } @conference {17641, title = {Optimizing epidemic protection for socially essential workers}, booktitle = {Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium}, series = {IHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {31 - 40}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Public-health policy makers have many tools to mitigate an epidemic{\textquoteright}s effects. Most related research focuses on the direct effects on those infected (in terms of health, life, or productivity). Interventions including treatment, prophylaxis, quarantine, and social distancing are well studied in this context. These interventions do not address indirect effects due to the loss of critical services and infrastructures when too many of those responsible for their day-to-day operations fall ill. We examine, both analytically and through simulation, the protection of such essential subpopulations by sequestering them, effectively isolating them into groups during an epidemic. We develop a framework for studying the benefits of sequestering and heuristics for when to sequester. We also prove a key property of sequestering placement which helps partition the subpopulations optimally. Thus we provide a first step toward determining how to allocate resources between the direct protection of a population, and protection of those responsible for critical services.}, keywords = {epidemiology, OPTIMIZATION, public health informatics}, isbn = {978-1-4503-0781-9}, doi = {10.1145/2110363.2110371}, url = {http://doi.acm.org/10.1145/2110363.2110371}, author = {Barrett,Chris and Beckman,Richard and Bisset,Keith and Chen,Jiangzhuo and DuBois,Thomas and Eubank,Stephen and Kumar,V. S. Anil and Lewis,Bryan and Marathe,Madhav V. and Srinivasan, Aravind and Stretz,Paula E.} } @article {19255, title = {Preparation and probing of coherent vibrational wave packets in the ground electronic state of HD^{+}}, journal = {Physical Review A}, volume = {85}, year = {2012}, month = {2012}, abstract = {We have investigated the formation of coherent vibrational wave packets in the ground electronic state of HD+ on exposure to intense ultrashort laser pulses of wavelength 1060 nm. The effects of the duration and field strength of the pulse on the final composition of the residual bound nuclear wave packet generated by such impulsive excitations have been studied. The resulting wave packet is allowed to evolve freely on the potential surface for some time, after which a weak pulse of sufficiently large duration is used for probing its composition. This pulse can cause only single-photon dissociation. The simulations have been performed with different probe wavelengths for accessing information about different portions of the wave packet in the vibrational quantum number space. Our aim was to investigate the extent to which information obtained from the kinetic-energy spectra of the photofragments induced by the probe pulse can be correlated to the structure of the wave packet. Simple time-dependent perturbation calculations have also been performed for obtaining the relative strengths of photofragment signals arising from different vibrational levels due to wave-packet dissociation. A comparison with our numerical results indicates that though the general features of the photofragment kinetic-energy spectra from a wave packet are consistent with the perturbation theory results in the intensity regime studied, dynamical evolution during a long pulse can modify the relative heights of the kinetic-energy peaks through nonperturbative interactions in some cases.}, url = {http://link.aps.org/doi/10.1103/PhysRevA.85.033424}, author = {Bhattacharya, Rangana and Chatterjee, Souvik and Bhattacharyya, Shuvra S.} } @article {19254, title = {Prototyping scalable digital signal processing systems for radio astronomy using dataflow models}, journal = {Radio Science}, volume = {47}, year = {2012}, month = {2012}, pages = {n/a - n/a}, abstract = {There is a growing trend toward using high-level tools for design and implementation of radio astronomy digital signal processing (DSP) systems. Such tools, for example, those from the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER), are usually platform-specific, and lack high-level, platform-independent, portable, scalable application specifications. This limits the designer{\textquoteright}s ability to experiment with designs at a high-level of abstraction and early in the development cycle. We address some of these issues using a model-based design approach employing dataflow models. We demonstrate this approach by applying it to the design of a tunable digital downconverter (TDD) used for narrow-bandwidth spectroscopy. Our design is targeted toward an FPGA platform, called theInterconnect Break-out Board (IBOB), that is available from the CASPER. We use the term TDD to refer to a digital downconverter for which the decimation factor and center frequency can be reconfigured without the need for regenerating the hardware code. Such a design is currently not available in the CASPER DSP library. The work presented in this paper focuses on two aspects. First, we introduce and demonstrate a dataflow-based design approach using thedataflow interchange format (DIF) tool for high-level application specification, and we integrate this approach with the CASPER tool flow. Secondly, we explore the trade-off between the flexibility of TDD designs and the low hardware cost of fixed-configuration digital downconverter (FDD) designs that use the available CASPER DSP library. We further explore this trade-off in the context of a two-stage downconversion scheme employing a combination of TDD or FDD designs.}, keywords = {dataflow models, digital downconverter, Digital signal processing, model-based design, radio astronomy, rapid prototyping}, isbn = {1944-799X}, url = {http://onlinelibrary.wiley.com/doi/10.1029/2011RS004924/abstract}, author = {Sane, N. and Ford, J. and Harris, A. I. and Bhattacharyya, Shuvra S.} } @article {19668, title = {Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS}, journal = {Molecular Systems Biology}, volume = {8}, year = {2012}, month = {2012/01/01/}, abstract = {Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele-specific manner (cis-acting) or it can affect both alleles of a gene (trans-acting). Differential allele-specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis-acting regulatory variation. While microarrays and high-throughput sequencing have enabled genome-wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography-coupled mass spectrometry (LC-MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species.Synopsis A novel strategy for the quantitative measurement of allele-specific protein expression is used to infer the contributions of cis- and trans-acting factors influencing the divergence of protein levels between yeast species. Rigorous experimental controls and analyses confirm the accuracy of the new strategy for the quantitative measurement of allele-specific protein expression by high-throughput mass spectrometry.Analysis of allele-specific protein expression in an interspecies yeast hybrid and protein expression differences between species reveals that both cis-effects and trans-effects contribute to protein expression divergence between two yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus. }, keywords = {allele specific, divergence, mass spectrometry, protein expression, proteomics}, url = {http://msb.embopress.org/content/8/1/602}, author = {Zia Khan and Bloom, Joshua S. and Amini, Sasan and Singh, Mona and Perlman, David H. and Caudy, Amy A. and Kruglyak, Leonid} } @conference {19318, title = {A Random Forest System Combination Approach for Error Detection in Digital Dictionaries}, booktitle = {Innovative hybrid approaches to the processing of textual data, EACL 2012 Workshop}, year = {2012}, month = {04/2012}, pages = {78-86}, abstract = {When digitizing a print bilingual dictionary, whether via optical character recognition or manual entry, it is inevitable that errors are introduced into the electronic version that is created. We investigate automating the process of detecting errors in an XML representation of a digitized print dictionary using a hybrid approach that combines rule-based, feature-based, and language model-based methods. We investigate combining methods and show that using random forests is a promising approach. We find that in isolation, unsupervised methods rival the performance of supervised methods. Random forests typically require training data so we investigate how we can apply random forests to combine individual base methods that are themselves unsupervised without requiring large amounts of training data. Experiments reveal empirically that a relatively small amount of data is sufficient and can potentially be further reduced through specific selection criteria. }, author = {Bloodgood,Michael and Ye,Peng and Rodrigues,Paul and Zajic, David and David Doermann} } @article {18712, title = {Rpn1 and Rpn2 coordinate ubiquitin processing factors at the proteasome}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, year = {2012}, month = {2012/02/08/}, abstract = {Substrates tagged with (poly)ubiquitin for degradation can be targeted directly to the 26S proteasome where they are proteolysed. Independently, ubiquitin-conjugates may also be delivered by bivalent shuttles. The majority of shuttles attach to the proteasome through a ubiquitin-like domain (UBL) while anchoring cargo at a C-terminal polyubiquitin-binding domain(s). We found that two shuttles of this class, Rad23 and Dsk2, dock at two different receptors embedded within a single subunit of the 19S proteasome regulatory particle (RP), Rpn1. Their association/dissociation constants and affinities for Rpn1 are similar. In contrast, another UBL-containing protein, the deubiquitinase Ubp6, is also anchored by Rpn1, yet dissociates slower, thus behaving as a sometimes proteasome subunit distinct from transiently-associated shuttles. Two neighboring subunits, Rpn10 and Rpn13, show a marked preference for polyubiquitin over UBLs. Rpn10 attaches to the central solenoid portion of Rpn1 although this association is stabilized by the presence of a third subunit, Rpn2. Rpn13 binds directly to the C-terminal portion of Rpn2. These intrinsic polyubiquitin receptors may compete with substrate shuttles for their polyubiquitin-conjugates, thereby aiding release of the emptied shuttles. By binding multiple ubiquitin-processing factors simultaneously, Rpn1 is uniquely suited to coordinate substrate recruitment, deubiquitination, and movement towards the catalytic core. The broad range of affinities for ubiquitin, ubiquitin-like, and non-ubiquitin signals by adjacent yet non-overlapping sites all within the Base illustrates a hub of activity that coordinates the intricate relay of substrates within the proteasome, and consequently influences substrate residency time and commitment to degradation.}, keywords = {deubiquitination, Proteasome, solenoid, Surface plasmon resonance (SPR), ubiquitin, Ubiquitin-dependent protease}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.M111.316323}, url = {http://www.jbc.org/content/early/2012/02/08/jbc.M111.316323}, author = {Rosenzweig,Rina and Bronner,Vered and Zhang,Daoning and Fushman, David and Glickman,Michael H.} } @article {12421, title = {SITS: A Hierarchical Nonparametric Model using Speaker Identity for Topic Segmentation in Multiparty Conversations}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {One of the key tasks for analyzing conversa- tional data is segmenting it into coherent topic segments. However, most models of topic segmentation ignore the social aspect of con- versations, focusing only on the words used. We introduce a hierarchical Bayesian nonpara- metric model, Speaker Identity for Topic Seg- mentation (SITS), that discovers (1) the top- ics used in a conversation, (2) how these top- ics are shared across conversations, (3) when these topics shift, and (4) a person-specific tendency to introduce new topics. We eval- uate against current unsupervised segmenta- tion models to show that including person- specific information improves segmentation performance on meeting corpora and on po- litical debates. Moreover, we provide evidence that SITS captures an individual{\textquoteright}s tendency to introduce new topics in political contexts, via analysis of the 2008 US presidential debates and the television program Crossfire.}, author = {Nguyen,Viet-An and Jordan Boyd-Graber and Resnik, Philip} } @article {17929, title = {Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs}, journal = {Journal of Computing and Information Science in Engineering}, year = {2012}, month = {2012///}, abstract = {In this paper, we introduce a GPU-based framework forsimulating particle trajectories under both static and dynamic force fields. By exploiting the highly parallel nature of the problem and making efficient use of the available hardware, our simulator exhibits a significant speedup over its CPU- based analog. We apply our framework to a specific experi- mental simulation: the computation of trapping probabilities associated with micron-sized silica beads in optical trapping workbenches. When evaluating large numbers of trajectories (4096), we see approximately a 356 times speedup of the GPU-based simulator over its CPU-based counterpart. }, author = {Patro,R. and Dickerson,J. P. and Bista,S. and Gupta,S.K. and Varshney, Amitabh} } @article {19132, title = {Structure, function and diversity of the healthy human microbiome}, journal = {Nature}, volume = {486}, year = {2012}, month = {2012}, pages = {207 - 214}, abstract = {Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat{\textquoteright}s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81{\textendash}99\% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.}, author = {Huttenhower, C. and Gevers, D. and Knight,R. and Abubucker, S. and Badger, J.H. and Chinwalla, A.T. and Creasy, H.H. and Earl, A.M. and Fitzgerald, M.G. and Fulton, R.S. and others} } @conference {19374, title = {Sub-cellular feature detection and automated extraction of collocalized actin and myosin regions}, booktitle = {the 2nd ACM SIGHIT symposiumProceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI {\textquoteright}12}, year = {2012}, pages = {399}, publisher = {ACM Press}, organization = {ACM Press}, address = {Miami, Florida, USANew York, New York, USA}, isbn = {9781450307819}, doi = {10.1145/211036310.1145/2110363.2110409}, author = {Martineau, Justin and Mokashi,Ronil and Chapman, David and Grasso, Michael and Brady,Mary and Yesha,Yelena and Yesha,Yaacov and Cardone, Antonio and Dima, Alden} } @article {12858, title = {Temporal and Spatial Variability in the Distribution of Vibrio vulnificus in the Chesapeake Bay: A Hindcast Study}, journal = {EcoHealth}, year = {2012}, month = {2012///}, pages = {1 - 12}, abstract = {Vibrio vulnificus, an estuarine bacterium, is the causative agent of seafood-related gastroenteritis, primary septicemia, and wound infections worldwide. It occurs as part of the normal microflora of coastal marine environments and can be isolated from water, sediment, and oysters. Hindcast prediction was undertaken to determine spatial and temporal variability in the likelihood of occurrence of V. vulnificus in surface waters of the Chesapeake Bay. Hindcast predictions were achieved by forcing a multivariate habitat suitability model with simulated sea surface temperature and salinity in the Bay for the period between 1991 and 2005 and the potential hotspots of occurrence of V. vulnificus in the Chesapeake Bay were identified. The likelihood of occurrence of V. vulnificus during high and low rainfall years was analyzed. From results of the study, it is concluded that hindcast prediction yields an improved understanding of environmental conditions associated with occurrence of V. vulnificus in the Chesapeake Bay.}, doi = {10.1007/s10393-011-0736-4}, author = {Banakar,V. and Constantin de Magny,G. and Jacobs,J. and Murtugudde,R. and Huq,A. and J. Wood,R. and Rita R Colwell} } @article {12420, title = {Topic Models for Dynamic Translation Model Adaptation}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {We propose an approach that biases machine translation systems toward relevant transla- tions based on topic-specific contexts, where topics are induced in an unsupervised way using topic models; this can be thought of as inducing subcorpora for adaptation with- out any human annotation. We use these topic distributions to compute topic-dependent lex- ical weighting probabilities and directly in- corporate them into our translation model as features. Conditioning lexical probabilities on the topic biases translations toward topic- relevant output, resulting in significant im- provements of up to 1 BLEU and 3 TER on Chinese to English translation over a strong baseline.}, author = {Vladimir Eidelman and Jordan Boyd-Graber and Resnik, Philip} } @conference {19465, title = {You{\textquoteright}Re Capped: Understanding the Effects of Bandwidth Caps on Broadband Use in the Home}, booktitle = {SIGCHI {\textquoteright}12}, series = {CHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {3021 - 3030}, publisher = {ACM}, organization = {ACM}, abstract = {Bandwidth caps, a limit on the amount of data users can upload and download in a month, are common globally for both home and mobile Internet access. With caps, each bit of data consumed comes at a cost against a monthly quota or a running tab. Yet, relatively little work has considered the implications of this usage-based pricing model on the user experience. In this paper, we present results from a qualitative study of households living with bandwidth caps. Our findings suggest home users grapple with three uncertainties regarding their bandwidth usage: invisible balances, mysterious processes, and multiple users. We discuss how these uncertainties impact their usage and describe the potential for better tools to help monitor and manage data caps. We conclude that as a community we need to cater for users under Internet cost constraints.}, keywords = {Bandwidth, bandwidth cap, data cap, Internet, metered use, pricing, usage-based billing, usage-based pricing}, isbn = {978-1-4503-1015-4}, url = {http://doi.acm.org/10.1145/2207676.2208714}, author = {Marshini Chetty and Banks, Richard and Brush, A.J. and Donner, Jonathan and Grinter, Rebecca} } @article {19650, title = {Accurate proteome-wide protein quantification from high-resolution 15N mass spectra}, journal = {Genome Biology}, volume = {12}, year = {2011}, month = {2011/12/19/}, abstract = {In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.PMID: 22182234 }, isbn = {1465-6906}, url = {http://genomebiology.com/2011/12/12/R122/abstract}, author = {Zia Khan and Amini, Sasan and Bloom, Joshua S. and Ruse, Cristian and Caudy, Amy A. and Kruglyak, Leonid and Singh, Mona and Perlman, David H. and Tavazoie, Saeed} } @conference {18330, title = {Active inference for retrieval in camera networks}, booktitle = {Person-Oriented Vision (POV), 2011 IEEE Workshop on}, year = {2011}, month = {2011/01//}, pages = {13 - 20}, publisher = {IEEE}, organization = {IEEE}, abstract = {We address the problem of searching camera network videos to retrieve frames containing specified individuals. We show the benefit of utilizing a learned probabilistic model that captures dependencies among the cameras. In addition, we develop an active inference framework that can request human input at inference time, directing human attention to the portions of the videos whose correct annotation would provide the biggest performance improvements. Our primary contribution is to show that by mapping video frames in a camera network onto a graphical model, we can apply collective classification and active inference algorithms to significantly increase the performance of the retrieval system, while minimizing the number of human annotations required.}, isbn = {978-1-61284-036-9}, doi = {10.1109/POV.2011.5712363}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5712363\&tag=1}, author = {Daozheng Chen and Bilgic,Mustafa and Getoor, Lise and Jacobs, David W. and Mihalkova,Lilyana and Tom Yeh} } @conference {14431, title = {Active inference for retrieval in camera networks}, booktitle = {Person-Oriented Vision (POV), 2011 IEEE Workshop on}, year = {2011}, month = {2011/01//}, pages = {13 - 20}, abstract = {We address the problem of searching camera network videos to retrieve frames containing specified individuals. We show the benefit of utilizing a learned probabilistic model that captures dependencies among the cameras. In addition, we develop an active inference framework that can request human input at inference time, directing human attention to the portions of the videos whose correct annotation would provide the biggest performance improvements. Our primary contribution is to show that by mapping video frames in a camera network onto a graphical model, we can apply collective classification and active inference algorithms to significantly increase the performance of the retrieval system, while minimizing the number of human annotations required.}, keywords = {active, annotation;probabilistic, frame;cameras;inference, inference;camera, mechanisms;probability;search, model;human, model;retrieval, network;graphical, problem;video, problems;video, processing;, retrieval;video, signal, system;searching}, doi = {10.1109/POV.2011.5712363}, author = {Daozheng Chen and Bilgic,M. and Getoor, Lise and Jacobs, David W. and Mihalkova,L. and Tom Yeh} } @article {19279, title = {Analysis of SystemC actor networks for efficient synthesis}, journal = {ACM Trans. Embed. Comput. Syst.}, volume = {10}, year = {2011}, month = {2011}, pages = {18:1 - 18:34}, abstract = {Applications in the signal processing domain are often modeled by dataflow graphs. Due to heterogeneous complexity requirements, these graphs contain both dynamic and static dataflow actors. In previous work, we presented a generalized clustering approach for these heterogeneous dataflow graphs in the presence of unbounded buffers. This clustering approach allows the application of static scheduling methodologies for static parts of an application during embedded software generation for multiprocessor systems. It systematically exploits the predictability and efficiency of the static dataflow model to obtain latency and throughput improvements. In this article, we present a generalization of this clustering technique to dataflow graphs with bounded buffers, therefore enabling synthesis for embedded systems without dynamic memory allocation. Furthermore, a case study is given to demonstrate the performance benefits of the approach.}, keywords = {actor-oriented design, clustering, Dataflow analysis, scheduling}, isbn = {1539-9087}, url = {http://doi.acm.org/10.1145/1880050.1880054}, author = {Falk, Joachim and Zebelein, Christian and Keinert, Joachim and Haubelt, Christian and Teich, Juergen and Bhattacharyya, Shuvra S.} } @conference {19269, title = {Applying graphics processor acceleration in a software defined radio prototyping environment}, booktitle = {2011 22nd IEEE International Symposium on Rapid System Prototyping (RSP)}, year = {2011}, month = {2011}, pages = {67 - 73}, abstract = {With higher bandwidth requirements and more complex protocols, software defined radio (SDR) has ever growing computational demands. SDR applications have different levels of parallelism that can be exploited on multicore platforms, but design and programming difficulties have inhibited the adoption of specialized multicore platforms like graphics processors (GPUs). In this work we propose a new design flow that augments a popular existing SDR development environment (GNU Radio), with a dataflow foundation and a stand-alone GPU accelerated library. The approach gives an SDR developer the ability to prototype a GPU accelerated application and explore its design space fast and effectively. We demonstrate this design flow on a standard SDR benchmark and show that deciding how to utilize a GPU can be non-trivial for even relatively simple applications.}, keywords = {Acceleration, coprocessors, dataflow foundation, GNU radio, Graphics processing unit, graphics processor acceleration, Kernel, Libraries, multicore platforms, Multicore processing, PARALLEL PROCESSING, Pipelines, Protocols, software defined radio prototyping environment, software radio, stand-alone GPU accelerated library}, author = {Plishker,W. and Zaki, G.F. and Bhattacharyya, Shuvra S. and Clancy, C. and Kuykendall, J.} } @article {18547, title = {Architecting for innovation}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011///}, pages = {24 - 36}, abstract = {We argue that the biggest problem with the current Internet architecture is not a particular functional deficiency, but its inability to accommodate innovation. To address this problem we propose a minimal architectural "framework" in which comprehensive architectures can reside. The proposed Framework for Internet Innovation (FII) --- which is derived from the simple observation that network interfaces should be extensible and abstract --- allows for a diversity of architectures to coexist, communicate, and evolve. We demonstrate FII{\textquoteright}s ability to accommodate diversity and evolution with a detailed examination of how information flows through the architecture and with a skeleton implementation of the relevant interfaces.}, keywords = {diversity, Evolution, innovation, internet architecture}, isbn = {0146-4833}, doi = {10.1145/2002250.2002256}, url = {http://doi.acm.org/10.1145/2002250.2002256}, author = {Koponen,Teemu and Shenker,Scott and Balakrishnan,Hari and Feamster, Nick and Ganichev,Igor and Ghodsi,Ali and Godfrey,P. Brighten and McKeown,Nick and Parulkar,Guru and Raghavan,Barath and Rexford,Jennifer and Arianfar,Somaya and Kuptsov,Dmitriy} } @article {12114, title = {An assessment of systems and software engineering scholars and institutions (2003{\textendash}2007 and 2004{\textendash}2008)}, journal = {Journal of Systems and Software}, volume = {84}, year = {2011}, month = {2011/01//}, pages = {162 - 168}, abstract = {An ongoing, annual survey of publications in systems and software engineering identifies the top 15 scholars and institutions in the field over a 5-year period. Each ranking is based on the weighted scores of the number of papers published in TSE, TOSEM, JSS, SPE, EMSE, IST, and Software of the corresponding period. This report summarizes the results for 2003{\textendash}2007 and 2004{\textendash}2008. The top-ranked institution is Korea Advanced Institute of Science and Technology, Korea for 2003{\textendash}2007, and Simula Research Laboratory, Norway for 2004{\textendash}2008, while Magne J{\o}rgensen is the top-ranked scholar for both periods.}, keywords = {Research publications, Systems and software engineering, Top institutions, Top scholars}, isbn = {0164-1212}, doi = {10.1016/j.jss.2010.09.036}, url = {http://www.sciencedirect.com/science/article/pii/S0164121210002682}, author = {Wong,W. Eric and Tse,T.H. and Glass,Robert L. and Basili, Victor R. and Chen,T.Y.} } @inbook {18819, title = {Automated Planning Logic Synthesis for Autonomous Unmanned Vehicles in Competitive Environments with Deceptive Adversaries}, booktitle = {New Horizons in Evolutionary Robotics}, series = {Studies in Computational Intelligence}, volume = {341}, year = {2011}, month = {2011///}, pages = {171 - 193}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We developed a new approach for automated synthesis of a planning logic for autonomous unmanned vehicles. This new approach can be viewed as an automated iterative process during which an initial version of a logic is synthesized and then gradually improved by detecting and fixing its shortcomings. This is achieved by combining data mining for extraction of vehicle{\textquoteright}s states of failure and Genetic Programming (GP) technique for synthesis of corresponding navigation code. We verified the feasibility of the approach using unmanned surface vehicles (USVs) simulation. Our focus was specifically on the generation of a planning logic used for blocking the advancement of an intruder boat towards a valuable target. Developing autonomy logic for this behavior is challenging as the intruder{\textquoteright}s attacking logic is human-competitive with deceptive behavior so the USV is required to learn specific maneuvers for specific situations to do successful blocking. We compared the performance of the generated blocking logic to the performance of logic that was manually implemented. Our results show that the new approach was able to synthesize a blocking logic with performance closely approaching the performance of the logic coded by hand.}, keywords = {engineering}, isbn = {978-3-642-18271-6}, url = {http://www.springerlink.com/content/f454477212518671/abstract/}, author = {Svec,Petr and Gupta, Satyandra K.}, editor = {Doncieux,St{\'e}phane and Bred{\`e}che,Nicolas and Mouret,Jean-Baptiste} } @article {16247, title = {Bacillus Anthracis Comparative Genome Analysis in Support of the Amerithrax Investigation}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {108}, year = {2011}, month = {2011/03/22/}, pages = {5027 - 5032}, abstract = {Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on microbial genotyping schemes based on a small portion of a genome sequence. Amerithrax, the investigation into the anthrax letter attacks, applied high-resolution whole-genome sequencing and comparative genomics to identify key genetic features of the letters{\textquoteright} Bacillus anthracis Ames strain. During systematic microbiological analysis of the spore material from the letters, we identified a number of morphological variants based on phenotypic characteristics and the ability to sporulate. The genomes of these morphological variants were sequenced and compared with that of the B. anthracis Ames ancestor, the progenitor of all B. anthracis Ames strains. Through comparative genomics, we identified four distinct loci with verifiable genetic mutations. Three of the four mutations could be directly linked to sporulation pathways in B. anthracis and more specifically to the regulation of the phosphorylation state of Spo0F, a key regulatory protein in the initiation of the sporulation cascade, thus linking phenotype to genotype. None of these variant genotypes were identified in single-colony environmental B. anthracis Ames isolates associated with the investigation. These genotypes were identified only in B. anthracis morphotypes isolated from the letters, indicating that the variants were not prevalent in the environment, not even the environments associated with the investigation. This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.1016657108}, url = {http://www.pnas.org/content/108/12/5027}, author = {Rasko,David A and Worsham,Patricia L and Abshire,Terry G and Stanley,Scott T and Bannan,Jason D and Wilson,Mark R and Langham,Richard J and Decker,R. Scott and Jiang,Lingxia and Read,Timothy D. and Phillippy,Adam M and Salzberg,Steven L. and Pop, Mihai and Van Ert,Matthew N and Kenefic,Leo J and Keim,Paul S and Fraser-Liggett,Claire M and Ravel,Jacques} } @conference {12398, title = {Believe Me{\textemdash}We Can Do This! Annotating Persuasive Acts in Blog Text}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, author = {Anand,P. and King,J. and Jordan Boyd-Graber and Wagner,E. and Martell,C. and Oard, Douglas and Resnik, Philip} } @article {12984, title = {Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?}, journal = {Systematic BiologySyst Biol}, volume = {60}, year = {2011}, month = {2011/12/01/}, pages = {782 - 796}, abstract = {This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45\% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78{\textendash}85\% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A {\textquotedblleft}more-genes-only{\textquotedblright} data set (41 taxa{\texttimes}26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.}, keywords = {Ditrysia, gene sampling, Hexapoda, Lepidoptera, missing data, molecular phylogenetics, nuclear genes, taxon sampling}, isbn = {1063-5157, 1076-836X}, doi = {10.1093/sysbio/syr079}, url = {http://sysbio.oxfordjournals.org/content/60/6/782}, author = {Cho,Soowon and Zwick,Andreas and Regier,Jerome C and Mitter,Charles and Cummings, Michael P. and Yao,Jianxiu and Du,Zaile and Zhao,Hong and Kawahara,Akito Y and Weller,Susan and Davis,Donald R and Baixeras,Joaquin and Brown,John W and Parr,Cynthia} } @conference {12105, title = {A case study of measuring process risk for early insights into software safety}, booktitle = {Software Engineering (ICSE), 2011 33rd International Conference on}, year = {2011}, month = {2011/05//}, pages = {623 - 632}, abstract = {In this case study, we examine software safety risk in three flight hardware systems in NASA{\textquoteright}s Constellation spaceflight program. We applied our Technical and Process Risk Measurement (TPRM) methodology to the Constellation hazard analysis process to quantify the technical and process risks involving software safety in the early design phase of these projects. We analyzed 154 hazard reports and collected metrics to measure the prevalence of software in hazards and the specificity of descriptions of software causes of hazardous conditions. We found that 49-70\% of 154 hazardous conditions could be caused by software or software was involved in the prevention of the hazardous condition. We also found that 12-17\% of the 2013 hazard causes involved software, and that 23-29\% of all causes had a software control. The application of the TRPM methodology identified process risks in the application of the hazard analysis process itself that may lead to software safety risk.}, keywords = {analysis;software, and, computing;risk, constellation, control;software, Hardware, maintenance;, measurement;aerospace, measurement;software, NASA, process, program;TPRM;flight, risk, safety;technical, spaceflight, systems;process}, doi = {10.1145/1985793.1985881}, author = {Layman,L. and Basili, Victor R. and Zelkowitz, Marvin V and Fisher,K.L.} } @conference {18667, title = {Characterizing Attackers and Attacks: An Empirical Study}, year = {2011}, month = {2011/12//}, pages = {174 - 183}, abstract = {This paper describes an empirical research study to characterize attackers and attacks against targets of opportunity. A honey net infrastructure was built and deployed over 167 days that leveraged three different honey pot configurations and a SSH-based authentication proxy to attract and follow attackers over several weeks. A total of 211 attack sessions were recorded and evidence was collected at each stage of the attack sequence: from discovery to intrusion and exploitation of rogue software. This study makes two important contributions: 1) we introduce a new approach to measure attacker skills, and 2) we leverage keystroke profile analysis to differentiate attackers beyond their IP address of origin.}, keywords = {attack sessions, attacker characterization, attacker skill measurement, honey net infrastructure, honey pot configurations, IP address, keystroke profile analysis, opportunity target, rogue software exploitation, security of data, SSH-based authentication proxy}, doi = {10.1109/PRDC.2011.29}, author = {Salles-Loustau,G. and Berthier,R. and Collange,E. and Sobesto,B. and Michel Cukier} } @conference {14326, title = {CHI 2011 sustainability community invited panel: challenges ahead}, booktitle = {2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {73 - 76}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {As part of a new CHI Sustainability Community, focused on environmental sustainability, this panel will discuss specific ways in which HCI research will be critical in finding solutions to this global challenge. While research to date has primarily focused on the end consumer, the panel will be challenged with enlarging the discussion to include the designer as a target user and to consider interfaces and interactions that support sustainable design and sustainable manufacturing, as well as sustainable consumption. Specifically, to make real progress, we seek to enumerate ways that HCI needs to grow, as well as to find ways that can help more HCI researchers to become involved.}, keywords = {design, Environment, sustainability; community, user behavior}, doi = {10.1145/1979482.1979484}, url = {http://doi.acm.org/10.1145/1979482.1979484}, author = {Khan,Azam and Bartram,Lyn and Blevis,Eli and DiSalvo,Carl and Jon Froehlich and Kurtenbach,Gordon} } @article {12869, title = {Clonal transmission, dual peak, and off-season cholera in Bangladesh}, journal = {Infection Ecology \& Epidemiology}, volume = {1}, year = {2011}, month = {08/2011}, abstract = {Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March{\textendash}May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March{\textendash}May and September{\textendash}November) pattern in the city of Dhaka that is bordered by a heavily polluted freshwater river system and flood embankment. In August 2007, extreme flooding was accompanied by an unusually severe diarrhea outbreak in Dhaka that resulted in a record high illness. This study was aimed to understand the unusual outbreak and if it was related to the circulation of a new V. cholerae clone. Nineteen V. cholerae isolated during the peak of the 2007 outbreak were subjected to extensive phenotypic and molecular analyses, including multi-locus genetic screening by polymerase chain reaction (PCR), sequence-typing of the ctxB gene, and pulsed-field gel electrophoresis (PFGE). Factors associated with the unusual incidence of cholera were determined and analysis of the disease severity was done. Overall, microbiological and molecular data confirmed that the hypervirulent V. cholerae was O1 biotype El Tor (ET) that possessed cholera toxin (CT) of the classical biotype. The PFGE (NotI) and dendrogram clustering confirmed that the strains were clonal and related to the pre-2007 variant ET from Dhaka and Matlab and resembled one of two distinct clones of the variant ET confirmed to be present in the estuarine ecosystem of Bangladesh. Results of the analyses of both diarrheal case data for three consecutive years (2006{\textendash}2008) and regional hydroclimatology over three decades (1980{\textendash}2009) clearly indicate that the pattern of cholera occurring in Dhaka, and not seen at other endemic sites, was associated with flood waters transmitting the infectious clone circulating via the fecal-oral route during and between the dual seasonal cholera peaks in Dhaka. Circular river systems and flood embankment likely facilitate transmission of infectious V. cholerae throughout the year that leads to both sudden and off-season outbreaks in the densely populated urban ecosystem of Dhaka. Clonal recycling of hybrid El Tor with increasing virulence in a changing climate and in a region with a growing urban population represents a serious public health concern for Bangladesh.}, doi = {10.3402/iee.v1i0.7273}, author = {Alam,M. and Islam,A. and Bhuiyan,N. A. and Rahim,N. and Hossain,A. and Khan,G. Y. and Ahmed,D. and Watanabe,H. and Izumiya,H. and Faruque,A. S. G. and Rita R Colwell} } @conference {12401, title = {Comparing values and sentiment using Mechanical Turk}, booktitle = {Proceedings of the 2011 iConference}, series = {iConference {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {783 - 784}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Human values can help to explain people{\textquoteright}s sentiment toward current events. In this experiment, we compare people{\textquoteright}s values with their agreement or disagreement with paragraphs that were classified as either supporting or opposing a specific topic. We found that five value types have statistically significant agreement (p<0.001) for both the supporting and opposing paragraphs, in opposite directions. We hope to use these paragraph ratings to train an automatic text classifier to agree or disagree with paragraphs based on a specific value profile.}, keywords = {human values, sentiment analysis, text classification}, isbn = {978-1-4503-0121-3}, doi = {10.1145/1940761.1940903}, url = {http://doi.acm.org/10.1145/1940761.1940903}, author = {Templeton,Thomas Clay and Fleischmann,Kenneth R. and Jordan Boyd-Graber} } @conference {12986, title = {Computing the Tree of Life: Leveraging the Power of Desktop and Service Grids}, booktitle = {Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on}, year = {2011}, month = {2011/05//}, pages = {1896 - 1902}, abstract = {The trend in life sciences research, particularly in molecular evolutionary systematics, is toward larger data sets and ever-more detailed evolutionary models, which can generate substantial computational loads. Over the past several years we have developed a grid computing system aimed at providing researchers the computational power needed to complete such analyses in a timely manner. Our grid system, known as The Lattice Project, was the first to combine two models of grid computing - the service model, which mainly federates large institutional HPC resources, and the desktop model, which harnesses the power of PCs volunteered by the general public. Recently we have developed a "science portal" style web interface that makes it easier than ever for phylogenetic analyses to be completed using GARLI, a popular program that uses a maximum likelihood method to infer the evolutionary history of organisms on the basis of genetic sequence data. This paper describes our approach to scheduling thousands of GARLI jobs with diverse requirements to heterogeneous grid resources, which include volunteer computers running BOINC software. A key component of this system provides a priori GARLI runtime estimates using machine learning with random forests.}, keywords = {(artificial, (mathematics);user, analysis;science, BOINC, computation;grid, computational, computing, computing;information, computing;machine, data;grid, estimation;portals;trees, evolutionary, Grid, grids;service, handling;evolutionary, history;evolutionary, intelligence);maximum, interface;computational, interfaces;, jobs;HPC, learning;maximum, likelihood, load;Internet;data, method;molecular, model;genetic, model;substantial, portal;service, power;data, project;life, resource;lattice, resource;Web, sequence, services;learning, sets;evolutionary, software;GARLI, system;heterogeneous, systematics;phylogenetic, tree}, doi = {10.1109/IPDPS.2011.344}, author = {Bazinet,A. L and Cummings, Michael P.} } @conference {13531, title = {Correcting Errors in Digital Lexicographic Resources Using a Dictionary Manipulation Language}, booktitle = {Electronic lexicography in the 21st century: new applications for new users (eLEX2011)}, year = {2011}, month = {2011///}, pages = {297 - 301}, abstract = {We describe a paradigm for combining manual and automatic error correction of noisy structured lexicographic data. Modifications to the structure and underlying text of the lexicographic data are expressed in a simple, interpreted programming language. Dictionary Manipulation Language (DML) commands identify nodes by unique identifiers, and manipulations are performed using simple commands such as create, move, set text, etc. Corrected lexicons are produced by applying sequences of DML commands to the source version of the lexicon. DML commands can be written manually to repair one-off errors or generated automatically to correct recurring problems. We discuss advantages of the paradigm for the task of editing digital bilingual dictionaries.}, author = {Zajic, David and Maxwell,Michael and David Doermann and Rodrigues,Paul and Bloodgood,Michael} } @conference {13081, title = {Creating contextual help for GUIs using screenshots}, booktitle = {Proceedings of the 24th annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {145 - 154}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Contextual help is effective for learning how to use GUIs by showing instructions and highlights on the actual interface rather than in a separate viewer. However, end-users and third-party tech support typically cannot create contextual help to assist other users because it requires programming skill and source code access. We present a creation tool for contextual help that allows users to apply common computer skills-taking screenshots and writing simple scripts. We perform pixel analysis on screenshots to make this tool applicable to a wide range of applications and platforms without source code access. We evaluated the tool{\textquoteright}s usability with three groups of participants: developers, in-structors, and tech support. We further validated the applicability of our tool with 60 real tasks supported by the tech support of a university campus.}, keywords = {contextual help, help, pixel analysis}, isbn = {978-1-4503-0716-1}, doi = {10.1145/2047196.2047214}, url = {http://doi.acm.org/10.1145/2047196.2047214}, author = {Tom Yeh and Chang,Tsung-Hsiang and Xie,Bo and Walsh,Greg and Watkins,Ivan and Wongsuphasawat,Krist and Huang,Man and Davis, Larry S. and Bederson, Benjamin B.} } @article {19266, title = {Dataflow-based Design and Implementation of Image Processing Applications}, year = {2011}, month = {2011}, abstract = {Dataflow is a well known computational model and is widely used forexpressing the functionality of digital signal processing (DSP) applications, such as audio and video data stream processing, digital communications, and image processing. These applications usually require real-time processing capabilities and have critical performance constraints. Dataflow provides a formal mechanism for describing specifications of DSP applications, imposes minimal data-dependency constraints in specifications, and is effective in exposing and exploiting task or data level parallelism for achieving high performance implementations. To demonstrate dataflow-based design methods in a manner that is concrete and easily adapted to different platforms and back-end design tools, we present in this report a number of case studies based on the lightweight dataflow (LWDF) programming methodology. LWDF is designed as a "minimalistic" approach for integrating coarse grain dataflow programming structures into arbitrary simulation- or platform-oriented languages, such as C, C++, CUDA, MATLAB, SystemC, Verilog, and VHDL. In particular, LWDF requires minimal dependence on specialized tools or libraries. This feature --- together with the rigorous adherence to dataflow principles throughout the LWDF design framework --- allows designers to integrate and experiment with dataflow modeling approaches relatively quickly and flexibly into existing design methodologies and processes. }, keywords = {Technical Report}, isbn = {UMIACS-TR-2011-11}, doi = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/11403}, author = {Chung-Ching Shen and Plishker,William and Bhattacharyya, Shuvra S.} } @article {19273, title = {Dataflow-Based Implementation of Layered Sensing Applications}, year = {2011}, month = {2011}, abstract = {This report describes a new dataflow-based technology and associated design tools for high-productivity design, analysis, and optimization of layered sensing software for signal processing systems. Our approach provides novel capabilities, based on the principles of task-level dataflow analysis, for exploring and optimizing interactions across application behavior; operational context; high performance embedded processing platforms, and implementation constraints. Particularly, we introduce and deliver novel software tools, called the targeted dataflow interchange format (TDIF) and Dataflow Interchange Format Markup Language (DIFML), for design and implementation of layered sensing and signal processing systems. The TDIF-CUDA (Compute Unified Device Architecture) environment is a graphics processing unit targeted software synthesis tool that provides a unique integration of dynamic dataflow modeling; retargetable actor construction; software synthesis; and instrumentation-based schedule evaluation and tuning. The DIFML package is a software package for the DIFML format, which is an Extensible Markup Language (XML)-based format for exchanging information between DIF and other tools.}, keywords = {*COMPUTER AIDED DESIGN, *DATA FUSION, *DATAFLOW, *LAYERS, *SOFTWARE TOOLS, COMPUTER PROGRAMMING AND SOFTWARE, DETECTION, High performance computing, LAYERED SENSING, OPTIMIZATION, Signal processing, synthesis, T2KA}, author = {Bhattacharyya, Shuvra S. and Chung-Ching Shen and Plishker,William and Sane, Nimish and Wu, Hsiang-Huang and Gu, Ruirui} } @conference {17861, title = {Decentralized, accurate, and low-cost network bandwidth prediction}, booktitle = {2011 Proceedings IEEE INFOCOM}, year = {2011}, month = {2011/04/10/15}, pages = {6 - 10}, publisher = {IEEE}, organization = {IEEE}, abstract = {The distributed nature of modern computing makes end-to-end prediction of network bandwidth increasingly important. Our work is inspired by prior work that treats the Internet and bandwidth as an approximate tree metric space. This paper presents a decentralized, accurate, and low cost system that predicts pairwise bandwidth between hosts. We describe an algorithm to construct a distributed tree that embeds bandwidth measurements. The correctness of the algorithm is provable when driven by precise measurements. We then describe three novel heuristics that achieve high accuracy for predicting bandwidth even with imprecise input data. Simulation experiments with a real-world dataset confirm that our approach shows high accuracy with low cost.}, keywords = {accuracy, approximate tree metric space, Bandwidth, bandwidth allocation, bandwidth measurement, decentralized low cost system, distributed tree, end-to-end prediction, Extraterrestrial measurements, Internet, low-cost network bandwidth prediction, Measurement uncertainty, pairwise bandwidth, Peer to peer computing, Prediction algorithms, trees (mathematics)}, isbn = {978-1-4244-9919-9}, doi = {10.1109/INFCOM.2011.5935251}, author = {Sukhyun Song and Keleher,P. and Bhattacharjee, Bobby and Sussman, Alan} } @book {15188, title = {Decision and Game Theory for Security: Second International Conference, GameSec 2011, College Park, MD, Maryland, USA, November 14-15, 2011, Proceedings}, year = {2011}, month = {2011/12/27/}, publisher = {Springer}, organization = {Springer}, abstract = {This book constitutes the refereed proceedings of the Second International Conference on Decision and Game Theory for Security, GameSec 2011, held in College Park, Maryland, USA, in November 2011. The 16 revised full papers and 2 plenary keynotes presented were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on attacks, adversaries, and game theory, wireless adhoc and sensor networks, network games, security insurance, security and trust in social networks and security investments.}, keywords = {Business \& Economics / Information Management, Computers / Hardware / Network Hardware, Computers / Information Technology, Computers / Programming / Algorithms, Computers / Security / General, Mathematics / Applied, Mathematics / Game Theory, Mathematics / General}, isbn = {9783642252792}, author = {Baras,John S and Katz, Jonathan and Altman,Eitan} } @article {18827, title = {Design and fabrication of miniature compliant hinges for multi-material compliant mechanisms}, journal = {The International Journal of Advanced Manufacturing Technology}, volume = {57}, year = {2011}, month = {2011///}, pages = {437 - 452}, abstract = {Multi-material molding (MMM) enables the creation of multi-material mechanisms that combine compliant hinges, serving as revolute joints, and rigid links in a single part. There are three important challenges in creating these structures: (1) bonding between the materials used, (2) the ability of the hinge to transfer the required loads in the mechanism while allowing for the prescribed degree(s) of freedom, and (3) incorporating the process-specific requirements in the design stage. This paper presents the approach for design and fabrication of miniature compliant hinges in multi-material compliant mechanisms. The methodology described in this paper allows for the concurrent design of the part and the manufacturing process. For the first challenge, mechanical interlocking strategies are presented. For the second challenge, the development of a simulation-based optimization model of the hinge is presented, involving functional and manufacturing constrains. For the third challenge, the development of hinge positioning features and gate positioning constraints is presented. The developed MMM process is described, along with the main constraints and performance measures. This includes the process sequence, the mold cavity design, gate selection, and runner system development. A case study is presented to demonstrate the feasibility of creating multi-material mechanisms with miniature hinges serving as joints through MMM process. The approach described in this paper was utilized to design a drive mechanism for a flapping wing micro air vehicle. The methods described in this paper are applicable to any lightweight, load-bearing compliant mechanism manufactured using multi-material injection molding.}, keywords = {engineering}, isbn = {0268-3768}, doi = {10.1007/s00170-011-3301-y}, url = {http://www.springerlink.com/content/ul641k1v50360607/abstract/}, author = {Bejgerowski,Wojciech and Gerdes,John and Gupta, Satyandra K. and Bruck,Hugh} } @conference {19260, title = {Design methods for Wireless Sensor Network Building Energy Monitoring Systems}, booktitle = {2011 IEEE 36th Conference on Local Computer Networks (LCN)}, year = {2011}, month = {2011}, pages = {974 - 981}, abstract = {In this paper, we present a new energy analysis method for evaluating energy consumption of embedded sensor nodes at the application level and the network level. Then we apply the proposed energy analysis method to develop new energy management schemes in order to maximize lifetime for Wireless Sensor Network Building Energy Monitoring Systems (WSNBEMS). At the application level, we develop a new design approach that uses dataflow techniques to model the application-level interfacing behavior between the processor and sensors on an embedded sensor node. At the network level, we analyze the energy consumption of the IEEE 802.15.4 MAC functionality. Based on our techniques for modeling and energy analysis, we have implemented an optimized WSNBEMS for a real building, and validated our energy analysis techniques through measurements on this implementation. The performance of our implementation is also evaluated in terms of monitoring accuracy and energy consumption savings. We have demonstrated that by applying the proposed scheme, system lifetime can be improved significantly without affecting monitoring accuracy.}, keywords = {Analytical models, application-level interfacing behavior, building energy monitoring system, Buildings, dataflow technique, embedded sensor node, energy analysis method, Energy consumption, energy management systems, Energy resolution, IEEE 802.15.4 MAC functionality, Monitoring, OPTIMIZATION, wireless sensor network, Wireless sensor networks, WSNBEMS, Zigbee}, author = {Cho, Inkeun and Chung-Ching Shen and Potbhare, S. and Bhattacharyya, Shuvra S. and Goldsman,N.} } @conference {19263, title = {A design tool for efficient mapping of multimedia applications onto heterogeneous platforms}, booktitle = {2011 IEEE International Conference on Multimedia and Expo (ICME)}, year = {2011}, month = {2011}, pages = {1 - 6}, abstract = {Development of multimedia systems on heterogeneous platforms is a challenging task with existing design tools due to a lack of rigorous integration between high level abstract modeling, and low level synthesis and analysis. In this paper, we present a new dataflow-based design tool, called the targeted dataflow interchange format (TDIF), for design, analysis, and implementation of embedded software for multimedia systems. Our approach provides novel capabilities, based on the principles of task-level dataflow analysis, for exploring and optimizing interactions across application behavior; operational context; heterogeneous platforms, including high performance embedded processing architectures; and implementation constraints.}, keywords = {Dataflow graphs, design tools, embedded signal processing, software synthesis}, author = {Chung-Ching Shen and Wu, Hsiang-Huang and Sane, N. and Plishker,W. and Bhattacharyya, Shuvra S.} } @conference {13535, title = {Detecting Structural Irregularity in Electronic Dictionaries Using Language Modeling}, booktitle = {Electronic lexicography in the 21st century: new applications for new users (eLEX2011)}, year = {2011}, month = {2011///}, pages = {227 - 232}, abstract = {Dictionaries are often developed using Extensible Markup Language (XML)-based standards. Very often, these standards allow many high-level repeating elements to represent lexical entries, and utilize descendants of these repeating elements to represent the structure within each lexical entry, in the form of an XML tree. In many cases, dictionaries are published that have errors and inconsistencies that would be too expensive to find manually. This paper discusses a method for dictionary writers to audit structural regularity across entries in a dictionary, quickly, by using statistical language modelling. The approach learns the patterns of XML nodes that could occur within an XML tree, and then calculates the probability of each XML tree in the dictionary against these patterns to look for entries that diverge from the norm.}, author = {Rodrigues,Paul and Zajic, David and Bloodgood,Michael and Ye,Peng and David Doermann} } @article {15470, title = {Developing a Single Model and Test Prioritization Strategies for Event-Driven Software}, journal = {Software Engineering, IEEE Transactions on}, volume = {37}, year = {2011}, month = {2011///}, pages = {48 - 64}, abstract = {Event-Driven Software (EDS) can change state based on incoming events; common examples are GUI and Web applications. These EDSs pose a challenge to testing because there are a large number of possible event sequences that users can invoke through a user interface. While valuable contributions have been made for testing these two subclasses of EDS, such efforts have been disjoint. This work provides the first single model that is generic enough to study GUI and Web applications together. In this paper, we use the model to define generic prioritization criteria that are applicable to both GUI and Web applications. Our ultimate goal is to evolve the model and use it to develop a unified theory of how all EDS should be tested. An empirical study reveals that the GUI and Web-based applications, when recast using the new model, show similar behavior. For example, a criterion that gives priority to all pairs of event interactions did well for GUI and Web applications; another criterion that gives priority to the smallest number of parameter value settings did poorly for both. These results reinforce our belief that these two subclasses of applications should be modeled and studied together.}, keywords = {EDS, event-driven software, graphical user interface, Graphical user interfaces, GUI testing, Internet, program testing, service-oriented architecture, test prioritization strategy, Web application testing}, isbn = {0098-5589}, doi = {10.1109/TSE.2010.12}, author = {Bryce,R.C. and Sampath,S. and Memon, Atif M.} } @article {19656, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization}, journal = {Nature Medicine}, volume = {17}, year = {2011}, month = {2011/09//}, pages = {1101 - 1108}, abstract = {Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin{\textendash}dependent epithelial traits and Sec23a-mediated tumor cell secretome.View full text }, isbn = {1078-8956}, url = {http://www.nature.com/nm/journal/v17/n9/abs/nm.2401.html}, author = {Korpal, Manav and Ell, Brian J. and Buffa, Francesca M. and Ibrahim, Toni and Blanco, Mario A. and Celi{\`a}-Terrassa, Toni and Mercatali, Laura and Zia Khan and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A. and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L. and Kang, Yibin} } @inbook {12455, title = {Distributed Sensing and Processing for Multi-Camera Networks}, booktitle = {Distributed Video Sensor NetworksDistributed Video Sensor Networks}, year = {2011}, month = {2011///}, pages = {85 - 101}, publisher = {Springer London}, organization = {Springer London}, abstract = {Sensor networks with large numbers of cameras are becoming increasingly prevalent in a wide range of applications, including video conferencing, motion capture, surveillance, and clinical diagnostics. In this chapter, we identify some of the fundamental challenges in designing such systems: robust statistical inference, computationally efficiency, and opportunistic and parsimonious sensing. We show that the geometric constraints induced by the imaging process are extremely useful for identifying and designing optimal estimators for object detection and tracking tasks. We also derive pipelined and parallelized implementations of popular tools used for statistical inference in non-linear systems, of which multi-camera systems are examples. Finally, we highlight the use of the emerging theory of compressive sensing in reducing the amount of data sensed and communicated by a camera network.}, isbn = {978-0-85729-127-1}, url = {http://dx.doi.org/10.1007/978-0-85729-127-1_6}, author = {Sankaranarayanan,Aswin C. and Chellapa, Rama and Baraniuk,Richard G.}, editor = {Bhanu,Bir and Ravishankar,Chinya V. and Roy-Chowdhury,Amit K. and Aghajan,Hamid and Terzopoulos,Demetri} } @article {19267, title = {The DSPCAD Integrative Command Line Environment: Introduction to DICE Version 1.1}, year = {2011}, month = {2011}, abstract = {DICE (the DSPCAD Integrative Command Line Environment) is a package of utilities that facilitates efficient management of software projects. Key areas of emphasis in DICE are cross-platform operation, support for projects that integrate heterogeneous programming languages, and support for applying and integrating different kinds of design and testing methodologies. The package is being developed at the University of Maryland to facilitate the research and teaching of methods for implementation, testing, evolution, and revision of engineering software. The package is also being developed as a foundation for developing experimental research software for techniques and tools in the area of computer-aided design (CAD) of digital signal processing (DSP) systems. The package is intended for cross-platform operation, and is currently being developed and used actively on the Linux, Mac OS, Solaris, and Windows (equipped with Cygwin) platforms. This report provides an introduction to DICE, and provides background on some of the key features in DICE Version 1.1. This report also gives a brief introduction to dicelang, which is a plug-in package for DICE that provides additional utilities, libraries, and tools for managing software projects in specific programming languages.}, keywords = {*SOFTWARE ENGINEERING, COMPUTER PROGRAMMING, COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER PROGRAMS, DICE(COMPUTER PROGRAM), programming languages, Project management}, author = {Bhattacharyya, Shuvra S. and Plishker,William and Chung-Ching Shen and Sane, Nimish and Zaki, George} } @article {19257, title = {The DSPCAD Lightweight Dataflow Environment: Introduction to LIDE Version 0.1}, year = {2011}, month = {2011}, abstract = {LIDE (the DSPCAD Lightweight Dataflow Environment) is a flexible,lightweight design environment that allows designers to experiment with dataflow-based approaches for design and implementation of digital signal processing (DSP) systems. LIDE contains libraries of dataflow graph elements (primitive actors, hierarchical actors, and edges) and utilities that assist designers in modeling, simulating, and implementing DSP systems using formal dataflow techniques. The libraries of dataflow graph elements (mainly actors) contained in LIDE provide useful building blocks that can be used to construct signal processing applications, and that can be used as examples that designers can adapt to create their own, customized LIDE actors. Furthermore, by using LIDE along with the DSPCAD Integrative Command Line Environment (DICE), designers can efficiently create and execute unit tests for user-designed actors. This report provides an introduction to LIDE. The report includes details on the process for setting up the LIDE environment, and covers methods for using pre-designed libraries of graph elements, as well as creating user-designed libraries and associated utilities using the C language. The report also gives an introduction to the C language plug-in for dicelang. This plug-in, called dicelang-C, provides features for efficient C-based project development and maintenance that are useful to apply when working with LIDE. }, keywords = {Technical Report}, isbn = {UMIACS-TR-2011-17}, doi = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/12147}, author = {Chung-Ching Shen and Wang, Lai-Huei and Cho, Inkeun and Kim, Scott and Won, Stephen and Plishker,William and Bhattacharyya, Shuvra S.} } @article {14430, title = {Dynamic Processing Allocation in Video}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {33}, year = {2011}, month = {2011/11//}, pages = {2174 - 2187}, abstract = {Large stores of digital video pose severe computational challenges to existing video analysis algorithms. In applying these algorithms, users must often trade off processing speed for accuracy, as many sophisticated and effective algorithms require large computational resources that make it impractical to apply them throughout long videos. One can save considerable effort by applying these expensive algorithms sparingly, directing their application using the results of more limited processing. We show how to do this for retrospective video analysis by modeling a video using a chain graphical model and performing inference both to analyze the video and to direct processing. We apply our method to problems in background subtraction and face detection, and show in experiments that this leads to significant improvements over baseline algorithms.}, keywords = {algorithms;digital, allocation;video, analysis;computer, background, detection;graphical, detection;resource, graphics;face, model;resource, processing;, processing;face, recognition;object, signal, subtraction;baseline, video}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2011.55}, author = {Daozheng Chen and Bilgic,M. and Getoor, Lise and Jacobs, David W.} } @article {14485, title = {Eighth workshop on mining and learning with graphs}, journal = {SIGKDD Explor. Newsl.}, volume = {12}, year = {2011}, month = {2011/03//}, pages = {63 - 65}, abstract = {The Eighth Workshop on Mining and Learning with Graphs (MLG)1was held at KDD 2010 in Washington DC. It brought together a variete of researchers interested in analyzing data that is best represented as a graph. Examples include the WWW, social networks, biological networks, communication networks, and many others. The importance of being able to effectively mine and learn from such data is growing, as more and more structured and semi-structured data is becoming available. This is a problem across widely different fields such as economics, statistics, social science, physics and computer science, and is studied within a variety of sub-disciplines of machine learning and data mining including graph mining, graphical models, kernel theory, statistical relational learning, etc. The objective of this workshop was to bring together practitioners from these various fields and areas to foster a rich discussion of which problems we work on, how we frame them in the context of graphs, which tools and algorithms we apply and our general findings and lessons learned. This year{\textquoteright}s workshop was very successful with well over 100 attendees, excellent keynote speakers and papers. This is a rapidly growing area and we believe that this community is only in its infancy. We hope that the readers will join us next year for MLG 2011.}, keywords = {data mining, dynamic network analysis, graph mining, kernel methods, link mining, machine learning, network analysis, pattern recognition, relational learning, scalable graph mining, statistical relational learning}, isbn = {1931-0145}, doi = {10.1145/1964897.1964915}, url = {http://doi.acm.org/10.1145/1964897.1964915}, author = {Brefeld,Ulf and Getoor, Lise and Macskassy,Sofus A.} } @article {16040, title = {Empirical Studies in Information Visualization: Seven Scenarios}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {PP}, year = {2011}, month = {2011///}, pages = {1 - 1}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluating visual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, evaluating visualization algorithms, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios distinguish different study goals and types of research questions and are illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. Scenarios can be used to choose appropriate research questions and goals and the provided examples can be consulted for guidance on how to design one{\textquoteright}s own study.}, isbn = {1077-2626}, doi = {10.1109/TVCG.2011.279}, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @article {18526, title = {The Evolution of Network Configuration: A Tale of Two Campuses}, journal = {Networks}, volume = {7}, year = {2011}, month = {2011///}, pages = {18 - 18}, abstract = {Studying network configuration evolution can improve our under- standing of the evolving complexity of networks and can be helpful in making network configuration less error-prone. Unfortunately, the nature of changes that operators make to network configuration is poorly understood. Towards improving our understanding, we examine and analyze five years of router, switch, and firewall con- figurations from two large campus networks using the logs from version control systems used to store the configurations. We study how network configuration is distributed across different network operations tasks and how the configuration for each task evolves over time, for different types of devices and for different loca- tions in the network. To understand the trends of how configura- tion evolves over time, we study the extent to which configuration for various tasks are added, modified, or deleted. We also study whether certain devices experience configuration changes more fre- quently than others, as well as whether configuration changes tend to focus on specific portions of the configuration (or on specific tasks). We also investigate when network operators make configu- ration changes of various types. Our results concerning configura- tion changes can help the designers of configuration languages un- derstand which aspects of configuration might be more automated or tested more rigorously and may ultimately help improve config- uration languages.}, author = {Kim,H. and Benson,T. and Akella,A. and Feamster, Nick} } @article {19272, title = {Exploiting Statically Schedulable Regions in Dataflow Programs}, journal = {Journal of Signal Processing Systems}, volume = {63}, year = {2011}, month = {2011}, pages = {129 - 142}, abstract = {Dataflow descriptions have been used in a wide range of Digital Signal Processing (DSP) applications, such as multi-media processing, and wireless communications. Among various forms of dataflow modeling, Synchronous Dataflow (SDF) is geared towards static scheduling of computational modules, which improves system performance and predictability. However, many DSP applications do not fully conform to the restrictions of SDF modeling. More general dataflow models, such as CAL (Eker and Janneck 2003), have been developed to describe dynamically-structured DSP applications. Such generalized models can express dynamically changing functionality, but lose the powerful static scheduling capabilities provided by SDF. This paper focuses on the detection of SDF-like regions in dynamic dataflow descriptions{\textemdash}in particular, in the generalized specification framework of CAL. This is an important step for applying static scheduling techniques within a dynamic dataflow framework. Our techniques combine the advantages of different dataflow languages and tools, including CAL (Eker and Janneck 2003), DIF (Hsu et al. 2005) and CAL2C (Roquier et al. 2008). In addition to detecting SDF-like regions, we apply existing SDF scheduling techniques to exploit the static properties of these regions within enclosing dynamic dataflow models. Furthermore, we propose an optimized approach for mapping SDF-like regions onto parallel processing platforms such as multi-core processors.}, keywords = {Cal, Circuits and Systems, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow, DIF, Electrical Engineering, Image Processing and Computer Vision, multicore processors, pattern recognition, Quasi-static scheduling, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-009-0445-1}, author = {Gu, Ruirui and Janneck, J{\"o}rn W. and Raulet, Micka{\"e}l and Bhattacharyya, Shuvra S.} } @inbook {12462, title = {Face Tracking and Recognition in a Camera Network}, booktitle = {Multibiometrics for Human IdentificationMultibiometrics for Human Identification}, year = {2011}, month = {2011///}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, isbn = {9780511921056}, url = {http://dx.doi.org/10.1017/CBO9780511921056}, author = {Bhanu,Bir and Govindaraju,Venu} } @article {15752, title = {Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {79}, year = {2011}, month = {2011/07/01/}, pages = {2268 - 2281}, abstract = {We present and evaluate a rigid-body, deterministic, molecular docking method, called ELMDOCK, that relies solely on the three-dimensional structure of the individual components and the overall rotational diffusion tensor of the complex, obtained from nuclear spin-relaxation measurements. We also introduce a docking method, called ELMPATIDOCK, derived from ELMDOCK and based on the new concept of combining the shape-related restraints from rotational diffusion with those from residual dipolar couplings, along with ambiguous contact/interface-related restraints obtained from chemical shift perturbations. ELMDOCK and ELMPATIDOCK use two novel approximations of the molecular rotational diffusion tensor that allow computationally efficient docking. We show that these approximations are accurate enough to properly dock the two components of a complex without the need to recompute the diffusion tensor at each iteration step. We analyze the accuracy, robustness, and efficiency of these methods using synthetic relaxation data for a large variety of protein-protein complexes. We also test our method on three protein systems for which the structure of the complex and experimental relaxation data are available, and analyze the effect of flexible unstructured tails on the outcome of docking. Additionally, we describe a method for integrating the new approximation methods into the existing docking approaches that use the rotational diffusion tensor as a restraint. The results show that the proposed docking method is robust against experimental errors in the relaxation data or structural rearrangements upon complex formation and is computationally more efficient than current methods. The developed approximations are accurate enough to be used in structure refinement protocols. Proteins 2011; {\textcopyright} 2011 Wiley-Liss, Inc.}, keywords = {diffusion-guided molecular assembly, ellipsoid model, ELM, PATI, protein complexes, residual dipolar couplings, rigid-body docking}, isbn = {1097-0134}, doi = {10.1002/prot.23053}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.23053/full}, author = {Berlin,Konstantin and O{\textquoteright}Leary, Dianne P. and Fushman, David} } @book {15187, title = {GameSec{\textquoteright}11: Proceedings of the Second international conference on Decision and Game Theory for Security}, year = {2011}, month = {2011///}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, isbn = {978-3-642-25279-2}, editor = {Baras,John S and Katz, Jonathan and Altman,Eitan} } @conference {17184, title = {HCI for peace: from idealism to concrete steps}, booktitle = {PART 2 {\textemdash}{\textemdash}{\textemdash}{\textendash} Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {613 - 616}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This panel will contribute diverse perspectives on the use of computer technology to promote peace and prevent armed conflict. These perspectives include: the use of social media to promote democracy and citizen participation, the role of computers in helping people communicate across division lines in zones of conflict, how persuasive technology can promote peace, and how interaction design can play a role in post-conflict reconciliation.}, keywords = {cyprus, peace, persuasive technology, post-conflict reconciliation, social media, value sensitive design, war}, doi = {10.1145/1979482.1979493}, url = {http://doi.acm.org/10.1145/1979482.1979493}, author = {Hourcade,Juan Pablo and Bullock-Rest,Natasha E. and Friedman,Batya and Nelson,Mark and Shneiderman, Ben and Zaphiris,Panayiotis} } @inbook {19277, title = {Heterogeneous Design in Functional DIF}, booktitle = {Transactions on High-Performance Embedded Architectures and Compilers IV}, series = {Lecture Notes in Computer Science}, year = {2011}, month = {2011}, pages = {391 - 408}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Dataflow formalisms have provided designers of digital signal processing (DSP) systems with analysis and optimizations for many years. As system complexity increases, designers are relying on more types of dataflow models to describe applications while retaining these implementation benefits. The semantic range of DSP-oriented dataflow models has expanded to cover heterogeneous models and dynamic applications, but efficient design, simulation, and scheduling of such applications has not. To facilitate implementing heterogeneous applications, we utilize a new dataflow model of computation and show how actors designed in other dataflow models are directly supported by this framework, allowing system designers to immediately compose and simulate actors from different models. Using examples, we show how this approach can be applied to quickly describe and functionally simulate a heterogeneous dataflow-based application such that a designer may analyze and tune trade-offs among different models and schedules for simulation time, memory consumption, and schedule size.}, keywords = {Arithmetic and Logic Structures, Computer Communication Networks, Dataflow, heterogeneous, Input/Output and Data Communications, Logic Design, Processor Architectures, Programming Languages, Compilers, Interpreters, Signal processing}, isbn = {978-3-642-24567-1, 978-3-642-24568-8}, url = {http://link.springer.com/chapter/10.1007/978-3-642-24568-8_20}, author = {Plishker,William and Sane, Nimish and Kiemb, Mary and Bhattacharyya, Shuvra S.}, editor = {Stenstr{\"o}m, Per} } @article {13942, title = {A Hierarchical Algorithm for Fast Debye Summation with Applications to Small Angle Scattering}, journal = {Technical Reports from UMIACS}, year = {2011}, month = {2011/09/01/}, abstract = {Debye summation, which involves the summation of sinc functions of distances between all pair of atoms in three dimensional space, arises in computations performed in crystallography, small/wide angle X-ray scattering (SAXS/WAXS) and small angle neutron scattering (SANS). Direct evaluation of Debye summation has quadratic complexity, which results in computational bottleneck when determining crystal properties, or running structure refinement protocols that involve SAXS or SANS, even for moderately sized molecules. We present a fast approximation algorithm that efficiently computes the summation to any prescribed accuracy epsilon in linear time. The algorithm is similar to the fast multipole method (FMM), and is based on a hierarchical spatial decomposition of the molecule coupled with local harmonic expansions and translation of these expansions. An even more efficient implementation is possible when the scattering profile is all that is required, as in small angle scattering reconstruction (SAS) of macromolecules. We examine the relationship of the proposed algorithm to existing approximate methods for profile computations, and provide detailed description of the algorithm, including error bounds and algorithms for stable computation of the translation operators. Our theoretical and computational results show orders of magnitude improvement in computation complexity over existing methods, while maintaining prescribed accuracy.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/11857}, author = {Gumerov, Nail A. and Berlin,Konstantin and Fushman, David and Duraiswami, Ramani} } @article {14865, title = {Illumination modeling for face recognition}, journal = {Handbook of face recognition}, year = {2011}, month = {2011///}, pages = {169 - 195}, abstract = {In this chapter, we show that effective systems can account for the effects of lighting using fewer than 10 degrees of freedom. This can have considerable impact on the speed and accuracy of recognition systems. We will describe theoretical results that, with some simplifying assumptions, prove the validity of low-dimensional, linear approximations to the set of images produced by a face.}, doi = {10.1007/978-0-85729-932-1_7}, author = {Basri,R. and Jacobs, David W.} } @conference {12446, title = {Illumination robust dictionary-based face recognition}, booktitle = {2011 18th IEEE International Conference on Image Processing (ICIP)}, year = {2011}, month = {2011/09/11/14}, pages = {777 - 780}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we present a face recognition method based on simultaneous sparse approximations under varying illumination. Our method consists of two main stages. In the first stage, a dictionary is learned for each face class based on given training examples which minimizes the representation error with a sparseness constraint. In the second stage, a test image is projected onto the span of the atoms in each learned dictionary. The resulting residual vectors are then used for classification. Furthermore, to handle changes in lighting conditions, we use a relighting approach based on a non-stationary stochastic filter to generate multiple images of the same person with different lighting. As a result, our algorithm has the ability to recognize human faces with good accuracy even when only a single or a very few images are provided for training. The effectiveness of the proposed method is demonstrated on publicly available databases and it is shown that this method is efficient and can perform significantly better than many competitive face recognition algorithms.}, keywords = {albedo, approximation theory, classification, competitive face recognition algorithms, Databases, Dictionaries, Face, face recognition, face recognition method, filtering theory, human face recognition, illumination robust dictionary-based face recognition, illumination variation, image representation, learned dictionary, learning (artificial intelligence), lighting, lighting conditions, multiple images, nonstationary stochastic filter, publicly available databases, relighting, relighting approach, representation error, residual vectors, Robustness, simultaneous sparse approximations, simultaneous sparse signal representation, sparseness constraint, Training, varying illumination, vectors}, isbn = {978-1-4577-1304-0}, doi = {10.1109/ICIP.2011.6116670}, author = {Patel, Vishal M. and Tao Wu and Biswas,S. and Phillips,P.J. and Chellapa, Rama} } @inbook {19034, title = {Implicit Authentication through Learning User Behavior}, booktitle = {Information Security}, series = {Lecture Notes in Computer Science}, volume = {6531}, year = {2011}, month = {2011}, pages = {99 - 113}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Users are increasingly dependent on mobile devices. However, current authentication methods like password entry are significantly more frustrating and difficult to perform on these devices, leading users to create and reuse shorter passwords and pins, or no authentication at all. We present implicit authentication - authenticating users based on behavior patterns. We describe our model for performing implicit authentication and assess our techniques using more than two weeks of collected data from over 50 subjects.}, keywords = {Computer science}, isbn = {978-3-642-18177-1}, url = {http://www.springerlink.com/content/m57u551u3133475m/abstract/}, author = {Elaine Shi and Niu, Yuan and Jakobsson, Markus and Chow, Richard}, editor = {Burmester, Mike and Tsudik, Gene and Magliveras, Spyros and Ilic, Ivana} } @article {19689, title = {Interactive topic modeling}, year = {2011}, month = {2011/00/19}, pages = {248 - 257}, publisher = {Association for Computational Linguistics}, abstract = {Abstract Topic models have been used extensively as a tool for corpus exploration, and a cottage industry has developed to tweak topic models to better encode human intuitions or to better model data. However, creating such extensions requires expertise in machine ...}, url = {http://dl.acm.org/citation.cfm?id=2002472.2002505}, author = {Hu, Yuening and Jordan Boyd-Graber and Satinoff, Brianna} } @conference {12218, title = {IP geolocation in metropolitan areas}, booktitle = {Proceedings of the ACM SIGMETRICS joint international conference on Measurement and modeling of computer systems}, series = {SIGMETRICS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {155 - 156}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Current IP geoloation techniques can geolocate an IP address to a region approximately 700 square miles, roughly the size of a metropolitan area. We model geolocation as a pattern-recognition problem, and introduce techniques that geolocate addresses to within 5 miles inside a metropolitan area. We propose two complementary algorithms: The first algorithm, Pattern Based Geolocation (PBG), models the distribution of latencies to the target and compares it to those of the reference landmarks to resolve an address to within 5 miles in a metropolitan area. The second approach, Perturbation Augmented PBG (PAPBG), provides higher resolution by sending extra traffic in the network. While sending an aggregate of 600 Kbps extra traffic to 20 nodes for approximately 2 minutes, PAPBG geolocates addresses to within 3 miles.}, keywords = {geolocation, pattern recognition, perturbation}, isbn = {978-1-4503-0814-4}, doi = {10.1145/1993744.1993803}, url = {http://doi.acm.org/10.1145/1993744.1993803}, author = {Singh,Satinder Pal and Baden,Randolph and Lee,Choon and Bhattacharjee, Bobby and La,Richard and Shayman,Mark} } @article {13274, title = {An iterative algorithm for homology computation on simplicial shapes}, journal = {Computer-Aided Design}, volume = {43}, year = {2011}, month = {2011/11//}, pages = {1457 - 1467}, abstract = {We propose a new iterative algorithm for computing the homology of arbitrary shapes discretized through simplicial complexes. We demonstrate how the simplicial homology of a shape can be effectively expressed in terms of the homology of its sub-components. The proposed algorithm retrieves the complete homological information of an input shape including the Betti numbers, the torsion coefficients and the representative homology generators.To the best of our knowledge, this is the first algorithm based on the constructive Mayer{\textendash}Vietoris sequence, which relates the homology of a topological space to the homologies of its sub-spaces, i.e. the sub-components of the input shape and their intersections. We demonstrate the validity of our approach through a specific shape decomposition, based only on topological properties, which minimizes the size of the intersections between the sub-components and increases the efficiency of the algorithm. }, keywords = {Computational topology, Generators, Mayer{\textendash}Vietoris sequence, shape decomposition, simplicial complexes, Z -homology}, isbn = {0010-4485}, doi = {10.1016/j.cad.2011.08.015}, url = {http://www.sciencedirect.com/science/article/pii/S0010448511002144}, author = {Boltcheva,Dobrina and Canino,David and Merino Aceituno,Sara and L{\'e}on,Jean-Claude and De Floriani, Leila and H{\'e}troy,Franck} } @article {15167, title = {Limits on the power of zero-knowledge proofs in cryptographic constructions}, journal = {Theory of Cryptography}, year = {2011}, month = {2011///}, pages = {559 - 578}, abstract = {For over 20 years, black-box impossibility results have been used to argue the infeasibility of constructing certain cryptographic primitives (e.g., key agreement) from others (e.g., one-way functions). A widely recognized limitation of such impossibility results, however, is that they say nothing about the usefulness of (known) nonblack-box techniques. This is unsatisfying, as we would at least like to rule out constructions using the set of techniques we have at our disposal.With this motivation in mind, we suggest a new framework for black-box constructions that encompasses constructions with a nonblack-box flavor: specifically, those that rely on zero-knowledge proofs relative to some oracle. We show that our framework is powerful enough to capture the Naor-Yung/Sahai paradigm for building a (shielding) CCA-secure public-key encryption scheme from a CPA-secure one, something ruled out by prior black-box separation results. On the other hand, we show that several black-box impossibility results still hold even in a setting that allows for zero-knowledge proofs. }, doi = {10.1007/978-3-642-19571-6_34}, author = {Brakerski,Z. and Katz, Jonathan and Segev,G. and Yerukhimovich,A.} } @conference {14830, title = {Localizing parts of faces using a consensus of exemplars}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {545 - 552}, abstract = {We present a novel approach to localizing parts in images of human faces. The approach combines the output of local detectors with a non-parametric set of global models for the part locations based on over one thousand hand-labeled exemplar images. By assuming that the global models generate the part locations as hidden variables, we derive a Bayesian objective function. This function is optimized using a consensus of models for these hidden variables. The resulting localizer handles a much wider range of expression, pose, lighting and occlusion than prior ones. We show excellent performance on a new dataset gathered from the internet and show that our localizer achieves state-of-the-art performance on the less challenging BioID dataset.}, keywords = {Bayesian, faces;lighting;occlusion;pose;Bayes, function;exemplar, images;expression;face, localization;human, methods;face, objective, part, recognition;}, doi = {10.1109/CVPR.2011.5995602}, author = {Belhumeur,P. N. and Jacobs, David W. and Kriegman, D.J. and Kumar,N.} } @article {12864, title = {Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios}, journal = {The ISME Journal}, volume = {6}, year = {2011}, month = {2011/07/14/}, pages = {21 - 30}, abstract = {The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45\% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, doi = {10.1038/ismej.2011.89}, url = {http://www.nature.com/ismej/journal/v6/n1/full/ismej201189a.html?WT.ec_id=ISMEJ-201201}, author = {Vezzulli,Luigi and Brettar,Ingrid and Pezzati,Elisabetta and Reid,Philip C. and Rita R Colwell and H{\"o}fle,Manfred G. and Pruzzo,Carla} } @conference {17904, title = {MDMap: A system for data-driven layout and exploration of molecular dynamics simulations}, booktitle = {Biological Data Visualization (BioVis), 2011 IEEE Symposium on}, year = {2011}, month = {2011/10//}, pages = {111 - 118}, abstract = {Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. The transitions amongst the states together with their frequencies represent the flow of a biomolecule through the trajectory space. MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. We compare and contrast multiple presentations of the state transition diagrams, such as conformational embedding, and spectral, hierarchical, and force-directed graph layouts. We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains.}, keywords = {computing;digital, driven, DYNAMICS, exploration;data, folding, graph;stochastic, landscapes;data, layout;molecular, MDMap;biomolecular, method;stochastic, processes;, simulation;graph, simulations;state, simulations;trajectory, space;biology, theory;molecular, time-varying, transition}, doi = {10.1109/BioVis.2011.6094055}, author = {Patro,R. and Ip, Cheuk Yiu and Bista,S. and Cho,S.S. and Thirumalai,D. and Varshney, Amitabh} } @article {16039, title = {Medication Reconciliation: Work Domain Ontology, Prototype Development, and a Predictive Model}, journal = {AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc}, volume = {2011}, year = {2011}, month = {2011///}, pages = {878 - 887}, abstract = {Medication errors can result from administration inaccuracies at any point of care and are a major cause for concern. To develop a successful Medication Reconciliation (MR) tool, we believe it necessary to build a Work Domain Ontology (WDO) for the MR process. A WDO defines the explicit, abstract, implementation-independent description of the task by separating the task from work context, application technology, and cognitive architecture. We developed a prototype based upon the WDO and designed to adhere to standard principles of interface design. The prototype was compared to Legacy Health System{\textquoteright}s and Pre-Admission Medication List Builder MR tools via a Keystroke-Level Model analysis for three MR tasks. The analysis found the prototype requires the fewest mental operations, completes tasks in the fewest steps, and completes tasks in the least amount of time. Accordingly, we believe that developing a MR tool, based upon the WDO and user interface guidelines, improves user efficiency and reduces cognitive load.}, isbn = {1942-597X}, author = {Markowitz,Eliz and Bernstam,Elmer V. and Herskovic,Jorge and Zhang,Jiajie and Shneiderman, Ben and Plaisant, Catherine and Johnson,Todd R.} } @conference {19262, title = {Methods for design and implementation of dynamic signal processing systems}, booktitle = {2011 International Conference on Embedded Computer Systems (SAMOS)}, year = {2011}, month = {2011}, pages = {i - i}, abstract = {Summary form only given. Dynamic signal processing systems, where significant changes in functionality and computational structure must be achieved while applications are running, are becoming increasingly important as computational platforms become more powerful, and feature-sets of DSP-powered products become more sophisticated. This talk covers two new, complementary dataflow models of computation that are being developed in the Maryland DSPCAD Research Group to help address the challenges of structured design, simulation, and synthesis of dynamic signal processing systems. The first of these models, called enable-invoke dataflow (EIDF), is aimed improving the predictability of actor invocation and the efficiency with which dynamic scheduling techniques can be realized. The second model, called the dataflow schedule graph (DSG), provides a formal framework for representing and analyzing dataflow graph schedules that is rooted in formal dataflow semantics, and accommodates a wide range of schedule classes, including static, quasi-static, and dynamic schedules, as well as both sequential and parallel schedule formats. In this talk, I will present the EIDF and DSG models and discuss their potential to improve the processes by which dynamic signal processing systems are developed.}, keywords = {actor invocation predictability, complementary dataflow models, Computational modeling, computational structure, COMPUTERS, data flow graphs, dataflow schedule graph, DSG models, DSP-powered products, Dynamic scheduling, dynamic scheduling techniques, dynamic signal processing systems, Educational institutions, EIDF models, enable-invoke dataflow, formal dataflow semantics, functionality structure, Laboratories, Maryland DSPCAD Research Group, quasi-static schedules, Schedules, scheduling, Signal processing, static schedules}, author = {Bhattacharyya, Shuvra S.} } @article {19276, title = {Model-based precision analysis and optimization for digital signal processors}, journal = {Proceedings of the European Signal Processing Conference}, year = {2011}, month = {2011}, pages = {506 - 510}, abstract = {Embedded signal processing has witnessed explosive growth in re-cent years in both scientific and consumer applications, driving the need for complex, high-performance signal processing systems that are largely application driven. In order to efficiently implement these systems on programmable platforms such as digital signal processors (DSPs), it is important to analyze and optimize the ap- plication design from early stages of the design process. A key per- formance concern for designers is choosing the data format. In this work, we propose a systematic and efficient design flow involving model-based design to analyze application data sets and precision requirements. We demonstrate this design flow with an exploration study into the required precision for eigenvalue decomposition (EVD) using the Jacobi algorithm. We demonstrate that with a high degree of structured analysis and automation, we are able to analyze the data set to derive an efficient data format, and optimize important parts of the algorithm with respect to precision. }, author = {Kedilaya, Soujanya and Plishker,William and Purkovic, Aleksandar and Johnson, Brian and Bhattacharyya, Shuvra S.} } @conference {19270, title = {A Model-Based Schedule Representation for Heterogeneous Mapping of Dataflow Graphs}, booktitle = {2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)}, year = {2011}, month = {2011}, pages = {70 - 81}, abstract = {Dataflow-based application specifications are widely used in model-based design methodologies for signal processing systems. In this paper, we develop a new model called the dataflow schedule graph (DSG) for representing a broad class of dataflow graph schedules. The DSG provides a graphical representation of schedules based on dataflow semantics. In conventional approaches, applications are represented using dataflow graphs, whereas schedules for the graphs are represented using specialized notations, such as various kinds of sequences or looping constructs. In contrast, the DSG approach employs dataflow graphs for representing both application models and schedules that are derived from them. Our DSG approach provides a precise, formal framework for unambiguously representing, analyzing, manipulating, and interchanging schedules. We develop detailed formulations of the DSG representation, and present examples and experimental results that demonstrate the utility of DSGs in the context of heterogeneous signal processing system design.}, keywords = {Computational modeling, data flow graphs, dataflow schedule graph, dataflow semantics, dataflow-based application specifications, Dynamic scheduling, heterogeneous mapping, heterogeneous signal processing system design, model-based design methodologies, model-based schedule representation, Processor scheduling, Program processors, Schedules, semantics, Signal processing, synchronization}, author = {Wu, Hsiang-Huang and Chung-Ching Shen and Sane, N. and Plishker,W. and Bhattacharyya, Shuvra S.} } @conference {19261, title = {Modeling and optimization of dynamic signal processing in resource-aware sensor networks}, booktitle = {2011 8th IEEE International Conference on Advanced Video and Signal-Based Surveillance (AVSS)}, year = {2011}, month = {2011}, pages = {449 - 454}, abstract = {Sensor node processing in resource-aware sensor networks is often critically dependent on dynamic signal processing functionality - i.e., signal processing functionality in which computational structure must be dynamically assessed and adapted based on time-varying environmental conditions, operating constraints or application requirements. In dynamic signal processing systems, it is important to provide flexibility for run-time adaptation of application behavior and execution characteristics, but in the domain of resource-aware sensor networks, such flexibility cannot come with significant costs in terms of power consumption overhead or reduced predictability. In this paper, we review a variety of complementary models of computation that are being developed as part of the dataflow interchange format (DIF) project to facilitate efficient and reliable implementation of dynamic signal processing systems. We demonstrate these methods in the context of resource-aware sensor networks.}, keywords = {Adaptation models, Aerodynamics, Computational modeling, data flow graphs, dataflow interchange format, Dynamic scheduling, dynamic signal processing, power consumption overhead, Program processors, resource-aware sensor networks, run-time adaptation, Schedules, sensor node processing, Signal processing, Wireless sensor networks}, author = {Bhattacharyya, Shuvra S. and Plishker,W. and Sane, N. and Chung-Ching Shen and Wu, Hsiang-Huang} } @conference {12406, title = {Modeling diverse standpoints in text classification: learning to be human by modeling human values}, booktitle = {Proceedings of the 2011 iConference}, series = {iConference {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {672 - 673}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {An annotator{\textquoteright}s classification of a text not only tells us something about the intent of the text{\textquoteright}s author, it also tells us something about the annotator{\textquoteright}s standpoint. To understand authorial intent, we can consider all of these diverse standpoints, as well as the extent to which the annotators{\textquoteright} standpoints affect their perceptions of authorial intent. To model human behavior, it is important to model humans{\textquoteright} unique standpoints. Human values play an especially important role in determining human behavior and how people perceive the world around them, so any effort to model human behavior and perception can benefit from an effort to understand and model human values. Instead of training humans to obscure their standpoints and act like computers, we should teach computers to have standpoints of their own.}, keywords = {diversity, framing theory, machine learning, standpoint epistemology, value sensitive computing}, isbn = {978-1-4503-0121-3}, doi = {10.1145/1940761.1940863}, url = {http://doi.acm.org/10.1145/1940761.1940863}, author = {Fleischmann,Kenneth R. and Templeton,Thomas Clay and Jordan Boyd-Graber} } @conference {18861, title = {Multi-material compliant mechanisms for mobile millirobots}, year = {2011}, month = {2011/05//}, pages = {3169 - 3174}, abstract = {This paper describes a new process for fabricating planar, multi-material, compliant mechanisms, intended for use in small scale robotics. The process involves laser cutting the mechanism geometry from a rigid material, and refilling the joint areas with a second, elastomeric material. This method allows for a large set of potential materials, with a wide range of material properties, to be used in combination to create mechanisms with highly tailored mechanical properties. These multi-material compliant mechanisms have minimum feature sizes of approximately 100 $\#$x00B5;m and have demonstrated long lifetimes, easily surviving 100,000 bending cycles. We also present the first use of these compliant mechanisms in a 2.5cm $\#$x00D7; 2.5cm $\#$x00D7; 7.5cm, 6g hexapod. This hexapod has been demonstrated moving at speeds up to 6 cm/s, with a predicted maximum speed of up to 17 cm/s.}, doi = {10.1109/ICRA.2011.5980543}, author = {Vogtmann,Dana E. and Gupta, Satyandra K. and Bergbreiter,Sarah} } @article {19268, title = {Multithreaded Simulation for Synchronous Dataflow Graphs}, journal = {ACM Trans. Des. Autom. Electron. Syst.}, volume = {16}, year = {2011}, month = {2011}, pages = {25:1 - 25:23}, abstract = {For system simulation, Synchronous DataFlow (SDF) has been widely used as a core model of computation in design tools for digital communication and signal processing systems. The traditional approach for simulating SDF graphs is to compute and execute static schedules in single-processor desktop environments. Nowadays, however, multicore processors are increasingly popular desktop platforms for their potential performance improvements through thread-level parallelism. Without novel scheduling and simulation techniques that explicitly explore thread-level parallelism for executing SDF graphs, current design tools gain only minimal performance improvements on multicore platforms. In this article, we present a new multithreaded simulation scheduler, called MSS, to provide simulation runtime speedup for executing SDF graphs on multicore processors. MSS strategically integrates graph clustering, intracluster scheduling, actor vectorization, and intercluster buffering techniques to construct InterThread Communication (ITC) graphs at compile-time. MSS then applies efficient synchronization and dynamic scheduling techniques at runtime for executing ITC graphs in multithreaded environments. We have implemented MSS in the Advanced Design System (ADS) from Agilent Technologies. On an Intel dual-core, hyper-threading (4 processing units) processor, our results from this implementation demonstrate up to 3.5 times speedup in simulating modern wireless communication systems (e.g., WCDMA3G, CDMA 2000, WiMax, EDGE, and Digital TV).}, keywords = {multithreaded simulation, scheduling, Synchronous dataflow}, isbn = {1084-4309}, url = {http://doi.acm.org/10.1145/1970353.1970358}, author = {Chia-Jui Hsu and Pino, Jos{\'e} Luis and Bhattacharyya, Shuvra S.} } @conference {14902, title = {Odd Leaf Out: Improving Visual Recognition with Games}, booktitle = {Privacy, security, risk and trust (passat), 2011 ieee third international conference on and 2011 ieee third international conference on social computing (socialcom)}, year = {2011}, month = {2011/10//}, pages = {87 - 94}, abstract = {A growing number of projects are solving complex computational and scientific tasks by soliciting human feedback through games. Many games with a purpose focus on generating textual tags for images. In contrast, we introduce a new game, Odd Leaf Out, which provides players with an enjoyable and educational game that serves the purpose of identifying misclassification errors in a large database of labeled leaf images. The game uses a novel mechanism to solicit useful information from players{\textquoteright} incorrect answers. A study of 165 players showed that game data can be used to identify mislabeled leaves much more quickly than would have been possible using a computer vision algorithm alone. Domain novices and experts were equally good at identifying mislabeled images, although domain experts enjoyed the game more. We discuss the successes and challenges of this new game, which can be applied to other domains with labeled image datasets.}, keywords = {algorithm;educational, classification;object, computational, computing;botany;computer, datasets;misclassification, errors;scientific, feedback;labeled, game;human, games;computer, games;image, image, leaf, Odd, Out;complex, recognition;, recognition;biology, tags;visual, tasks;computer, tasks;textual, VISION}, doi = {10.1109/PASSAT/SocialCom.2011.225}, author = {Hansen,D. L and Jacobs, David W. and Lewis,D. and Biswas,A. and Preece,J. and Rotman,D. and Stevens,E.} } @article {19271, title = {Overview of the MPEG Reconfigurable Video Coding Framework}, journal = {Journal of Signal Processing Systems}, volume = {63}, year = {2011}, month = {2011}, pages = {251 - 263}, abstract = {Video coding technology in the last 20 years has evolved producing a variety of different and complex algorithms and coding standards. So far the specification of such standards, and of the algorithms that build them, has been done case by case providing monolithic textual and reference software specifications in different forms and programming languages. However, very little attention has been given to provide a specification formalism that explicitly presents common components between standards, and the incremental modifications of such monolithic standards. The MPEG Reconfigurable Video Coding (RVC) framework is a new ISO standard currently under its final stage of standardization, aiming at providing video codec specifications at the level of library components instead of monolithic algorithms. The new concept is to be able to specify a decoder of an existing standard or a completely new configuration that may better satisfy application-specific constraints by selecting standard components from a library of standard coding algorithms. The possibility of dynamic configuration and reconfiguration of codecs also requires new methodologies and new tools for describing the new bitstream syntaxes and the parsers of such new codecs. The RVC framework is based on the usage of a new actor/ dataflow oriented language called CAL for the specification of the standard library and instantiation of the RVC decoder model. This language has been specifically designed for modeling complex signal processing systems. CAL dataflow models expose the intrinsic concurrency of the algorithms by employing the notions of actor programming and dataflow. The paper gives an overview of the concepts and technologies building the standard RVC framework and the non standard tools supporting the RVC model from the instantiation and simulation of the CAL model to software and/or hardware code synthesis.}, keywords = {CAL actor language, Circuits and Systems, Code synthesis, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow programming, Electrical Engineering, Image Processing and Computer Vision, pattern recognition, Reconfigurable Video Coding, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-009-0399-3}, author = {Bhattacharyya, Shuvra S. and Eker, Johan and Janneck, J{\"o}rn W. and Lucarz, Christophe and Mattavelli, Marco and Raulet, Micka{\"e}l} } @article {19722, title = {ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.}, journal = {BMC Bioinformatics}, volume = {12}, year = {2011}, month = {2011}, pages = {434}, abstract = {

BACKGROUND: Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies.

RESULTS: Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather than by relying on prebuilt protein families or fixed sequence similarity thresholds. Double Partial Phylogenetic Profiling (DPPP) is a related procedure that begins with a single sequence and searches for optimal granularities for its surrounding protein family in order to generate the best query profiles for PPP. We present ProPhylo, a high-performance software package for phylogenetic profiling studies through creating individually optimized protein family boundaries. ProPhylo provides precomputed databases for immediate use and tools for manipulating the taxonomic profiles used as queries.

CONCLUSION: ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from ftp://ftp.jcvi.org/pub/data/ppp/.

}, keywords = {algorithms, Archaea, Archaeal Proteins, DNA, Methane, Phylogeny, software}, issn = {1471-2105}, doi = {10.1186/1471-2105-12-434}, author = {Basu, Malay K and Jeremy D Selengut and Haft, Daniel H} } @article {18793, title = {Recent advances and future challenges in automated manufacturing planning}, journal = {Journal of Computing and Information Science in Engineering}, volume = {11}, year = {2011}, month = {2011///}, pages = {021006 - 021006}, author = {Bourne,D. and Corney,J. and Gupta,S.K.} } @conference {17338, title = {Re-engineering health care with information technology: the role of computer-human interaction}, booktitle = {PART 2 {\textemdash}{\textemdash}{\textemdash}{\textendash} Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {451 - 454}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {There is critical, nation-wide need to improve health care and its cost. Health information technology has great promise that is yet to be realized. In this panel four noted experts will discuss key issues that should drive health IT, and the challenges for the CHI community to play a leading role.}, keywords = {clinical workflow, electronic medical records, health information technology visualization, healthcare informatics, participatory design, usability standards \&$\#$38; evaluation}, doi = {10.1145/1979482.1979490}, url = {http://doi.acm.org/10.1145/1979482.1979490}, author = {Butler,Keith and Payne,Thomas and Shneiderman, Ben and Brennan,Patricia and Zhang,Jiajie} } @article {16033, title = {Research Directions in Data Wrangling: Visualizations and Transformations for Usable and Credible Data}, journal = {Information VisualizationInformation Visualization}, volume = {10}, year = {2011}, month = {2011/10/01/}, pages = {271 - 288}, abstract = {In spite of advances in technologies for working with data, analysts still spend an inordinate amount of time diagnosing data quality issues and manipulating data into a usable form. This process of {\textquoteleft}data wrangling{\textquoteright} often constitutes the most tedious and time-consuming aspect of analysis. Though data cleaning and integration arelongstanding issues in the database community, relatively little research has explored how interactive visualization can advance the state of the art. In this article, we review the challenges and opportunities associated with addressing data quality issues. We argue that analysts might more effectively wrangle data through new interactive systems that integrate data verification, transformation, and visualization. We identify a number of outstanding research questions, including how appropriate visual encodings can facilitate apprehension of missing data, discrepant values, and uncertainty; how interactive visualizations might facilitate data transform specification; and how recorded provenance and social interaction might enable wider reuse, verification, and modification of data transformations.}, keywords = {data cleaning, data quality, data transformation, Uncertainty, Visualization}, isbn = {1473-8716, 1473-8724}, doi = {10.1177/1473871611415994}, url = {http://ivi.sagepub.com/content/10/4/271}, author = {Kandel,Sean and Heer,Jeffrey and Plaisant, Catherine and Kennedy,Jessie and Van Ham,Frank and Riche,Nathalie Henry and Weaver,Chris and Lee,Bongshin and Brodbeck,Dominique and Buono,Paolo} } @article {16041, title = {Seven guiding scenarios for information visualization evaluation}, volume = {2011-992-04}, year = {2011}, month = {2011///}, institution = {Department of Computer Science, University of Calgary}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluatingvisual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, automated evaluation of visualizations, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios are described through their goals, the types of questions they embody and illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. For example, if the research goals or evaluative questions are known they can be used to map to specific scenarios, where practical existing examples can be considered for effective evaluation approaches. }, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @conference {12413, title = {Simulating Audiences: Automating Analysis of Values, Attitudes, and Sentiment}, booktitle = {Privacy, Security, Risk and Trust (PASSAT), 2011 IEEE Third International Conference on and 2011 IEEE Third International Confernece on Social Computing (SocialCom)}, year = {2011}, month = {2011/10/09/11}, pages = {734 - 737}, publisher = {IEEE}, organization = {IEEE}, abstract = {Current events such as the Park51 Project in downtown Manhattan create "critical discourse moments," explosions of discourse around a topic that can be exploited for data gathering. Policymakers have a need to understand the dynamics of public discussion in real time. Human values, which are cognitively related to attitudes and serve as reference points in moral argument, are important indicators of what{\textquoteright}s at stake in a public controversy. This work shows that it is possible to link values data with reader behavior to infer values implicit in a topical corpus, and that it is possible to automate this process using machine learning.}, keywords = {audience simulation, behavioural sciences computing, crowdsourcing, Educational institutions, human values, HUMANS, learning (artificial intelligence), machine learning, moral argument, natural language processing, Park51 project, Presses, public controversy, public discussion, Security, social sciences computing, support vector machines, Weaving}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.238}, author = {Templeton,T.C. and Fleischmann,K.R. and Jordan Boyd-Graber} } @article {17909, title = {Social Snapshot: A System for Temporally Coupled Social Photography}, journal = {Computer Graphics and Applications, IEEE}, volume = {31}, year = {2011}, month = {2011/02//jan}, pages = {74 - 84}, abstract = {Social Snapshot actively acquires and reconstructs temporally dynamic data. The system enables spatiotemporal 3D photography using commodity devices, assisted by their auxiliary sensors and network functionality. It engages users, making them active rather than passive participants in data acquisition.}, keywords = {3D, acquisition;data, acquisition;photography;social, computing;, coupled, data, photography;data, photography;temporally, reconstruction;social, sciences, snapshot;spatiotemporal, social}, isbn = {0272-1716}, doi = {10.1109/MCG.2010.107}, author = {Patro,R. and Ip, Cheuk Yiu and Bista,S. and Varshney, Amitabh} } @article {17744, title = {SYSTEM AND METHOD FOR DATA MANAGEMENT IN LARGE DATA NETWORKS}, volume = {WO/2011/032077}, year = {2011}, month = {2011/03//}, abstract = {A system and method for storing an input data network, in the form of graph is provided. The system includes a master node and a plurality of slave nodes. The master node is operable to receive the data network in the form of a graph, the graph including a plurality of vertices connected by edges; calculate a probability of co-retrieval for each of the plurality of vertices; and assign each of the plurality of vertices to one of the plurality of compute nodes based on the calculated probability of co-retrieval. Another method and system are provided for converting a dataset into a graph based index and storing the index on disk. Respective systems and methods of querying such data networks are also provided.}, author = {BROECHELER,M. and V.S. Subrahmanian and Pugliese, A.} } @conference {19258, title = {Teaching cross-platform design and testing methods for embedded systems using DICE}, series = {WESE {\textquoteright}11}, year = {2011}, month = {2011}, pages = {38 - 45}, publisher = {ACM}, organization = {ACM}, abstract = {DICE (the DSPCAD Integrative Command Line Environment) is a package of utilities that facilitates efficient management of software projects. Key areas of emphasis in DICE are cross-platform operation, support for projects that integrate heterogeneous programming languages, and support for applying and integrating different kinds of design and testing methodologies. The package is being developed at the University of Maryland to facilitate the research and teaching of methods for implementation, testing, evolution, and revision of engineering software. The platform- and language-independent focus of DICE makes it an effective vehicle for teaching high-productivity, high-reliability methods for design and implementation of embedded systems for a variety of courses. In this paper, we provide an overview of features of DICE --- particularly as they relate to testing driven design practices --- that are useful in embedded systems education, and discuss examples and experiences of applying the tool in courses at the University of Maryland aimed at diverse groups of students --- undergraduate programming concepts for engineers, graduate VLSI architectures (aimed at research-oriented students), and graduate FPGA system design (aimed at professional Master{\textquoteright}s students).}, isbn = {978-1-4503-1046-8}, url = {http://doi.acm.org/10.1145/2077370.2077376}, author = {Bhattacharyya, Shuvra S. and Plishker,William and Gupta, Ayush and Chung-Ching Shen} } @article {12860, title = {Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus}, journal = {The ISME Journal}, volume = {6}, year = {2011}, month = {2011/12/08/}, pages = {835 - 846}, abstract = {Sea surface temperatures (SST) are rising because of global climate change. As a result, pathogenic Vibrio species that infect humans and marine organisms during warmer summer months are of growing concern. Coral reefs, in particular, are already experiencing unprecedented degradation worldwide due in part to infectious disease outbreaks and bleaching episodes that are exacerbated by increasing SST. For example, Vibrio coralliilyticus, a globally distributed bacterium associated with multiple coral diseases, infects corals at temperatures above 27 {\textdegree}C. The mechanisms underlying this temperature-dependent pathogenicity, however, are unknown. In this study, we identify potential virulence mechanisms using whole genome sequencing of V. coralliilyticus ATCC (American Type Culture Collection) BAA-450. Furthermore, we demonstrate direct temperature regulation of numerous virulence factors using proteomic analysis and bioassays. Virulence factors involved in motility, host degradation, secretion, antimicrobial resistance and transcriptional regulation are upregulated at the higher virulent temperature of 27 {\textdegree}C, concurrent with phenotypic changes in motility, antibiotic resistance, hemolysis, cytotoxicity and bioluminescence. These results provide evidence that temperature regulates multiple virulence mechanisms in V. coralliilyticus, independent of abundance. The ecological and biological significance of this temperature-dependent virulence response is reinforced by climate change models that predict tropical SST to consistently exceed 27 {\textdegree}C during the spring, summer and fall seasons. We propose V. coralliilyticus as a model Gram-negative bacterium to study temperature-dependent pathogenicity in Vibrio-related diseases.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, doi = {10.1038/ismej.2011.154}, url = {http://www.nature.com/ismej/journal/v6/n4/full/ismej2011154a.html}, author = {Kimes,Nikole E. and Grim,Christopher J. and Johnson,Wesley R. and Hasan,Nur A. and Tall,Ben D. and Kothary,Mahendra H. and Kiss,Hajnalka and Munk,A. Christine and Tapia,Roxanne and Green,Lance and Detter,Chris and Bruce,David C. and Brettin,Thomas S. and Rita R Colwell and Morris,Pamela J.} } @article {11903, title = {Threat-Aware Clustering in Wireless Sensor Networks}, journal = {IFIP Advances in Information and Communication Technology (AICT)}, volume = {264}, year = {2011}, month = {2011///}, pages = {1 - 12}, author = {Abd-Almageed, Wael and Blace,R.E. and Eltoweissy,M.} } @conference {17979, title = {Toolchain for Programming, Simulating and Studying the XMT Many-Core Architecture}, booktitle = {Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on}, year = {2011}, month = {2011/05//}, pages = {1282 - 1291}, abstract = {The Explicit Multi-Threading (XMT) is a general-purpose many-core computing platform, with the vision of a 1000-core chip that is easy to program but does not compromise on performance. This paper presents a publicly available tool chain for XMT, complete with a highly configurable cycle-accurate simulator and an optimizing compiler. The XMT tool chain has matured and has been validated to a point where its description merits publication. In particular, research and experimentation enabled by the tool chain played a central role in supporting the ease-of-programming and performance aspects of the XMT architecture. The compiler and the simulator are also important milestones for an efficient programmer{\textquoteright}s workflow from PRAM algorithms to programs that run on the shared memory XMT hardware. This workflow is a key component in accomplishing the dual goal of ease-of-programming and performance. The applicability of our tool chain extends beyond specific XMT choices. It can be used to explore the much greater design space of shared memory many-cores by system researchers or by programmers. As the tool chain can practically run on any computer, it provides a supportive environment for teaching parallel algorithmic thinking with a programming component. Unobstructed by techniques such as decomposition-first and programming for locality, this environment may be useful in deferring the teaching of these techniques, when desired, to more advanced or platform-specific courses.}, keywords = {algorithm;XMT, architecture;XMT, architectures;shared, chain;cycle-accurate, compiler;programmer, compilers;parallel, component;shared, computing;optimizing, hardware;shared, many-core, many-core;concurrency, memory, multithreading;general-purpose, PRAM, simulator;ease-of-programming;explicit, systems;, theory;multi-threading;optimising, tool, workflow;programming, XMT}, doi = {10.1109/IPDPS.2011.270}, author = {Keceli,F. and Tzannes,A. and Caragea,G.C. and Barua,R. and Vishkin, Uzi} } @article {19256, title = {Topological Patterns for Scalable Representation and Analysis of Dataflow Graphs}, journal = {Journal of Signal Processing Systems}, volume = {65}, year = {2011}, month = {2011}, pages = {229 - 244}, abstract = {Tools for designing signal processing systems with their semantic foundation in dataflow modeling often use high-level graphical user interfaces (GUIs) or text based languages that allow specifying applications as directed graphs. Such graphical representations serve as an initial reference point for further analysis and optimizations that lead to platform-specific implementations. For large-scale applications, the underlying graphs often consist of smaller substructures that repeat multiple times. To enable more concise representation and direct analysis of such substructures in the context of high level DSP specification languages and design tools, we develop the modeling concept of topological patterns, and propose ways for supporting this concept in a high-level language. We augment the dataflow interchange format (DIF) language{\textemdash}a language for specifying DSP-oriented dataflow graphs{\textemdash}with constructs for supporting topological patterns, and we show how topological patterns can be effective in various aspects of embedded signal processing design flows using specific application examples.}, keywords = {Circuits and Systems, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow graphs, Electrical Engineering, High-level languages, Image Processing and Computer Vision, model-based design, pattern recognition, Signal processing systems, Signal, Image and Speech Processing, Topological patterns}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-011-0610-1}, author = {Sane, Nimish and Kee, Hojin and Seetharaman, Gunasekaran and Bhattacharyya, Shuvra S.} } @inbook {12458, title = {Tracking and Identification via Object Reflectance Using a Hyperspectral Video Camera}, booktitle = {Machine Vision Beyond Visible SpectrumMachine Vision Beyond Visible Spectrum}, series = {Augmented Vision and Reality}, volume = {1}, year = {2011}, month = {2011///}, pages = {201 - 219}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and particle filters to simultaneously track and identify an object based on its reflectance spectra is proposed. By exploiting high-resolution spectral features in the visible and near-infrared regimes, the framework is able to track objects that appear featureless to the human eye. For example, we demonstrate that near-IR spectra of human skin can also be used to distinguish different people in a video sequence. These capabilities are illustrated using experiments conducted on real hyperspectral video data.}, isbn = {978-3-642-11568-4}, url = {http://dx.doi.org/10.1007/978-3-642-11568-4_9}, author = {Nguyen,Hien Van and Banerjee,Amit and Burlina,Philippe and Broadwater,Joshua and Chellapa, Rama}, editor = {Hammoud,Riad and Fan,Guoliang and McMillan,Robert W. W. and Ikeuchi,Katsushi and Hammoud,Riad I. and Wolff,Lawrence B.} } @conference {17442, title = {TreeVersity: Comparing tree structures by topology and node{\textquoteright}s attributes differences}, booktitle = {2011 IEEE Conference on Visual Analytics Science and Technology (VAST)}, year = {2011}, month = {2011/10/23/28}, pages = {275 - 276}, publisher = {IEEE}, organization = {IEEE}, abstract = {It is common to classify data in hierarchies, they provide a comprehensible way of understanding big amounts of data. From budgets to organizational charts or even the stock market, trees are everywhere and people find them easy to use. However when analysts need to compare two versions of the same tree structure, or two related taxonomies, the task is not so easy. Much work has been done on this topic, but almost all of it has been restricted to either compare the trees by topology, or by the node attribute values. With this project we are proposing TreeVersity, a framework for comparing tree structures, both by structural changes and by differences in the node attributes. This paper is based on our previous work on comparing traffic agencies using LifeFlow [1, 2] and on a first prototype of TreeVersity.}, keywords = {Computer science, data classification, Data visualization, Educational institutions, hierarchy, Image color analysis, LifeFlow, node attributes differences, Pattern classification, structural changes, Topology, topology attributes differences, traffic agencies, tree structures comparison, trees (mathematics), TreeVersity, Vegetation, Visualization}, isbn = {978-1-4673-0015-5}, doi = {10.1109/VAST.2011.6102471}, author = {Gomez,J.A.G. and Buck-Coleman,A. and Plaisant, Catherine and Shneiderman, Ben} } @conference {16034, title = {TreeVersity: Comparing tree structures by topology and node{\textquoteright}s attributes differences}, booktitle = {Visual Analytics Science and Technology (VAST), 2011 IEEE Conference on}, year = {2011}, month = {2011/10//}, pages = {275 - 276}, abstract = {It is common to classify data in hierarchies, they provide a comprehensible way of understanding big amounts of data. From budgets to organizational charts or even the stock market, trees are everywhere and people find them easy to use. However when analysts need to compare two versions of the same tree structure, or two related taxonomies, the task is not so easy. Much work has been done on this topic, but almost all of it has been restricted to either compare the trees by topology, or by the node attribute values. With this project we are proposing TreeVersity, a framework for comparing tree structures, both by structural changes and by differences in the node attributes. This paper is based on our previous work on comparing traffic agencies using LifeFlow [1, 2] and on a first prototype of TreeVersity.}, keywords = {(mathematics);, agencies;tree, attributes, changes;topology, classification;hierarchy;node, classification;trees, comparison;pattern, differences;structural, differences;traffic, LifeFlow;TreeVersity;data, STRUCTURES}, doi = {10.1109/VAST.2011.6102471}, author = {Gomez,J.A.G. and Buck-Coleman,A. and Plaisant, Catherine and Shneiderman, Ben} } @article {19264, title = {Using the DSPCAD Integrative Command-Line Environment: User{\textquoteright}s Guide for DICE Version 1.1}, year = {2011}, month = {2011}, abstract = {This document provides instructions on setting up, starting up, andbuilding DICE and its key companion packages, dicemin and dicelang. This installation process is based on a general set of conventions, which we refer to as the DICE organizational conventions, for software packages. The DICE organizational conventions are specified in this report. These conventions are applied in DICE, dicemin, and dicelang, and also to other software packages that are developed in the Maryland DSPCAD Research Group. }, keywords = {Technical Report}, isbn = {UMIACS-TR-2011-13}, doi = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/11804}, author = {Bhattacharyya, Shuvra S. and Chung-Ching Shen and Plishker,William and Sane, Nimish and Zaki, George} } @article {12417, title = {Using Variational Inference and MapReduce to Scale Topic Modeling}, journal = {arXiv:1107.3765}, year = {2011}, month = {2011/07/19/}, abstract = {Latent Dirichlet Allocation (LDA) is a popular topic modeling technique for exploring document collections. Because of the increasing prevalence of large datasets, there is a need to improve the scalability of inference of LDA. In this paper, we propose a technique called ~\emph{MapReduce LDA} (Mr. LDA) to accommodate very large corpus collections in the MapReduce framework. In contrast to other techniques to scale inference for LDA, which use Gibbs sampling, we use variational inference. Our solution efficiently distributes computation and is relatively simple to implement. More importantly, this variational implementation, unlike highly tuned and specialized implementations, is easily extensible. We demonstrate two extensions of the model possible with this scalable framework: informed priors to guide topic discovery and modeling topics from a multilingual corpus.}, keywords = {Computer Science - Artificial Intelligence, Computer Science - Distributed, Parallel, and Cluster Computing}, url = {http://arxiv.org/abs/1107.3765}, author = {Zhai,Ke and Jordan Boyd-Graber and Asadi,Nima} } @article {14412, title = {Value of information lattice: exploiting probabilistic independence for effective feature subset acquisition}, journal = {Journal of Artificial Intelligence Research}, volume = {41}, year = {2011}, month = {2011/05//}, pages = {69 - 95}, abstract = {We address the cost-sensitive feature acquisition problem, where misclassifying an instance is costly but the expected misclassification cost can be reduced by acquiring the values of the missing features. Because acquiring the features is costly as well, the objective is to acquire the right set of features so that the sum of the feature acquisition cost and misclassification cost is minimized. We describe the Value of Information Lattice (VOILA), an optimal and eficient feature subset acquisition framework. Unlike the common practice, which is to acquire features greedily, VOILA can reason with subsets of features. VOILA eficiently searches the space of possible feature subsets by discovering and exploiting conditional independence properties between the features and it reuses probabilistic inference computations to further speed up the process. Through empirical evaluation on five medical datasets, we show that the greedy strategy is often reluctant to acquire features, as it cannot forecast the benefit of acquiring multiple features in combination.}, isbn = {1076-9757}, url = {http://dl.acm.org/citation.cfm?id=2051237.2051240}, author = {Bilgic,Mustafa and Getoor, Lise} } @conference {19259, title = {Vectorization and mapping of software defined radio applications on heterogeneous multi-processor platforms}, booktitle = {2011 IEEE Workshop on Signal Processing Systems (SiPS)}, year = {2011}, month = {2011}, pages = {31 - 36}, abstract = {A variety of multiprocessor architectures have proliferated even for off-the-shelf computing platforms. To improve performance and productivity for common heterogeneous systems, we have developed a workflow to generate efficient solutions. By starting with a formal description of an application and the mapping problem we are able to generate a range of designs that efficiently trade-of latency and throughput. In this approach, efficient utilization of SIMD cores is achieved by applying extensive block processing in conjunction with efficient mapping and scheduling. We demonstrate our approach through an integration into the GNU Radio environment for software defined radio system design.}, keywords = {Benchmark testing, block processing, Design methodology, formal description, GNU radio environment, Graphic Processor Unit, Graphics processing unit, heterogeneous multiprocessor platform, mapping problem, Multicore processing, Multiprocessing systems, multiprocessor architecture, multiprocessor scheduling, operating systems (computers), PARALLEL PROCESSING, Processor scheduling, Schedules, SIMD core, Software Defined Radio, software defined radio system design, software radio, telecommunication computing, Throughput, vectorization, workflow}, author = {Zaki, G.F. and Plishker,W. and Bhattacharyya, Shuvra S. and Clancy, C. and Kuykendall, J.} } @conference {19464, title = {Why is My Internet Slow?: Making Network Speeds Visible}, booktitle = {SIGCHI {\textquoteright}11}, series = {CHI {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {1889 - 1898}, publisher = {ACM}, organization = {ACM}, abstract = {With widespread broadband adoption, more households report experiencing sub-optimal speeds. Not only are slow speeds frustrating, they may indicate consumers are not receiving the services they are paying for from their internet service providers. Yet, determining the speed and source of slow-downs is difficult because few tools exist for broadband management. We report on results of a field trial with 10 households using a visual network probe designed to address these problems. We describe the results of the study and provide design implications for future tools. More importantly, we argue that tools like this can educate and empower consumers by making broadband speeds and sources of slow-downs more visible.}, keywords = {broadband speed, broadband tools, home networks}, isbn = {978-1-4503-0228-9}, url = {http://doi.acm.org/10.1145/1978942.1979217}, author = {Marshini Chetty and Haslem, David and Baird, Andrew and Ofoha, Ugochi and Sumner, Bethany and Grinter, Rebecca} } @article {14355, title = {Active inference for collective classification}, journal = {AAAI{\textquoteright}10}, year = {2010}, month = {2010///}, abstract = {Labeling nodes in a network is an important problem that has seen a growing interest. A number of methods that exploit both local and relational information have been developed for this task. Acquiring the labels for a few nodes at inference time can greatly improve the ac- curacy, however the question of figuring out which node labels to acquire is challenging. Previous approaches have been based on simple structural properties. Here, we present a novel technique, which we refer to as re- flect and correct, that can learn and predict when the un- derlying classification system is likely to make mistakes and it suggests acquisitions to correct those mistakes.}, author = {Bilgic,M. and Getoor, Lise} } @article {14396, title = {Active learning for networked data}, journal = {ICML{\textquoteright}10}, year = {2010}, month = {2010///}, abstract = {We introduce a novel active learning algo-rithm for classification of network data. In this setting, training instances are connected by a set of links to form a network, the labels of linked nodes are correlated, and the goal is to exploit these dependencies and accu- rately label the nodes. This problem arises in many domains, including social and biologi- cal network analysis and document classifica- tion, and there has been much recent interest in methods that collectively classify the nodes in the network. While in many cases labeled examples are expensive, often network infor- mation is available. We show how an active learning algorithm can take advantage of net- work structure. Our algorithm effectively ex- ploits the links between instances and the in- teraction between the local and collective as- pects of a classifier to improve the accuracy of learning from fewer labeled examples. We ex- periment with two real-world benchmark col- lective classification domains, and show that we are able to achieve extremely accurate re- sults even when only a small fraction of the data is labeled. }, author = {Bilgic,M. and Mihalkova,L. and Getoor, Lise} } @article {12495, title = {Adaptive Threshold Estimation via Extreme Value Theory}, journal = {Signal Processing, IEEE Transactions on}, volume = {58}, year = {2010}, month = {2010/02//}, pages = {490 - 500}, abstract = {Determining a detection threshold to automatically maintain a low false alarm rate is a challenging problem. In a number of different applications, the underlying parametric assumptions of most automatic target detection algorithms are invalid. Therefore, thresholds derived using these incorrect distribution assumptions do not produce desirable results when applied to real sensor data. Monte Carlo methods for threshold determination work well but tend to perform poorly when targets are present. In order to mitigate these effects, we propose an algorithm using extreme value theory through the use of the generalized Pareto distribution (GPD) and a Kolmogorov-Smirnov statistical test. Unlike previous work based on GPD estimates, this algorithm incorporates a way to adaptively maintain low false alarm rates in the presence of targets. Both synthetic and real-world detection results demonstrate the usefulness of this algorithm.}, keywords = {detection;, detection;Pareto, distribution;adaptive, distribution;signal, estimation;extreme, estimation;signal, Kolmogorov-Smirnov, Pareto, statistical, test;adaptive, theory;generalized, threshold, value}, isbn = {1053-587X}, doi = {10.1109/TSP.2009.2031285}, author = {Broadwater, J.B. and Chellapa, Rama} } @conference {12122, title = {Are developers complying with the process: an XP study}, booktitle = {Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement}, series = {ESEM {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {14:1{\textendash}14:10 - 14:1{\textendash}14:10}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Adapting new software processes and practices in organizational and academic environments requires training the developers and validating the applicability of the newly introduced activities. Investigating process conformance during training and understanding if programmers are able and willing to follow the specific steps are crucial to evaluating whether the process improves various software product quality factors. In this paper we present a process model independent approach to detect process non-conformance. Our approach is based on non-intrusively collected data captured by a version control system and provides the project manager with timely updates. Further, we provide evidence of the applicability of our approach by investigating process conformance in a five day training class on eXtreme Programming (XP) practices at the Leibniz Universit{\"a}t Hannover. Our results show that the approach enabled researchers to formulate minimal intrusive methods to check for conformance and that for the majority of the investigated XP practices violations could be detected.}, keywords = {process conformance, process improvement, XP programming}, isbn = {978-1-4503-0039-1}, doi = {10.1145/1852786.1852805}, url = {http://doi.acm.org/10.1145/1852786.1852805}, author = {Zazworka, Nico and Stapel,Kai and Knauss,Eric and Shull, Forrest and Basili, Victor R. and Schneider,Kurt} } @conference {19284, title = {Automated generation of an efficient MPEG-4 Reconfigurable Video Coding decoder implementation}, booktitle = {2010 Conference on Design and Architectures for Signal and Image Processing (DASIP)}, year = {2010}, month = {2010}, pages = {265 - 272}, abstract = {This paper proposes an automatic design flow from user-friendly design to efficient implementation of video processing systems. This design flow starts with the use of coarse-grain dataflow representations based on the CAL language, which is a complete language for dataflow programming of embedded systems. Our approach integrates previously developed techniques for detecting synchronous dataflow (SDF) regions within larger CAL networks, and exploiting the static structure of such regions using analysis tools in The Dataflow interchange format Package (TDP). Using a new XML format that we have developed to exchange dataflow information between different dataflow tools, we explore systematic implementation of signal processing systems using CAL, SDF-like region detection, TDP-based static scheduling, and CAL-to-C (CAL2C) translation. Our approach, which is a novel integration of three complementary dataflow tools - the CAL parser, TDP, and CAL2C - is demonstrated on an MPEG Reconfigurable Video Coding (RVC) decoder.}, keywords = {automated generation, automatic design flow, CAL language, CAL networks, CAL-to-C translation, CAL2C translation, coarse-grain dataflow representations, Computational modeling, data flow computing, dataflow information, Dataflow programming, decoding, Digital signal processing, Libraries, MPEG-4 reconfigurable video coding decoder implementation, parallel languages, SDF detection, synchronous dataflow detection, TDP, TDP-based static scheduling, The Dataflow interchange format Package, Transform coding, user-friendly design, video coding, video processing systems, XML, XML format}, author = {Gu, Ruirui and Piat, J. and Raulet, M. and Janneck, J.W. and Bhattacharyya, Shuvra S.} } @article {12220, title = {Brief announcement: decentralized network bandwidth prediction}, journal = {Distributed Computing}, year = {2010}, month = {2010///}, pages = {198 - 200}, abstract = {Distributed applications can often benefit from knowledge of the bandwidth between hosts, without performing measurements between all host pairs. For example, if a peer-to-peer (P2P) computational grid system predicts pairwise bandwidth between all nodes in the system, that information could increase overall system performance by finding high-bandwidth nodes to store large scientific input or output datasets. Another possible beneficiary is a P2P online game, which can provide users a seamless gaming experience by selecting a coordinator node that has high-bandwidth connections to the players in a game region.}, author = {Song,S. and Keleher,P. and Bhattacharjee, Bobby and Sussman, Alan} } @conference {19295, title = {Buffer management for multi-application image processing on multi-core platforms: Analysis and case study}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010}, pages = {1662 - 1665}, abstract = {Due to the limited amounts of on-chip memory, large volumes of data, and performance and power consumption overhead associated with interprocessor communication, efficient management of buffer memory is critical to multi-core image processing. To address this problem, this paper develops new modeling and analysis techniques based on dataflow representations, and demonstrates these techniques on a multi-core implementation case study involving multiple, concurrently-executing image processing applications. Our techniques are based on careful representation and exploitation of frame- or block-based operations, which involve repeated invocations of the same computations across regularly- arranged subsets of data. Using these new approaches to manage block-based image data, this paper demonstrates methods to analyze synchronization overhead and FIFO buffer sizes when mapping image processing applications onto heterogeneous, multi core architectures.}, keywords = {block-based image data, buffer memory management, buffer storage, concurrently-executing image processing application, data flow computing, data flow representation, data subset, Dataflow, Digital signal processing, Energy consumption, Energy management, Engineering management, FIFO buffer sizes, Hardware, Image analysis, IMAGE PROCESSING, image processing application, image representation, interprocessor communication, memory architecture, Memory management, multiapplication image processing, multicore image processing, multiprocessing, on-chip memory, power consumption, power consumption overhead, Runtime, scheduling, set theory, shared memory, storage management chips, synchronization overhead}, author = {Ko,Dong-Ik and Won, N. and Bhattacharyya, Shuvra S.} } @conference {16682, title = {cdec: A decoder, alignment, and learning framework for finite-state and context-free translation models}, booktitle = {Proceedings of the ACL 2010 System Demonstrations}, year = {2010}, month = {2010///}, pages = {7 - 12}, author = {Dyer,C. and Weese,J. and Setiawan,H. and Lopez,A. and Ture,F. and Eidelman,V. and Ganitkevitch,J. and Blunsom,P. and Resnik, Philip} } @article {18501, title = {Chipping away at censorship firewalls with user-generated content}, journal = {Proc. 19th USENIX Security Symposium, Washington, DC}, year = {2010}, month = {2010///}, abstract = {Oppressive regimes and even democratic governmentsrestrict Internet access. Existing anti-censorship systems often require users to connect through proxies, but these systems are relatively easy for a censor to discover and block. This paper offers a possible next step in the cen- sorship arms race: rather than relying on a single system or set of proxies to circumvent censorship firewalls, we explore whether the vast deployment of sites that host user-generated content can breach these firewalls. To ex- plore this possibility, we have developed Collage, which allows users to exchange messages through hidden chan- nels in sites that host user-generated content. Collage has two components: a message vector layer for embedding content in cover traffic; and a rendezvous mechanism to allow parties to publish and retrieve messages in the cover traffic. Collage uses user-generated content (e.g., photo-sharing sites) as {\textquotedblleft}drop sites{\textquotedblright} for hidden messages. To send a message, a user embeds it into cover traffic and posts the content on some site, where receivers retrieve this content using a sequence of tasks. Collage makes it difficult for a censor to monitor or block these messages by exploiting the sheer number of sites where users can exchange messages and the variety of ways that a mes- sage can be hidden. Our evaluation of Collage shows that the performance overhead is acceptable for sending small messages (e.g., Web articles, email). We show how Collage can be used to build two applications: a direct messaging application, and a Web content delivery system. }, author = {Burnett,S. and Feamster, Nick and Vempala,S.} } @conference {18556, title = {Circumventing censorship with collage}, booktitle = {Proceedings of the ACM SIGCOMM 2010 conference}, series = {SIGCOMM {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {471 - 472}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Oppressive regimes and even democratic governments restrict Internet access. Existing anti-censorship systems often require users to connect through proxies, but these systems are relatively easy for a censor to discover and block. We explore a possible next step in the censorship arms race: rather than relying on a single system or set of proxies to circumvent censorship firewalls, we use the vast deployment of sites that host user-generated content to breach these firewalls. We have developed Collage, which allows users to exchange messages through hidden channels in sites that host user-generated content. To send a message, a user embeds it into cover traffic and posts the content on some site, where receivers retrieve this content. Collage makes it difficult for a censor to monitor or block these messages by exploiting the sheer number of sites where users can exchange messages and the variety of ways that a message can be hidden. We have built a censorship-resistant news reader using Collage that can retrieve from behind a censorship firewall and show Collage{\textquoteright}s effectiveness with a live demonstration of its complete infrastructure.}, keywords = {Availability, censorship}, isbn = {978-1-4503-0201-2}, doi = {10.1145/1851182.1851269}, url = {http://doi.acm.org/10.1145/1851182.1851269}, author = {Burnett,Sam and Feamster, Nick and Vempala,Santosh} } @conference {13937, title = {Clear Panels: a technique to design mobile application interactivity}, booktitle = {Proceedings of the 8th ACM Conference on Designing Interactive Systems}, year = {2010}, month = {2010///}, pages = {360 - 363}, author = {Brown,Q. and Bonsignore,E. and Hatley,L. and Druin, Allison and Walsh,G. and Foss,E. and Brewer,R. and Hammer,J. and Golub,E.} } @article {15326, title = {Coherent turbulent motions in a Mach 3 boundary layer}, journal = {Bulletin of the American Physical Society}, volume = {55}, year = {2010}, month = {2010///}, author = {Beekman,I. and Kan,Y. C and Priebe,S. and Martin, M.P} } @article {15366, title = {Common Mode Analysis of Ethernet Transformers}, journal = {Magnetics Letters, IEEE}, volume = {1}, year = {2010}, month = {2010///}, abstract = {In this letter, a distributed model for Ethernet transformers subject to common mode signals is developed.Explicit formulas for transfer functions are derived and illustrated by numerical examples. }, author = {Bowen,D. and Mayergoyz, Issak D and Krafft,C. and Kroop,D.} } @article {12881, title = {Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae}, journal = {BMC Microbiology}, volume = {10}, year = {2010}, month = {2010///}, abstract = {In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Results Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15\% divergence (88 to 85\% ANI and 92 to 91\% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95\% and AAI <96\% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59\%) and 2058 ORFs (56\%) with the published core genome of V. cholerae and 2956 (82\%) and 3048 ORFs (84\%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81\% Vibrio sp. RC341 and 81\% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Conclusions Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.}, author = {Bradd,H. and Christopher,G. and Nur,H. and Seon-Young,C. and Jongsik,C. and Thomas,B. and David,B. and Jean,C. and Chris,D. J. and Cliff,H. and Rita R Colwell} } @inbook {12500, title = {Compressive Acquisition of Dynamic Scenes}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6311}, year = {2010}, month = {2010///}, pages = {129 - 142}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Compressive sensing (CS) is a new approach for the acquisition and recovery of sparse signals and images that enables sampling rates significantly below the classical Nyquist rate. Despite significant progress in the theory and methods of CS, little headway has been made in compressive video acquisition and recovery. Video CS is complicated by the ephemeral nature of dynamic events, which makes direct extensions of standard CS imaging architectures and signal models infeasible. In this paper, we develop a new framework for video CS for dynamic textured scenes that models the evolution of the scene as a linear dynamical system (LDS). This reduces the video recovery problem to first estimating the model parameters of the LDS from compressive measurements, from which the image frames are then reconstructed. We exploit the low-dimensional dynamic parameters (the state sequence) and high-dimensional static parameters (the observation matrix) of the LDS to devise a novel compressive measurement strategy that measures only the dynamic part of the scene at each instant and accumulates measurements over time to estimate the static parameters. This enables us to considerably lower the compressive measurement rate considerably. We validate our approach with a range of experiments including classification experiments that highlight the effectiveness of the proposed approach.}, isbn = {978-3-642-15548-2}, url = {http://dx.doi.org/10.1007/978-3-642-15549-9_10}, author = {Sankaranarayanan,Aswin and Turaga,Pavan and Baraniuk,Richard and Chellapa, Rama}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @article {12463, title = {Compressive Video Acquisition, Fusion and Processing}, year = {2010}, month = {2010/12/14/}, abstract = {Modern developments in sensor technology, signal processing, and wireless communications have enabled the conception and deployment of large-scale networked sensing systems spanning numerous collection platforms and varied modalities. These systems have the potential to make intelligent decisions by integrating information from massive amounts of sensor data. Before such benefits can be achieved, significant advances must be made in methods for communicating, fusing, and processing this evergrowing volume of diverse data. In this one-year research project, we aimed to expose the fundamental issues and pave the way for further careful study of compressive approaches to video acquisition, fusion, and processing. In doing so, we developed a theoretical definition of video temporal bandwidth and applied the theory to compressive sampling and reconstruction. We created a new framework for compressive video sensing based on linear dynamical systems, lowering the compressive measurement rate. Finally, we applied our own joint manifold model to a variety of relevant image processing problems, demonstrating the model{\textquoteright}s effectiveness and ability to overcome noise and occlusion obstacles. We also showed how joint manifold models can discover an object{\textquoteright}s trajectory, an important step towards video fusion.}, keywords = {*DATA FUSION, *DETECTORS, *SIGNAL PROCESSING, *VIDEO SIGNALS, ACQUISITION, COLLECTION, COMMUNICATION AND RADIO SYSTEMS, COMPRESSIVE PROPERTIES, COMPRESSIVE SAMPLING, compressive sensing, COMPRESSIVE VIDEO, decision making, DEPLOYMENT, DETECTION, DYNAMICS, IMAGE PROCESSING, Linear systems, Linearity, MANIFOLDS(ENGINES), measurement, MISCELLANEOUS DETECTION AND DETECTORS, MODELS, sampling, THEORY, TRAJECTORIES}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA533703}, author = {Baraniuk,Richard G. and Chellapa, Rama and Wakin,Michael} } @article {14371, title = {Computing marginal distributions over continuous markov networks for statistical relational learning}, journal = {Advances in Neural Information Processing Systems (NIPS)}, year = {2010}, month = {2010///}, abstract = {Continuous Markov random fields are a general formalism to model joint proba-bility distributions over events with continuous outcomes. We prove that marginal computation for constrained continuous MRFs is $\#$P-hard in general and present a polynomial-time approximation scheme under mild assumptions on the struc- ture of the random field. Moreover, we introduce a sampling algorithm to com- pute marginal distributions and develop novel techniques to increase its effi- ciency. Continuous MRFs are a general purpose probabilistic modeling tool and we demonstrate how they can be applied to statistical relational learning. On the problem of collective classification, we evaluate our algorithm and show that the standard deviation of marginals serves as a useful measure of confidence. }, author = {Br{\"o}cheler,M. and Getoor, Lise} } @conference {17747, title = {COSI: Cloud Oriented Subgraph Identification in Massive Social Networks}, booktitle = {Advances in Social Networks Analysis and Mining (ASONAM), 2010 International Conference on}, year = {2010}, month = {2010/08//}, pages = {248 - 255}, abstract = {Subgraph matching is a key operation on graph data. Social network (SN) providers may want to find all subgraphs within their social network that match certain query graph patterns. Unfortunately, subgraph matching is NP-complete, making its application to massive SNs a major challenge. Past work has shown how to implement subgraph matching on a single processor when the graph has 10-25M edges. In this paper, we show how to use cloud computing in conjunction with such existing single processor methods to efficiently match complex subgraphs on graphs as large as 778M edges. A cloud consists of one master compute node and k slave compute nodes. We first develop a probabilistic method to estimate probabilities that a vertex will be retrieved by a random query and that a pair of vertices will be successively retrieved by a random query. We use these probability estimates to define edge weights in an SN and to compute minimal edge cuts to partition the graph amongst k slave nodes. We develop algorithms for both master and slave nodes that try to minimize communication overhead. The resulting COSI system can answer complex queries over real-world SN data containing over 778M edges very efficiently.}, keywords = {(online);, answering;social, complexity;data, computing;edge, data;graph, estimation;query, handling;graph, matching;Internet;computational, matching;probability;query, network;subgraph, networking, NP-complete;cloud, pattern;probability, processing;social, theory;pattern, weight;graph}, doi = {10.1109/ASONAM.2010.80}, author = {Bröcheler,M. and Pugliese, A. and V.S. Subrahmanian} } @conference {18940, title = {Crowdsourcing the evaluation of a domain-adapted named entity recognition system}, series = {HLT {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {345 - 348}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Named entity recognition systems sometimes have difficulty when applied to data from domains that do not closely match the training data. We first use a simple rule-based technique for domain adaptation. Data for robust validation of the technique is then generated, and we use crowdsourcing techniques to show that this strategy produces reliable results even on data not seen by the rule designers. We show that it is possible to extract large improvements on the target data rapidly at low cost using these techniques.}, isbn = {1-932432-65-5}, url = {http://dl.acm.org/citation.cfm?id=1857999.1858050}, author = {Sayeed,Asad B. and Meyer,Timothy J. and Nguyen,Hieu C. and Buzek,Olivia and Weinberg, Amy} } @article {14545, title = {Deploying sensor networks with guaranteed fault tolerance}, journal = {IEEE/ACM Transactions on Networking (TON)}, volume = {18}, year = {2010}, month = {2010///}, pages = {216 - 228}, author = {Bredin,J. L and Demaine,E. D and Hajiaghayi, Mohammad T. and Rus,D.} } @conference {18826, title = {Design and Fabrication of a Multi-Material Compliant Flapping Wing Drive Mechanism for Miniature Air Vehicles}, year = {2010}, month = {2010///}, pages = {69 - 80}, publisher = {ASME}, organization = {ASME}, abstract = {Successful realization of a flapping wing micro air vehicle (MAV) requires development of a light weight drive mechanism converting the rotary motion of the motor into flapping motion of the wings. Low weight of the drive mechanism is required to maximize the payload and battery capacity. In order to make flapping wing MAVs attractive in search, rescue, and recovery missions, they should be disposable from the cost point of view. Injection molded compliant drive mechanisms are an attractive design option to satisfy the weight, efficiency and cost requirements. In the past, we have successfully used multi-piece molding to create mechanisms utilizing distributed compliance for smaller MAVs. However, as the size of the MAV increases, mechanisms with distributed compliance exhibit excessive deformation. Therefore localizing rather than distributing the compliance in the mechanism becomes a more attractive option. Local compliance can be realized through multimaterial designs. A multi-material injection molded mechanism additionally offers reduction in the number of parts. This paper describes an approach for determining the drive mechanism shape and size that meets both the functional design and multi-material molding requirements. The design generated by the approach described in this paper was utilized to realize a flapping wing MAV with significant enhancements in the payload capabilities.}, isbn = {978-0-7918-4410-6}, doi = {10.1115/DETC2010-28519}, url = {http://link.aip.org/link/ASMECP/v2010/i44106/p69/s1\&Agg=doi}, author = {Bejgerowski,Wojciech and Gerdes,John W. and Gupta, Satyandra K. and Bruck,Hugh A. and Wilkerson,Stephen} } @article {19280, title = {Design and implementation of embedded computer vision systems based on particle filters}, journal = {Computer Vision and Image Understanding}, volume = {114}, year = {2010}, month = {2010}, pages = {1203 - 1214}, abstract = {Particle filtering methods are gradually attaining significant importance in a variety of embedded computer vision applications. For example, in smart camera systems, object tracking is a very important application and particle filter based tracking algorithms have shown promising results with robust tracking performance. However, most particle filters involve vast amount of computational complexity, thereby intensifying the challenges faced in their real-time, embedded implementation. Many of these applications share common characteristics, and the same system design can be reused by identifying and varying key system parameters and varying them appropriately. In this paper, we present a System-on-Chip (SoC) architecture involving both hardware and software components for a class of particle filters. The framework uses parameterization to enable fast and efficient reuse of the architecture with minimal re-design effort for a wide range of particle filtering applications as well as implementation platforms. Using this framework, we explore different design options for implementing three different particle filtering applications on field-programmable gate arrays (FPGAs). The first two applications involve particle filters with one-dimensional state transition models, and are used to demonstrate the key features of the framework. The main focus of this paper is on design methodology for hardware/software implementation of multi-dimensional particle filter application and we explore this in the third application which is a 3D facial pose tracking system for videos. In this multi-dimensional particle filtering application, we extend our proposed architecture with models for hardware/software co-design so that limited hardware resources can be utilized most effectively. Our experiments demonstrate that the framework is easy and intuitive to use, while providing for efficient design and implementation. We present different memory management schemes along with results on trade-offs between area (FPGA resource requirement) and execution speed.}, keywords = {design space exploration, Particle filters, Reconfigurable platforms}, isbn = {1077-3142}, url = {http://www.sciencedirect.com/science/article/pii/S1077314210000950}, author = {Sankalita Saha and Bambha, Neal K. and Bhattacharyya, Shuvra S.} } @conference {19281, title = {Design and implementation of real-time signal processing applications on heterogeneous multiprocessor arrays}, booktitle = {2010 Conference Record of the Forty Fourth Asilomar Conference on Signals, Systems and Computers (ASILOMAR)}, year = {2010}, month = {2010}, pages = {2121 - 2125}, abstract = {Processing structures based on arrays of computational elements form an important class of architectures, which includes field programmable gate arrays (FPGAs), systolic arrays, and various forms of multicore processors. A wide variety of design methods and tools have been targeted to regular processing arrays involving homogeneous processing elements. In this paper, we introduce the concept of field programmable X arrays (FPXAs) as an abstract model for design and implementation of heterogeneous multiprocessor arrays for signal processing systems. FPXAs are abstract structures that can be targeted for implementation on application-specific integrated circuits, FPGAs, or other kinds of reconfigurable processors. FPXAs can also be mapped onto multicore processors for flexible emulation. We discuss the use of dataflow models as an integrated application representation and intermediate representation for efficient specification and mapping of signal processing systems on FPXAs. We demonstrate our proposed models and techniques with a case study involving the embedding of an application-specific FPXA system on an off-the-shelf FPGA device.}, keywords = {application specific integrated circuits, application-specific integrated circuits, computational elements, Computer architecture, decoding, Field programmable gate arrays, field programmable X arrays, FPGA, FPXA, Integrated circuit modeling, Logic Design, microprocessor chips, multicore processors, multiprocessor arrays, real-time signal processing, reconfigurable architectures, reconfigurable processors, Routing, Signal processing, Signal processing systems, systolic arrays, Viterbi algorithm}, author = {Wu, Hsiang-Huang and Chung-Ching Shen and Bhattacharyya, Shuvra S. and Compton, K. and Schulte, M. and Wolf, M. and Zhang, Tong} } @article {18828, title = {Developing a Stochastic Dynamic Programming Framework for Optical Tweezer-Based Automated Particle Transport Operations}, journal = {Automation Science and Engineering, IEEE Transactions on}, volume = {7}, year = {2010}, month = {2010/04//}, pages = {218 - 227}, abstract = {Automated particle transport using optical tweezers requires the use of motion planning to move the particle while avoiding collisions with randomly moving obstacles. This paper describes a stochastic dynamic programming based motion planning framework developed by modifying the discrete version of an infinite-horizon partially observable Markov decision process algorithm. Sample trajectories generated by this algorithm are presented to highlight effectiveness in crowded scenes and flexibility. The algorithm is tested using silica beads in a holographic tweezer set-up and data obtained from the physical experiments are reported to validate various aspects of the planning simulation framework. This framework is then used to evaluate the performance of the algorithm under a variety of operating conditions.}, keywords = {holographic tweezer set-up, holography, infinite-horizon partially observable Markov decision process algorithm, Markov processes, motion planning framework, optical tweezer-based automated particle transport operations, optical tweezers, radiation pressure, silica beads, stochastic dynamic programming framework, stochastic programming}, isbn = {1545-5955}, doi = {10.1109/TASE.2009.2026056}, author = {Banerjee,A. G. and Pomerance,A. and Losert,W. and Gupta,S.K.} } @article {12876, title = {Diversity and distribution of cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/08/}, pages = {198 - 207}, abstract = {Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47\% of 83 non-O1, non-O139 strains and 16\% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2010.00139.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00139.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Purdy,Alexandra E. and Balch,Deborah and Liz{\'a}rraga-Partida,Marcial Leonardo and Islam,Mohammad Sirajul and Martinez-Urtaza,Jaime and Huq,Anwar and Rita R Colwell and Bartlett,Douglas H.} } @article {18539, title = {Don{\textquoteright}t Configure the Network, Program It! Domain-Specific Programming Languages for Network Systems}, volume = {YALEU/DCS/RR-1432}, year = {2010}, month = {2010///}, institution = {Yale University}, abstract = {Network operators must configure networks to accomplish critical, complex, and often conflicting requirements: they must ensure good performance while maintaining security, and satisfy contractual obligations while ensuring profitable use of interdomain connections. Unfortunately, today they have no choice but to implement these high-level goals by configuring hundreds of individual network devices. These interact in complex and unexpected ways, often resulting in misconfigurations or downtime. We propose a new approach: rather than configure individual network devices, operators should program the network holistically, according to high-level policies. Towards this goal, we present Nettle, a system for clearly and concisely expressing network requirements together with mechanisms to control the network accordingly. At the lowest level, we rely on OpenFlow switches for programmable network hardware. On top of this layer, we build an extensible family of embedded domain-specific languages (EDSLs), each aimed at different operational concerns and provide convenient ways to sensibly combine expressions in these languages. We present a case study demonstrating a DSL for networks that provides fine-grained, dynamic access control policies.}, author = {Feamster, Nick and Voellmy,A. and Agarwal,A. and Hudak,P. and Burnett,S. and Launchbury,J.} } @conference {12221, title = {Don{\textquoteright}t love thy nearest neighbor}, booktitle = {Proceedings of the 9th international conference on Peer-to-peer systems}, series = {IPTPS{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {5 - 5}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, url = {http://dl.acm.org/citation.cfm?id=1863145.1863150}, author = {Lumezanu,Cristian and Levin,Dave and Han,Bo and Spring, Neil and Bhattacharjee, Bobby} } @inbook {19300, title = {Dynamic and Multidimensional Dataflow Graphs}, booktitle = {Handbook of Signal Processing Systems}, year = {2010}, month = {2010}, pages = {899 - 930}, publisher = {Springer US}, organization = {Springer US}, abstract = {Much of the work to date on dataflow models for signal processing system design has focused decidable dataflow models that are best suited for onedimensional signal processing. In this chapter, we review more general dataflow modeling techniques that are targeted to applications that include multidimensional signal processing and dynamic dataflow behavior. As dataflow techniques are applied to signal processing systems that are more complex, and demand increasing degrees of agility and flexibility, these classes of more general dataflow models are of correspondingly increasing interest. We begin with a discussion of two dataflow modeling techniques - multi-dimensional synchronous dataflow and windowed dataflow - that are targeted towards multidimensional signal processing applications. We then provide a motivation for dynamic dataflow models of computation, and review a number of specific methods that have emerged in this class of models. Our coverage of dynamic dataflowmodels in this chapter includes Boolean dataflow, the stream-based function model, CAL, parameterized dataflow, and enable-invoke dataflow.}, keywords = {Communications Engineering, Networks, Computer Systems Organization and Communication Networks, Processor Architectures, Signal, Image and Speech Processing}, isbn = {978-1-4419-6344-4, 978-1-4419-6345-1}, url = {http://link.springer.com/chapter/10.1007/978-1-4419-6345-1_32}, author = {Bhattacharyya, Shuvra S. and Deprettere, Ed F. and Keinert, Joachim}, editor = {Bhattacharyya, Shuvra S. and Deprettere, Ed F. and Leupers, Rainer and Takala, Jarmo} } @conference {12222, title = {The effect of packet loss on redundancy elimination in cellular wireless networks}, booktitle = {Proceedings of the 10th annual conference on Internet measurement}, series = {IMC {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {294 - 300}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network-level redundancy elimination (RE) algorithms reduce traffic volume on bandwidth-constrained network paths by avoiding the transmission of repeated byte sequences. Previous work shows that RE can suppress the transmission of 20-50\% bytes when deployed at ISP access links or between routers. In this paper, we focus on the challenges of deploying RE in cellular networks. The potential benefifit is substantial, since cellular networks have a growing subscriber base and network links, including wired backhaul, are often oversubscribed. Using three large traces captured at two North American and one European wireless network providers, we show that RE can reduce the bandwidth consumption of the majority of mobile users by at least 10\%. However, cellular links have much higher packet loss rates than their wired counterparts, which makes applying RE much more difficult. Our experiments also show that the loss of only a few packets can disrupt RE and eliminate the bandwidth savings. We propose informed marking, a lightweight scheme that detects lost packets and prevents RE algorithms from using them for future encodings. We implement RE with informed marking and deploy it in a real-world cellular network. Our results show that with informed marking, more than 60\% of the bandwidth savings of RE are preserved, even when packet loss rates are high.}, keywords = {cellular networks, loss, redundancy elimination}, isbn = {978-1-4503-0483-2}, doi = {10.1145/1879141.1879179}, url = {http://doi.acm.org/10.1145/1879141.1879179}, author = {Lumezanu,Cristian and Guo,Katherine and Spring, Neil and Bhattacharjee, Bobby} } @article {12477, title = {An Efficient and Robust Algorithm for Shape Indexing and Retrieval}, journal = {Multimedia, IEEE Transactions on}, volume = {12}, year = {2010}, month = {2010/08//}, pages = {372 - 385}, abstract = {Many shape matching methods are either fast but too simplistic to give the desired performance or promising as far as performance is concerned but computationally demanding. In this paper, we present a very simple and efficient approach that not only performs almost as good as many state-of-the-art techniques but also scales up to large databases. In the proposed approach, each shape is indexed based on a variety of simple and easily computable features which are invariant to articulations, rigid transformations, etc. The features characterize pairwise geometric relationships between interest points on the shape. The fact that each shape is represented using a number of distributed features instead of a single global feature that captures the shape in its entirety provides robustness to the approach. Shapes in the database are ordered according to their similarity with the query shape and similar shapes are retrieved using an efficient scheme which does not involve costly operations like shape-wise alignment or establishing correspondences. Depending on the application, the approach can be used directly for matching or as a first step for obtaining a short list of candidate shapes for more rigorous matching. We show that the features proposed to perform shape indexing can be used to perform the rigorous matching as well, to further improve the retrieval performance.}, keywords = {activity, algorithm;shape, classification;human, databases;robust, estimation;large, indexing;shape, MATCHING, matching;image, methods;shape, pose, recognition;, retrieval;image, retrieval;indexing;shape}, isbn = {1520-9210}, doi = {10.1109/TMM.2010.2050735}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @conference {19289, title = {Efficient static buffering to guarantee throughput-optimal FPGA implementation of synchronous dataflow graphs}, booktitle = {2010 International Conference on Embedded Computer Systems (SAMOS)}, year = {2010}, month = {2010}, pages = {136 - 143}, abstract = {When designing DSP applications for implementation on field programmable gate arrays (FPGAs), it is often important to minimize consumption of limited FPGA resources while satisfying real-time performance constraints. In this paper, we develop efficient techniques to determine dataflow graph buffer sizes that guarantee throughput-optimal execution when mapping synchronous dataflow (SDF) representations of DSP applications onto FPGAs. Our techniques are based on a novel two-actor SDF graph Model (TASM), which efficiently captures the behavior and costs associated with SDF graph edges (flow-graph connections). With our proposed techniques, designers can automatically generate upper bounds on SDF graph buffer distributions that realize maximum achievable throughput performance for the corresponding applications. Furthermore, our proposed technique is characterized by low polynomial time complexity, which is useful for rapid prototyping in DSP system design.}, keywords = {buffer memory, circuit complexity, Complexity theory, Computational modeling, data flow graphs, Digital signal processing, digital signal processing chips, DSP system design, efficient static buffering, Field programmable gate arrays, FPGA, graph buffer distributions, integrated circuit design, low polynomial time complexity, Random access memory, Schedules, SDF graph edges, Signal processing systems, Synchronous dataflow, synchronous dataflow graph mapping, Throughput, throughput-optimal execution, throughput-optimal FPGA implementation, two-actor SDF graph model, upper bounds}, author = {Kee, Hojin and Bhattacharyya, Shuvra S. and Kornerup, J.} } @article {15383, title = {Electromagnetic Modeling of Ethernet Transformers}, journal = {Magnetics, IEEE Transactions on}, volume = {46}, year = {2010}, month = {2010/02//}, pages = {563 - 569}, abstract = {The unique features of Ethernet transformers are reviewed, and novel testing techniques for identification of lumped parameters of equivalent circuits are presented. To account for the distributed nature of the cross-winding and intrawinding capacitances, novel distributed models for electromagnetic analysis of Ethernet transformers are presented.}, keywords = {analysis;electromagnetic, area, capacitances;lumped, circuits;ethernet, circuits;local, cross-winding;distributed, modeling;equivalent, models;electromagnetic, networks;lumped, networks;transformer, parameter, parameters;novel, techniques;capacitance;equivalent, Testing, transformers;intrawinding, windings;transformers;}, isbn = {0018-9464}, doi = {10.1109/TMAG.2009.2033203}, author = {Bowen,D. and Mayergoyz, Issak D and Krafft,C.} } @article {19293, title = {Energy-driven distribution of signal processing applications across wireless sensor networks}, journal = {ACM Trans. Sen. Netw.}, volume = {6}, year = {2010}, month = {2010}, pages = {24:1 - 24:32}, abstract = {Wireless sensor network (WSN) applications have been studied extensively in recent years. Such applications involve resource-limited embedded sensor nodes that have small size and low power requirements. Based on the need for extended network lifetimes in WSNs in terms of energy use, the energy efficiency of computation and communication operations in the sensor nodes becomes critical. Digital Signal Processing (DSP) applications typically require intensive data processing operations and as a result are difficult to implement directly in resource-limited WSNs. In this article, we present a novel design methodology for modeling and implementing computationally intensive DSP applications applied to wireless sensor networks. This methodology explores efficient modeling techniques for DSP applications, including data sensing and processing; derives formulations of Energy-Driven Partitioning (EDP) for distributing such applications across wireless sensor networks; and develops efficient heuristic algorithms for finding partitioning results that maximize the network lifetime. To address such an energy-driven partitioning problem, this article provides a new way of aggregating data and reducing communication traffic among nodes based on application analysis. By considering low data token delivery points and the distribution of computation in the application, our approach finds energy-efficient trade-offs between data communication and computation.}, keywords = {DSP, Energy efficiency, network lifetime, Speech recognition, Wireless sensor networks}, isbn = {1550-4859}, url = {http://doi.acm.org/10.1145/1754414.1754420}, author = {Chung-Ching Shen and Plishker, William L. and Ko,Dong-Ik and Bhattacharyya, Shuvra S. and Goldsman,Neil} } @conference {16685, title = {Error driven paraphrase annotation using Mechanical Turk}, booktitle = {Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon{\textquoteright}s Mechanical Turk}, year = {2010}, month = {2010///}, pages = {217 - 221}, author = {Buzek,O. and Resnik, Philip and Bederson, Benjamin B.} } @article {15882, title = {Evaluation of information retrieval for E-discovery}, journal = {Artificial Intelligence and Law}, volume = {18}, year = {2010}, month = {2010/08/10/}, pages = {347 - 386}, isbn = {0924-8463, 1572-8382}, doi = {10.1007/s10506-010-9093-9}, url = {http://www.springerlink.com/content/m700w2k26n264u01/}, author = {Oard, Douglas and Baron,Jason R. and Hedin,Bruce and Lewis,David D. and Tomlinson,Stephen} } @inbook {12995, title = {Evolutionary framework for Lepidoptera model systems}, booktitle = {Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera}, year = {2010}, month = {2010///}, pages = {1 - 24}, publisher = {Taylor \& Francis}, organization = {Taylor \& Francis}, address = {Boca Raton}, abstract = {{\textquotedblleft}Model systems{\textquotedblright} are specific organisms upon which detailed studies have been conducted examining a fundamental biological question. If the studies are robust, their results can be extrapolated among an array of organisms that possess features in common with the subject organism. The true power of model systems lies in the ability to extrapolate these details across larger groups of organisms. In order to generalize these results, comparative studies are essential and require that model systems be placed into their evolutionary or phylogenetic context. This chapter examines model systems in the insect order Lepidoptera from the perspective of several different superfamilies. Historically, many species of Lepidoptera have been essential in the development of invaluable model systems in the fields of development biology, genetics, molecular biology, physiology, co-evolution, population dynamics, and ecology.}, author = {Roe,A. and Weller,S. and Baixeras,J. and Brown,J. W and Cummings, Michael P. and Davis,DR and Horak,M and Kawahara,A. Y and Mitter,C and Parr,C.S. and Regier,J. C and Rubinoff,D and Simonsen,TJ and Wahlberg,N and Zwick,A.}, editor = {Goldsmith,M and Marec,F} } @inbook {14196, title = {An Experimental Study of Color-Based Segmentation Algorithms Based on the Mean-Shift Concept}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6312}, year = {2010}, month = {2010///}, pages = {506 - 519}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We point out a difference between the original mean-shift formulation of Fukunaga and Hostetler and the common variant in the computer vision community, namely whether the pairwise comparison is performed with the original or with the filtered image of the previous iteration. This leads to a new hybrid algorithm, called Color Mean Shift, that roughly speaking, treats color as Fukunaga{\textquoteright}s algorithm and spatial coordinates as Comaniciu{\textquoteright}s algorithm. We perform experiments to evaluate how different kernel functions and color spaces affect the final filtering and segmentation results, and the computational speed, using the Berkeley and Weizmann segmentation databases. We conclude that the new method gives better results than existing mean shift ones on four standard comparison measures ( improvement on RAND and BDE measures respectively for color images), with slightly higher running times ( ). Overall, the new method produces segmentations comparable in quality to the ones obtained with current state of the art segmentation algorithms.}, isbn = {978-3-642-15551-2}, url = {http://dx.doi.org/10.1007/978-3-642-15552-9_37}, author = {Bitsakos,K. and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @inbook {17598, title = {Fault-Tolerant Facility Location: A Randomized Dependent LP-Rounding Algorithm}, booktitle = {Integer Programming and Combinatorial OptimizationInteger Programming and Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {6080}, year = {2010}, month = {2010///}, pages = {244 - 257}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, isbn = {978-3-642-13035-9}, url = {http://dx.doi.org/10.1007/978-3-642-13036-6_19}, author = {Byrka,Jaroslaw and Srinivasan, Aravind and Swamy,Chaitanya}, editor = {Eisenbrand,Friedrich and Shepherd,F.} } @article {16265, title = {Finishing genomes with limited resources: lessons from an ensemble of microbial genomes}, journal = {BMC Genomics}, volume = {11}, year = {2010}, month = {2010/04/16/}, pages = {242 - 242}, abstract = {While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-11-242}, url = {http://www.biomedcentral.com/1471-2164/11/242}, author = {Nagarajan,Niranjan and Cook,Christopher and Di Bonaventura,Maria Pia and Ge,Hong and Richards,Allen and Bishop-Lilly,Kimberly A and DeSalle,Robert and Read,Timothy D. and Pop, Mihai} } @conference {19297, title = {FPGA-based design and implementation of the 3GPP-LTE physical layer using parameterized synchronous dataflow techniques}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010}, pages = {1510 - 1513}, abstract = {Synchronous dataflow (SDF) is an ubiquitous dataflow model of computation that has been studied extensively for efficient simulation and software synthesis of DSP applications. In recent years, parameterized SDF (PSDF) has evolved as a useful framework for modeling SDF graphs in which arbitrary parameters can be changed dynamically. However, the potential to enable efficient hardware synthesis has been treated relatively sparsely in the literature for SDF and even more so for the newer, more general PSDF model. This paper investigates efficient FPGA-based design and implementation of the physical layer for 3GPP-Long Term Evolution (LTE), a next generation cellular standard. To capture the SDF behavior of the functional core of LTE along with higher level dynamics in the standard, we use a novel PSDF-based FPGA architecture framework. We implement our PSDF-based, LTE design framework using National Instrument{\textquoteright}s LabVIEW FPGA, a recently-introduced commercial platform for reconfigurable hardware implementation. We show that our framework can effectively model the dynamics of the LTE protocol, while also providing a synthesis framework for efficient FPGA implementation.}, keywords = {3G mobile communication, 3GPP-long term evolution, 3GPP-LTE physical layer, 4G communication systems, Computational modeling, data flow analysis, data flow graphs, Dataflow modeling, Digital signal processing, DSP applications, Field programmable gate arrays, FPGA architecture framework, FPGA implementation, FPGA-based design, Hardware, hardware synthesis, Instruments, LabVIEW FPGA, Logic Design, LTE, next generation cellular standard, parameterized synchronous data flow technique, Pervasive computing, Physical layer, Physics computing, Production, PSDF graph, reconfigurable hardware implementation, Runtime, software synthesis, Ubiquitous Computing, ubiquitous data flow model}, author = {Kee, Hojin and Bhattacharyya, Shuvra S. and Wong, I. and Yong Rao} } @article {12219, title = {A general framework for efficient geographic routing in wireless networks}, journal = {Computer Networks}, volume = {54}, year = {2010}, month = {2010/04/08/}, pages = {844 - 861}, abstract = {We propose a new link metric called normalized advance (NADV) for geographic routing in multihop wireless networks. NADV selects neighbors with the optimal trade-off between proximity and link cost. Coupled with the local next hop decision in geographic routing, NADV enables an adaptive and efficient cost-aware routing strategy. Depending on the objective or message priority, applications can use the NADV framework to minimize various types of link cost.We present efficient methods for link cost estimation and perform detailed experiments in simulated environments. Our results show that NADV outperforms current schemes in many aspects: for example, in high noise environments with frequent packet losses, the use of NADV leads to 81\% higher delivery ratio. When compared to centralized routing under certain settings, geographic routing using NADV finds paths whose cost is close to the optimum. We also conducted experiments in Emulab testbed and the results demonstrate that our proposed approach performs well in practice. }, keywords = {Geographic routing, Link cost estimation, Routing metric, Wireless multihop networks}, isbn = {1389-1286}, doi = {10.1016/j.comnet.2009.09.013}, url = {http://www.sciencedirect.com/science/article/pii/S1389128609002904}, author = {Lee,Seungjoon and Bhattacharjee, Bobby and Banerjee,Suman and Han,Bo} } @article {12871, title = {Genome Sequence of Hybrid Vibrio Cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. Cholerae}, journal = {Journal of BacteriologyJ. Bacteriol.}, volume = {192}, year = {2010}, month = {2010/07/01/}, pages = {3524 - 3533}, abstract = {The genomes of Vibrio cholerae O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33, and altered O1 El Tor CIRS101 were sequenced. All three strains were found to belong to the phylocore group 1 clade of V. cholerae, which includes the 7th-pandemic O1 El Tor and serogroup O139 isolates, despite displaying certain characteristics of the classical biotype. All three strains were found to harbor a hybrid variant of CTXΦ and an integrative conjugative element (ICE), leading to their establishment as successful clinical clones and the displacement of prototypical O1 El Tor. The absence of strain- and group-specific genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most likely factor in the recent establishment of dominance of V. cholerae CIRS101 over the other two hybrid strains.}, isbn = {0021-9193, 1098-5530}, doi = {10.1128/JB.00040-10}, url = {http://jb.asm.org/content/192/13/3524}, author = {Grim,Christopher J. and Hasan,Nur A. and Taviani,Elisa and Haley,Bradd and Jongsik Chun and Brettin,Thomas S. and Bruce,David C. and Detter,J. Chris and Han,Cliff S. and Chertkov,Olga and Challacombe,Jean and Huq,Anwar and Nair,G. Balakrish and Rita R Colwell} } @article {17970, title = {Global Contours}, volume = {CS-TR-4957}, year = {2010}, month = {2010/05/05/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {We present a multi-scale approach that uses Laplacian eigenvectorsto extract globally significant contours from an image. The input images are mapped into the Laplacian space by using Laplacian eigenvectors. This mapping causes globally significant pixels along the contours to expand in the Laplacian space. The measure of the expansion is used to compute the Global Contours. We apply our scheme to real color images and compare it with several other methods that compute image and color saliency. The contours calculated by our method reflect global properties of the image and are complementary to classic center-surround image saliency methods. We believe that hybrid image saliency algorithms that combine our method of Global Contours with center-surround image saliency algorithms will be able to better characterize the most important regions of images than those from just using contours calculated using bottom-up approaches. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/10072}, author = {Bista, Sujal and Varshney, Amitabh} } @book {19354, title = {Handbook of Signal Processing Systems}, year = {2010}, month = {2010}, pages = {1099}, publisher = {Springer}, organization = {Springer}, abstract = {The Handbook is organized in four parts. The first part motivates representative applications that drive and apply state-of-the art methods for design and implementation of signal processing systems; the second part discusses architectures for implementing these applications; the third part focuses on compilers and simulation tools; and the fourth part describes models of computation and their associated design tools and methodologies.}, keywords = {Computers / Information Theory, Technology \& Engineering / Electrical, Technology \& Engineering / Signals \& Signal Processing}, isbn = {9781441963451}, author = {Bhattacharyya, Shuvra S. and Deprettere, Ed F.} } @conference {12403, title = {Holistic sentiment analysis across languages: multilingual supervised latent Dirichlet allocation}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, series = {EMNLP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {45 - 55}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {In this paper, we develop multilingual supervised latent Dirichlet allocation (MlSLDA), a probabilistic generative model that allows insights gleaned from one language{\textquoteright}s data to inform how the model captures properties of other languages. MlSLDA accomplishes this by jointly modeling two aspects of text: how multilingual concepts are clustered into thematically coherent topics and how topics associated with text connect to an observed regression variable (such as ratings on a sentiment scale). Concepts are represented in a general hierarchical framework that is flexible enough to express semantic ontologies, dictionaries, clustering constraints, and, as a special, degenerate case, conventional topic models. Both the topics and the regression are discovered via posterior inference from corpora. We show MlSLDA can build topics that are consistent across languages, discover sensible bilingual lexical correspondences, and leverage multilingual corpora to better predict sentiment.}, url = {http://dl.acm.org/citation.cfm?id=1870658.1870663}, author = {Jordan Boyd-Graber and Resnik, Philip} } @article {12875, title = {Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {76}, year = {2010}, month = {2010/03/15/}, pages = {1996 - 2001}, abstract = {The Ibis T5000 is a novel diagnostic platform that couples PCR and mass spectrometry. In this study, we developed an assay that can identify all known pathogenic Vibrio species and field-tested it using natural water samples from both freshwater lakes and the Georgian coastal zone of the Black Sea. Of the 278 total water samples screened, 9 different Vibrio species were detected, 114 (41\%) samples were positive for V. cholerae, and 5 (0.8\%) samples were positive for the cholera toxin A gene (ctxA). All ctxA-positive samples were from two freshwater lakes, and no ctxA-positive samples from any of the Black Sea sites were detected.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01919-09}, url = {http://aem.asm.org/content/76/6/1996}, author = {Whitehouse,Chris A. and Baldwin,Carson and Sampath,Rangarajan and Blyn,Lawrence B. and Melton,Rachael and Li,Feng and Hall,Thomas A. and Harpin,Vanessa and Matthews,Heather and Tediashvili,Marina and Jaiani,Ekaterina and Kokashvili,Tamar and Janelidze,Nino and Grim,Christopher and Rita R Colwell and Huq,Anwar} } @inbook {16274, title = {Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets}, booktitle = {Bioinformatics Research and Applications}, series = {Lecture Notes in Computer Science}, volume = {6053}, year = {2010}, month = {2010///}, pages = {101 - 112}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge. We show that MetaPath outperforms other common approaches when evaluated on simulated datasets. We also demonstrate the power of our methods in analyzing two, publicly available, metagenomic datasets: a comparison of the gut microbiome of obese and lean twins; and a comparison of the gut microbiome of infant and adult subjects. We demonstrate that the subpathways identified by our method provide valuable insights into the biological activities of the microbiome.}, isbn = {978-3-642-13077-9}, url = {http://dx.doi.org/10.1007/978-3-642-13078-6_12}, author = {Liu,Bo and Pop, Mihai}, editor = {Borodovsky,Mark and Gogarten,Johann and Przytycka,Teresa and Rajasekaran,Sanguthevar} } @conference {12429, title = {Image classification of vascular smooth muscle cells}, booktitle = {Proceedings of the 1st ACM International Health Informatics Symposium}, series = {IHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {484 - 486}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {cell biology, digital image processing, machine learning}, isbn = {978-1-4503-0030-8}, doi = {10.1145/1882992.1883068}, url = {http://doi.acm.org/10.1145/1882992.1883068}, author = {Grasso,Michael A. and Mokashi,Ronil and Dalvi,Darshana and Cardone, Antonio and Dima,Alden A. and Bhadriraju,Kiran and Plant,Anne L. and Brady,Mary and Yesha,Yaacov and Yesha,Yelena} } @conference {16692, title = {Improving translation via targeted paraphrasing}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, year = {2010}, month = {2010///}, pages = {127 - 137}, author = {Resnik, Philip and Buzek,O. and Hu,C. and Kronrod,Y. and Quinn,A. and Bederson, Benjamin B.} } @inbook {17635, title = {On k-Column Sparse Packing Programs}, booktitle = {Integer Programming and Combinatorial OptimizationInteger Programming and Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {6080}, year = {2010}, month = {2010///}, pages = {369 - 382}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We consider the class of packing integer programs (PIPs) that are column sparse, where there is a specified upper bound k on the number of constraints that each variable appears in. We give an improved (ek + o(k))-approximation algorithm for k-column sparse PIPs. Our algorithm is based on a linear programming relaxation, and involves randomized rounding combined with alteration. We also show that the integrality gap of our LP relaxation is at least 2k - 1; it is known that even special cases of k-column sparse PIPs are (klogk)-hard to approximate.We generalize our result to the case of maximizing monotone submodular functions over k-column sparse packing constraints, and obtain an e2ke-1+o(k) -approximation algorithm. In obtaining this result, we prove a new property of submodular functions that generalizes the fractionally subadditive property, which might be of independent interest. }, isbn = {978-3-642-13035-9}, url = {http://dx.doi.org/10.1007/978-3-642-13036-6_28}, author = {Bansal,Nikhil and Korula,Nitish and Nagarajan,Viswanath and Srinivasan, Aravind}, editor = {Eisenbrand,Friedrich and Shepherd,F.} } @conference {17986, title = {Lazy binary-splitting: a run-time adaptive work-stealing scheduler}, booktitle = {Proceedings of the 15th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming}, series = {PPoPP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {179 - 190}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present Lazy Binary Splitting (LBS), a user-level scheduler of nested parallelism for shared-memory multiprocessors that builds on existing Eager Binary Splitting work-stealing (EBS) implemented in Intel{\textquoteright}s Threading Building Blocks (TBB), but improves performance and ease-of-programming. In its simplest form (SP), EBS requires manual tuning by repeatedly running the application under carefully controlled conditions to determine a stop-splitting-threshold (sst)for every do-all loop in the code. This threshold limits the parallelism and prevents excessive overheads for fine-grain parallelism. Besides being tedious, this tuning also over-fits the code to some particular dataset, platform and calling context of the do-all loop, resulting in poor performance portability for the code. LBS overcomes both the performance portability and ease-of-programming pitfalls of a manually fixed threshold by adapting dynamically to run-time conditions without requiring tuning. We compare LBS to Auto-Partitioner (AP), the latest default scheduler of TBB, which does not require manual tuning either but lacks context portability, and outperform it by 38.9\% using TBB{\textquoteright}s default AP configuration, and by 16.2\% after we tuned AP to our experimental platform. We also compare LBS to SP by manually finding SP{\textquoteright}s sst using a training dataset and then running both on a different execution dataset. LBS outperforms SP by 19.5\% on average. while allowing for improved performance portability without requiring tedious manual tuning. LBS also outperforms SP with sst=1, its default value when undefined, by 56.7\%, and serializing work-stealing (SWS), another work-stealer by 54.7\%. Finally, compared to serializing inner parallelism (SI) which has been used by OpenMP, LBS is 54.2\% faster.}, keywords = {Dynamic scheduling, load balancing, nested parallelism, thread scheduling, work stealing}, isbn = {978-1-60558-877-3}, doi = {10.1145/1693453.1693479}, url = {http://doi.acm.org/10.1145/1693453.1693479}, author = {Tzannes,Alexandros and Caragea,George C. and Barua,Rajeev and Vishkin, Uzi} } @inbook {12142, title = {Learning Through Application: The Maturing ofthe QIP in the SEL}, booktitle = {Making Software: What Really Works, and Why We Believe ItMaking Software: What Really Works, and Why We Believe It}, year = {2010}, month = {2010///}, pages = {65 - 65}, publisher = {O{\textquoteright}Reilly Media, Inc.}, organization = {O{\textquoteright}Reilly Media, Inc.}, isbn = {9780596808327}, author = {Basili, Victor R.} } @conference {19282, title = {A Lightweight Dataflow Approach for Design and Implementation of SDR Systems}, booktitle = {Wireless Innovation Conference and Product Exposition, Washington DC, USA}, year = {2010}, month = {2010}, abstract = {Model-based design methods based on dataflow modelsof computation are attractive for design and implementation of wireless communication systems because of their intuitive correspondence to communication system block diagrams, and the formal structure that is exposed through formal dataflow representations (e.g., see [2]). In this paper, we introduce a novel lightweight dataflow (LWDF) programming model for model-based design and implementation of wireless communication and software-defined radio systems. The approach is suitable for improving the productivity of the design process; the agility with which designs can be retargeted across different platforms; and the quality of derived implementations. By {\textquotedblleft}lightweight{\textquotedblright}, we meant that the programming model is designed to be minimally intrusive on existing design processes, and require minimal dependence on specialized tools or libraries. This allows designers to integrate and experiment with dataflow modeling approaches relatively quickly and flexibly into existing design methodologies and processes. }, url = {http://www.researchgate.net/publication/228788399_A_lightweight_dataflow_approach_for_design_and_implementation_of_SDR_systems/file/d912f511472fa25833.pdf}, author = {Chung-Ching Shen and Plishker,William and Wu, Hsiang-Huang and Bhattacharyya, Shuvra S.} } @mastersthesis {12404, title = {Linguistic Extensions of Topic Models}, year = {2010}, month = {2010///}, school = {Princeton University}, abstract = {Topic models like latent Dirichlet allocation (LDA) provide a framework for analyzinglarge datasets where observations are collected into groups. Although topic modeling has been fruitfully applied to problems social science, biology, and computer vision, it has been most widely used to model datasets where documents are modeled as exchangeable groups of words. In this context, topic models discover topics, distribu- tions over words that express a coherent theme like {\textquotedblleft}business{\textquotedblright} or {\textquotedblleft}politics.{\textquotedblright} While one of the strengths of topic models is that they make few assumptions about the underlying data, such a general approach sometimes limits the type of problems topic models can solve. When we restrict our focus to natural language datasets, we can use insights from linguistics to create models that understand and discover richer language patterns. In this thesis, we extend LDA in three different ways: adding knowledge of word mean- ing, modeling multiple languages, and incorporating local syntactic context. These extensions apply topic models to new problems, such as discovering the meaning of ambiguous words, extend topic models for new datasets, such as unaligned multi- lingual corpora, and combine topic models with other sources of information about documents{\textquoteright} context. }, author = {Jordan Boyd-Graber} } @article {12144, title = {Linking Software Development and Business Strategy Through Measurement}, journal = {Computer}, volume = {43}, year = {2010}, month = {2010/04//}, pages = {57 - 65}, abstract = {The GQM+Strategies approach extends the goal/question/metric paradigm for measuring the success or failure of goals and strategies, adding enterprise-wide support for determining action on the basis of measurement results. An organization can thus integrate its measurement program across all levels.}, keywords = {approach;business, aspects;software, development;organisational, engineering;, GQM+Strategies, program;software, strategy;enterprise, support;measurement, wide}, isbn = {0018-9162}, doi = {10.1109/MC.2010.108}, author = {Basili, Victor R. and Lindvall,M. and Regardie,M. and Seaman,C. and Heidrich,J. and Munch,J. and Rombach,D. and Trendowicz,A.} } @conference {19290, title = {Loop transformations for interface-based hierarchies IN SDF graphs}, booktitle = {2010 21st IEEE International Conference on Application-specific Systems Architectures and Processors (ASAP)}, year = {2010}, month = {2010}, pages = {341 - 344}, abstract = {Data-flow has proven to be an attractive computation model for programming digital signal processing (DSP) applications. A restricted version of data-flow, termed synchronous data-flow (SDF), offers strong compile-time predictability properties, but has limited expressive power. A new type of hierarchy (Interface-based SDF) has been proposed allowing more expressivity while maintaining its predictability. One of the main problems with this hierarchical SDF model is the lack of trade-off between parallelism and network clustering. This paper presents a systematic method for applying an important class of loop transformation techniques in the context of interface-based SDF semantics. The resulting approach provides novel capabilities for integrating parallelism extraction properties of the targeted loop transformations with the useful modeling, analysis, and code reuse properties provided by SDF.}, keywords = {Application software, code generation, Computer architecture, Computer interfaces, Data-Flow programming, Digital signal processing, Loop parallelization, PARALLEL PROCESSING, Power engineering computing, Power system modeling, Processor scheduling, Programming profession, scheduling, SDF graph, system recovery}, author = {Piat, J. and Bhattacharyya, Shuvra S. and Raulet, M.} } @article {19287, title = {A Low-overhead Scheduling Methodology for Fine-grained Acceleration of Signal Processing Systems}, journal = {Journal of Signal Processing Systems}, volume = {60}, year = {2010}, month = {2010}, pages = {333 - 343}, abstract = {Fine-grained accelerators have the potential to deliver significant benefits in various platforms for embedded signal processing. Due to the moderate complexity of their targeted operations, these accelerators must be managed with minimal run-time overhead. In this paper, we present a methodology for applying flow-shop scheduling techniques to make effective, low-overhead use of fine-grained DSP accelerators. We formulate the underlying scheduling approach in terms of general flow-shop scheduling concepts, and demonstrate our methodology concretely by applying it to MPEG-4 video decoding. We present quantitative experiments on a soft processor that runs on a field-programmable gate array, and provide insight on trends and trade-offs among different flow-shop scheduling approaches when applied to run-time management of fine-grained acceleration.}, url = {http://link.springer.com/article/10.1007/s11265-009-0366-z}, author = {Boutellier, Jani and Bhattacharyya, Shuvra S. and Silv{\'e}n, Olli} } @article {17621, title = {LP-rounding algorithms for facility-location problems}, journal = {arXiv:1007.3611}, year = {2010}, month = {2010/07/21/}, abstract = {We study LP-rounding approximation algorithms for metric uncapacitated facility-location problems. We first give a new analysis for the algorithm of Chudak and Shmoys, which differs from the analysis of Byrka and Aardal in that now we do not need any bound based on the solution to the dual LP program. Besides obtaining the optimal bifactor approximation as do Byrka and Aardal, we can now also show that the algorithm with scaling parameter equaling 1.58 is, in fact, an 1.58-approximation algorithm. More importantly, we suggest an approach based on additional randomization and analyses such as ours, which could achieve or approach the conjectured optimal 1.46...--approximation for this basic problem. Next, using essentially the same techniques, we obtain improved approximation algorithms in the 2-stage stochastic variant of the problem, where we must open a subset of facilities having only stochastic information about the future demand from the clients. For this problem we obtain a 2.2975-approximation algorithm in the standard setting, and a 2.4957-approximation in the more restricted, per-scenario setting. We then study robust fault-tolerant facility location, introduced by Chechik and Peleg: solutions here are designed to provide low connection cost in case of failure of up to $k$ facilities. Chechik and Peleg gave a 6.5-approximation algorithm for $k=1$ and a ($7.5k + 1.5$)-approximation algorithm for general $k$. We improve this to an LP-rounding $(k+5+4/k)$-approximation algorithm. We also observe that in case of oblivious failures the expected approximation ratio can be reduced to $k + 1.5$, and that the integrality gap of the natural LP-relaxation of the problem is at least $k + 1$.}, keywords = {Computer Science - Data Structures and Algorithms}, url = {http://arxiv.org/abs/1007.3611}, author = {Byrka,Jaroslaw and Ghodsi,Mohammadreza and Srinivasan, Aravind} } @conference {12223, title = {Maranello: practical partial packet recovery for 802.11}, booktitle = {Proceedings of the 7th USENIX conference on Networked systems design and implementation}, series = {NSDI{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {14 - 14}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Partial packet recovery protocols attempt to repair corrupted packets instead of retransmitting them in their entirety. Recent approaches have used physical layer confidence estimates or additional error detection codes embedded in each transmission to identify corrupt bits, or have applied forward error correction to repair without such explicit knowledge. In contrast to these approaches, our goal is a practical design that simultaneously: (a) requires no extra bits in correct packets, (b) reduces recovery latency, except in rare instances, (c) remains compatible with existing 802.11 devices by obeying timing and backoff standards, and (d) can be incrementally deployed on widely available access points and wireless cards. In this paper, we design, implement, and evaluate Maranello, a novel partial packet recovery mechanism for 802.11. In Maranello, the receiver computes checksums over blocks in corrupt packets and bundles these checksums into a negative acknowledgment sent when the sender expects to receive an acknowledgment. The sender then retransmits only those blocks for which the checksum is incorrect, and repeats this partial retransmission until it receives an acknowledgment. Successful transmissions are not burdened by additional bits and the receiver needs not infer which bits were corrupted. We implemented Maranello using OpenFWWF (open source firmware for Broadcom wireless cards) and deployed it in a small testbed. We compare Maranello to alternative recovery protocols using a trace-driven simulation and to 802.11 using a live implementation under various channel conditions. To our knowledge, Maranello is the first partial packet recovery design to be implemented in commonly available firmware.}, url = {http://dl.acm.org/citation.cfm?id=1855711.1855725}, author = {Han,Bo and Schulman,Aaron and Gringoli,Francesco and Spring, Neil and Bhattacharjee, Bobby and Nava,Lorenzo and Ji,Lusheng and Lee,Seungjoon and Miller,Robert} } @conference {12405, title = {Measuring transitivity using untrained annotators}, booktitle = {Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon{\textquoteright}s Mechanical Turk}, series = {CSLDAMT {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {188 - 194}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Hopper and Thompson (1980) defined a multi-axis theory of transitivity that goes beyond simple syntactic transitivity and captures how much "action" takes place in a sentence. Detecting these features requires a deep understanding of lexical semantics and real-world pragmatics. We propose two general approaches for creating a corpus of sentences labeled with respect to the Hopper-Thompson transitivity schema using Amazon Mechanical Turk. Both approaches assume no existing resources and incorporate all necessary annotation into a single system; this is done to allow for future generalization to other languages. The first task attempts to use language-neutral videos to elicit human-composed sentences with specified transitivity attributes. The second task uses an iterative process to first label the actors and objects in sentences and then annotate the sentences{\textquoteright} transitivity. We examine the success of these techniques and perform a preliminary classification of the transitivity of held-out data.}, url = {http://dl.acm.org/citation.cfm?id=1866696.1866726}, author = {Madnani,Nitin and Jordan Boyd-Graber and Resnik, Philip} } @conference {19286, title = {Methods for efficient implementation of Model Predictive Control on multiprocessor systems}, booktitle = {2010 IEEE International Conference on Control Applications (CCA)}, year = {2010}, month = {2010}, pages = {1357 - 1362}, abstract = {Model Predictive Control (MPC) has been used in a wide range of application areas including chemical engineering, food processing, automotive engineering, aerospace, and metallurgy. An important limitation on the application of MPC is the difficulty in completing the necessary computations within the sampling interval. Recent trends in computing hardware towards greatly increased parallelism offer a solution to this problem. This paper describes modeling and analysis tools to facilitate implementing the MPC algorithms on parallel computers, thereby greatly reducing the time needed to complete the calculations. The use of these tools is illustrated by an application to a class of MPC problems.}, keywords = {Computational modeling, COMPUTERS, Equations, Hardware, Linear systems, Mathematical model, model predictive control, MPC algorithms, Multiprocessing systems, Multiprocessor systems, parallel computers, predictive control, Program processors}, author = {Gu, Ruirui and Bhattacharyya, Shuvra S. and Levine,W. S} } @article {13708, title = {A modality lexicon and its use in automatic tagging}, journal = {Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC{\textquoteright}10)}, year = {2010}, month = {2010///}, pages = {1402 - 1407}, abstract = {This paper describes our resource-building results for an eight-week JHU Human Language Technology Center of Excellence SummerCamp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation. Specifically, we describe the construction of a modality annotation scheme, a modality lexicon, and two automated modality taggers that were built using the lexicon and annotation scheme. Our annotation scheme is based on identifying three components of modality: a trigger, a target and a holder. We describe how our modality lexicon was produced semi-automatically, expanding from an initial hand-selected list of modality trigger words and phrases. The resulting expanded modality lexicon is being made publicly available. We demonstrate that one tagger{\textemdash}a structure-based tagger{\textemdash}results in precision around 86\% (depending on genre) for tagging of a standard LDC data set. In a machine translation application, using the structure-based tagger to annotate English modalities on an English-Urdu training corpus improved the translation quality score for Urdu by 0.3 Bleu points in the face of sparse training data. }, author = {Baker,K. and Bloodgood,M. and Dorr, Bonnie J and Filardo,N.W. and Levin,L. and Piatko,C.} } @conference {12407, title = {Modeling perspective using adaptor grammars}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, series = {EMNLP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {284 - 292}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Strong indications of perspective can often come from collocations of arbitrary length; for example, someone writing get the government out of my X is typically expressing a conservative rather than progressive viewpoint. However, going beyond unigram or bigram features in perspective classification gives rise to problems of data sparsity. We address this problem using nonparametric Bayesian modeling, specifically adaptor grammars (Johnson et al., 2006). We demonstrate that an adaptive na{\"\i}ve Bayes model captures multiword lexical usages associated with perspective, and establishes a new state-of-the-art for perspective classification results using the Bitter Lemons corpus, a collection of essays about mid-east issues from Israeli and Palestinian points of view.}, url = {http://dl.acm.org/citation.cfm?id=1870658.1870686}, author = {Hardisty,Eric A. and Jordan Boyd-Graber and Resnik, Philip} } @inbook {16823, title = {Multidimensional data structures for spatial applications}, booktitle = {Algorithms and theory of computation handbookAlgorithms and theory of computation handbook}, year = {2010}, month = {2010///}, pages = {6 - 6}, publisher = {Chapman \& Hall/CRC}, organization = {Chapman \& Hall/CRC}, abstract = {An overview is presented of a number of representations of multidimensional data that arise in spatial applications. Multidimensional spatial data consists of points as well as objects that have extent such as line segments, rectangles, regions, and volumes. The points may have locational as well as nonlocational attributes. The focus is on spatial data which is a subset of multidimensional data consisting of points with locational attributes and objects with extent. The emphasis is on hierarchical representations based on the "divide-and-conquer" problem-solving paradigm. They are of interest because they enable focusing computational resources on the interesting subsets of data. Thus, there is no need to expend work where the payoff is small. These representations are of use in operations such as range searching and finding nearest neighbors.}, isbn = {978-1-58488-822-2}, url = {http://dl.acm.org/citation.cfm?id=1882757.1882763}, author = {Samet, Hanan}, editor = {Atallah,Mikhail J. and Blanton,Marina} } @conference {18641, title = {Nfsight: netflow-based network awareness tool}, year = {2010}, month = {2010///}, abstract = {Network awareness is highly critical for network and se-curity administrators. It enables informed planning and management of network resources, as well as detection and a comprehensive understanding of malicious activ- ity. It requires a set of tools to efficiently collect, process, and represent network data. While many such tools al- ready exist, there is no flexible and practical solution for visualizing network activity at various granularities, and quickly gaining insights about the status of network as- sets. To address this issue, we developed Nfsight, a Net- Flow processing and visualization application designed to offer a comprehensive network awareness solution. Nfsight constructs bidirectional flows out of the unidi- rectional NetFlow flows and leverages these bidirectional flows to provide client/server identification and intrusion detection capabilities. We present in this paper the in- ternal architecture of Nfsight, the evaluation of the ser- vice, and intrusion detection algorithms. We illustrate the contributions of Nfsight through several case studies conducted by security administrators on a large univer- sity network. }, url = {http://www.usenix.org/event/lisa10/tech/full_papers/Berthier.pdf}, author = {Berthier,R. and Michel Cukier and Hiltunen,M. and Kormann,D. and Vesonder,G. and Sheleheda,D.} } @article {16049, title = {Non-visual exploration of geographic maps: Does sonification help?}, journal = {Disability \& Rehabilitation: Assistive Technology}, volume = {5}, year = {2010}, month = {2010/05//}, pages = {164 - 174}, abstract = {Purpose. This study aims at evaluating the effectiveness of sonification as a mean to provide access to geo-referenced information to users with visual impairments.Method. Thiry-five participants (10 congenitally blind, 10 with acquired blindness and 15 blindfolded sighted) completed four tasks of progressive difficulty. During each task, participants first explored a sonified map by using either a tablet or a keyboard to move across regions and listened to sounds giving information about the current location. Then the participants were asked to identify, among four tactile maps, the one that crossmodally corresponds to the sonifed map they just explored. Finally, participants answered a self-report questionnaire of understanding and satisfaction. Results. Participants achieved high accuracy in all of the four tactile map discrimination tasks. No significant performance difference was found neither between subjects that used keyboard or tablet, nor between the three groups of blind and sighted participants. Differences between groups and interfaces were found in the usage strategies. High levels of satisfaction and understanding of the tools and tasks emerged from users{\textquoteright} reports. }, isbn = {1748-3107, 1748-3115}, doi = {10.3109/17483100903100277}, url = {http://informahealthcare.com/doi/abs/10.3109/17483100903100277}, author = {Delogu,Franco and Palmiero,Massimiliano and Federici,Stefano and Plaisant, Catherine and Zhao,Haixia and Belardinelli,Olivetti} } @conference {12151, title = {Obtaining valid safety data for software safety measurement and process improvement}, booktitle = {Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement}, series = {ESEM {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {46:1{\textendash}46:4 - 46:1{\textendash}46:4}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We report on a preliminary case study to examine software safety risk in the early design phase of the NASA Constellation spaceflight program. Our goal is to provide NASA quality assurance managers with information regarding the ongoing state of software safety across the program. We examined 154 hazard reports created during the preliminary design phase of three major flight hardware systems within the Constellation program. Our purpose was two-fold: 1) to quantify the relative importance of software with respect to system safety; and 2) to identify potential risks due to incorrect application of the safety process, deficiencies in the safety process, or the lack of a defined process. One early outcome of this work was to show that there are structural deficiencies in collecting valid safety data that make software safety different from hardware safety. In our conclusions we present some of these deficiencies.}, keywords = {case study, NASA, risk analysis, safety metrics}, isbn = {978-1-4503-0039-1}, doi = {10.1145/1852786.1852846}, url = {http://doi.acm.org/10.1145/1852786.1852846}, author = {Basili, Victor R. and Zelkowitz, Marvin V and Layman,Lucas and Dangle,Kathleen and Diep,Madeline} } @conference {15104, title = {Overcoming the Hole in the Bucket: Public-Key Cryptography Resilient to Continual Memory Leakage}, booktitle = {Foundations of Computer Science (FOCS), 2010 51st Annual IEEE Symposium on}, year = {2010}, month = {2010/10//}, pages = {501 - 510}, abstract = {In recent years, there has been a major effort to design cryptographic schemes that remain secure even when arbitrary information about the secret key is leaked (e.g., via side-channel attacks). We explore the possibility of achieving security under emphcontinual leakage from the emphentire secret key by designing schemes in which the secret key is updated over time. In this model, we construct public-key encryption schemes, digital signatures, and identity-based encryption schemes that remain secure even if an attacker can leak a constant fraction of the secret memory (including the secret key) in each time period between key updates. We also consider attackers who may probe the secret memory during the updates themselves. We stress that we allow unrestricted leakage, without the assumption that {\textquotedblleft}only computation leaks information{\textquotedblright}. Prior to this work, constructions of public-key encryption schemes secure under continual leakage were not known even under this assumption.}, keywords = {continual, cryptography;, cryptography;public-key, encryption, key, key;digital, leakage;cryptographic, memory, schemes;digital, schemes;public-key, schemes;secret, signatures;identity-based, signatures;public}, doi = {10.1109/FOCS.2010.55}, author = {Brakerski,Z. and Kalai,Y.T. and Katz, Jonathan and Vaikuntanathan,V.} } @article {12224, title = {Overlay Networking and Resiliency}, journal = {Guide to Reliable Internet Services and Applications}, year = {2010}, month = {2010///}, pages = {221 - 251}, author = {Bhattacharjee, Bobby and Rabinovich,M.} } @conference {12485, title = {Pose-robust albedo estimation from a single image}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {2683 - 2690}, abstract = {We present a stochastic filtering approach to perform albedo estimation from a single non-frontal face image. Albedo estimation has far reaching applications in various computer vision tasks like illumination-insensitive matching, shape recovery, etc. We extend the formulation proposed in that assumes face in known pose and present an algorithm that can perform albedo estimation from a single image even when pose information is inaccurate. 3D pose of the input face image is obtained as a byproduct of the algorithm. The proposed approach utilizes class-specific statistics of faces to iteratively improve albedo and pose estimates. Illustrations and experimental results are provided to show the effectiveness of the approach. We highlight the usefulness of the method for the task of matching faces across variations in pose and illumination. The facial pose estimates obtained are also compared against ground truth.}, keywords = {3D, albedo, estimation;, estimation;shape, Face, filtering;face, image;single, image;stochastic, information;pose-robust, matching;pose, nonfrontal, pose;class-specific, recognition;filtering, recovery;single, statistics;computer, theory;pose, vision;illumination-insensitive}, doi = {10.1109/CVPR.2010.5539987}, author = {Biswas,S. and Chellapa, Rama} } @article {12877, title = {The pre-seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/01/}, pages = {208 - 216}, abstract = {Vibrio cholerae O1 El Tor BX 330286 was isolated from a water sample in Australia in 1986, 9 years after an indigenous outbreak of cholera occurred in that region. This environmental strain encodes virulence factors highly similar to those of clinical strains, suggesting an ability to cause disease in humans. We demonstrate its high similarity in gene content and genome-wide nucleotide sequence to clinical V. cholerae strains, notably to pre-seventh pandemic O1 El Tor strains isolated in 1910 (V. cholerae NCTC 8457) and 1937 (V. cholerae MAK 757), as well as seventh pandemic strains isolated after 1960 globally. Here we demonstrate that this strain represents a transitory clone with shared characteristics between pre-seventh and seventh pandemic strains of V. cholerae. Interestingly, this strain was isolated 25 years after the beginning of the seventh pandemic, suggesting the environment as a genome reservoir in areas where cholera does not occur in sporadic, endemic or epidemic form.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2010.00141.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00141.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Haley,Bradd J. and Grim,Christopher J. and Hasan,Nur A. and Taviani,Elisa and Jongsik Chun and Brettin,Thomas S. and Bruce,David C. and Challacombe,Jean F. and Detter,J. Chris and Han,Cliff S. and Huq,Anwar and Nair,G. Balakrish and Rita R Colwell} } @article {14466, title = {Probabilistic similarity logic}, journal = {Proceedings of the Conference on Uncertainty in Artificial Intelligence}, year = {2010}, month = {2010///}, abstract = {Many machine learning applications require theability to learn from and reason about noisy multi-relational data. To address this, several ef- fective representations have been developed that provide both a language for expressing the struc- tural regularities of a domain, and principled sup- port for probabilistic inference. In addition to these two aspects, however, many applications also involve a third aspect{\textendash}the need to reason about similarities{\textendash}which has not been directly supported in existing frameworks. This paper introduces probabilistic similarity logic (PSL), a general-purpose framework for joint reason- ing about similarity in relational domains that incorporates probabilistic reasoning about sim- ilarities and relational structure in a principled way. PSL can integrate any existing domain- specific similarity measures and also supports reasoning about similarities between sets of en- tities. We provide efficient inference and learn- ing techniques for PSL and demonstrate its ef- fectiveness both in common relational tasks and in settings that require reasoning about similarity. }, author = {Br{\"o}cheler,M. and Mihalkova,L. and Getoor, Lise} } @article {16391, title = {The problem with zoning: nonlinear effects of interactions between location preferences and externalities on land use and utility}, journal = {Environment and Planning B: Planning and Design}, volume = {37}, year = {2010}, month = {2010///}, pages = {408 - 428}, author = {Zellner,M.L. and Riolo,R.L. and Rand, William and Brown,D.G. and Page,S.E. and Fernandez,L.E.} } @conference {19291, title = {Rapid prototyping for digital signal processing systems using Parameterized Synchronous Dataflow graphs}, booktitle = {2010 21st IEEE International Symposium on Rapid System Prototyping (RSP)}, year = {2010}, month = {2010}, pages = {1 - 7}, abstract = {Parameterized Synchronous Dataflow (PSDF) has been used previously for abstract scheduling and as a model for architecting embedded software and FPGA implementations. PSDF has been shown to be attractive for these purposes due to its support for flexible dynamic reconfiguration, and efficient quasi-static scheduling. To apply PSDF techniques more deeply into the design flow, support for comprehensive functional simulation and efficient hardware mapping is important. By building on the DIF (Dataflow Interchange Format), which is a design language and associated software package for developing and experimenting with dataflow-based design techniques for signal processing systems, we have developed a tool for functional simulation of PSDF specifications. This simulation tool allows designers to model applications in PSDF and simulate their functionality, including use of the dynamic parameter reconfiguration capabilities offered by PSDF. Based on this simulation tool, we also present a systematic design methodology for applying PSDF to the design and implementation of digital signal processing systems, with emphasis on FPGA-based systems for signal processing. We demonstrate capabilities for rapid and accurate prototyping offered by our proposed design methodology, along with its novel support for PSDF-based FPGA system implementation.}, keywords = {abstract scheduling, Computational modeling, Computer architecture, data flow graphs, dataflow based design, dataflow interchange format, design flow, design language, Digital signal processing, digital signal processing systems, dynamic parameter reconfiguration, Dynamic scheduling, efficient hardware mapping, efficient quasistatic scheduling, Embedded software, embedded systems, Field programmable gate arrays, flexible dynamic reconfiguration, FPGA based systems, FPGA implementations, functional simulation, Hardware, parameterized synchronous dataflow graphs, rapid prototyping, Schedules, scheduling, semantics, simulation tool, software package, systematic design methodology}, author = {Wu, Hsiang-Huang and Kee, Hojin and Sane, N. and Plishker,W. and Bhattacharyya, Shuvra S.} } @conference {17984, title = {Resource-Aware Compiler Prefetching for Many-Cores}, booktitle = {Parallel and Distributed Computing (ISPDC), 2010 Ninth International Symposium on}, year = {2010}, month = {2010/07//}, pages = {133 - 140}, abstract = {Super-scalar, out-of-order processors that can have tens of read and write requests in the execution window place significant demands on Memory Level Parallelism (MLP). Multi-and many-cores with shared parallel caches further increase MLP demand. Current cache hierarchies however have been unable to keep up with this trend, with modern designs allowing only 4-16 concurrent cache misses. This disconnect is exacerbated by recent highly parallel architectures (e.g. GPUs) where power and area per-core budget favor lighter cores with less resources. Support for hardware and software prefetch increase MLP pressure since these techniques overlap multiple memory requests with existing computation. In this paper, we propose and evaluate a novel Resource-Aware Prefetching (RAP) compiler algorithm that is aware of the number of simultaneous prefetches supported, and optimized for the same. We show that in situations where not enough resources are available to issue prefetch instructions for all references in a loop, it is more beneficial to decrease the prefetch distance and prefetch for as many references as possible, rather than use a fixed prefetched distance and skip prefetching for some references, as in current approaches. We implemented our algorithm in a GCC-derived compiler and evaluated its performance using an emerging fine-grained many-core architecture. Our results show that the RAP algorithm outperforms a well-known loop prefetching algorithm by up to 40.15\% and the state-of-the art GCC implementation by up to 34.79\%. Moreover, we compare the RAP algorithm with a simple hardware prefetching mechanism, and show improvements of up to 24.61\%.}, keywords = {algorithm;memory, architecture;hardware-software, architectures;parallel, architectures;resource, aware, caches;super-scalar, compiler, compiler;Multicore, compilers;parallel, GCC-derived, level, management;, many-core, memories;storage, out-of-order, Parallel, parallelism;parallel, prefetch;loop, prefetching, prefetching;shared, processor;fine-grained, processors;multiprocessing, systems;optimising}, doi = {10.1109/ISPDC.2010.16}, author = {Caragea,G.C. and Tzannes,A. and Keceli,F. and Barua,R. and Vishkin, Uzi} } @conference {12490, title = {The role of geometry in age estimation}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010/03/14/19}, pages = {946 - 949}, publisher = {IEEE}, organization = {IEEE}, abstract = {Understanding and modeling of aging in human faces is an important problem in many real-world applications such as biometrics, authentication, and synthesis. In this paper, we consider the role of geometric attributes of faces, as described by a set of landmark points on the face, in age perception. Towards this end, we show that the space of landmarks can be interpreted as a Grassmann manifold. Then the problem of age estimation is posed as a problem of function estimation on the manifold. The warping of an average face to a given face is quantified as a velocity vector that transforms the average to a given face along a smooth geodesic in unit-time. This deformation is then shown to contain important information about the age of the face. We show in experiments that exploiting geometric cues in a principled manner provides comparable performance to several systems that utilize both geometric and textural cues. We show results on age estimation using the standard FG-Net dataset and a passport dataset which illustrate the effectiveness of the approach.}, keywords = {age estimation, Aging, Biometrics, computational geometry, Face, Face Geometry, Facial animation, Feature extraction, function estimation problem, geometric face attributes, Geometry, Grassmann manifold, human face modeling, human face understanding, HUMANS, Mouth, regression, Regression analysis, SHAPE, Solid modeling, solid modelling, velocity vector}, isbn = {978-1-4244-4295-9}, doi = {10.1109/ICASSP.2010.5495292}, author = {Turaga,P. and Biswas,S. and Chellapa, Rama} } @conference {19285, title = {Scalable representation of dataflow graph structures using topological patterns}, booktitle = {2010 IEEE Workshop on Signal Processing Systems (SIPS)}, year = {2010}, month = {2010}, pages = {13 - 18}, abstract = {Tools for designing signal processing systems with their semantic foundation in dataflow modeling often use high-level graphical user interface (GUI) or text based languages that allow specifying applications as directed graphs. Such graphical representations serve as an initial reference point for further analysis and optimizations that lead to platform-specific implementations. For large-scale applications, the underlying graphs often consist of smaller substructures that repeat multiple times. To enable more concise representation and direct analysis of such substructures in the context of high level DSP specification languages and design tools, we develop the modeling concept of topological patterns, and propose ways for supporting this concept in a high-level language. We augment the DIF language - a language for specifying DSP-oriented dataflow graphs - with constructs for supporting topological patterns, and we show how topological patterns can be effective in various aspects of embedded signal processing design flows using specific application examples.}, keywords = {arrays, data flow graphs, Dataflow graphs, DIF language, Digital signal processing, directed graphs, DSP specification languages, embedded signal processing design flows, embedded systems, Field programmable gate arrays, graphical user interface, Graphical user interfaces, High-level languages, modelbased design, optimisation, optimizations, scalable dataflow graph structures representation, semantics, Signal processing, Signal processing systems, Specification languages, text based languages, Topological patterns, Topology, Transform coding}, author = {Sane, N. and Kee, Hojin and Seetharaman, G. and Bhattacharyya, Shuvra S.} } @article {19283, title = {Selective excitation of LI2 by chirped laser pulses with all possible interstate radiative couplings}, journal = {The Journal of Chemical Physics}, volume = {133}, year = {2010}, month = {2010}, pages = {164313 - 164313-9}, abstract = {We have numerically explored the feasibility and the mechanism of population transfer to the excited E 1Σg electronic state of Li2 from the v = 0 level of the ground electronic state X 1Σg using the A 1Σu state as an intermediate. In this system, the use of transform limited pulses with a frequency difference greater than the maximum Rabi frequency does not produce population transfer when all possible radiative couplings are taken into account. We have employed two synchronous pulses far detuned from the allowed transition frequencies, mainly with the lower frequency pulse positively chirped, and both pulses coupling the successive pair of states, X-A and A-E. The adiabaticity of the process has been investigated by a generalized Floquet calculation in the basis of 12 field dressed molecular states, and the results have been compared with those obtained from the full solution of time dependent Schr{\"o}dinger equation. The conventional representation of the process in terms of three (or four) adiabatic potentials is not valid. It has been found that for cases of almost complete population transfer in full calculations with the conservation of the vibrational quantum number, adiabatic passage is attained with the 12 state Floquet model but not with the six state model. The agreement between the full calculations and the 12 state Floquet calculations is generally good when the transfer is adiabatic. Another characteristic feature of this work is the gaining of control over the vibrational state preparation in the final electronic state by careful tuning of the laser parameters as well as the chirp rate sign. This causes time dependent changes in the adiabatic potentials and nonadiabatic transfers can be made to occur between them.}, isbn = {00219606}, url = {http://jcp.aip.org/resource/1/jcpsa6/v133/i16/p164313_s1}, author = {Chatterjee, Souvik and Bhattacharyya, Shuvra S.} } @article {19298, title = {Signal Processing on Platforms with Multiple Cores: Part 2-Applications and Design [From the Guest Editors]}, journal = {IEEE Signal Processing Magazine}, volume = {27}, year = {2010}, month = {2010}, pages = {20 - 21}, abstract = {Platforms with multiple cores are now prevalent everywhere from desktops and graphics processors to laptops and embedded systems. By adding more parallel computational resources while managing power consumption, multicore platforms offer better programmability, performance, and power efficiency. Signal processing systems of tomorrow will be and must be implemented on platforms with multiple cores. Writing efficient parallel applications that utilize the computing capability of many processing cores require some effort. Signal processing algorithm designers must understand the nuances of a multicore computing engine; only then can the tremendous computing power that such platforms provide be harnessed efficiently. To give a thorough perspective of the area, we have organized two special issues on this topic.}, keywords = {Concurrent computing, Embedded system, Energy management, Graphics, Multicore processing, Portable computers, Resource management, Signal design, Signal processing, Signal processing algorithms}, isbn = {1053-5888}, author = {Chen,Y. and Chakrabarti,C. and Bhattacharyya, Shuvra S. and Bougard, B.} } @inbook {19044, title = {Signatures of Reputation}, booktitle = {Financial Cryptography and Data Security}, series = {Lecture Notes in Computer Science}, volume = {6052}, year = {2010}, month = {2010}, pages = {400 - 407}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, keywords = {Computer science}, isbn = {978-3-642-14576-6}, url = {http://www.springerlink.com/content/8484428n77226512/abstract/}, author = {Bethencourt, John and Elaine Shi and Song, Dawn}, editor = {Sion, Radu} } @conference {19296, title = {Simulating dynamic communication systems using the core functional dataflow model}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010}, pages = {1538 - 1541}, abstract = {The latest communication technologies invariably consist of modules with dynamic behavior. There exists a number of design tools for communication system design with their foundation in dataflow modeling semantics. These tools must not only support the functional specification of dynamic communication modules and subsystems but also provide accurate estimation of resource requirements for efficient simulation and implementation. We explore this trade-off - between flexible specification of dynamic behavior and accurate estimation of resource requirements - using a representative application employing an adaptive modulation scheme. We propose an approach for precise modeling of such applications based on a recently-introduced form of dynamic dataflow called core functional dataflow. From our proposed modeling approach, we show how parameterized looped schedules can be generated and analyzed to simulate applications with low run-time overhead as well as guaranteed bounded memory execution. We demonstrate our approach using the Advanced Design System from Agilent Technologies, Inc., which is a commercial tool for design and simulation of communication systems.}, keywords = {adaptive modulation, Analytical models, Application software, Computational modeling, core functional dataflow model, Dataflow, dataflow modeling semantics, design tools, Digital signal processing, dynamic communication systems, functional specification, Hardware, modeling and simulation, Power system modeling, Predictive models, Processor scheduling, Production, Signal processing, software tools, wireless communication}, author = {Sane, N. and Chia-Jui Hsu and Pino,J. L and Bhattacharyya, Shuvra S.} } @article {15397, title = {On Stability of Magnetization Dynamics in Nanoparticles}, journal = {Magnetics, IEEE Transactions on}, volume = {46}, year = {2010}, month = {2010/06//}, pages = {1718 - 1721}, abstract = {It is rigorously demonstrated that spatially uniform magnetization oscillations in sufficiently small ellipsoidal nanoparticles can be unconditionally stable with respect to spatially nonuniform perturbations. The proof reveals the dominant stabilizing effect of exchange field which is mathematically manifested through the Poincare inequality.}, keywords = {(electron);magnetic, DYNAMICS, ellipsoidal, field;magnetization, inequality;exchange, INTERACTIONS, magnetization, nanoparticles;spatially, nonuniform, oscillations;spin-wave, particles;magnetisation;nanoparticles;spin, perturbations;exchange, perturbations;spatially, Poincare, stability;small, uniform, waves;}, isbn = {0018-9464}, doi = {10.1109/TMAG.2009.2039119}, author = {Mayergoyz, Issak D and Serpico,C. and Bertotti,G.} } @article {18757, title = {Stochastic simulations with graphics hardware: Characterization of accuracy and performance}, journal = {Journal of Computing and Information Science in Engineering}, volume = {10}, year = {2010}, month = {2010///}, pages = {011010 - 011010}, author = {Balijepalli,A. and LeBrun,T. W. and Gupta,S.K.} } @article {15811, title = {Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings}, journal = {J. Am. Chem. Soc.}, volume = {132}, year = {2010}, month = {2010///}, pages = {8961 - 8972}, abstract = {We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein?protein complex by utilizing the RDCs? sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein?protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein?protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes.We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein?protein complex by utilizing the RDCs? sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein?protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein?protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes. }, isbn = {0002-7863}, doi = {10.1021/ja100447p}, url = {http://dx.doi.org/10.1021/ja100447p}, author = {Berlin,Konstantin and O{\textquoteright}Leary,Dianne P. and Fushman, David} } @article {18601, title = {SwitchBlade: a platform for rapid deployment of network protocols on programmable hardware}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {40}, year = {2010}, month = {2010/08//}, pages = {183 - 194}, abstract = {We present SwitchBlade, a platform for rapidly deploying custom protocols on programmable hardware. SwitchBlade uses a pipeline-based design that allows individual hardware modules to be enabled or disabled on the fly, integrates software exception handling, and provides support for forwarding based on custom header fields. SwitchBlade{\textquoteright}s ease of programmability and wire-speed performance enables rapid prototyping of custom data-plane functions that can be directly deployed in a production network. SwitchBlade integrates common packet-processing functions as hardware modules, enabling different protocols to use these functions without having to resynthesize hardware. SwitchBlade{\textquoteright}s customizable forwarding engine supports both longest-prefix matching in the packet header and exact matching on a hash value. SwitchBlade{\textquoteright}s software exceptions can be invoked based on either packet or flow-based rules and updated quickly at runtime, thus making it easy to integrate more flexible forwarding function into the pipeline. SwitchBlade also allows multiple custom data planes to operate in parallel on the same physical hardware, while providing complete isolation for protocols running in parallel. We implemented SwitchBlade using NetFPGA board, but SwitchBlade can be implemented with any FPGA. To demonstrate SwitchBlade{\textquoteright}s flexibility, we use SwitchBlade to implement and evaluate a variety of custom network protocols: we present instances of IPv4, IPv6, Path Splicing, and an OpenFlow switch, all running in parallel while forwarding packets at line rate.}, keywords = {netfpga, network virtualization}, isbn = {0146-4833}, doi = {10.1145/1851275.1851206}, url = {http://doi.acm.org/10.1145/1851275.1851206}, author = {Anwer,Muhammad Bilal and Motiwala,Murtaza and Bin Tariq,Mukarram and Feamster, Nick} } @article {12415, title = {Syntactic Topic Models}, journal = {arXiv:1002.4665v1}, year = {2010}, month = {2010/02/24/}, abstract = {The syntactic topic model (STM) is a Bayesian nonparametric model of language that discovers latent distributions of words (topics) that are both semantically and syntactically coherent. The STM models dependency parsed corpora where sentences are grouped into documents. It assumes that each word is drawn from a latent topic chosen by combining document-level features and the local syntactic context. Each document has a distribution over latent topics, as in topic models, which provides the semantic consistency. Each element in the dependency parse tree also has a distribution over the topics of its children, as in latent-state syntax models, which provides the syntactic consistency. These distributions are convolved so that the topic of each word is likely under both its document and syntactic context. We derive a fast posterior inference algorithm based on variational methods. We report qualitative and quantitative studies on both synthetic data and hand-parsed documents. We show that the STM is a more predictive model of language than current models based only on syntax or only on topics.}, keywords = {Computer Science - Artificial Intelligence, Computer Science - Computation and Language, Mathematics - Statistics Theory}, url = {http://arxiv.org/abs/1002.4665}, author = {Jordan Boyd-Graber and Blei,David M.} } @conference {13925, title = {Toque: designing a cooking-based programming language for and with children}, booktitle = {Proceedings of the 28th international conference on Human factors in computing systems}, year = {2010}, month = {2010///}, pages = {2417 - 2426}, author = {Tarkan,S. and Sazawal,V. and Druin, Allison and Golub,E. and Bonsignore,E. M and Walsh,G. and Atrash,Z.} } @conference {12480, title = {Tracking via object reflectance using a hyperspectral video camera}, booktitle = {2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)}, year = {2010}, month = {2010/06/13/18}, pages = {44 - 51}, publisher = {IEEE}, organization = {IEEE}, abstract = {Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and the mean shift algorithm to simultaneously track the object based on its reflectance spectra is proposed. The combination of spectral detection and motion prediction enables the tracker to be robust against abrupt motions, and facilitate fast convergence of the mean shift tracker. In addition, the system achieves good computational efficiency by using random projection to reduce spectral dimension. The tracker has been evaluated on real hyperspectral video data.}, keywords = {Computer vision, electronic design, hyperspectral datacubes, hyperspectral image analysis, Hyperspectral imaging, Hyperspectral sensors, hyperspectral video camera, Image motion analysis, Image sensors, lighting, Motion estimation, motion prediction, Object detection, object reflectance tracking, random projection, Reflectivity, robust methods, Robustness, sensor design, spectral detection, Surveillance, tracking, Video surveillance}, isbn = {978-1-4244-7029-7}, doi = {10.1109/CVPRW.2010.5543780}, author = {Nguyen,Hien Van and Banerjee, A. and Chellapa, Rama} } @article {19299, title = {Utilizing Hierarchical Multiprocessing for Medical Image Registration}, journal = {IEEE Signal Processing Magazine}, volume = {27}, year = {2010}, month = {2010}, pages = {61 - 68}, abstract = {This work discusses an approach to utilize hierarchical multiprocessing in the context of medical image registration. By first organizing application parallelism into a domain-specific taxonomy, an algorithm is structured to target a set of multicore platforms.The approach on a cluster of graphics processing units (GPUs) requiring the use of two parallel programming environments to achieve fast execution times is demonstrated.There is negligible loss in accuracy for rigid registration when employing GPU acceleration, but it does adversely effect our nonrigid registration implementation due to our usage of a gradient descent approach.}, keywords = {Acceleration, application parallelism, Biomedical imaging, domain-specific taxonomy, GPU acceleration, gradient descent approach, Graphics processing unit, hierarchical multiprocessing, image registration, Magnetic resonance imaging, Medical diagnostic imaging, medical image processing, medical image registration, multicore platform set, Multicore processing, PARALLEL PROCESSING, parallel programming, Robustness, Signal processing algorithms, Ultrasonic imaging}, isbn = {1053-5888}, author = {Plishker,W. and Dandekar,O. and Bhattacharyya, Shuvra S. and Shekhar,R.} } @conference {18355, title = {VizWiz: nearly real-time answers to visual questions}, booktitle = {Proceedings of the 23nd annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {333 - 342}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The lack of access to visual information like text labels, icons, and colors can cause frustration and decrease independence for blind people. Current access technology uses automatic approaches to address some problems in this space, but the technology is error-prone, limited in scope, and quite expensive. In this paper, we introduce VizWiz, a talking application for mobile phones that offers a new alternative to answering visual questions in nearly real-time - asking multiple people on the web. To support answering questions quickly, we introduce a general approach for intelligently recruiting human workers in advance called quikTurkit so that workers are available when new questions arrive. A field deployment with 11 blind participants illustrates that blind people can effectively use VizWiz to cheaply answer questions in their everyday lives, highlighting issues that automatic approaches will need to address to be useful. Finally, we illustrate the potential of using VizWiz as part of the participatory design of advanced tools by using it to build and evaluate VizWiz::LocateIt, an interactive mobile tool that helps blind people solve general visual search problems.}, keywords = {blind users, non-visual interfaces, real-time human computation}, isbn = {978-1-4503-0271-5}, doi = {10.1145/1866029.1866080}, url = {http://doi.acm.org/10.1145/1866029.1866080}, author = {Bigham,Jeffrey P. and Jayant,Chandrika and Ji,Hanjie and Little,Greg and Miller,Andrew and Miller,Robert C. and Miller,Robin and Tatarowicz,Aubrey and White,Brandyn and White,Samual and Tom Yeh} } @conference {18356, title = {VizWiz::LocateIt - enabling blind people to locate objects in their environment}, booktitle = {Computer Vision and Pattern Recognition Workshops (CVPRW), 2010 IEEE Computer Society Conference on}, year = {2010}, month = {2010/06//}, pages = {65 - 72}, publisher = {IEEE}, organization = {IEEE}, abstract = {Blind people face a number of challenges when interacting with their environments because so much information is encoded visually. Text is pervasively used to label objects, colors carry special significance, and items can easily become lost in surroundings that cannot be quickly scanned. Many tools seek to help blind people solve these problems by enabling them to query for additional information, such as color or text shown on the object. In this paper we argue that many useful problems may be better solved by directly modeling them as search problems, and present a solution called VizWiz::LocateIt that directly supports this type of interaction. VizWiz::LocateIt enables blind people to take a picture and ask for assistance in finding a specific object. The request is first forwarded to remote workers who outline the object, enabling efficient and accurate automatic computer vision to guide users interactively from their existing cellphones. A two-stage algorithm is presented that uses this information to guide users to the appropriate object interactively from their phone.}, isbn = {978-1-4244-7029-7}, doi = {10.1109/CVPRW.2010.5543821}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5543821}, author = {Bigham,Jeffrey P. and Jayant,Chandrika and Miller,Andrew and White,Brandyn and Tom Yeh} } @article {18925, title = {When is it better not to look ahead?}, journal = {Artificial Intelligence}, volume = {174}, year = {2010}, month = {2010/11//}, pages = {1323 - 1338}, abstract = {In situations where one needs to make a sequence of decisions, it is often believed that looking ahead will help produce better decisions. However, it was shown 30 years ago that there are {\textquotedblleft}pathological{\textquotedblright} situations in which looking ahead is counterproductive. Two long-standing open questions are (a) what combinations of factors have the biggest influence on whether lookahead pathology occurs, and (b) whether it occurs in real-world decision-making.This paper includes simulation results for several synthetic game-tree models, and experimental results for three well-known board games: two chess endgames, kalah (with some modifications to facilitate experimentation), and the 8-puzzle. The simulations show the interplay between lookahead pathology and several factors that affect it; and the experiments confirm the trends predicted by the simulation models. The experiments also show that lookahead pathology is more common than has been thought: all three games contain situations where it occurs. }, keywords = {Game-tree search, Lookahead pathology, minimax}, isbn = {0004-3702}, doi = {10.1016/j.artint.2010.08.002}, url = {http://www.sciencedirect.com/science/article/pii/S0004370210001402}, author = {Nau, Dana S. and Lu{\v s}trek,Mitja and Parker,Austin and Bratko,Ivan and Gams,Matja{\v z}} } @conference {19463, title = {Who{\textquoteright}s Hogging the Bandwidth: The Consequences of Revealing the Invisible in the Home}, booktitle = {SIGCHI {\textquoteright}10}, series = {CHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {659 - 668}, publisher = {ACM}, organization = {ACM}, abstract = {As more technologies enter the home, householders are burdened with the task of digital housekeeping-managing and sharing digital resources like bandwidth. In response to this, we created and evaluated a domestic tool for bandwidth management called Home Watcher. Our field trial showed that when resource contention amongst different household members is made visible, people{\textquoteright}s understanding of bandwidth changes and household politics are revealed. In this paper, we describe the consequences of showing real time resource usage in a home, and how this varies depending on the social make up of the household.}, keywords = {bandwidth monitoring, home broadband, home networks}, isbn = {978-1-60558-929-9}, url = {http://doi.acm.org/10.1145/1753326.1753423}, author = {Marshini Chetty and Banks, Richard and Harper, Richard and Regan, Tim and Sellen, Abigail and Gkantsidis, Christos and Karagiannis, Thomas and Key, Peter} } @conference {15456, title = {Workshop on experimental evaluation of software and systems in computer science (Evaluate 2010)}, booktitle = {Proceedings of the ACM international conference companion on Object oriented programming systems languages and applications companion}, series = {SPLASH {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {291 - 292}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We call ourselves {\textquoteright}computer scientists{\textquoteright}, but are we scientists? If we are scientists, then we must practice the scientific method. This includes a solid experimental evaluation. In our experience, our experimental methodology is ad hoc at best, and nonexistent at worst. This workshop brings together experts from different areas of computer science to discuss, explore, and attempt to identify the principles of sound experimental evaluation}, keywords = {Evaluation, METHODOLOGY}, isbn = {978-1-4503-0240-1}, doi = {10.1145/1869542.1869618}, url = {http://doi.acm.org/10.1145/1869542.1869618}, author = {Blackburn,Steven M. and Diwan,Amer and Hauswirth,Matthias and Memon, Atif M. and Sweeney,Peter F.} } @article {14650, title = {Young Proteins Experience More Variable Selection Pressures Than Old Proteins}, journal = {Genome ResearchGenome Res.}, volume = {20}, year = {2010}, month = {2010/11/01/}, pages = {1574 - 1581}, abstract = {It is well known that young proteins tend to experience weaker purifying selection and evolve more quickly than old proteins. Here, we show that, in addition, young proteins tend to experience more variable selection pressures over time than old proteins. We demonstrate this pattern in three independent taxonomic groups: yeast, Drosophila, and mammals. The increased variability of selection pressures on young proteins is highly significant even after controlling for the fact that young proteins are typically shorter and experience weaker purifying selection than old proteins. The majority of our results are consistent with the hypothesis that the function of a young gene tends to change over time more readily than that of an old gene. At the same time, our results may be caused in part by young genes that serve constant functions over time, but nevertheless appear to evolve under changing selection pressures due to depletion of adaptive mutations. In either case, our results imply that the evolution of a protein-coding sequence is partly determined by its age and origin, and not only by the phenotypic properties of the encoded protein. We discuss, via specific examples, the consequences of these findings for understanding of the sources of evolutionary novelty.}, isbn = {1088-9051, 1549-5469}, doi = {10.1101/gr.109595.110}, url = {http://genome.cshlp.org/content/20/11/1574}, author = {Vishnoi,Anchal and Kryazhimskiy,Sergey and Bazykin,Georgii A and Hannenhalli, Sridhar and Plotkin,Joshua B.} } @article {12533, title = {Age progression in human faces: A survey}, journal = {Journal of Visual Languages and Computing}, volume = {15}, year = {2009}, month = {2009///}, pages = {3349 - 3361}, abstract = {Facial aging, a new dimension that has recently beenadded to the problem of face recognition, poses interesting theo- retical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community, has recently found enhanced interest in the computer vision community. How do humans perceive age ? What constitutes an age-invariant signature that can be derived from faces ? How compactly can the facial growth event be described ? How does facial aging impact recognition performance ? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification etc. and offer insights into future research on this topic. }, author = {Ramanathan,N. and Chellapa, Rama and Biswas,S.} } @article {18784, title = {Algorithms for extraction of nanowire lengths and positions from optical section microscopy image sequence}, journal = {Journal of Computing and Information Science in Engineering}, volume = {9}, year = {2009}, month = {2009///}, pages = {041007 - 041007}, author = {Peng,T. and Balijepalli,A. and Gupta,S.K. and LeBrun,T. W.} } @conference {12229, title = {All Bits Are Not Equal - A Study of IEEE 802.11 Communication Bit Errors}, booktitle = {INFOCOM 2009, IEEE}, year = {2009}, month = {2009/04//}, pages = {1602 - 1610}, abstract = {In IEEE 802.11 Wireless LAN (WLAN) systems, techniques such as acknowledgement, retransmission, and transmission rate adaptation, are frame-level mechanisms designed for combating transmission errors. Recently sub-frame level mechanisms such as frame combining have been proposed by the research community. In this paper, we present results obtained from our bit error study for identifying sub-frame error patterns because we believe that identifiable bit error patterns can potentially introduce new opportunities in channel coding, network coding, forward error correction (FEC), and frame combining mechanisms. We have constructed a number of IEEE 802.11 wireless LAN testbeds and conducted extensive experiments to study the characteristics of bit errors and their location distribution. Conventional wisdom dictates that bit error probability is the result of channel condition and ought to follow corresponding distribution. However our measurement results identify three repeatable bit error patterns that are not induced by channel conditions. We have verified that such error patterns are present in WLAN transmissions in different physical environments and across different wireless LAN hardware platforms. We also discuss our current hypotheses for the reasons behind these bit error probability patterns and how identifying these patterns may help improving WLAN transmission robustness.}, keywords = {802.11, bit, coding;error, coding;forward, coding;subframe, combining, Communication, correction;frame, correction;wireless, error, errors;channel, errors;wireless, IEEE, LAN;, LAN;channel, mechanisms;network, patterns;transmission, statistics;forward}, doi = {10.1109/INFCOM.2009.5062078}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Bhattacharjee, Bobby and Miller,R.R.} } @article {15377, title = {Analytical Description of Quasi-Random Magnetization Relaxation to Equilibrium}, journal = {Magnetics, IEEE Transactions on}, volume = {45}, year = {2009}, month = {2009/11//}, pages = {5224 - 5227}, abstract = {The Landau-Lifshitz (LL) dynamics of a uniformly magnetized particle is considered. The LL equation is written in the form of a Hamiltonian perturbed dynamical system. By using suitable averaging technique, the equation for the slow dynamics of the energy is derived. The averaging technique breaks up in the case of separatrix crossing. It is shown that, in the limit of small damping, the separatrix crossing can be described by using a probabilistic approach.}, keywords = {approach;quasirandom, crossing;uniformly, dynamical, dynamics;averaging, Hamiltonian, magnetization, magnetized, particle;magnetic, particles;magnetic, perturbed, relaxation;magnetisation;probability;, relaxation;separatrix, system;Landau-Lifshitz, technique;damping;probabilistic}, isbn = {0018-9464}, doi = {10.1109/TMAG.2009.2031067}, author = {Serpico,C. and d{\textquoteright}Aquino,M. and Bertotti,G. and Mayergoyz, Issak D} } @conference {16974, title = {Analyzing (social media) networks with NodeXL}, booktitle = {Proceedings of the fourth international conference on Communities and technologies}, series = {C\&$\#$38;T {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {255 - 264}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present NodeXL, an extendible toolkit for network overview, discovery and exploration implemented as an add-in to the Microsoft Excel 2007 spreadsheet software. We demonstrate NodeXL data analysis and visualization features with a social media data sample drawn from an enterprise intranet social network. A sequence of NodeXL operations from data import to computation of network statistics and refinement of network visualization through sorting, filtering, and clustering functions is described. These operations reveal sociologically relevant differences in the patterns of interconnection among employee participants in the social media space. The tool and method can be broadly applied.}, keywords = {excel, network analysis, social media, social network, spreadsheet, Visualization}, isbn = {978-1-60558-713-4}, doi = {10.1145/1556460.1556497}, url = {http://doi.acm.org/10.1145/1556460.1556497}, author = {Smith,Marc A. and Shneiderman, Ben and Milic-Frayling,Natasa and Mendes Rodrigues,Eduarda and Barash,Vladimir and Dunne,Cody and Capone,Tony and Perer,Adam and Gleave,Eric} } @conference {18659, title = {Analyzing the process of installing rogue software}, year = {2009}, month = {2009/07/29/2}, pages = {560 - 565}, abstract = {This practical experience report presents the results of an experiment aimed at understanding the sequence of malicious actions following a remote compromise. The type of rogue software installed during attacks was used to classify and understand sequences of malicious actions. For this experiment, we used four Linux target computers running SSH with simple passwords. During the eight-month data collection period, we recorded a total of 1,171 attack sessions. In these sessions, attackers typed a total of 20,335 commands that we categorized into 24 specific actions. These actions were analyzed based on the type of rogue software installed by attackers.}, keywords = {Linux, Linux target computers, malicious actions, rogue software installation, security of data}, doi = {10.1109/DSN.2009.5270293}, author = {Berthier,R. and Arjona,J. and Michel Cukier} } @article {12531, title = {An architectural level design methodology for smart camera applications}, journal = {International Journal of Embedded Systems}, volume = {4}, year = {2009}, month = {2009///}, pages = {83 - 97}, abstract = {Today{\textquoteright}s embedded computing applications are characterised by increased functionality, and hence increased design complexity and processing requirements. The resulting design spaces are vast and designers are typically able to evaluate only small subsets of solutions due to lack of efficient design tools. In this paper, we propose an architectural level design methodology that provides a means for a comprehensive design space exploration for smart camera applications and enable designers to select higher quality solutions and provides substantial savings on the overall cost of the system. We present efficient, accurate and intuitive models for performance estimation and validate them with experiments.}, author = {Saha,S. and Kianzad,V. and Schlessman,J. and Aggarwal,G. and Bhattacharyya, Shuvra S. and Chellapa, Rama and Wolf,W.} } @article {12113, title = {An assessment of systems and software engineering scholars and institutions (2002{\textendash}2006)}, journal = {Journal of Systems and Software}, volume = {82}, year = {2009}, month = {2009/08//}, pages = {1370 - 1373}, abstract = {This paper summarizes a survey of publications in the field of systems and software engineering from 2002 to 2006. The survey is an ongoing, annual event that identifies the top 15 scholars and institutions over a 5-year period. The rankings are calculated based on the number of papers published in TSE, TOSEM, JSS, SPE, EMSE, IST, and Software. The top-ranked institution is Korea Advanced Institute of Science and Technology, Korea, and the top-ranked scholar is Magne J{\o}rgensen of Simula Research Laboratory, Norway.}, keywords = {Research publications, Systems and software engineering, Top institutions, Top scholars}, isbn = {0164-1212}, doi = {10.1016/j.jss.2009.06.018}, url = {http://www.sciencedirect.com/science/article/pii/S0164121209001265}, author = {Wong,W. Eric and Tse,T.H. and Glass,Robert L. and Basili, Victor R. and Chen,T.Y.} } @conference {12399, title = {Better vocabularies for assistive communication aids: connecting terms using semantic networks and untrained annotators}, booktitle = {Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility}, series = {Assets {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {171 - 178}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The difficulties of navigating vocabulary in an assistive communication device are exacerbated for individuals with lexical access disorders like those due to aphasia. We present the design and implementation of a vocabulary network based on WordNet, a resource that attempts to model human semantic memory, that enables users to find words easily. To correct for the sparsity of links among words, we augment WordNet with additional connections derived from human judgments of semantic similarity collected in an online experiment. We evaluate the resulting system, the visual vocabulary for aphasia (ViVA), and describe its potential to adapt to a user{\textquoteright}s profile and enable faster search and improved navigation.}, keywords = {adaptive tools, aphasia, assistive communication, semantic networks, visual vocabularies}, isbn = {978-1-60558-558-1}, doi = {10.1145/1639642.1639673}, url = {http://doi.acm.org/10.1145/1639642.1639673}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Fellbaum,Christiane and Cook,Perry} } @conference {12227, title = {Channel Access Throttling for Improving WLAN QoS}, booktitle = {Sensor, Mesh and Ad Hoc Communications and Networks, 2009. SECON {\textquoteright}09. 6th Annual IEEE Communications Society Conference on}, year = {2009}, month = {2009/06//}, pages = {1 - 9}, abstract = {The de facto QoS channel access method for the IEEE 802.11 Wireless LANs is the Enhanced Distributed Channel Access (EDCA) mechanism, which differentiates transmission treatments for data frames belonging to different traffic categories with four different levels of channel access priority. In this paper, we propose extending EDCA with Channel Access Throttling (CAT) for more flexible and efficient QoS support. By assigning different member stations different channel access parameters, CAT differentiates channel access priorities not between traffic categories but between member stations. Then by dynamically changing the channel access parameters of each member station based on a pre-computed schedule, CAT enables EDCA WLANs the benefits of scheduled access QoS. We also present evaluation results of CAT obtained from both simulations and experiments conducted using off-the-shelf WLAN hardware and open-source device driver. Our results show that CAT can proportionally partition channel capacity, significantly improve performance of multimedia applications, effectively achieve performance protection for admitted flows, and increase per cell VoIP call capacity by up to 41\%.}, keywords = {802.11, access, area, call, capacity;data, capacity;quality, capacity;WLAN, categories;transmission, channel, device, distributed, driver;quality, facto, frames;de, IEEE, LAN;, LAN;VoIP, local, mechanism;member, method;enhanced, multimedia, network;wireless, networks;channel, of, parameters;channel, priority;channel, QoS, QoS;channel, service;telecommunication, service;traffic, standards;telecommunication, stations;open-source, throttling;channel, traffic;wireless, treatments;wireless, wireless}, doi = {10.1109/SAHCN.2009.5168915}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Miller,R.R. and Bhattacharjee, Bobby} } @conference {12226, title = {Channel Access Throttling for Overlapping BSS Management}, booktitle = {Communications, 2009. ICC {\textquoteright}09. IEEE International Conference on}, year = {2009}, month = {2009/06//}, pages = {1 - 6}, abstract = {Multiple co-channel WLAN BSSes (i.e., WLAN cells) overlapping in coverage are generally considered undesirable because members of the OBSSes compete for channel access, which typically increases the contention level of wireless medium access and reduces overall system performance. In this paper, we propose to use channel access throttling (CAT) for managing Wireless LAN radio resources for overlapping BSSes (OBSSes). CAT provides an access point (AP) of each BSS with a mechanism to control channel access parameters of its member stations on the fly. By coordinating the CAT operations of the OBSS APs, we can enable privileged channel access to an individual BSS at a particular time, for example, by assigning high priority access parameters to member stations associated with the BSS. By controlling how much each BSS may be given the privileged channel access, we can also achieve a proportional partitioning of channel capacity among OBSSes. We present evaluation results obtained from both simulations and experiments using testbed built with commercial off-the-shelf (COTS) WLAN hardware and open-source device driver. Our results show that with CAT, not only can we proportionally partition channel capacity among the OBSSes, but also improve channel utilization efficiency and increase overall capacity.}, keywords = {access, access;cellular, allocation;channel, BSS, capacity;computer, capacity;proportional, cell;open-source, channel, channels;, co-channel, device, driver;overlapping, efficiency;high-priority, LAN;wireless, management;partition, management;wireless, medium, network, parameters;multiple, partitioning;radio, radio;channel, resources;wireless, throttling;channel, utilization, WLAN}, doi = {10.1109/ICC.2009.5198815}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Miller,R.R. and Bhattacharjee, Bobby} } @article {18772, title = {Characterization and control of pin diameter during in-mold assembly of mesoscale revolute joints}, journal = {North American Manufacturing Research Institute}, volume = {37}, year = {2009}, month = {2009///}, abstract = {Macro-scale revolute joints can be formed byfirst molding the hole and then molding the pin inside the hole. As the pin shrinks during the solidification process, it moves away from the hole and provides the clearance for the joint to function. The value of clearance in the macro- scale joint can be controlled by carefully selecting the process parameters and the material for the pin. However, in order for this strategy to work at the mesoscale, it requires the use of very thin cores to form sub-millimeter holes. Such thin cores are very difficult to make, are easily damaged during the molding process, and very difficult to retract from the hole. Our previous work has shown that making the pins first and then creating holes on the top of pins leads to successful mesoscale joints. This strategy is counter intuitive based on our experiences at the macro-scale. At the macroscale, as the hole shrinks on top of the pin, the joint is jammed. So a fundamental question is why this counter-intuitive strategy works at the mesoscale. In this paper we show that at the mesoscale, the joint jamming is prevented because of the deformation of the pin under the compressive loading during the second stage molding. We also describe features in the mold that can control the pin deformation and hence control the joint parameters. We present experimental data and computational models to show how mesoscale revolute joints can be formed. }, url = {http://web.mit.edu/arvinda/www/NAMRI_2009_draft.pdf}, author = {Ananthanarayanan,A. and Gupta,S.K. and Bruck,H. A.} } @conference {18555, title = {Characterizing VLAN-induced sharing in a campus network}, booktitle = {Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference}, series = {IMC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {116 - 121}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many enterprise, campus, and data-center networks have complex layer-2 virtual LANs ("VLANs") below the IP layer. The interaction between layer-2 and IP topologies in these VLANs introduces hidden dependencies between IP level network and the physical infrastructure that has implications for network management tasks such as planning for capacity or reliability, and for fault diagnosis. This paper characterizes the extent and effect of these dependencies in a large campus network. We first present the design and implementation of EtherTrace, a tool that we make publicly available, which infers the layer-2 topology using data passively collected from Ethernet switches. Using this tool, we infer the layer-2 topology for a large campus network and compare it with the IP topology. We find that almost 70\% of layer-2 edges are shared by 10 or more IP edges, and a single layer-2 edge may be shared by as many as 34 different IP edges. This sharing of layer-2 edges and switches among IP paths commonly results from trunking multiple VLANs to the same access router, or from colocation of academic departments that share layer-2 infrastructure, but have logically separate IP subnet and routers. We examine how this sharing affects the accuracy and specificity of fault diagnosis. For example, applying network tomography to the IP topology to diagnose failures caused by layer-2 devices results in only 54\% accuracy, compared to 100\% accuracy when our tomography algorithm takes input across layers.}, keywords = {network diagnosis, network virtualization, VLAN, vlan-induced dependency}, isbn = {978-1-60558-771-4}, doi = {10.1145/1644893.1644907}, url = {http://doi.acm.org/10.1145/1644893.1644907}, author = {Bin Tariq,Mukarram and Mansy,Ahmed and Feamster, Nick and Ammar,Mostafa} } @inbook {14493, title = {Collective classification for text classification}, booktitle = {Text Mining: Classification, Clustering, and ApplicationsText Mining: Classification, Clustering, and Applications}, year = {2009}, month = {2009///}, pages = {51 - 69}, author = {Namata,G. and Sen,P. and Bilgic,M. and Getoor, Lise} } @inbook {14382, title = {Collective relational clustering}, booktitle = {Constrained Clustering: Advances in Algorithms, Theory, and ApplicationsConstrained Clustering: Advances in Algorithms, Theory, and Applications}, year = {2009}, month = {2009///}, pages = {221 - 244}, author = {Bhattacharya,I. and Getoor, Lise} } @article {12518, title = {Computational methods for modeling facial aging: A survey}, journal = {Journal of Visual Languages \& Computing}, volume = {20}, year = {2009}, month = {2009/06//}, pages = {131 - 144}, abstract = {Facial aging, a new dimension that has recently been added to the problem of face recognition, poses interesting theoretical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community has recently found enhanced interest in the computer vision community. How do humans perceive age? What constitutes an age-invariant signature that can be derived from faces? How compactly can the facial growth event be described? How does facial aging impact recognition performance? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification, etc. and offer insights into future research on this topic.}, keywords = {age estimation, Age progression, Craniofacial growth, face recognition}, isbn = {1045-926X}, doi = {10.1016/j.jvlc.2009.01.011}, url = {http://www.sciencedirect.com/science/article/pii/S1045926X09000032}, author = {Ramanathan,Narayanan and Chellapa, Rama and Biswas,Soma} } @conference {12402, title = {Connections between the lines: augmenting social networks with text}, booktitle = {Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining}, series = {KDD {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {169 - 178}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network data is ubiquitous, encoding collections of relationships between entities such as people, places, genes, or corporations. While many resources for networks of interesting entities are emerging, most of these can only annotate connections in a limited fashion. Although relationships between entities are rich, it is impractical to manually devise complete characterizations of these relationships for every pair of entities on large, real-world corpora. In this paper we present a novel probabilistic topic model to analyze text corpora and infer descriptions of its entities and of relationships between those entities. We develop variational methods for performing approximate inference on our model and demonstrate that our model can be practically deployed on large corpora such as Wikipedia. We show qualitatively and quantitatively that our model can construct and annotate graphs of relationships and make useful predictions.}, keywords = {Graphical models, social network learning, statistical topic models}, isbn = {978-1-60558-495-9}, doi = {10.1145/1557019.1557044}, url = {http://doi.acm.org/10.1145/1557019.1557044}, author = {Chang,Jonathan and Jordan Boyd-Graber and Blei,David M.} } @conference {12230, title = {CPM: Adaptive Video-on-Demand with Cooperative Peer Assists and Multicast}, booktitle = {INFOCOM 2009, IEEE}, year = {2009}, month = {2009/04//}, pages = {91 - 99}, abstract = {We present CPM, a unified approach that exploits server multicast, assisted by peer downloads, to provide efficient video-on-demand (VoD) in a service provider environment. We describe our architecture and show how CPM is designed to dynamically adapt to a wide range of situations including highly different peer-upload bandwidths, content popularity, user request arrival patterns, video library size, and subscriber population. We demonstrate the effectiveness of CPM using simulations (based on an actual implementation codebase) across the range of situations described above and show that CPM does significantly better than traditional unicast, different forms of multicast, as well as peer-to-peer schemes. Along with synthetic parameters, we augment our experiments using data from a deployed VoD service to evaluate the performance of CPM.}, keywords = {assists;multicast;peer-to-peer, communication;peer-to-peer, computing;video, CPM;cooperative, demand;, on, parameters;video-on-demand;multicast, peer, schemes;synthetic}, doi = {10.1109/INFCOM.2009.5061910}, author = {Gopalakrishnan,V. and Bhattacharjee, Bobby and Ramakrishnan,K.K. and Jana,R. and Srivastava,D.} } @article {14603, title = {CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/11/18/}, pages = {R131 - R131}, abstract = {CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF{\textquoteright}s functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-11-r131}, url = {http://genomebiology.com/2009/10/11/R131}, author = {Essien,Kobby and Vigneau,Sebastien and Apreleva,Sofia and Singh,Larry N. and Bartolomei,Marisa S. and Hannenhalli, Sridhar} } @conference {18798, title = {A Decoupled and Prioritized Stochastic Dynamic Programming Approach for Automated Transport of Multiple Particles Using Optical Tweezers}, volume = {6}, year = {2009}, month = {2009///}, pages = {785 - 796}, publisher = {ASME}, organization = {ASME}, address = {San Diego, California, USA}, abstract = {Automated transport of multiple particles using optical tweezers requires the use of motion planning to move them simultaneously while avoiding collisions amongst themselves and with randomly moving obstacles. This paper develops a decoupled and prioritized stochastic dynamic programming based motion planning framework by sequentially applying a partially observable Markov decision process algorithm on every particle that needs to be transported. An iterative version of a maximum bipartite graph matching algorithm is used to assign given goal locations to such particles. The algorithm for individual particle transport is validated using silica beads in a holographic tweezer set-up. Once the individual plans are computed, a three-step method consisting of clustering, classification, and branch and bound optimization is employed to determine the final collision-free paths. Simulation results in the form of sample trajectories and performance characterization plots are presented to illustrate the usefulness of the developed approach.}, isbn = {978-0-7918-4903-3}, doi = {10.1115/DETC2009-87113}, url = {http://link.aip.org/link/ASMECP/v2009/i49033/p785/s1\&Agg=doi}, author = {Banerjee,Ashis Gopal and Losert,Wolfgang and Gupta, Satyandra K.} } @conference {12416, title = {The design of ViVA: a mixed-initiative visual vocabulary for aphasia}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {4015 - 4020}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we present the design of ViVA, a visual vocabulary for aphasia. Aphasia is an acquired language disorder that causes variability of impairments affecting individual{\textquoteright}s ability to speak, comprehend, read and write. Existing communication aids lack flexibility and adequate customization functionality failing to address this variability and to satisfy individual user needs. We tackle these shortcomings by incorporating adaptive and adaptable capabilities in ViVA which is designed to assist communication for users suffering from aphasia. The visual vocabulary for aphasia implements a novel approach that organizes the words in the vocabulary according to user preferences, word usage and certain semantic measures, thus continuously tailoring the tool to the user{\textquoteright}s profile.}, keywords = {adaptive and adaptable interfaces, assistive communication tools, multi-modal interfaces}, isbn = {978-1-60558-247-4}, doi = {10.1145/1520340.1520610}, url = {http://doi.acm.org/10.1145/1520340.1520610}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Cook,Perry R.} } @conference {13916, title = {Designing the reading experience for scanned multi-lingual picture books on mobile phones}, booktitle = {Proceedings of the 9th ACM/IEEE-CS joint conference on Digital libraries}, year = {2009}, month = {2009///}, pages = {305 - 308}, author = {Bederson, Benjamin B. and Quinn,A. and Druin, Allison} } @conference {18562, title = {Detecting network neutrality violations with causal inference}, booktitle = {Proceedings of the 5th international conference on Emerging networking experiments and technologies}, series = {CoNEXT {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {289 - 300}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present NANO, a system that detects when ISPs apply policies that discriminate against specific classes of applications, users, or destinations. Existing systems for detecting discrimination are typically specific to an application or to a particular discrimination mechanism and rely on active measurement tests. Unfortunately, ISPs can change discrimination policies and mechanisms, and they can evade these tests by giving probe traffic higher priority. NANO detects ISP discrimination by passively collecting performance data from clients. To distinguish discrimination from other causes of degradation (e.g., overload, misconfiguration, failure), NANO establishes a causal relationship between an ISP and observed performance by adjusting for confounding factors. NANO agents deployed at participating clients across the Internet collect performance data for selected services and report this information to centralized servers, which analyze the measurements to establish causal relationship between an ISP and performance degradations. We have implemented NANO and deployed clients in a controlled environment on Emulab. We run a combination of controlled experiments on Emulab and wide-area experiments on PlanetLab that show that NANO can determine the extent and criteria for discrimination for a variety of discrimination policies and applications.}, keywords = {causal inference, network neutrality}, isbn = {978-1-60558-636-6}, doi = {10.1145/1658939.1658972}, url = {http://doi.acm.org/10.1145/1658939.1658972}, author = {Bin Tariq,Mukarram and Motiwala,Murtaza and Feamster, Nick and Ammar,Mostafa} } @article {14472, title = {Distinguishing knowledge vs social capital in social media with roles and context}, journal = {Proceedings of the ICWSM}, volume = {9}, year = {2009}, month = {2009///}, abstract = {Social media communities (e.g. Wikipedia, Flickr, Live Q\&A) give rise to distinct types of content, foremost among which are relational content (discussion, chat) and factual content (answering questions, problem-solving). Both users and researchers are increasingly interested in developing strategies that can rapidly distinguish these types of content. While many text-based and structural strategies are possible, we extend two bodies of research that show how social context, and the social roles of answerers can predict content type. We test our framework on a dataset of manually labeled contributions to Microsoft{\textquoteright}s Live Q\&A and find that it reliably extracts factual and relational messages from the data.}, author = {Barash,V. and Smith,M. and Getoor, Lise and Welser,H. T} } @article {17095, title = {Do you know the way to SNA?: A process model for analyzing and visualizing social media data}, journal = {University of Maryland Tech Report: HCIL-2009-17}, year = {2009}, month = {2009///}, abstract = {Traces of activity left by social media users can shed lighton individual behavior, social relationships, and community efficacy. Tools and processes to analyze social traces are essential for enabling practitioners to study and nurture meaningful and sustainable social interaction. Yet such tools and processes remain in their infancy. We conducted a study of 15 graduate students who were learning to apply Social Network Analysis (SNA) to data from online communities. Based on close observations of their emergent practices, we derived the Network Analysis and Visualization (NAV) process model and identified stages where intervention from peers, experts, and an SNA tool were most useful. We show how the NAV model informs the design of SNA tools and services, education practices, and support for social media practitioners. }, author = {Hansen,D. L and Rotman,D. and Bonsignore,E. and Milic-Frayling,N. and Rodrigues,E.M. and Smith,M. and Shneiderman, Ben} } @article {15382, title = {Electromagnetic Analysis of Plasmon-Resonance Based All-Optical Magnetic Recording}, journal = {Magnetics, IEEE Transactions on}, volume = {45}, year = {2009}, month = {2009/03//}, pages = {1634 - 1637}, abstract = {The electromagnetic analysis of plasmon-resonance-based all-optical magnetic recording is performed. This analysis is based on the treatment of plasmon resonances as an eigenvalue problem for specific boundary integral equations. The plasmon modes which can be excited in circular nanoholes and cylindrical nanoshells by circularly polarized light are theoretically and numerically studied. Dramatic enhancement of circularly polarized light intensity on the nanoscale through the excitation of specific plasmon modes in uniaxial nanostructures is demonstrated.}, keywords = {Ag;boundary, all-optical, analysis;magnetization, and, based, effects;nanoparticles;silver;surface, eigenfunctions;magnetic, equations;circular, equations;eigenvalues, integral, intensity;cylindrical, light, magnetic, modes;plasmon-resonance, nanoholes;circularly, nanoshells;eigenvalue, nanostructures;boundary, plasmon, polarized, problem;electromagnetic, recording;magnetisation, recording;silver;uniaxial, resonance;, reversal;magneto-optical, reversals;nanoparticle;plasmon}, isbn = {0018-9464}, doi = {10.1109/TMAG.2009.2012762}, author = {Mayergoyz, Issak D and Zhang,Zhenyu and McAvoy,P. and Bowen,D. and Krafft,C.} } @article {16404, title = {The emergence of zoning policy games in exurban jurisdictions: Informing collective action theory}, journal = {Land Use Policy}, volume = {26}, year = {2009}, month = {2009/04//}, pages = {356 - 367}, abstract = {Theoretical urban policy literature predicts the likelihood of free riding in the management of common goods such as forested open space; such outcome is often characterized as a Prisoner{\textquoteright}s Dilemma game. Numerous cases exist in which neighboring jurisdictions cooperate to maintain public goods, challenging the expected results, yet theoretical explanations of these cases have not been fully developed. In this paper, we use an agent-based model to explore how underlying micro-behaviors affect the payoffs obtained by two neighboring municipalities in a hypothetical exurban area. Payoffs are measured in terms of regional forested space and of local tax revenue at the end of the agent-based simulations; the municipalities affect these payoffs through their choice of residential zoning policies and the spillover effect between the neighboring jurisdictions. Zoning restrictions influence the conversion of farmland into residential subdivisions of different types, and consequently the location of heterogeneous residential households in the region. Developers and residents respond to the changing landscape characteristics, thus establishing a feedback between early and future land-use patterns. The structure of the simulated payoffs is analyzed using standard game theory. Our analysis shows that a variety of games, in addition to Prisoner{\textquoteright}s Dilemma, can emerge between the neighboring jurisdictions. Other games encourage coordination or subsidization, offering some explanations for the unexpected observations. The game realized in any given context depends on the initial characteristics of the landscape, the value given to the objectives each township seeks to maximize, and the income distribution of the population.}, keywords = {Agent-based modeling, game theory, Land-use policy, Local government cooperation, Scale interaction}, isbn = {0264-8377}, doi = {10.1016/j.landusepol.2008.04.004}, url = {http://www.sciencedirect.com/science/article/pii/S0264837708000604}, author = {Zellner,Moira L. and Page,Scott E. and Rand, William and Brown,Daniel G. and Robinson,Derek T. and Nassauer,Joan and Low,Bobbi} } @conference {18829, title = {Enhanced force measurement techniques to extend optical trapping towards nanoscale manipulation}, year = {2009}, month = {2009/07//}, pages = {13 - 16}, abstract = {We have developed a new force measurement technique based on the random thermal motion of a nanoparticle in an optical trap. We demonstrate this method, in one-dimension, through numerical simulations and laboratory experiments. We show that computer simulations successfully recover the profile of the optical trapping force, beyond the inflection point of the trapping potential for a range of particle sizes. We show, through laboratory experiments, that this technique is effective in recovering higher order terms, in a power series expansion of the trapping force, beyond the widely reported linear trap stiffness. We also show that the first order (stiffness) term in our series expansion is consistent with values reported in the literature.}, keywords = {Brownian motion, extend optical trapping, Fokker-Planck equation, force measurement, inflection point, linear trap stiffness, nanoparticle, nanoparticles, nanoscale manipulation, nanotechnology, optical trapping force, power series expansion, radiation pressure, random thermal motion}, author = {Balijepalli,A. and LeBrun,T. W. and Gorman,J. J. and Gupta,S.K.} } @article {18655, title = {An evaluation of connection characteristics for separating network attacks}, journal = {International Journal of Security and Networks}, volume = {4}, year = {2009}, month = {2009/01/01/}, pages = {110 - 124}, abstract = {The goal of this paper is to evaluate the efficiency of connection characteristics to separate different attack families that target a single TCP port. Identifying the most relevant characteristics might allow statistically separating attack families without systematically using forensics. This study is based on a dataset collected over 117 days using a test-bed of two high interaction honeypots. The results indicated that to separate unsuccessful from successful attacks in malicious traffic: the number of bytes is a relevant characteristic; time-based characteristics are poor characteristics; using combinations of characteristics does not improve the efficiency of separating attacks.}, doi = {10.1504/IJSN.2009.02343}, url = {http://dx.doi.org/10.1504/IJSN.2009.02343}, author = {Berthier,Robin and Michel Cukier} } @article {12997, title = {Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development}, journal = {Sci Transl Med}, volume = {1}, year = {2009}, month = {2009/10//}, pages = {2ra5 - 2ra5}, abstract = {Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine.}, doi = {10.1126/scitranslmed.3000257}, author = {Takala,S. L and Coulibaly,D. and Thera,M. A and Batchelor,A. H and Cummings, Michael P. and Escalante,A. A and Ouattara,A. and Traor{\'e},K. and Niangaly,A. and Djimd{\'e},A. A and Doumbo,OK and Plowe,CV} } @inbook {12526, title = {Face Recognition from Video}, booktitle = {The Essential Guide to Video Processing (Second Edition)The Essential Guide to Video Processing (Second Edition)}, year = {2009}, month = {2009///}, pages = {653 - 688}, publisher = {Academic Press}, organization = {Academic Press}, address = {Boston}, isbn = {978-0-12-374456-2}, url = {http://www.sciencedirect.com/science/article/pii/B9780123744562000232}, author = {Zhou,Shaohua Kevin and Chellapa, Rama and Aggarwal,Gaurav}, editor = {Al Bovik} } @conference {17531, title = {Fighting Spam with the NeighborhoodWatch DHT}, booktitle = {IEEE INFOCOM 2009}, year = {2009}, month = {2009/04/19/25}, pages = {1755 - 1763}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we present DHTBL, an anti-spam blacklist built upon a novel secure distributed hash table (DHT). We show how DHTBL can be used to replace existing DNS-based blacklists (DNSBLs) of IP addresses of mail relays that forward spam. Implementing a blacklist on a DHT improves resilience to DoS attacks and secures message delivery, when compared to DNSBLs. However, due to the sensitive nature of the blacklist, storing the data in a peer-to-peer DHT would invite attackers to infiltrate the system. Typical DHTs can withstand fail-stop failures, but malicious nodes may provide incorrect routing information, refuse to return published items, or simply ignore certain queries. The neighborhoodwatch DHT is resilient to malicious nodes and maintains the O(logiV) bounds on routing table size and expected lookup time. NeighborhoodWatch depends on two assumptions in order to make these guarantees: (1) the existence of an on-line trusted authority that periodically contacts and issues signed certificates to each node, and (2) for every sequence of k + 1 consecutive nodes in the ID space, at least one is alive and non-malicious. We show how NeighborhoodWatch maintains many of its security properties even when the second assumption is violated. Honest nodes in NeighborhoodWatch can detect malicious behavior and expel the responsible nodes from the DHT.}, keywords = {Communications Society, computer crime, cryptography, Databases, IP addresses, IP networks, on-line trusted authority, Peer to peer computing, peer-to-peer computing, peer-to-peer distributed hash table, Postal services, Relays, Resilience, Routing, Security, table size routing, Unsolicited electronic mail}, isbn = {978-1-4244-3512-8}, doi = {10.1109/INFCOM.2009.5062095}, author = {Bender,A. and Sherwood,R. and Monner,D. and Goergen,N. and Spring, Neil and Bhattacharjee, Bobby} } @inbook {16263, title = {Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information}, booktitle = {Research in Computational Molecular Biology}, series = {Lecture Notes in Computer Science}, volume = {5541}, year = {2009}, month = {2009///}, pages = {400 - 417}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Hierarchical clustering is a popular method for grouping together similar elements based on a distance measure between them. In many cases, annotations for some elements are known beforehand, which can aid the clustering process. We present a novel approach for decomposing a hierarchical clustering into the clusters that optimally match a set of known annotations, as measured by the variation of information metric. Our approach is general and does not require the user to enter the number of clusters desired. We apply it to two biological domains: finding protein complexes within protein interaction networks and identifying species within metagenomic DNA samples. For these two applications, we test the quality of our clusters by using them to predict complex and species membership, respectively. We find that our approach generally outperforms the commonly used heuristic methods.}, isbn = {978-3-642-02007-0}, url = {http://dx.doi.org/10.1007/978-3-642-02008-7_29}, author = {Navlakha,Saket and White,James and Nagarajan,Niranjan and Pop, Mihai and Kingsford, Carl}, editor = {Batzoglou,Serafim} } @conference {17168, title = {First Steps to Netviz Nirvana: Evaluating Social Network Analysis with NodeXL}, booktitle = {International Conference on Computational Science and Engineering, 2009. CSE {\textquoteright}09}, volume = {4}, year = {2009}, month = {2009/08/29/31}, pages = {332 - 339}, publisher = {IEEE}, organization = {IEEE}, abstract = {Social Network Analysis (SNA) has evolved as a popular, standard method for modeling meaningful, often hidden structural relationships in communities. Existing SNA tools often involve extensive pre-processing or intensive programming skills that can challenge practitioners and students alike. NodeXL, an open-source template for Microsoft Excel, integrates a library of common network metrics and graph layout algorithms within the familiar spreadsheet format, offering a potentially low-barrier-to-entry framework for teaching and learning SNA. We present the preliminary findings of 2 user studies of 21 graduate students who engaged in SNA using NodeXL. The majority of students, while information professionals, had little technical background or experience with SNA techniques. Six of the participants had more technical backgrounds and were chosen specifically for their experience with graph drawing and information visualization. Our primary objectives were (1) to evaluate NodeXL as an SNA tool for a broad base of users and (2) to explore methods for teaching SNA. Our complementary dual case-study format demonstrates the usability of NodeXL for a diverse set of users, and significantly, the power of a tightly integrated metrics/visualization tool to spark insight and facilitate sense-making for students of SNA.}, keywords = {Computer science, computer science education, data visualisation, Data visualization, Educational institutions, graph drawing, graph layout algorithm, Information services, Information Visualization, Internet, Libraries, Microsoft Excel open-source template, MILC, multi-dimensional in-depth long-term case studies, Netviz Nirvana, NodeXL, Open source software, Programming profession, SNA, social network analysis, Social network services, social networking (online), spreadsheet programs, structural relationship, teaching, visual analytics, visualization tool, Web sites}, isbn = {978-1-4244-5334-4}, doi = {10.1109/CSE.2009.120}, author = {Bonsignore,E. M and Dunne,C. and Rotman,D. and Smith,M. and Capone,T. and Hansen,D. L and Shneiderman, Ben} } @article {12178, title = {From New Zealand to Mongolia: Co-designing and deploying a digital library for the world{\textquoteright}s children}, journal = {Special issue of Children, Youth and Environments: Children in Technological Environments: Interaction, Development, and Design}, year = {2009}, month = {2009///}, author = {Druin, Allison and Bederson, Benjamin B. and Rose,A. and Weeks,A.} } @article {18764, title = {Generating simplified trapping probability models from simulation of optical tweezers system}, journal = {Journal of Computing and Information Science in Engineering}, volume = {9}, year = {2009}, month = {2009///}, pages = {021003 - 021003}, author = {Banerjee,A. G. and Balijepalli,A. and Gupta,S.K. and LeBrun,T. W.} } @article {12896, title = {Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains}, journal = {Nature}, year = {2009}, month = {2009///}, abstract = {Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a {\textquoteright}shift{\textquoteright} between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a {\textquoteright}drift{\textquoteright} between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.}, keywords = {59; CHOLERA; GENES; GENETICS; GENOTYPE; ISLANDS; ORIGIN; PHENOTYPE; PUBLIC HEALTH; RECOMBINATION; STRAINS; TOXINS}, url = {http://www.osti.gov/energycitations/servlets/purl/962365-icnke9/}, author = {Brettin,Thomas S[Los Alamos National Laboratory and Bruce,David C[Los Alamos National Laboratory and Challacombe,Jean F[Los Alamos National Laboratory and Detter,John C[Los Alamos National Laboratory and Han,Cliff S[Los Alamos National Laboratory and Munik,A. C[Los Alamos National Laboratory and Chertkov,Olga[Los Alamos National Laboratory and Meincke,Linda[Los Alamos National Laboratory and Saunders,Elizabeth[Los Alamos National Laboratory and Choi,Seon Y[SEOUL NATL UNIV and Haley,Bradd J[U MARYLAND and Taviani,Elisa[U MARYLAND and Jeon,Yoon-Seong[INTL VACCINE INST SEOUL and Kim,Dong Wook[INTL VACCINE INST SEOUL and Lee,Jae-Hak[SEOUL NATL UNIV and Walters,Ronald A[PNNL and Hug,Anwar[NATL INST CHOLERIC ENTERIC DIS and Rita R Colwell} } @article {14553, title = {Hat guessing games}, journal = {SIAM review}, volume = {51}, year = {2009}, month = {2009///}, pages = {399 - 413}, author = {Butler,S. and Hajiaghayi, Mohammad T. and Kleinberg,R. D and Leighton,T.} } @conference {12238, title = {Identifying close friends on the internet}, booktitle = {Proc. of workshop on Hot Topics in Networks (HotNets-VIII)}, year = {2009}, month = {2009///}, abstract = {Online Social Networks (OSNs) encourage users to createan online presence that reflects their offline identity. OSNs create the illusion that these online accounts correspond to the correct offline person, but in reality the OSN lacks the re- sources to detect impersonation. We propose that OSN users identify each other based on interaction and experience. We believe that impersonation can be thwarted by users who possess exclusive shared knowledge, secret informa- tion shared only between a pair of OSN friends. We describe existing protocols that use shared secrets to exchange public keys without revealing those secrets to attackers. We present results from a user study on Facebook to show that users do share exclusive knowledge with their Facebook friends and attackers are rarely able to guess that knowledge. Finally, we show that friend identification can be extended using a web of trust built on the OSN friend graph. }, author = {Baden,R. and Spring, Neil and Bhattacharjee, Bobby} } @conference {14560, title = {Improved approximation algorithms for prize-collecting Steiner tree and TSP}, booktitle = {2009 50th Annual IEEE Symposium on Foundations of Computer Science}, year = {2009}, month = {2009///}, pages = {427 - 436}, author = {Archer,A. and Bateni,M. H and Hajiaghayi, Mohammad T. and Karloff,H.} } @article {15763, title = {Improvement and analysis of computational methods for prediction of residual dipolar couplings}, journal = {Journal of Magnetic Resonance}, volume = {201}, year = {2009}, month = {2009/11//}, pages = {25 - 33}, abstract = {We describe a new, computationally efficient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a molecule. This method is applicable to bicelles, PEG/hexanol, and other alignment media that can be modeled by steric restrictions introduced by a planar barrier. This method is used to further explore and compare various representations of protein shape by an equivalent ellipsoid. We also examine the accuracy of the alignment tensor and residual dipolar couplings (RDC) prediction using various ab initio methods. We separately quantify the inaccuracy in RDC prediction caused by the inaccuracy in the orientation and in the magnitude of the alignment tensor, concluding that orientation accuracy is much more important in accurate prediction of RDCs.}, keywords = {Ab initio prediction, Alignment tensor, PALES, Residual dipolar coupling}, isbn = {1090-7807}, doi = {10.1016/j.jmr.2009.07.028}, url = {http://www.sciencedirect.com/science/article/pii/S1090780709002304}, author = {Berlin,Konstantin and O{\textquoteright}Leary,Dianne P. and Fushman, David} } @conference {15863, title = {Improving search effectiveness in the legal e-discovery process using relevance feedback}, booktitle = {Proceedings of the global E-Discovery/E-Disclosure workshop on electronically stored information in discovery at the 12th international conference on artificial intelligence and law (ICAIL09 DESI Workshop). DESI Press, Barcelona}, year = {2009}, month = {2009///}, author = {Zhao,F.C. and Oard, Douglas and Baron,J.R.} } @inbook {18850, title = {In Situ Characterization and Modeling of Strains near Embedded Electronic Components During Processing and Break-in for Multifunctional Polymer Structures}, booktitle = {Advances in Mathematical Modeling and Experimental Methods for Materials and Structures}, series = {Solid Mechanics and Its Applications}, volume = {168}, year = {2009}, month = {2009///}, pages = {145 - 159}, publisher = {Springer Netherlands}, organization = {Springer Netherlands}, abstract = {Emerging molding concepts, such as in-mold assembly, are enabling electronic structures to be directly embedded in thermoplastic polymers to provide integrated packaging for better protection and a more multifunctional structure in {\textquotedblleft}in-mold assembly processes{\textquotedblright}. During the molding process, stress can develop at the interface of the polymer and embedded electronic component due to shrinkage of the polymer that precipitates fracture or fatigue during the life cycle of the product. Additionally, the interaction between a mold and the polymer melt is altered in a multi-stage molding process where a polymer for superior impact protection can be molded over another polymer that is more compatible with the embedded electronic component. Currently, we do not fully understand the impact of various parameters governing the in-mold assembly process on the residual strains that develop in polymers around embedded electronic components in order to develop process models. Therefore, in this chapter experiments are presented that are designed and executed to measure the strains involved and the manner in which they develop. An in situ open mold experiment is employed using the full-field deformation technique of Digital Image Correlation (DIC) to characterize the displacement and corresponding strain fields that evolve near embedded electronic elements as the polymer shrinks from the molten to the solid state during processes and during break-in of the electronic component. It was determined that the use of multi-stage molding may reduce the residual stresses in addition to providing superior impact protection. However, there was a higher concentration of strain near the polymer-component interface during break-due to lower thermal conductivity. Experimental data was consistent with a thermomechanical model up until the point of failure.}, keywords = {engineering}, isbn = {978-90-481-3467-0}, url = {http://www.springerlink.com/content/lh52x2475g7x00k7/abstract/}, author = {Gershon,Alan L. and Gyger,Lawrence S. and Bruck,Hugh A. and Gupta, Satyandra K.}, editor = {Gilat,Rivka and Banks-Sills,Leslie and Gladwell,G. M. L.} } @conference {15491, title = {An Initial Characterization of Industrial Graphical User Interface Systems}, booktitle = {Software Testing Verification and Validation, 2009. ICST {\textquoteright}09. International Conference on}, year = {2009}, month = {2009/04//}, pages = {11 - 20}, abstract = {To date we have developed and applied numerous model-based GUI testing techniques; however, we are unable to provide definitive improvement schemes to real-world GUI test planners, as our data was derived from open source applications, small compared to industrial systems. This paper presents a study of three industrial GUI-based software systems developed at ABB, including data on classified defects detected during late-phase testing and customer usage, test suites, and source code change metrics. The results show that (1) 50\% of the defects found through the GUI are categorized as data access and handling, control flow and sequencing, correctness, and processing defects, (2) system crashes exposed defects 12-19\% of the time, and (3) GUI and non-GUI components are constructed differently, in terms of source code metrics.}, keywords = {Graphical user interfaces, GUI-based software systems, industrial graphical user interface systems, model-based GUI testing techniques, program testing, software metrics, source code change metrics}, doi = {10.1109/ICST.2009.11}, author = {Brooks,P.A. and Robinson,B.P. and Memon, Atif M.} } @article {19460, title = {The Ins and Outs of Home Networking: The Case for Useful and Usable Domestic Networking}, journal = {ACM Trans. Comput.-Hum. Interact.}, volume = {16}, year = {2009}, month = {2009/06//}, pages = {8:1 - 8:28}, abstract = {Householders are increasingly adopting home networking as a solution to the demands created by the presence of multiple computers, devices, and the desire to access the Internet. However, current network solutions are derived from the world of work (and initially the military) and provide poor support for the needs of the home. We present the key findings to emerge from empirical studies of home networks in the UK and US. The studies reveal two key kinds of work that effective home networking relies upon: one, the technical work of setting up and maintaining the home network, and the other, the collaborative and socially organized work of the home which the network is embedded in and supports. The two are thoroughly intertwined and rely upon one another for their realization, yet neither is adequately supported by current networking technologies and applications. Explication of the {\textquotedblleft}work to make the home network work{\textquotedblright} opens up the design space for the continued integration of the home network in domestic life and elaboration of future support. Key issues for development include the development of networking facilities that do not require advanced networking knowledge, that are flexible and support the local social order of the home and the evolution of its routines, and which ultimately make the home network visible and accountable to household members.}, keywords = {home networking, Human computer interaction}, isbn = {1073-0516}, url = {http://doi.acm.org/10.1145/1534903.1534905}, author = {Grinter, Rebecca E. and Edwards, W. Keith and Marshini Chetty and Poole, Erika S. and Sung, Ja-Young and Yang, Jeonghwa and Crabtree, Andy and Tolmie, Peter and Rodden, Tom and Greenhalgh, Chris and Benford, Steve} } @article {18751, title = {Integrated product and process design for a flapping wing drive mechanism}, journal = {Journal of Mechanical Design}, volume = {131}, year = {2009}, month = {2009///}, pages = {061006 - 061006}, author = {Bejgerowski,W. and Ananthanarayanan,A. and Mueller,D. and Gupta,S.K.} } @conference {17242, title = {Interacting with eHealth: towards grand challenges for HCI}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, year = {2009}, month = {2009///}, pages = {3309 - 3312}, abstract = {While health records are increasingly stored electronically, we, as citizens, have little access to this data about ourselves. We are not used to thinking of these official records either as ours or as useful to us. We increasingly turn to the Web, however, to query any ache, pain or health goal we may have before consulting with health care professionals. Likewise, for proactive health care such as nutrition or fitness, or to find fellow-sufferers for post diagnosis support, we turn to online resources. There is a potential disconnect between points at which professional and lay eHealth data and resources intersect for preventative or proactive health care. Such gaps in information sharing may have direct impact on practices we decide to take up, the care we seek, or the support professionals offer. In this panel, we consider several places within proactive, preventative health care in particular HCI has a role towards enhancing health knowledge discovery and health support interaction. Our goal is to demonstrate how now is the time for eHealth to come to the forefront of the HCI research agenda.}, author = {Andr{\'e},P. and White,R. and Tan,D. and Berners-Lee,T. and Consolvo,S. and Jacobs,R. and Kohane,I. and Le Dantec,C.A. and Mamykina,L. and Marsden,G.} } @inbook {13797, title = {Interlingual annotation of multilingual text corpora and FrameNet}, booktitle = {Multilingual FrameNets in Computational LexicographyMultilingual FrameNets in Computational Lexicography}, volume = {200}, year = {2009}, month = {2009/07/14/}, pages = {287 - 318}, publisher = {Mouton de Gruyter}, organization = {Mouton de Gruyter}, address = {Berlin, New York}, isbn = {978-3-11-021296-9, 978-3-11-021297-6}, url = {http://www.degruyter.com/view/books/9783110212976/9783110212976.4.287/9783110212976.4.287.xml}, author = {Farwell,David and Dorr, Bonnie J and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Green,Rebecca and Levin,Lori and Miller,Keith and Mitamura,Teruko and Rambow,Owen and Reeder,Flo and Siddharthan,Advaith}, editor = {Bisang,Walter and Hock,Hans Henrich and Winter,Werner and Boas,Hans C.} } @conference {15485, title = {Introducing a test suite similarity metric for event sequence-based test cases}, booktitle = {Software Maintenance, 2009. ICSM 2009. IEEE International Conference on}, year = {2009}, month = {2009/09//}, pages = {243 - 252}, abstract = {Most of today{\textquoteright}s event driven software (EDS) systems are tested using test cases that are carefully constructed as sequences of events; they test the execution of an event in the context of its preceding events. Because sizes of these test suites can be extremely large, researchers have developed techniques, such as reduction and minimization, to obtain test suites that are ldquosimilarrdquo to the original test suite, but smaller. Existing similarity metrics mostly use code coverage; they do not consider the contextual relationships between events. Consequently, reduction based on such metrics may eliminate desirable test cases. In this paper, we present a new parameterized metric, CONTeSSi(n) which uses the context of n preceding events in test cases to develop a new context-aware notion of test suite similarity for EDS. This metric is defined and evaluated by comparing four test suites for each of four open source applications. Our results show that CONT eSSi(n) is a better indicator of the similarity of EDS test suites than existing metrics.}, keywords = {event driven software systems, event sequence-based test cases, open source systems, program testing, public domain software, software metrics, Software testing, test suite similarity metric}, doi = {10.1109/ICSM.2009.5306305}, author = {Brooks,P.A. and Memon, Atif M.} } @conference {19455, title = {It{\textquoteright}s Not Easy Being Green: Understanding Home Computer Power Management}, booktitle = {SIGCHI {\textquoteright}09}, series = {CHI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1033 - 1042}, publisher = {ACM}, organization = {ACM}, abstract = {Although domestic computer use is increasing, most efforts to reduce energy use through improved power management have focused on computers in the workplace. We studied 20 households to understand how people use power management strategies on their home computers. We saw computers in the home, particularly desktop computers, are left on much more than they are actively used suggesting opportunities for economic and energy savings. However, for most of our participants, the economic incentives were too minor to motivate them to turn off devices when not in use, especially given other frustrations such as long boot up times. We suggest research directions for home computer power management that could help users be more green without having to dramatically change their home computing habits.}, keywords = {home computer use, power management, Sustainability}, isbn = {978-1-60558-246-7}, url = {http://doi.acm.org/10.1145/1518701.1518860}, author = {Marshini Chetty and Brush, A.J. Bernheim and Meyers, Brian R. and Johns, Paul} } @article {14427, title = {Link-based active learning}, journal = {NIPS Workshop on Analyzing Networks and Learning with Graphs}, year = {2009}, month = {2009///}, abstract = {Supervised and semi-supervised data mining techniques require labeled data.However, labeling examples is costly for many real-world applications. To ad- dress this problem, active learning techniques have been developed to guide the labeling process in an effort to minimize the amount of labeled data without sac- rificing much from the quality of the learned models. Yet, most of the active learning methods to date have remained relatively agnostic to the rich structure offered by network data, often ignoring the relationships between the nodes of a network. On the other hand, the relational learning community has shown that the relationships can be very informative for various prediction tasks. In this paper, we propose different ways of adapting existing active learning work to network data while utilizing links to select better examples to label. }, author = {Bilgic,M. and Getoor, Lise} } @article {15768, title = {Locality bounds on hamiltonians for stabilizer codes}, journal = {Quantum Info. Comput.}, volume = {9}, year = {2009}, month = {2009/05//}, pages = {487 - 499}, abstract = {In this paper, we study the complexity of Hamiltonians whose groundstate is a stabilizer code. Weintroduce various notions of k-locality of a stabilizer code, inherited from the associated stabilizergroup. A choice of generators leads to a Hamiltonian with the code in its groundspace. We establishbounds on the locality of any other Hamiltonian whose groundspace contains such a code, whetheror not its Pauli tensor summands commute. Our results provide insight into the cost of creating anenergy gap for passive error correction and for adiabatic quantum computing. The results simplify inthe cases of XZ-split codes such as Calderbank-Shor-Steane stabilizer codes and topologically-orderedstabilizer codes arising from surface cellulations.}, isbn = {1533-7146}, url = {http://dl.acm.org/citation.cfm?id=2011791.2011800}, author = {Bullock,Stephen S. and O{\textquoteright}Leary, Dianne P.} } @article {12146, title = {Maturing Software Engineering Knowledge through Classifications: A Case Study on Unit Testing Techniques}, journal = {Software Engineering, IEEE Transactions on}, volume = {35}, year = {2009}, month = {2009/08//july}, pages = {551 - 565}, abstract = {Classification makes a significant contribution to advancing knowledge in both science and engineering. It is a way of investigating the relationships between the objects to be classified and identifies gaps in knowledge. Classification in engineering also has a practical application; it supports object selection. They can help mature software engineering knowledge, as classifications constitute an organized structure of knowledge items. Till date, there have been few attempts at classifying in software engineering. In this research, we examine how useful classifications in software engineering are for advancing knowledge by trying to classify testing techniques. The paper presents a preliminary classification of a set of unit testing techniques. To obtain this classification, we enacted a generic process for developing useful software engineering classifications. The proposed classification has been proven useful for maturing knowledge about testing techniques, and therefore, SE, as it helps to: 1) provide a systematic description of the techniques, 2) understand testing techniques by studying the relationships among techniques (measured in terms of differences and similarities), 3) identify potentially useful techniques that do not yet exist by analyzing gaps in the classification, and 4) support practitioners in testing technique selection by matching technique characteristics to project characteristics.}, keywords = {characteristic;project, characteristic;software, classification;matching, engineering, engineering;, knowledge;software, technique, techniques;program, Testing, testing;software, testing;unit}, isbn = {0098-5589}, doi = {10.1109/TSE.2009.13}, author = {Vegas,S. and Juristo,N. and Basili, Victor R.} } @article {14228, title = {MEASURING 1ST ORDER STRETCH WITH A SINGLE FILTER}, journal = {Relation}, volume = {10}, year = {2009}, month = {2009///}, pages = {691 - 691}, abstract = {We analytically develop a filter that is able to measurethe linear stretch of the transformation around a point, and present results of applying it to real signals. We show that this method is a real-time alternative solution for measuring local signal transformations. Experimentally, this method can accurately measure stretch, however, it is sensitive to shift. }, author = {Bitsakos,K. and Domke, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {19664, title = {Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays}, journal = {BMC Genomics}, volume = {10}, year = {2009}, month = {2009/12/01/}, pages = {1 - 10}, abstract = {Background High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression. Results Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae. Conclusion Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.}, keywords = {Animal Genetics and Genomics, Life Sciences, general, Microarrays, Microbial Genetics and Genomics, Plant Genetics \& Genomics, proteomics}, isbn = {1471-2164}, url = {http://link.springer.com/article/10.1186/1471-2164-10-221}, author = {Bloom, Joshua S. and Zia Khan and Kruglyak, Leonid and Singh, Mona and Caudy, Amy A.} } @article {17990, title = {Mesh-of-Trees and Alternative Interconnection Networks for Single-Chip Parallelism}, journal = {Very Large Scale Integration (VLSI) Systems, IEEE Transactions on}, volume = {17}, year = {2009}, month = {2009/10//}, pages = {1419 - 1432}, abstract = {In single-chip parallel processors, it is crucial to implement a high-throughput low-latency interconnection network to connect the on-chip components, especially the processing units and the memory units. In this paper, we propose a new mesh of trees (MoT) implementation of the interconnection network and evaluate it relative to metrics such as wire complexity, total register count, single switch delay, maximum throughput, tradeoffs between throughput and latency, and post-layout performance. We show that on-chip interconnection networks can provide higher bandwidth between processors and shared first-level cache than previously considered possible, facilitating greater scalability of memory architectures that require that. MoT is also compared, both analytically and experimentally, to some other traditional network topologies, such as hypercube, butterfly, fat trees and butterfly fat trees. When we evaluate a 64-terminal MoT network at 90-nm technology, concrete results show that MoT provides higher throughput and lower latency especially when the input traffic (or the on-chip parallelism) is high, at comparable area. A recurring problem in networking and communication is that of achieving good sustained throughput in contrast to just high theoretical peak performance that does not materialize for typical work loads. Our quantitative results demonstrate a clear advantage of the proposed MoT network in the context of single-chip parallel processing.}, keywords = {90, cache;single, complexity;multiprocessor, delay;single-chip, first-level, high-throughput, interconnection, low-latency, network;memory, network;shared, networks;network-on-chip;parallel, nm;wire, Parallel, parallelism;size, processing;, processor;single-chip, switch, topologies;on-chip, units;mesh-of-trees;network}, isbn = {1063-8210}, doi = {10.1109/TVLSI.2008.2003999}, author = {Balkan,A.O. and Gang Qu and Vishkin, Uzi} } @article {12888, title = {Microbial oceanography in a sea of opportunity}, journal = {Nature}, volume = {459}, year = {2009}, month = {2009/05/13/}, pages = {180 - 184}, abstract = {Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean{\textquoteright}s response to climate change, improving the predictive power of climate models.}, keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling, climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics}, isbn = {0028-0836}, doi = {10.1038/nature08056}, url = {http://www.nature.com/nature/journal/v459/n7244/abs/nature08056.html}, author = {Bowler,Chris and Karl,David M. and Rita R Colwell} } @article {15390, title = {Modeling and Testing of Ethernet Transformers}, journal = {Magnetics, IEEE Transactions on}, volume = {45}, year = {2009}, month = {2009/10//}, pages = {4793 - 4796}, abstract = {In this paper, novel techniques for the testing and identification of lumped parameters of equivalent circuits for Ethernet transformers are presented. It is demonstrated experimentally and theoretically that resonance phenomena may occur in the loop formed by leakage inductances and cross-winding capacitance. This resonance may corrupt the pass band of the transformers transfer characteristic for differential-mode signals.}, keywords = {area, capacitance;differential-mode, characteristic;local, Ethernet, identification;lumped, inductances;lumped, networks;transformers;, PARAMETERS, phenomena;transformers, signals;leakage, testing;resonance, transfer, transformers;cross-winding}, isbn = {0018-9464}, doi = {10.1109/TMAG.2009.2023918}, author = {Bowen,D. and Mayergoyz, Issak D and Zhang,Zhenyu and McAvoy,P. and Krafft,C. and Kroop,D.} } @article {14630, title = {Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/07/01/}, pages = {R72 - R72}, abstract = {Hundreds of proteins modulate neurotransmitter release and synaptic plasticity during neuronal development and in response to synaptic activity. The expression of genes in the pre- and post-synaptic neurons is under stringent spatio-temporal control, but the mechanism underlying the neuronal expression of these genes remains largely unknown.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-7-r72}, url = {http://genomebiology.com/2009/10/7/R72}, author = {Liu,Rui and Hannenhalli, Sridhar and Bucan,Maja} } @conference {12408, title = {Multilingual topic models for unaligned text}, booktitle = {Proceedings of the Twenty-Fifth Conference on Uncertainty in Artificial Intelligence}, series = {UAI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {75 - 82}, publisher = {AUAI Press}, organization = {AUAI Press}, address = {Arlington, Virginia, United States}, abstract = {We develop the multilingual topic model for unaligned text (MuTo), a probabilistic model of text that is designed to analyze corpora composed of documents in two languages. From these documents, MuTo uses stochastic EM to simultaneously discover both a matching between the languages and multilingual latent topics. We demonstrate that MuTo is able to find shared topics on real-world multilingual corpora, successfully pairing related documents across languages. MuTo provides a new framework for creating multilingual topic models without needing carefully curated parallel corpora and allows applications built using the topic model formalism to be applied to a much wider class of corpora.}, isbn = {978-0-9749039-5-8}, url = {http://dl.acm.org/citation.cfm?id=1795114.1795124}, author = {Jordan Boyd-Graber and Blei,David M.} } @article {12887, title = {New records of phytoplankton for Bangladesh. 9. Some rare and a new species}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {16}, year = {2009}, month = {2009/06/25/}, abstract = {Ten taxa belonging to Chlorophyceae, Cyanophyceae, Bacillariophyceae and Euglenophyceae, and one with an uncertain taxonomic position have been described in this paper. Of these, 10 taxa have been found to be globally rare and new records for Bangladesh, whereas Strombomonas islamii Khondker sp. nov. has been described as new to science.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v16i1.2734}, url = {http://www.banglajol.info/bd/index.php/BJPT/article/viewArticle/2734}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {15391, title = {Nonlinear Resonant and Chaotic Dynamics in Microwave Assisted Magnetization Switching}, journal = {Magnetics, IEEE Transactions on}, volume = {45}, year = {2009}, month = {2009/10//}, pages = {3950 - 3953}, abstract = {The switching process of a uniformly magnetized magnetic nanoparticle is considered. The particle is subject to applied fields having both dc and linearly-polarized radio-frequency (RF) components. The possibility of using the RF power to obtain a reduced coercivity of the particle is related to the onset of chaotic magnetization dynamics for moderately low values of the RF field amplitude. Perturbation technique for the evaluation of the reduced coercive field is developed and applied to the microwave assisted switching of the particle. Numerical simulations confirm the predictions of the theory.}, keywords = {amplitude;chaotic, components;magnetic, dynamical, dynamics;coercive, dynamics;numerical, field, field;coercivity;linearly-polarized, force;magnetic, magnetization, nanoparticle;microwave-assisted, particles;magnetic, radiofrequency, resonant, RF, simulations;perturbation, switching;nanoparticles;nonlinear, switching;nonlinear, systems;perturbation, technique;chaos;coercive, theory;}, isbn = {0018-9464}, doi = {10.1109/TMAG.2009.2023242}, author = {d{\textquoteright}Aquino,M. and Serpico,C. and Bertotti,G. and Mayergoyz, Issak D and Bonin,R.} } @article {16606, title = {An oscillatory hebbian network model of short-term memory}, journal = {Neural computation}, volume = {21}, year = {2009}, month = {2009///}, pages = {741 - 761}, author = {Winder,R. K and Reggia, James A. and Weems,S. A and Bunting,M. F} } @article {16432, title = {Participatory simulation as a tool for agent-based simulation}, journal = {Proceedings of the International Conference on Agents and Artificial Intelligence (ICAART-09)}, year = {2009}, month = {2009///}, abstract = {Participatory simulation, as described by Wilensky \& Stroup (1999c), is a form of agent-based simulation inwhich multiple humans control or design individual agents in the simulation. For instance, in a participatory simulation of an ecosystem, fifty participants might each control the intake and output of one agent, such that the food web emerges from the interactions of the human-controlled agents. We argue that participatory simulation has been under-utilized outside of strictly educational contexts, and that it provides myriad benefits to designers of traditional agent-based simulations. These benefits include increased robustness of the model, increased comprehensibility of the findings, and simpler design of individual agent behaviors. To make this argument, we look to recent research such as that from crowdsourcing (von Ahn, 2005) and the reinforcement learning of autonomous agent behavior (Abbeel, 2008). }, author = {Berland,M. and Rand, William} } @conference {12237, title = {Persona: an online social network with user-defined privacy}, booktitle = {Proceedings of the ACM SIGCOMM 2009 conference on Data communication}, series = {SIGCOMM {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {135 - 146}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online social networks (OSNs) are immensely popular, with some claiming over 200 million users. Users share private content, such as personal information or photographs, using OSN applications. Users must trust the OSN service to protect personal information even as the OSN provider benefits from examining and sharing that information. We present Persona, an OSN where users dictate who may access their information. Persona hides user data with attribute-based encryption (ABE), allowing users to apply fine-grained policies over who may view their data. Persona provides an effective means of creating applications in which users, not the OSN, define policy over access to private data. We demonstrate new cryptographic mechanisms that enhance the general applicability of ABE. We show how Persona provides the functionality of existing online social networks with additional privacy benefits. We describe an implementation of Persona that replicates Facebook applications and show that Persona provides acceptable performance when browsing privacy-enhanced web pages, even on mobile devices.}, keywords = {ABE, Facebook, OSN, persona, privacy, social networks}, isbn = {978-1-60558-594-9}, doi = {10.1145/1592568.1592585}, url = {http://doi.acm.org/10.1145/1592568.1592585}, author = {Baden,Randy and Bender,Adam and Spring, Neil and Bhattacharjee, Bobby and Starin,Daniel} } @article {12232, title = {Persona : An Online Social Network with User-Defined Privacy Categories and Subject Descriptors}, journal = {Computer}, volume = {39}, year = {2009}, month = {2009///}, pages = {135 - 146}, abstract = {Online social networks (OSNs) are immensely popular, with some claiming over 200 million users. Users share private content, such as personal information or photographs, using OSN applications. Users must trust the OSN service to protect personal information even as the OSN provider benefits from examining and sharing that information. We present Persona, an OSN where users dictate who may access their information. Persona hides user data with attribute-based encryption (ABE), allowing users to apply fine-grained policies over who may view their data. Persona provides an effective means of creating applications in which users, not the OSN, define policy over access to private data. We demonstrate new cryptographic mechanisms that enhance the general applicability of ABE. We show how Persona provides the functionality of existing online social networks with additional privacy benefits. We describe an implementation of Persona that replicates Facebook applications and show that Persona provides acceptable performance when browsing privacy-enhanced web pages, even on mobile devices.}, doi = {10.1145/1594977.1592585}, author = {Starin,Daniel and Baden,Randy and Bender,Adam and Spring, Neil and Bhattacharjee, Bobby} } @article {19648, title = {A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009/07/01/}, pages = {1609 - 1616}, abstract = {Motivation: High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anchor points for genome{\textendash}genome comparisons.Results: We introduce a new algorithm for finding MEMs. The algorithm leverages a sparse suffix array (SA), a text index that stores every K-th position of the text. In contrast to a full text index that stores every position of the text, a sparse SA occupies much less memory. Even though we use a sparse index, the output of our algorithm is the same as a full text index algorithm as long as the space between the indexed suffixes is not greater than a minimum length of a MEM. By relying on partial matches and additional text scanning between indexed positions, the algorithm trades memory for extra computation. The reduced memory usage makes it possible to determine MEMs between significantly longer sequences. Availability: Source code for the algorithm is available under a BSD open source license at http://compbio.cs.princeton.edu/mems. The implementation can serve as a drop-in replacement for the MEMs algorithm in MUMmer 3. Contact: zkhan@cs.princeton.edu;mona@cs.princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online. }, isbn = {1367-4803, 1460-2059}, url = {http://bioinformatics.oxfordjournals.org/content/25/13/1609}, author = {Zia Khan and Bloom, Joshua S. and Kruglyak, Leonid and Singh, Mona} } @article {12892, title = {Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study}, journal = {EcoHealth}, volume = {6}, year = {2009}, month = {2009///}, pages = {378 - 389}, abstract = {Vibrio cholerae, the causative agent of cholera, is a naturally occurring inhabitant of the Chesapeake Bay and serves as a predictor for other clinically important vibrios, including Vibrio parahaemolyticus and Vibrio vulnificus. A system was constructed to predict the likelihood of the presence of V. cholerae in surface waters of the Chesapeake Bay, with the goal to provide forecasts of the occurrence of this and related pathogenic Vibrio spp. Prediction was achieved by driving an available multivariate empirical habitat model estimating the probability of V. cholerae within a range of temperatures and salinities in the Bay, with hydrodynamically generated predictions of ambient temperature and salinity. The experimental predictions provided both an improved understanding of the in situ variability of V. cholerae, including identification of potential hotspots of occurrence, and usefulness as an early warning system. With further development of the system, prediction of the probability of the occurrence of related pathogenic vibrios in the Chesapeake Bay, notably V. parahaemolyticus and V. vulnificus, will be possible, as well as its transport to any geographical location where sufficient relevant data are available.}, doi = {10.1007/s10393-009-0273-6}, author = {Constantin de Magny,G. and Long,W. and Brown,C. W. and Hood,R. R. and Huq,A. and Murtugudde,R. and Rita R Colwell} } @article {19667, title = {Protein quantification across hundreds of experimental conditions}, journal = {Proceedings of the National Academy of Sciences}, volume = {106}, year = {2009}, month = {2009/09/15/}, pages = {15544 - 15548}, abstract = {Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.}, keywords = {kd-tree, orthogonal range query, quantitative proteomics, space partitioning data structures, tandem mass spectrometry}, isbn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/content/106/37/15544}, author = {Zia Khan and Bloom, Joshua S. and Garcia, Benjamin A. and Singh, Mona and Kruglyak, Leonid} } @conference {12412, title = {Reading tea leaves: How humans interpret topic models}, booktitle = {Proceedings of the 23rd Annual Conference on Neural Information Processing Systems}, volume = {31}, year = {2009}, month = {2009///}, abstract = {Probabilistic topic models are a popular tool for the unsupervised analysis of text, providing both a predictive model of future text and a latent topic representation of the corpus. Practitioners typically assume that the latent space is semantically meaningful. It is used to check models, summarize the corpus, and guide explo- ration of its contents. However, whether the latent space is interpretable is in need of quantitative evaluation. In this paper, we present new quantitative methods for measuring semantic meaning in inferred topics. We back these measures with large-scale user studies, showing that they capture aspects of the model that are undetected by previous measures of model quality based on held-out likelihood. Surprisingly, topic models which perform better on held-out likelihood may infer less semantically meaningful topics.}, author = {Chang,J. and Jordan Boyd-Graber and Gerrish,S. and Wang,C. and Blei,D.M.} } @conference {14251, title = {Real-time shape retrieval for robotics using skip Tri-Grams}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems, 2009. IROS 2009}, year = {2009}, month = {2009/10/10/15}, pages = {4731 - 4738}, publisher = {IEEE}, organization = {IEEE}, abstract = {The real time requirement is an additional constraint on many intelligent applications in robotics, such as shape recognition and retrieval using a mobile robot platform. In this paper, we present a scalable approach for efficiently retrieving closed contour shapes. The contour of an object is represented by piecewise linear segments. A skip Tri-Gram is obtained by selecting three segments in the clockwise order while allowing a constant number of segments to be {\~A}‚{\^A}{\textquestiondown}skipped{\~A}‚{\^A}{\textquestiondown} in between. The main idea is to use skip Tri-Grams of the segments to implicitly encode the distant dependency of the shape. All skip Tri-Grams are used for efficiently retrieving closed contour shapes without pairwise matching feature points from two shapes. The retrieval is at least an order of magnitude faster than other state-of-the-art algorithms. We score 80\% in the Bullseye retrieval test on the whole MPEG 7 shape dataset. We further test the algorithm using a mobile robot platform in an indoor environment. 8 objects are used for testing from different viewing directions, and we achieve 82\% accuracy.}, keywords = {Bullseye retrieval test, Clocks, closed contour shape retrieval, Image retrieval, Image segmentation, Indexing, Information retrieval, Intelligent robots, Jacobian matrices, mobile robot, Mobile robots, MPEG 7 shape dataset, piecewise linear segments, Piecewise linear techniques, Real time systems, real-time shape retrieval, robot vision, SHAPE, shape recognition, shape representation, skip Tri-Grams, Testing}, isbn = {978-1-4244-3803-7}, doi = {10.1109/IROS.2009.5354738}, author = {Li,Yi and Bitsakos,K. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14368, title = {Reflect and correct: A misclassification prediction approach to active inference}, journal = {ACM Transactions on Knowledge Discovery from Data (TKDD)}, volume = {3}, year = {2009}, month = {2009/12//}, pages = {20:1{\textendash}20:32 - 20:1{\textendash}20:32}, abstract = {Information diffusion, viral marketing, graph-based semi-supervised learning, and collective classification all attempt to model and exploit the relationships among nodes in a network to improve the performance of node labeling algorithms. However, sometimes the advantage of exploiting the relationships can become a disadvantage. Simple models like label propagation and iterative classification can aggravate a misclassification by propagating mistakes in the network, while more complex models that define and optimize a global objective function, such as Markov random fields and graph mincuts, can misclassify a set of nodes jointly. This problem can be mitigated if the classification system is allowed to ask for the correct labels for a few of the nodes during inference. However, determining the optimal set of labels to acquire is intractable under relatively general assumptions, which forces us to resort to approximate and heuristic techniques. We describe three such techniques in this article. The first one is based on directly approximating the value of the objective function of label acquisition and greedily acquiring the label that provides the most improvement. The second technique is a simple technique based on the analogy we draw between viral marketing and label acquisition. Finally, we propose a method, which we refer to as reflect and correct, that can learn and predict when the classification system is likely to make mistakes and suggests acquisitions to correct those mistakes. We empirically show on a variety of synthetic and real-world datasets that the reflect and correct method significantly outperforms the other two techniques, as well as other approaches based on network structural measures such as node degree and network clustering.}, keywords = {active inference, collective classification, information diffusion, label acquisition, viral marketing}, isbn = {1556-4681}, doi = {10.1145/1631162.1631168}, url = {http://doi.acm.org/10.1145/1631162.1631168}, author = {Bilgic,Mustafa and Getoor, Lise} } @article {15119, title = {Ring signatures: Stronger definitions, and constructions without random oracles}, journal = {Journal of Cryptology}, volume = {22}, year = {2009}, month = {2009///}, pages = {114 - 138}, abstract = {Ring signatures, first introduced by Rivest, Shamir, and Tauman, enable a user to sign a message so that a ring of possible signers (of which the user is a member) is identified, without revealing exactly which member of that ring actually generated the signature. In contrast to group signatures, ring signatures are completely {\textquotedblleft}ad-hoc{\textquotedblright} and do not require any central authority or coordination among the various users (indeed, users do not even need to be aware of each other); furthermore, ring signature schemes grant users fine-grained control over the level of anonymity associated with any particular signature.This paper has two main areas of focus. First, we examine previous definitions of security for ring signature schemes and suggest that most of these prior definitions are too weak, in the sense that they do not take into account certain realistic attacks. We propose new definitions of anonymity and unforgeability which address these threats, and give separation results proving that our new notions are strictly stronger than previous ones. Second, we show the first constructions of ring signature schemes in the standard model. One scheme is based on generic assumptions and satisfies our strongest definitions of security. Two additional schemes are more efficient, but achieve weaker security guarantees and more limited functionality. }, doi = {10.1007/s00145-007-9011-9}, author = {Bender,A. and Katz, Jonathan and Morselli,R.} } @article {12520, title = {Robust Estimation of Albedo for Illumination-Invariant Matching and Shape Recovery}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {31}, year = {2009}, month = {2009/05//}, pages = {884 - 899}, abstract = {We present a nonstationary stochastic filtering framework for the task of albedo estimation from a single image. There are several approaches in the literature for albedo estimation, but few include the errors in estimates of surface normals and light source direction to improve the albedo estimate. The proposed approach effectively utilizes the error statistics of surface normals and illumination direction for robust estimation of albedo, for images illuminated by single and multiple light sources. The albedo estimate obtained is subsequently used to generate albedo-free normalized images for recovering the shape of an object. Traditional shape-from-shading (SFS) approaches often assume constant/piecewise constant albedo and known light source direction to recover the underlying shape. Using the estimated albedo, the general problem of estimating the shape of an object with varying albedo map and unknown illumination source is reduced to one that can be handled by traditional SFS approaches. Experimental results are provided to show the effectiveness of the approach and its application to illumination-invariant matching and shape recovery. The estimated albedo maps are compared with the ground truth. The maps are used as illumination-invariant signatures for the task of face recognition across illumination variations. The recognition results obtained compare well with the current state-of-the-art approaches. Impressive shape recovery results are obtained using images downloaded from the Web with little control over imaging conditions. The recovered shapes are also used to synthesize novel views under novel illumination conditions.}, keywords = {albedo estimation;error statistics;face recognition;illumination-invariant matching;nonstationary stochastic filtering;robust estimation;shape recovery;shape-from-shading approach;error statistics;face recognition;filtering theory;image matching;Algorithm, Automated;Photometry;Reproducibility of Results;Sensitivity and Specificity;, Computer-Assisted;Imaging, Three-Dimensional;Lighting;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2008.135}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @article {16525, title = {Running memory span: A comparison of behavioral capacity limits with those of an attractor neural network}, journal = {Cognitive Systems Research}, volume = {10}, year = {2009}, month = {2009/06//}, pages = {161 - 171}, abstract = {We studied a computational model of short term memory capacity that performs a simulated running memory span task using Hebbian learning and rapid decay of connection strengths to keep recent items active for later recall. This model demonstrates recall performance similar to humans performing the same task, with a capacity limit of approximately three items and a prominent recency effect. The model also shows that this capacity depends on decay to release the model from accumulating interference. Model findings are compared with data from two behavioral experiments that used varying task demands to tax memory capacity limits. Following additional theoretical predictions from the computational model, behavioral data support that when task demands require attention to be spread too thin to keep items available for later recall, capacity limits suffer. These findings are important both for understanding the mechanisms underlying short term memory capacity, and also to memory researchers interested in the role of attention in capacity limitations.}, keywords = {Attractor neural network, Computational model, Running span, Short term memory, Working memory capacity}, isbn = {1389-0417}, doi = {10.1016/j.cogsys.2008.09.001}, url = {http://www.sciencedirect.com/science/article/pii/S1389041708000569}, author = {Weems,Scott A. and Winder,Ransom K. and Bunting,Michael and Reggia, James A.} } @conference {17911, title = {Salient Clustering for View-dependent Multiresolution Rendering}, booktitle = {Computer Graphics and Image Processing (SIBGRAPI), 2009 XXII Brazilian Symposium on}, year = {2009}, month = {2009/10//}, pages = {56 - 63}, abstract = {Perceptual information is quickly gaining importance in mesh representation, analysis and rendering. User studies, eye tracking and other techniques are able to provide ever more useful insights for many user-centric systems, which form the bulk of computer graphics applications. In this work we build upon the concept of Mesh Saliency - an automatic measure of visual importance for triangle meshes based on models of low-level human visual attention - applying it to the problem of mesh segmentation and view-dependent rendering. We introduce a technique for segmentation that partitions an object into a set of face clusters, each encompassing a group of locally interesting features; Mesh Saliency is incorporated in a propagative mesh clustering framework, guiding cluster seed selection and triangle propagation costs and leading to a convergence of face clusters around perceptually important features. We compare our technique with different fully automatic segmentation algorithms, showing that it provides similar or better segmentation without the need for user input. We illustrate application of our clustering results through a saliency-guided view-dependent rendering system, achieving significant frame rate increases with little loss of visual detail.}, keywords = {(computer, algorithms;cluster, analysis;mesh, attention;mesh, AUTOMATIC, centred, clustering, clustering;rendering, clustering;user-centric, clusters;low-level, dependent, design;, framework;salient, graphics);user, graphics;face, human, information;propagative, mesh, multiresolution, rendering;image, representation;mesh, resolution;image, saliency;mesh, seed, segmentation, segmentation;pattern, segmentation;perceptual, selection;computer, system;view, visual}, doi = {10.1109/SIBGRAPI.2009.34}, author = {Barni,R. and Comba,J. and Varshney, Amitabh} } @conference {14562, title = {Scheduling to minimize staleness and stretch in real-time data warehouses}, booktitle = {Proceedings of the twenty-first annual symposium on Parallelism in algorithms and architectures}, year = {2009}, month = {2009///}, pages = {29 - 38}, author = {Bateni,M. H and Golab,L. and Hajiaghayi, Mohammad T. and Karloff,H.} } @conference {12154, title = {Scope error detection and handling concerning software estimation models}, booktitle = {Proceedings of the 2009 3rd International Symposium on Empirical Software Engineering and Measurement}, series = {ESEM {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {123 - 132}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {Over the last 25+ years, the software community has been searching for the best models for estimating variables of interest (e.g., cost, defects, and fault proneness). However, little research has been done to improve the reliability of the estimates. Over the last decades, scope error and error analysis have been substantially ignored by the community. This work attempts to fill this gap in the research and enhance a common understanding within the community. Results provided in this study can eventually be used to support human judgment-based techniques and be an addition to the portfolio. The novelty of this work is that, we provide a way of detecting and handling the scope error arising from estimation models. The answer whether or not scope error will occur is a pre-condition to safe use of an estimation model. We also provide a handy procedure for dealing with outliers as to whether or not to include them in the training set for building a new version of the estimation model. The majority of the work is empirically based, applying computational intelligence techniques to some COCOMO model variations with respect to a publicly available cost estimation data set in the PROMISE repository.}, isbn = {978-1-4244-4842-5}, doi = {10.1109/ESEM.2009.5316020}, url = {http://dx.doi.org/10.1109/ESEM.2009.5316020}, author = {Sarcia,Salvatore Alessandro and Basili, Victor R. and Cantone,Giovanni} } @article {13856, title = {Semantically informed machine translation (SIMT)}, journal = {SCALE summer workshop final report, Human Language Technology Center Of Excellence}, year = {2009}, month = {2009///}, author = {Baker,K. and Bethard,S. and Bloodgood,M. and Brown,R. and Callison-Burch,C. and Coppersmith,G. and Dorr, Bonnie J and Filardo,W. and Giles,K. and Irvine,A. and others} } @article {12882, title = {Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/10/01/}, pages = {6268 - 6274}, abstract = {Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41\%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23\%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94\%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., {\textquotedblleft}clonal cluster,{\textquotedblright} as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00266-09}, url = {http://aem.asm.org/content/75/19/6268}, author = {Alam,Munirul and Chowdhury,Wasimul B. and Bhuiyan,N. A. and Islam,Atiqul and Hasan,Nur A. and Nair,G. Balakrish and Watanabe,H. and Siddique,A. K. and Huq,Anwar and Sack,R. Bradley and Akhter,M. Z. and Grim,Christopher J. and Kam,K.-M. and Luey,C. K. Y. and Endtz,Hubert P. and Cravioto,Alejandro and Rita R Colwell} } @article {15151, title = {Signing a linear subspace: Signature schemes for network coding}, journal = {Public Key Cryptography{\textendash}PKC 2009}, year = {2009}, month = {2009///}, pages = {68 - 87}, abstract = {Network coding offers increased throughput and improved robustness to random faults in completely decentralized networks. In contrast to traditional routing schemes, however, network coding requires intermediate nodes to modify data packets en route; for this reason, standard signature schemes are inapplicable and it is a challenge to provide resilience to tampering by malicious nodes.We propose two signature schemes that can be used in conjunction with network coding to prevent malicious modification of data. Our schemes can be viewed as signing linear subspaces in the sense that a signature σ on a subspace V authenticates exactly those vectors in V. Our first scheme is (suitably) homomorphic and has constant public-key size and per-packet overhead. Our second scheme does not rely on random oracles and is based on weaker assumptions. We also prove a lower bound on the length of signatures for linear subspaces showing that our schemes are essentially optimal in this regard. }, doi = {10.1007/978-3-642-00468-1_5}, author = {Boneh,D. and Freeman,D. and Katz, Jonathan and Waters,B.} } @conference {12414, title = {Speaking through pictures: images vs. icons}, booktitle = {Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility}, series = {Assets {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {163 - 170}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {People with aphasia, a condition that impairs the ability to understand or generate written or spoken language, are aided by assistive technology that helps them communicate through a vocabulary of icons. These systems are akin to language translation systems, translating icon arrangements into spoken or written language and vice versa. However, these icon-based systems have little vocabulary breadth or depth, making it difficult for people with aphasia to apply their usage to multiple real world situations. Pictures from the web are numerous, varied, and easily accessible and thus, could potentially address the small size issues of icon-based systems. We present results from two studies that investigate this potential and demonstrate that images can be as effective as icons when used as a replacement for English language communication. The first study uses elderly subjects to investigate the efficacy of images vs. icons in conveying word meaning; the second study examines the retention of word-level meaning by both images and icons with a population of aphasics. We conclude that images collected from the web are as functional as icons in conveying information and thus, are feasible to use in assistive technology that supports people with aphasia.}, keywords = {aphasia, computerized visual communication (C-VIC), visual communication (VIC)}, isbn = {978-1-60558-558-1}, doi = {10.1145/1639642.1639672}, url = {http://doi.acm.org/10.1145/1639642.1639672}, author = {Ma,Xiaojuan and Jordan Boyd-Graber and Nikolova,Sonya and Cook,Perry R.} } @article {18807, title = {A survey of CAD model simplification techniques for physics-based simulation applications}, journal = {Computer-Aided Design}, volume = {41}, year = {2009}, month = {2009/02//}, pages = {65 - 80}, abstract = {Automated CAD model simplification plays an important role in effectively utilizing physics-based simulation during the product realization process. Currently a rich body of literature exists that describe many successful techniques for fully-automatic or semi-automatic simplification of CAD models for a wide variety of applications. The purpose of this paper is to compile a list of the techniques that are relevant for physics-based simulations problems and to characterize them based on their attributes. We have classified them into the following four categories: techniques based on surface entity based operators, volume entity based operators, explicit feature based operators, and dimension reduction operators. This paper also presents the necessary background information in the CAD model representation to assist the new readers. We conclude the paper by outlining open research directions in this field.}, keywords = {CAD model simplification, Physics-based simulation}, isbn = {0010-4485}, doi = {10.1016/j.cad.2008.11.009}, url = {http://www.sciencedirect.com/science/article/pii/S0010448508002285}, author = {Thakur,Atul and Banerjee,Ashis Gopal and Gupta, Satyandra K.} } @conference {12236, title = {Symbiotic relationships in internet routing overlays}, booktitle = {Proceedings of the 6th USENIX symposium on Networked systems design and implementation}, series = {NSDI{\textquoteright}09}, year = {2009}, month = {2009///}, pages = {467 - 480}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {We propose to construct routing overlay networks using the following principle: that overlay edges should be based on mutual advantage between pairs of hosts. Upon this principle, we design, implement, and evaluate Peer-Wise, a latency-reducing overlay network. To show the feasibility of PeerWise, we must show first that mutual advantage exists in the Internet: perhaps contrary to expectation, that there are not only "haves" and "have nots" of low-latency connectivity. Second, we must provide a scalable means of finding promising edges and overlay routes; we seek embedding error in network coordinates to expose both shorter-than-default "detour" routes and longer-than-expected default routes. We evaluate the cost of limiting PeerWise to mutually advantageous links, then build the intelligent components that put PeerWise into practice. We design and evaluate "virtual" network coordinates for destinations not participating in the overlay, neighbor selection algorithms to find promising relays, and relay selection algorithms to choose the neighbor to traverse for a good detour. Finally, we show that PeerWise is practical through a wide-area deployment and evaluation.}, url = {http://dl.acm.org/citation.cfm?id=1558977.1559009}, author = {Lumezanu,Cristian and Baden,Randy and Levin,Dave and Spring, Neil and Bhattacharjee, Bobby} } @article {18771, title = {A systematic approach for designing multifunctional thermally conducting polymer structures with embedded actuators}, journal = {Journal of Mechanical Design}, volume = {131}, year = {2009}, month = {2009///}, pages = {111009 - 111009}, author = {Bejgerowski,W. and Gupta,S.K. and Bruck,H. A.} } @conference {12318, title = {System-level Clustering and Timing Analysis for GALS-based Dataflow Architectures}, booktitle = {In Proceedings of the ACM International Workshop on Timing Issues in the Specification and Synthesis of Digital Systems, Austin, Texas, February 2009.}, year = {2009}, month = {2009///}, abstract = {In this paper, we propose an approach based ondataflow techniques for modeling application-specific, globally asynchronous, locally synchronous (GALS) architectures for digital signal processing (DSP) applications, and analyzing the performance of such architectures. Dataflow-based techniques are attractive for DSP applications because they allow applica- tion behavior to be represented formally, analyzed at a high level of abstraction, and synthesized to software/hardware implementations through an optimized, automated process. In our proposed methodology, we employ dataflow-based compu- tational models to expose relevant structure in the targeted applications, and facilitate the manual or automatic derivation of efficient implementations. We demonstrate the utility of our modeling and analysis techniques by applying them as core parts of a novel clustering algorithm that is geared towards optimizing the throughput of GALS-based DSP architectures. }, author = {Shen,C. and Bhattacharyya, Shuvra S.} } @conference {12228, title = {Systems-compatible incentives}, booktitle = {Game Theory for Networks, 2009. GameNets {\textquoteright}09. International Conference on}, year = {2009}, month = {2009/05//}, pages = {100 - 106}, abstract = {Selfish participants in a distributed system attempt to gain from the system without regard to how their actions may affect others. To maintain desirable system-wide properties in the presence of selfish users, designers are increasingly turning to the powerful mechanisms offered by economics and game theory. Combining the two fields of economics and systems design introduces new challenges of achieving incentive-compatibility in systems we can deploy in today{\textquoteright}s Internet. In this paper, we explore the interactions between systems and the mechanisms that give users incentives to cooperate. Using findings from recent work on incentive-compatible systems, we discuss several economic mechanisms and assumptions: money, punishment, and altruism. We seek to understand when these mechanisms violate system properties. Among the potential pitfalls we present is a phenomenon we call the price of altruism: altruistic peers can impose a loss of social good in some systems. We also discuss systems-compatible mechanisms that have been used in real, distributed systems, and attempt to extract the underlying design principles that have led to their success.}, keywords = {computing;, incentives;game, Internet;distributed, system;distributed, systems;game, systems;systems-compatible, theory;incentive-compatible, theory;peer-to-peer}, doi = {10.1109/GAMENETS.2009.5137390}, author = {Levin,D. and Spring, Neil and Bhattacharjee, Bobby} } @conference {19045, title = {TACKing Together Efficient Authentication, Revocation, and Privacy in VANETs}, year = {2009}, month = {2009}, pages = {1 - 9}, abstract = {Vehicular ad hoc networks (VANETs) require a mechanism to help authenticate messages, identify valid vehicles, and remove malevolent vehicles. A public key infrastructure (PKI) can provide this functionality using certificates and fixed public keys. However, fixed keys allow an eavesdropper to associate a key with a vehicle and a location, violating drivers{\textquoteright} privacy. In this work we propose a VANET key management scheme based on temporary anonymous certified keys (TACKs). Our scheme efficiently prevents eavesdroppers from linking a vehicle{\textquoteright}s different keys and provides timely revocation of misbehaving participants while maintaining the same or less overhead for vehicle-to-vehicle communication as the current IEEE 1609.2 standard for VANET security.}, keywords = {ad hoc networks, data privacy, eavesdropper, IEEE 1609.2 standard, Message authentication, mobile radio, public key cryptography, public key infrastructure, remove malevolent vehicle, telecommunication security, temporary anonymous certified key, valid vehicle identification, VANET key management, VANET security, vehicle-to-vehicle communication, Vehicles, vehicular ad hoc network}, author = {Studer, A. and Elaine Shi and Bai, Fan and Perrig, A.} } @conference {14658, title = {A theory of typed coercions and its applications}, booktitle = {Proceedings of the 14th ACM SIGPLAN international conference on Functional programming}, series = {ICFP {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {329 - 340}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A number of important program rewriting scenarios can be recast as type-directed coercion insertion. These range from more theoretical applications such as coercive subtyping and supporting overloading in type theories, to more practical applications such as integrating static and dynamically typed code using gradual typing, and inlining code to enforce security policies such as access control and provenance tracking. In this paper we give a general theory of type-directed coercion insertion. We specifically explore the inherent tradeoff between expressiveness and ambiguity--the more powerful the strategy for generating coercions, the greater the possibility of several, semantically distinct rewritings for a given program. We consider increasingly powerful coercion generation strategies, work out example applications supported by the increased power (including those mentioned above), and identify the inherent ambiguity problems of each setting, along with various techniques to tame the ambiguities.}, keywords = {coercion insertion, gradual typing, nonambiguity, provenance, type-directed translation}, isbn = {978-1-60558-332-7}, doi = {10.1145/1596550.1596598}, url = {http://doi.acm.org/10.1145/1596550.1596598}, author = {Swamy,Nikhil and Hicks, Michael W. and Bierman,Gavin M.} } @article {19726, title = {Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.}, journal = {Appl Environ Microbiol}, volume = {75}, year = {2009}, month = {2009 Apr}, pages = {2046-56}, abstract = {

The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.

}, keywords = {Anti-Bacterial Agents, bacteria, Biological Transport, Carbohydrate Metabolism, Cyanobacteria, DNA, Bacterial, Fungi, Genome, Bacterial, Macrolides, Molecular Sequence Data, Nitrogen, Phylogeny, Proteobacteria, Sequence Analysis, DNA, sequence homology, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.02294-08}, author = {Ward, Naomi L and Challacombe, Jean F and Janssen, Peter H and Henrissat, Bernard and Coutinho, Pedro M and Wu, Martin and Xie, Gary and Haft, Daniel H and Sait, Michelle and Badger, Jonathan and Barabote, Ravi D and Bradley, Brent and Brettin, Thomas S and Brinkac, Lauren M and Bruce, David and Creasy, Todd and Daugherty, Sean C and Davidsen, Tanja M and DeBoy, Robert T and Detter, J Chris and Dodson, Robert J and Durkin, A Scott and Ganapathy, Anuradha and Gwinn-Giglio, Michelle and Han, Cliff S and Khouri, Hoda and Kiss, Hajnalka and Kothari, Sagar P and Madupu, Ramana and Nelson, Karen E and Nelson, William C and Paulsen, Ian and Penn, Kevin and Ren, Qinghu and Rosovitz, M J and Jeremy D Selengut and Shrivastava, Susmita and Sullivan, Steven A and Tapia, Roxanne and Thompson, L Sue and Watkins, Kisha L and Yang, Qi and Yu, Chunhui and Zafar, Nikhat and Zhou, Liwei and Kuske, Cheryl R} } @article {18724, title = {Together, Rpn10 and Dsk2 Can Serve as a Polyubiquitin Chain-Length Sensor}, journal = {Molecular Cell}, volume = {36}, year = {2009}, month = {2009/12/24/}, pages = {1018 - 1033}, abstract = {SummaryAs a signal for substrate targeting, polyubiquitin meets various layers of receptors upstream to the 26S proteasome. We obtained structural information on two receptors, Rpn10 and Dsk2, alone and in complex with (poly)ubiquitin or with each other. A~hierarchy of affinities emerges with Dsk2 binding monoubiquitin tighter than Rpn10 does, whereas Rpn10 prefers the ubiquitin-like domain of Dsk2 to monoubiquitin, with increasing affinities for longer polyubiquitin chains. We demonstrated the formation of ternary complexes of both receptors simultaneously with (poly)ubiquitin and found that, depending on the ubiquitin chain length, the orientation of the resulting complex is entirely different, providing for alternate signals. Dynamic rearrangement provides a chain-length sensor, possibly explaining how accessibility of Dsk2 to the proteasome is limited unless it carries a properly tagged cargo. We propose a mechanism for a malleable ubiquitin signal that depends both on chain length and combination of receptors to produce tetraubiquitin as an efficient signal threshold. }, keywords = {Proteins, signaling}, isbn = {1097-2765}, doi = {10.1016/j.molcel.2009.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509008260}, author = {Zhang,Daoning and Chen,Tony and Ziv,Inbal and Rosenzweig,Rina and Matiuhin,Yulia and Bronner,Vered and Glickman,Michael H. and Fushman, David} } @conference {12163, title = {Tool supported detection and judgment of nonconformance in process execution}, booktitle = {Empirical Software Engineering and Measurement, 2009. ESEM 2009. 3rd International Symposium on}, year = {2009}, month = {2009/10//}, pages = {312 - 323}, abstract = {In the past decades the software engineering community has proposed a large collection of software development life cycles, models, and processes. The goal of a major set of these processes is to assure that the product is finished within time and budget, and that a predefined set of functional and nonfunctional requirements (e.g. quality goals) are satisfied at delivery time. Based upon the assumption that there is a real relationship between the process applied and the characteristics of the product developed from that process, we developed a tool supported approach that uses process nonconformance detection to identify potential risks in achieving the required process characteristics. In this paper we present the approach and a feasibility study that demonstrates its use on a large-scale software development project in the aerospace domain. We demonstrate that our approach, in addition to meeting the criteria above, can be applied to a real system of reasonable size; can represent a useful and adequate set of rules of relevance in such an environment; and can detect relevant examples of process nonconformance that provide useful insight to the project manager.}, keywords = {aerospace, community;tool, cycle;software, detection;software, development, domain;large-scale, engineering, execution;process, life, management;software, nonconformance, project;nonfunctional, requirement;process, software, supported, tools;}, doi = {10.1109/ESEM.2009.5315983}, author = {Zazworka, N. and Basili, Victor R. and Shull, F.} } @article {13026, title = {Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study}, journal = {BMC Evol Biol}, volume = {9}, year = {2009}, month = {2009///}, pages = {280 - 280}, abstract = {BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98\% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.}, doi = {10.1186/1471-2148-9-280}, author = {Regier,J. C and Zwick,A. and Cummings, Michael P. and Kawahara,A. Y and Cho,S. and Weller,S. and Roe,A. and Baixeras,J. and Brown,J. W and Parr,C. and Davis,DR and Epstein,M and Hallwachs,W and Hausmann,A and Janzen,DH and Kitching,IJ and Solis,MA and Yen,S-H and Bazinet,A. L and Mitter,C} } @inbook {12235, title = {Triangle Inequality and Routing Policy Violations in the Internet}, booktitle = {Passive and Active Network MeasurementPassive and Active Network Measurement}, series = {Lecture Notes in Computer Science}, volume = {5448}, year = {2009}, month = {2009///}, pages = {45 - 54}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Triangle inequality violations (TIVs) are the effect of packets between two nodes being routed on the longer direct path between them when a shorter detour path through an intermediary is available. TIVs are a natural, widespread and persistent consequence of Internet routing policies. By exposing opportunities to improve the delay between two nodes, TIVs can help myriad applications that seek to minimize end-to-end latency. However, sending traffic along the detour paths revealed by TIVs may influence Internet routing negatively. In this paper we study the interaction between triangle inequality violations and policy routing in the Internet. We use measured and predicted AS paths between Internet nodes to show that 25\% of the detour paths exposed by TIVs are in fact available to BGP but are simply deemed {\textquotedblleft}less efficient{\textquotedblright}. We also compare the AS paths of detours and direct paths and find that detours use AS edges that are rarely followed by default Internet paths, while avoiding others that BGP seems to prefer. Our study is important both for understanding the various interactions that occur at the routing layer as well as their effects on applications that seek to use TIVs to minimize latency.}, keywords = {Computer, Science}, isbn = {978-3-642-00974-7}, url = {http://dx.doi.org/10.1007/978-3-642-00975-4_5}, author = {Lumezanu,Cristian and Baden,Randy and Spring, Neil and Bhattacharjee, Bobby}, editor = {Moon,Sue and Teixeira,Renata and Uhlig,Steve} } @conference {12234, title = {Triangle inequality variations in the internet}, booktitle = {Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference}, series = {IMC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {177 - 183}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Triangle inequality violations (TIVs) are important for latency sensitive distributed applications. On one hand, they can expose opportunities to improve network routing by finding shorter paths between nodes. On the other hand, TIVs can frustrate network embedding or positioning systems that treat the Internet as a metric space where the triangle inequality holds. Even though triangle inequality violations are both significant and curious, their study has been limited to aggregate data sets that combine measurements taken over long periods of time. The limitations of these data sets open crucial questions in the design of systems that exploit (or avoid) TIVs: are TIVs stable or transient? Or are they illusions caused by aggregating measurements taken at different times? We collect latency matrices at varying sizes and time granularities and study dynamic properties of triangle inequality violations in the Internet. We show that TIVs are not results of measurement error and that their number varies with time. We examine how latency aggregates of data measured over longer periods of time preserve TIVs. Using medians to compute violations eliminates most of the TIVs that appear sporadically during the measurement but it misses many of the ones that are present for more than five hours.}, keywords = {latency, tiv, triangle inequality violation, variation}, isbn = {978-1-60558-771-4}, doi = {10.1145/1644893.1644914}, url = {http://doi.acm.org/10.1145/1644893.1644914}, author = {Lumezanu,Cristian and Baden,Randy and Spring, Neil and Bhattacharjee, Bobby} } @article {12233, title = {Understanding the design tradeoffs for cooperative streaming multicast}, year = {2009}, month = {2009///}, institution = {Technical report MPI-SWS-2009-002, Max Planck Institute for Software Systems}, abstract = {Video streaming over the Internet is rapidly increasing in popular-ity, but the availability and quality of the content is limited by the high bandwidth cost for server-based solutions. Cooperative end- system multicast (CEM) has emerged as a promising paradigm for content distribution in the Internet, because the bandwidth over- head of disseminating content is shared among the participants of the CEM overlay network. Several CEM systems have been pro- posed and deployed, but the tradeoffs inherent in the different de- signs are not well understood. In this work, we provide a common framework in which different CEM design choices can be empirically and systematically evalu- ated. Our results show that all CEM protocols are inherently lim- ited in certain aspects of their performance. We distill our observa- tions into a novel model that explains the inherent tradeoffs of CEM design choices and provides bounds on the practical performance limits of any future CEM protocol. In particular, the model conjec- tures that no CEM design can simultaneously achieve all three of low overhead, low lag, and high streaming quality. }, author = {Nandi,A. and Bhattacharjee, Bobby and Druschel,P.} } @article {12162, title = {The Use of Empirical Studies in the Development of High End Computing Applications}, year = {2009}, month = {2009/12//}, institution = {University of Maryland, College Park}, abstract = {This report provides a description of the research and development activities towards learning much about the development and measurement of productivity in high performance computing environments. Many objectives were accomplished including the development of a methodology for measuring productivity in the parallel programming domain. This methodology was tested over 25 times at 8 universities across the United States and can be used to aid other researchers studying similar environments. The productivity measurement methodology incorporates both development time and performance into a single productivity number. An Experiment Manager tool for collecting data on the development of parallel programs, as well as a suite of tools to aid in the capture and analysis of such data was also developed. Lastly, several large scale development environments were studied in order to better understand the environment used to build large parallel programming applications. That work also included several surveys and interviews with many professional programmers in these environments.}, keywords = {*COMPUTER PROGRAMMING, *EMPIRICAL STUDIES, *HPC(HIGH PERFORMANCE COMPUTING), *METHODOLOGY, *PARALLEL PROCESSING, *PARALLEL PROGRAMMING, *PRODUCTIVITY, *SOFTWARE ENGINEERING, *SOFTWARE METRICS, ADMINISTRATION AND MANAGEMENT, APMS(AUTOMATED PERFORMANCE MEASUREMENT SYSTEM), COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER SYSTEMS MANAGEMENT AND STANDARDS, data acquisition, efficiency, ENVIRONMENTS, HIGH END COMPUTING, HPCBUGBASE, HUMAN FACTORS ENGINEERING \& MAN MACHINE SYSTEM, learning, measurement, MPI(MESSAGE PASSING INTERFACE), PARALLEL ORIENTATION, PE62303E, PROGRAMMERS, SE(SOFTWARE ENGINEERING), SUPERVISORS, TEST AND EVALUATION, TEST FACILITIES, EQUIPMENT AND METEORS, TIME, tools, United States, WUAFRLT810HECA}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA511351}, author = {Basili, Victor R. and Zelowitz,Marvin V} } @article {12846, title = {Using formal specifications to support testing}, journal = {ACM Computing Surveys}, volume = {41}, year = {2009}, month = {2009/02/01/}, pages = {1 - 76}, isbn = {03600300}, doi = {10.1145/1459352.1459354}, url = {http://dl.acm.org/citation.cfm?id=1459352.1459354}, author = {Hierons,Robert M. and Krause,Paul and L{\"u}ttgen,Gerald and Simons,Anthony J. H. and Vilkomir,Sergiy and Woodward,Martin R. and Zedan,Hussein and Bogdanov,Kirill and Bowen,Jonathan P. and Cleaveland, Rance and Derrick,John and Dick,Jeremy and Gheorghe,Marian and Harman,Mark and Kapoor,Kalpesh} } @conference {12167, title = {Using uncertainty as a model selection and comparison criterion}, booktitle = {Proceedings of the 5th International Conference on Predictor Models in Software Engineering}, series = {PROMISE {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {18:1{\textendash}18:9 - 18:1{\textendash}18:9}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Over the last 25+ years, software estimation research has been searching for the best model for estimating variables of interest (e.g., cost, defects, and fault proneness). This research effort has not lead to a common agreement. One problem is that, they have been using accuracy as the basis for selection and comparison. But accuracy is not invariant; it depends on the test sample, the error measure, and the chosen error statistics (e.g., MMRE, PRED, Mean and Standard Deviation of error samples). Ideally, we would like an invariant criterion. In this paper, we show that uncertainty can be used as an invariant criterion to figure out which estimation model should be preferred over others. The majority of this work is empirically based, applying Bayesian prediction intervals to some COCOMO model variations with respect to a publicly available cost estimation data set coming from the PROMISE repository.}, keywords = {accuracy, Bayesian prediction intervals, Calibration, cost estimation, cost model, model evaluation, model selection, prediction interval, Uncertainty}, isbn = {978-1-60558-634-2}, doi = {10.1145/1540438.1540464}, url = {http://doi.acm.org/10.1145/1540438.1540464}, author = {Sarcia{\textquoteright},Salvatore Alessandro and Basili, Victor R. and Cantone,Giovanni} } @article {12538, title = {Video-Based Face Recognition Algorithms}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {193 - 216}, abstract = {Traditional face recognition systems have relied on a gallery of still images for learning and a probe of still images for recognition. While the advantage of using motion information in face videos has been widely recognized, computational models for video-based face recognition have only recently gained attention. This chapter reviews some recent advances in this novel framework. In particular, the utility of videos in enhancing performance of image-based tasks (such as recognition or localization) will be summarized. Subsequently, spatiotemporal video-based face recognition systems based on particle filters, hidden Markov models , and system theoretic approaches will be presented. Further, some useful face databases employable by researchers interested in this field will be described. Finally, some open research issues will be proposed and discussed.}, author = {Chellapa, Rama and Bicego, M. and Turaga,P.} } @conference {14849, title = {Visibility constraints on features of 3D objects}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {1231 - 1238}, abstract = {To recognize three-dimensional objects it is important to model how their appearances can change due to changes in viewpoint. A key aspect of this involves understanding which object features can be simultaneously visible under different viewpoints. We address this problem in an image-based framework, in which we use a limited number of images of an object taken from unknown viewpoints to determine which subsets of features might be simultaneously visible in other views. This leads to the problem of determining whether a set of images, each containing a set of features, is consistent with a single 3D object. We assume that each feature is visible from a disk of viewpoints on the viewing sphere. In this case we show the problem is NP-hard in general, but can be solved efficiently when all views come from a circle on the viewing sphere. We also give iterative algorithms that can handle noisy data and converge to locally optimal solutions in the general case. Our techniques can also be used to recover viewpoint information from the set of features that are visible in different images. We show that these algorithms perform well both on synthetic data and images from the COIL dataset.}, keywords = {3D, algorithms;synthetic, complexity;iterative, constraints;computational, data;synthetic, dataset;NP-hard;image-based, features;COIL, framework;iterative, images;three-dimensional, methods;object, object, recognition;, recognition;viewing, sphere;visibility}, doi = {10.1109/CVPR.2009.5206726}, author = {Basri,R. and Felzenszwalb,P. F and Girshick,R. B and Jacobs, David W. and Klivans,C. J} } @article {13105, title = {Visual Tag}, volume = {12/533,231}, year = {2009}, month = {2009/07//}, abstract = {An improved animal tag for application to an animal{\textquoteright}s ear which comprises a male portion that includes a flat segment and a projection segment, a female portion that includes a generally square or generally oval shaped flat segment and a raised segment with an aperture; wherein the projection segment of the male portion is adapted to be inserted through the animal{\textquoteright}s ear and into the aperture when pressure is applied thereto.}, url = {http://www.google.com/patents?id=ZXTTAAAAEBAJ}, author = {BRETEY,STEVE and Kuhnly,Keith and Davis, Larry S.} } @article {12225, title = {What a mesh: understanding the design tradeoffs for streaming multicast}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {37}, year = {2009}, month = {2009/10//}, pages = {85 - 86}, abstract = {Cooperative end-system multicast (CEM) is a promising paradigm for Internet video distribution. Several CEM systems have been proposed and deployed, but the tradeoffs inherent in the different designs are not well understood. In this work, we provide a common framework in which different CEM design choices can be empirically and systematically evaluated. Based on our results, we conjecture that all CEM systems must abide by a set of fundamental design constraints, which we express in a simple model. By necessity, existing system implementations couple the data- and control-planes and often use different transport protocols.}, isbn = {0163-5999}, doi = {10.1145/1639562.1639598}, url = {http://doi.acm.org/10.1145/1639562.1639598}, author = {Nandi,Animesh and Bhattacharjee, Bobby and Druschel,Peter} } @article {18544, title = {Accountable internet protocol (aip)}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {38}, year = {2008}, month = {2008/08//}, pages = {339 - 350}, abstract = {This paper presents AIP (Accountable Internet Protocol), a network architecture that provides accountability as a first-order property. AIP uses a hierarchy of self-certifying addresses, in which each component is derived from the public key of the corresponding entity. We discuss how AIP enables simple solutions to source spoofing, denial-of-service, route hijacking, and route forgery. We also discuss how AIP{\textquoteright}s design meets the challenges of scaling, key management, and traffic engineering.}, keywords = {accountability, address, internet architecture, scalability, Security}, isbn = {0146-4833}, doi = {10.1145/1402946.1402997}, url = {http://doi.acm.org/10.1145/1402946.1402997}, author = {Andersen,David G. and Balakrishnan,Hari and Feamster, Nick and Koponen,Teemu and Moon,Daekyeong and Shenker,Scott} } @article {13874, title = {The acl anthology reference corpus: A reference dataset for bibliographic research in computational linguistics}, journal = {Proc. of the 6th International Conference on Language Resources and Evaluation Conference (LREC{\textquoteright}08)}, year = {2008}, month = {2008///}, pages = {1755 - 1759}, abstract = {The ACL Anthology is a digital archive of conference and journal papers in natural language processing and computational linguistics.Its primary purpose is to serve as a reference repository of research results, but we believe that it can also be an object of study and a platform for research in its own right. We describe an enriched and standardized reference corpus derived from the ACL Anthology that can be used for research in scholarly document processing. This corpus, which we call the ACL Anthology Reference Corpus (ACL ARC), brings together the recent activities of a number of research groups around the world. Our goal is to make the corpus widely available, and to encourage other researchers to use it as a standard testbed for experiments in both bibliographic and bibliometric research. }, author = {Bird,S. and Dale,R. and Dorr, Bonnie J and Gibson,B. and Joseph,M.T. and Kan,M.Y. and Lee,D. and Powley,B. and Radev,D.R. and Tan,Y.F.} } @conference {12111, title = {Adopting Curvilinear Component Analysis to Improve Software Cost Estimation Accuracy. Model, Application Strategy, and an Experimental Verification}, booktitle = {In G. Visaggio (Ed.), 12 th International Conference on Evaluation and Assessment in Software Engineering. BCS eWIC}, year = {2008}, month = {2008///}, abstract = {Cost estimation is a critical issue for software organizations. Good estimates can help us make more informed decisions (controlling and planning software risks), if they are reliable (correct) and valid (stable). In this study, we apply a variable reduction technique (based on auto-associative feed--forward neural networks {\textendash} called Curvilinear component analysis) to log-linear regression functions calibrated with ordinary least squares. Based on a COCOMO 81 data set, we show that Curvilinear component analysis can improve the estimation model accuracy by turning the initial input variables into an equivalent and more compact representation. We show that, the models obtained by applying Curvilinear component analysis are more parsimonious, correct, and reliable.}, author = {Sarcia,Salvatore A. and Cantone,Giovanni and Basili, Victor R.} } @conference {17998, title = {An area-efficient high-throughput hybrid interconnection network for single-chip parallel processing}, booktitle = {Proceedings of the 45th annual Design Automation Conference}, series = {DAC {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {435 - 440}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Single-chip parallel processing requires high bandwidth between processors and on-chip memory modules. A recently proposed Mesh-of-Trees (MoT) network provides high throughput and low latency at relatively high area cost. In this paper, we introduce a hybrid MoT-BF network that combines MoT network with the area efficient butterfly network. We prove that the hybrid network reduces MoT network{\textquoteright}s area cost. Cycle-accurate simulation and post-layout results all show that significant area reduction can be achieved with negligible performance degradation, when operating at same clock rate.}, keywords = {hybrid networks, mesh-of-trees, on-chip networks}, isbn = {978-1-60558-115-6}, doi = {10.1145/1391469.1391583}, url = {http://doi.acm.org/10.1145/1391469.1391583}, author = {Balkan,Aydin O. and Gang Qu and Vishkin, Uzi} } @article {12158, title = {The ASC-Alliance Projects: A Case Study of Large-Scale Parallel Scientific Code Development}, journal = {Computer}, volume = {41}, year = {2008}, month = {2008/03//}, pages = {50 - 58}, abstract = {Computational scientists face many challenges when developing software that runs on large-scale parallel machines. However, software-engineering researchers haven{\textquoteright}t studied their software development processes in much detail. To better understand the nature of software development in this context, the authors examined five large-scale computational science software projects operated at the five ASC-Alliance centers.}, keywords = {ASC-Alliance, code, development;large-scale, development;parallel, engineering;, machines;software, Parallel, projects;computational, scale, Science, scientific, scientists;large, software, systems;parallel}, isbn = {0018-9162}, doi = {10.1109/MC.2008.101}, author = {Hochstein, L. and Basili, Victor R.} } @article {12112, title = {An assessment of systems and software engineering scholars and institutions (2001{\textendash}2005)}, journal = {Journal of Systems and Software}, volume = {81}, year = {2008}, month = {2008/06//}, pages = {1059 - 1062}, abstract = {This paper presents the findings of a five-year study of the top scholars and institutions in the systems and software engineering field, as measured by the quantity of papers published in the journals of the field in 2001{\textendash}2005. The top scholar is Magne J{\o}rgensen of Simula Research Laboratory, Norway, and the top institution is Korea Advanced Institute of Science and Technology, Korea.This paper is part of an ongoing study, conducted annually, that identifies the top 15 scholars and institutions in the most recent five-year period. }, keywords = {Research publications, Systems and software engineering, Top institutions, Top scholars}, isbn = {0164-1212}, doi = {10.1016/j.jss.2007.09.018}, url = {http://www.sciencedirect.com/science/article/pii/S0164121207002300}, author = {Wong,W. Eric and Tse,T.H. and Glass,Robert L. and Basili, Victor R. and Chen,T.Y.} } @conference {16073, title = {BELIV{\textquoteright}08: Beyond time and errors: novel evaluation methods for information visualization}, booktitle = {CHI {\textquoteright}08 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {3913 - 3916}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Information visualization systems allow users to produce insights, innovations and discoveries. Evaluating such tools is a challenging task and the goal of BELIV{\textquoteright}08 is to make a step ahead in the comprehension of such a complex activity. Current evaluation methods exhibit noticeable limitations and researchers in the area experiment some frustration with evaluation processes that are time consuming and too often leading to unsatisfactory results. The most used evaluation metrics such as task time completion and number of errors appear insufficient to quantify the quality of an information visualization system; thus the name of the workshop: "beyond time and errors".}, keywords = {Evaluation, Information Visualization}, isbn = {978-1-60558-012-8}, doi = {10.1145/1358628.1358955}, url = {http://doi.acm.org/10.1145/1358628.1358955}, author = {Bertini,Enrico and Perer,Adam and Plaisant, Catherine and Santucci,Giuseppe} } @conference {14205, title = {Bilateral symmetry of object silhouettes under perspective projection}, booktitle = {19th International Conference on Pattern Recognition, 2008. ICPR 2008}, year = {2008}, month = {2008/12/08/11}, pages = {1 - 4}, publisher = {IEEE}, organization = {IEEE}, abstract = {Symmetry is an important property of objects and is exhibited in different forms e.g., bilateral, rotational, etc. This paper presents an algorithm for computing the bilateral symmetry of silhouettes of shallow objects under perspective distortion, exploiting the invariance of the cross ratio to projective transformations. The basic idea is to use the cross ratio to compute a number of midpoints of cross sections and then fit a straight line through them. The goodness-of-fit determines the likelihood of the line to be the axis of symmetry. We analytically estimate the midpointpsilas location as a function of the vanishing point for a given object silhouette. Hence finding the symmetry axis amounts to a 2D search in the space of vanishing points. We present experiments on two datasets as well as Internet images of symmetric objects that validate our approach.}, keywords = {Automation, bilateral symmetry, Computer vision, Frequency, Image analysis, Image coding, Image reconstruction, Internet, Internet images, Object detection, object silhouettes, perspective distortion, perspective projection, SHAPE, symmetric objects}, isbn = {978-1-4244-2174-9}, doi = {10.1109/ICPR.2008.4761501}, author = {Bitsakos,K. and Yi,H. and Yi,L. and Ferm{\"u}ller, Cornelia} } @conference {12246, title = {Bittorrent is an auction: analyzing and improving bittorrent{\textquoteright}s incentives}, booktitle = {Proceedings of the ACM SIGCOMM 2008 conference on Data communication}, series = {SIGCOMM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {243 - 254}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Incentives play a crucial role in BitTorrent, motivating users to upload to others to achieve fast download times for all peers. Though long believed to be robust to strategic manipulation, recent work has empirically shown that BitTorrent does not provide its users incentive to follow the protocol. We propose an auction-based model to study and improve upon BitTorrent{\textquoteright}s incentives. The insight behind our model is that BitTorrent uses, not tit-for-tat as widely believed, but an auction to decide which peers to serve. Our model not only captures known, performance-improving strategies, it shapes our thinking toward new, effective strategies. For example, our analysis demonstrates, counter-intuitively, that BitTorrent peers have incentive to intelligently under-report what pieces of the file they have to their neighbors. We implement and evaluate a modification to BitTorrent in which peers reward one another with proportional shares of bandwidth. Within our game-theoretic model, we prove that a proportional-share client is strategy-proof. With experiments on PlanetLab, a local cluster, and live downloads, we show that a proportional-share unchoker yields faster downloads against BitTorrent and BitTyrant clients, and that under-reporting pieces yields prolonged neighbor interest.}, keywords = {auctions, bittorrent, incentive systems, proportional share, tit-for-tat}, isbn = {978-1-60558-175-0}, doi = {10.1145/1402958.1402987}, url = {http://doi.acm.org/10.1145/1402958.1402987}, author = {Levin,Dave and LaCurts,Katrina and Spring, Neil and Bhattacharjee, Bobby} } @article {14375, title = {Collective Classification in Network Data}, journal = {AI Magazine}, volume = {29}, year = {2008}, month = {2008/09/06/}, pages = {93 - 93}, abstract = {Collective Classification in Network Data}, isbn = {0738-4602}, doi = {10.1609/aimag.v29i3.2157}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/2157}, author = {Sen,Prithviraj and Namata,Galileo and Bilgic,Mustafa and Getoor, Lise and Galligher,Brian and Eliassi-Rad,Tina} } @conference {18681, title = {On the Comparison of Network Attack Datasets: An Empirical Analysis}, year = {2008}, month = {2008/12//}, pages = {39 - 48}, abstract = {Network malicious activity can be collected and reported by various sources using different attack detection solutions. The granularity of these solutions provides either very detailed information (intrusion detection systems, honeypots) or high-level trends (CAIDA, SANS). The problem for network security operators is often to select the sources of information to better protect their network. How much information from these sources is redundant and how much is unique? The goal of this paper is to show empirically that while some global attack events can be correlated across various sensors, the majority of incoming malicious activity has local specificities. This study presents a comparative analysis of four different attack datasets offering three different levels of granularity: 1) two high interaction honeynets deployed at two different locations (i.e., a corporate and an academic environment); 2) ATLAS which is a distributed network telescope from Arbor; and 3) Internet Protecttrade which is a global alerting service from AT amp;T.}, keywords = {ATLAS, distributed network telescope, Internet, intrusion detection systems, network attack datasets, network malicious activity, network security operators, security of data}, doi = {10.1109/HASE.2008.50}, author = {Berthier,R. and Korman,D. and Michel Cukier and Hiltunen,M. and Vesonder,G. and Sheleheda,D.} } @article {12898, title = {The Complete Genome Sequence of Thermococcus Onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism}, journal = {Journal of BacteriologyJ. Bacteriol.}, volume = {190}, year = {2008}, month = {2008/11/15/}, pages = {7491 - 7499}, abstract = {Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus.}, isbn = {0021-9193, 1098-5530}, doi = {10.1128/JB.00746-08}, url = {http://jb.asm.org/content/190/22/7491}, author = {Lee,Hyun Sook and Kang,Sung Gyun and Bae,Seung Seob and Lim,Jae Kyu and Cho,Yona and Kim,Yun Jae and Jeon,Jeong Ho and Cha,Sun-Shin and Kwon,Kae Kyoung and Kim,Hyung-Tae and Park,Cheol-Joo and Lee,Hee-Wook and Kim,Seung Il and Jongsik Chun and Rita R Colwell and Kim,Sang-Jin and Lee,Jung-Hyun} } @article {12569, title = {Compressive sensing for background subtraction}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {155 - 168}, abstract = {Compressive sensing (CS) is an emerging field that provides a framework for image recovery using sub-Nyquist sampling rates. The CS theory shows that a signal can be reconstructed from a small set of random projections, provided that the signal is sparse in some basis, e.g., wavelets. In this paper, we describe a method to directly recover background subtracted images using CS and discuss its applications in some communication constrained multi-camera computer vision problems. We show how to apply the CS theory to recover object silhouettes (binary background subtracted images) when the objects of interest occupy a small portion of the camera view, i.e., when they are sparse in the spatial domain. We cast the background subtraction as a sparse approximation problem and provide different solutions based on convex optimization and total variation. In our method, as opposed to learning the background, we learn and adapt a low dimensional compressed representation of it, which is sufficient to determine spatial innovations; object silhouettes are then estimated directly using the compressive samples without any auxiliary image reconstruction. We also discuss simultaneous appearance recovery of the objects using compressive measurements. In this case, we show that it may be necessary to reconstruct one auxiliary image. To demonstrate the performance of the proposed algorithm, we provide results on data captured using a compressive single-pixel camera. We also illustrate that our approach is suitable for image coding in communication constrained problems by using data captured by multiple conventional cameras to provide 2D tracking and 3D shape reconstruction results with compressive measurements.}, author = {Cevher, V. and Sankaranarayanan, A. and Duarte, M. and Reddy, D. and Baraniuk, R. and Chellapa, Rama} } @article {18823, title = {Content-based assembly search: A step towards assembly reuse}, journal = {Computer-Aided Design}, volume = {40}, year = {2008}, month = {2008/02//}, pages = {244 - 261}, abstract = {The increased use of CAD systems by product development organizations has resulted in the creation of large databases of assemblies. This explosion of assembly data is likely to continue in the future. In many situations, a text-based search alone may not be sufficient to search for assemblies and it may be desirable to search for assemblies based on the content of the assembly models. The ability to perform content-based searches on these databases is expected to help the designers in the following two ways. First, it can facilitate the reuse of existing assembly designs, thereby reducing the design time. Second, a lot of useful designs for manufacturing, and assembly knowledge are implicitly embedded in existing assemblies. Therefore a capability to locate existing assemblies and examine them can be used as a learning tool by designers to learn from the existing assembly designs. This paper describes a system for performing content-based searches on assembly databases. We identify templates for comprehensive search definitions and describe algorithms to perform content-based searches for mechanical assemblies. We also illustrate the capabilities of our system through several examples.}, keywords = {Assembly characteristics, Assembly mating conditions, Content-based assembly search, Graph compatibility}, isbn = {0010-4485}, doi = {10.1016/j.cad.2007.10.012}, url = {http://www.sciencedirect.com/science/article/pii/S0010448507002424}, author = {Deshmukh,Abhijit S. and Banerjee,Ashis Gopal and Gupta, Satyandra K. and Sriram,Ram D.} } @article {12127, title = {CrossTalk: The Journal of Defense Software Engineering. Volume 21, Number 10, October 2008}, year = {2008}, month = {2008///}, institution = {DTIC Document}, author = {Basili, Victor R. and Dangle,K. and Esker,L. and Marotta,F. and Rus,I. and Brosgol,B. M and Jamin,S. and Arthur,J. D and Ravichandar,R. and Wisnosky,D. E} } @conference {18692, title = {The Deployment of a Darknet on an Organization-Wide Network: An Empirical Analysis}, year = {2008}, month = {2008/12//}, pages = {59 - 68}, abstract = {Darknet sensors have the interesting property of collecting only suspicious traffic, including misconfiguration, backscatter and malicious traffic. The type of traffic collected highly depends on two parameters: the size and the location of the darknet sensor. The goals of this paper are to study empirically the relationship between these two parameters and to try to increase the volume of attackers detected by a given darknet sensor. Our empirical results reveal that on average, on a daily basis, 485 distinct external source IP addresses perform a TCP scan on one of the two /16 networks of our organizationpsilas network. Moreover, a given darknet sensor of 77 IP addresses deployed in the same /16 network collects on average attack traffic from 26\% of these attackers.}, keywords = {attack traffic, backscatter, darknet sensors, external source IP address, malicious traffic, organization network, organization-wide network, TCP scan, telecommunication congestion control, transmission control protocol, Transport protocols}, doi = {10.1109/HASE.2008.54}, author = {Berthier,R. and Michel Cukier} } @article {18768, title = {Development of a multi-piece multi-gate mold for manufacturing a flapping wing drive-mechanism}, journal = {Transactions of North American Manufacturing Research Institution of SME}, volume = {36}, year = {2008}, month = {2008///}, abstract = {Successful realization a flapping wing microair vehicle (MAV) requires development of a light weight drive-mechanism that can convert the continuous rotary motion to oscillatory flapping motion. Molded compliant drive-mechanisms are an attractive design option because of manufacturing scalability and reduction in the number of parts. The unique characteristics of this mechanism require development of a complex multi-piece multi-gate mold design. This paper describes a systematic approach for determining the part shape and size, optimizing the mold pieces, and placing the gates on the multi-piece mold. The novel aspects of this work include (1) selecting non-critical shape features to optimize the mold design and (2) the use of sacrificial structural elements to reduce the impact of the weld lines on the structural performance. The mold developed using our approach was utilized to realize a working flapping wing MAV. }, url = {http://web.mit.edu/arvinda/www/NAMRI_2008_Draft.pdf}, author = {Ananthanarayanan,A. and Bejgerowski,W. and Mueller,D. and Gupta,S.K.} } @article {17519, title = {Discarte: a disjunctive internet cartographer}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {38}, year = {2008}, month = {2008///}, pages = {303 - 314}, author = {Sherwood,R. and Bender,A. and Spring, Neil} } @article {14681, title = {Dynamic Rebinding for Marshalling and Update, Via Redex-Time and Destruct-Time Reduction}, journal = {Journal of Functional Programming}, volume = {18}, year = {2008}, month = {2008///}, pages = {437 - 502}, abstract = {Most programming languages adopt static binding, but for distributed programming an exclusive reliance on static binding is too restrictive: dynamic binding is required in various guises, for example, when a marshalled value is received from the network, containing identifiers that must be rebound to local resources. Typically, it is provided only by ad hoc mechanisms that lack clean semantics. In this paper, we adopt a foundational approach, developing core dynamic rebinding mechanisms as extensions to the simply typed call-by-value λ calculus. To do so, we must first explore refinements of the call-by-value reduction strategy that delay instantiation, to ensure computations make use of the most recent versions of rebound definitions. We introduce redex-time and destruct-time strategies. The latter forms the basis for a λmarsh calculus that supports dynamic rebinding of marshalled values, while remaining as far as possible statically typed. We sketch an extension of λmarsh with concurrency and communication, giving examples showing how wrappers for encapsulating untrusted code can be expressed. Finally, we show that a high-level semantics for dynamic updating can also be based on the destruct-time strategy, defining a λupdate calculus with simple primitives to provide type-safe updating of running code. We show how the ideas of this simple calculus extend to more real-world, module-level dynamic updating in the style of Erlang. We thereby establish primitives and a common semantic foundation for a variety of real-world dynamic rebinding requirements.}, doi = {10.1017/S0956796807006600}, author = {Sewell,Peter and Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Wansbrough,Keith} } @conference {14443, title = {Effective label acquisition for collective classification}, booktitle = {Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining}, series = {KDD {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {43 - 51}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Information diffusion, viral marketing, and collective classification all attempt to model and exploit the relationships in a network to make inferences about the labels of nodes. A variety of techniques have been introduced and methods that combine attribute information and neighboring label information have been shown to be effective for collective labeling of the nodes in a network. However, in part because of the correlation between node labels that the techniques exploit, it is easy to find cases in which, once a misclassification is made, incorrect information propagates throughout the network. This problem can be mitigated if the system is allowed to judiciously acquire the labels for a small number of nodes. Unfortunately, under relatively general assumptions, determining the optimal set of labels to acquire is intractable. Here we propose an acquisition method that learns the cases when a given collective classification algorithm makes mistakes, and suggests acquisitions to correct those mistakes. We empirically show on both real and synthetic datasets that this method significantly outperforms a greedy approximate inference approach, a viral marketing approach, and approaches based on network structural measures such as node degree and network clustering. In addition to significantly improving accuracy with just a small amount of labeled data, our method is tractable on large networks.}, keywords = {active inference, collective classification, label acquisition}, isbn = {978-1-60558-193-4}, doi = {10.1145/1401890.1401901}, url = {http://doi.acm.org/10.1145/1401890.1401901}, author = {Bilgic,Mustafa and Getoor, Lise} } @article {12239, title = {Efficient and Resilient Backbones for Multihop Wireless Networks}, journal = {Mobile Computing, IEEE Transactions on}, volume = {7}, year = {2008}, month = {2008/11//}, pages = {1349 - 1362}, abstract = {We consider the problem of finding "backbones" in multihop wireless networks. The backbone provides end-to-end connectivity, allowing nonbackbone nodes to save energy since they do not have to route nonlocal data or participate in the routing protocol. Ideally, such a backbone would be small, consist primarily of high capacity nodes, and remain connected even when nodes are mobile or fail. Unfortunately, it is often infeasible to construct a backbone that has all of these properties; e.g., a small optimal backbone is often too sparse to handle node failures or high mobility. We present a parameterized backbone construction algorithm that permits explicit trade-offs between backbone size, resilience to node movement and failure, energy consumption, and path lengths. We prove that our scheme can construct essentially best possible backbones (with respect to energy consumption and backbone size) when the network is relatively static. We generalize our scheme to build more robust structures better suited to networks with higher mobility. We present a distributed protocol based upon our algorithm and show that this protocol builds and maintains a connected backbone in dynamic networks. Finally, we present detailed packet-level simulation results to evaluate and compare our scheme with existing energy-saving techniques. Our results show that, depending on the network environment, our scheme increases network lifetimes by 20 percent to 220 percent without adversely affecting delivery ratio or end-to-end latency.}, keywords = {algorithm;protocols;wireless, backbone, channels;, CONSTRUCTION, distributed, networks;parameterized, protocol;multihop, wireless}, isbn = {1536-1233}, doi = {10.1109/TMC.2008.69}, author = {Lee,Seungjoon and Bhattacharjee, Bobby and Srinivasan, Aravind and Khuller, Samir} } @inbook {13365, title = {Energy Efficient Monitoring in Sensor Networks}, booktitle = {LATIN 2008: Theoretical InformaticsLATIN 2008: Theoretical Informatics}, series = {Lecture Notes in Computer Science}, volume = {4957}, year = {2008}, month = {2008///}, pages = {436 - 448}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper we study a set of problems related to efficient energy management for monitoring applications in wireless sensor networks. We study several generalizations of a basic problem called Set k -Cover, which can be described as follows: we are given a set of sensors, and a set of regions to be monitored. Each region can be monitored by a subset of the sensors. To increase the lifetime of the sensor network, we would like to partition the sensors into k sets (or time-slots) and activate each partition in a different time-slot. The goal is to find the partitioning that maximizes the coverage of the regions. This problem is known to be NP -hard. We first develop improved approximation algorithms for this problem based on its similarities to the max k -cut problem. We then consider a variation, called Set ( k , α )-cover, where each sensor is allowed to be active in α different time-slots. We develop a randomized routing algorithm for this problem. We then consider extensions where each sensor can monitor only a bounded number of regions in any time-slot. We develop the first approximation algorithms for this problem. An experimental evaluation of the algorithms we propose can be found in the full version of the paper.}, isbn = {978-3-540-78772-3}, url = {http://dx.doi.org/10.1007/978-3-540-78773-0_38}, author = {Deshpande, Amol and Khuller, Samir and Malekian,Azarakhsh and Toossi,Mohammed}, editor = {Laber,Eduardo and Bornstein,Claudson and Nogueira,Loana and Faria,Luerbio} } @article {16063, title = {Enhancing In-Car Navigation Systems with Personal Experience}, journal = {Transportation Research Record: Journal of the Transportation Research Board}, volume = {2064}, year = {2008}, month = {2008/12/01/}, pages = {33 - 42}, abstract = {Computers are extremely powerful for data processing but less adept at handling problems that involve subjective reasoning. People, on the other hand, are good at such tasks. A framework is presented for adding subjective human experience to in-car navigation systems. People often rely on personal experience when planning trips, choosing the route that is fastest, prettiest, or recommended by a friend. A set of methods was developed to help people record personal driving history, add textual annotations describing subjective experiences, and share data with friends and family or even the broader community. Users can then learn from personal data or harness the multiplicity of individual experiences to enjoy new routes. This approach can be used in conjunction with traditional in-car navigation systems.}, doi = {10.3141/2064-06}, url = {http://dx.doi.org/10.3141/2064-06}, author = {Bederson, Benjamin B. and Clamage,Aaron and Plaisant, Catherine} } @inbook {12117, title = {An Environment for Conducting Families of Software Engineering Experiments}, booktitle = {Software Development}, volume = {Volume 74}, year = {2008}, month = {2008///}, pages = {175 - 200}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. Understanding how to run such experiments, developing procedures to collect accurate data, and collecting data that is consistent across multiple studies are major problems. This paper describes an environment, the Experiment Manager that simplifies the process of collecting, managing, and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages in the high-performance computing domain on programmer productivity at multiple universities across the United States.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245808006050}, author = {Hochstein, Lorin and Nakamura,Taiga and Shull, Forrest and Zazworka, Nico and Basili, Victor R. and Zelkowitz, Marvin V}, editor = {Zelkowitz, Marvin V} } @article {12913, title = {Environmental signatures associated with cholera epidemics}, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, year = {2008}, month = {2008///}, pages = {17676 - 17676}, abstract = {The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998{\textendash}2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing }, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0809654105}, url = {http://www.pnas.org/content/105/46/17676}, author = {Constantin de Magny,G. and Murtugudde,R. and Sapiano,M. R. P. and Nizam,A. and Brown,C. W. and Busalacchi,A. J. and Yunus,M. and Nair,G. B. and Gil,A. I. and Lanata,C. F. and Rita R Colwell} } @article {12908, title = {Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons}, journal = {FEMS Microbiology Ecology}, volume = {64}, year = {2008}, month = {2008/04/01/}, pages = {45 - 54}, abstract = {Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002{\textendash}2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly β-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates.}, keywords = {ICE, integron, Mozambique, Vibrio}, isbn = {1574-6941}, doi = {10.1111/j.1574-6941.2008.00455.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2008.00455.x/full}, author = {Taviani,Elisa and Ceccarelli,Daniela and Lazaro,Nivalda and Bani,Stefania and Cappuccinelli,Piero and Rita R Colwell and Colombo,Mauro M.} } @inbook {12996, title = {Expanding the reach of Grid computing: combining Globus- and BOINC-based systems}, booktitle = {Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology}, series = {Wiley Book Series on Bioinformatics: Computational Techniques and Engineering}, year = {2008}, month = {2008///}, pages = {71 - 85}, publisher = {Wiley-Interscience}, organization = {Wiley-Interscience}, address = {Hoboken}, author = {Myers,D. S and Bazinet,A. L and Cummings, Michael P.}, editor = {Talbi,E-G and Zomaya,AY} } @article {16396, title = {Exurbia from the bottom-up: Confronting empirical challenges to characterizing a complex system}, journal = {Geoforum}, volume = {39}, year = {2008}, month = {2008/03//}, pages = {805 - 818}, abstract = {We describe empirical results from a multi-disciplinary project that support modeling complex processes of land-use and land-cover change in exurban parts of Southeastern Michigan. Based on two different conceptual models, one describing the evolution of urban form as a consequence of residential preferences and the other describing land-cover changes in an exurban township as a consequence of residential preferences, local policies, and a diversity of development types, we describe a variety of empirical data collected to support the mechanisms that we encoded in computational agent-based models. We used multiple methods, including social surveys, remote sensing, and statistical analysis of spatial data, to collect data that could be used to validate the structure of our models, calibrate their specific parameters, and evaluate their output. The data were used to investigate this system in the context of several themes from complexity science, including have (a) macro-level patterns; (b) autonomous decision making entities (i.e., agents); (c) heterogeneity among those entities; (d) social and spatial interactions that operate across multiple scales and (e) nonlinear feedback mechanisms. The results point to the importance of collecting data on agents and their interactions when producing agent-based models, the general validity of our conceptual models, and some changes that we needed to make to these models following data analysis. The calibrated models have been and are being used to evaluate landscape dynamics and the effects of various policy interventions on urban land-cover patterns.}, keywords = {Ecological effects, Land-cover change, Land-use change, spatial modeling, Urban sprawl}, isbn = {0016-7185}, doi = {10.1016/j.geoforum.2007.02.010}, url = {http://www.sciencedirect.com/science/article/pii/S0016718507000371}, author = {Brown,Daniel G. and Robinson,Derek T. and An,Li and Nassauer,Joan I. and Zellner,Moira and Rand, William and Riolo,Rick and Page,Scott E. and Low,Bobbi and Wang,Zhifang} } @conference {17537, title = {Fixing ally{\textquoteright}s growing pains with velocity modeling}, booktitle = {Proceedings of the 8th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {337 - 342}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Mapping the router topology is an important component of Internet measurement. Alias resolution, the process of mapping IP addresses to routers, is critical to accurate Internet mapping. Ally, a popular alias resolution tool, was developed to resolve aliases in individual ISPs, but its probabilistic accuracy and need to send O(n2) probes to infer aliases among n IP addresses make it unappealing for large-scale Internet mapping. In this paper, we present RadarGun, a tool that uses IP identifier velocity modeling to improve the accuracy and scalability of the Ally-based resolution technique. We provide analytical bounds on Ally{\textquoteright}s accuracy and validate our predicted aliases against Ally. Additionally, we show that velocity modeling requires only O(n) probes and thus scales to Internet-sized mapping efforts.}, keywords = {alias resolution, ally, ip identifier, velocity modeling}, isbn = {978-1-60558-334-1}, doi = {10.1145/1452520.1452560}, url = {http://doi.acm.org/10.1145/1452520.1452560}, author = {Bender,Adam and Sherwood,Rob and Spring, Neil} } @conference {12106, title = {A Framework for Software Engineering Experimental Replications}, booktitle = {Engineering of Complex Computer Systems, 2008. ICECCS 2008. 13th IEEE International Conference on}, year = {2008}, month = {2008/04/31/3}, pages = {203 - 212}, abstract = {Experimental replications are very important to the advancement of empirical software engineering. Replications are one of the key mechanisms to confirm previous experimental findings. They are also used to transfer experimental knowledge, to train people, and to expand a base of experimental evidence. Unfortunately, experimental replications are difficult endeavors. It is not easy to transfer experimental know-how and experimental findings. Based on our experience, this paper discusses this problem and proposes a Framework for Improving the Replication of Experiments (FIRE). The FIRE addresses knowledge sharing issues both at the intra-group (internal replications) and inter-group (external replications) levels. It encourages coordination of replications in order to facilitate knowledge transfer for lower cost, higher quality replications and more generalizable results.}, keywords = {engineering, engineering;, evidence;experimental, experimental, Experiments;experimental, for, Framework, Improving, knowledge, of, replication, replication;software, sharing;software, the, transfer;knowledge}, doi = {10.1109/ICECCS.2008.38}, author = {Mendonca,M.G. and Maldonado,J.C. and de Oliveira,M.C.F. and Carver, J. and Fabbri,C.P.F. and Shull, F. and Travassos,G.H. and Hohn,E.N. and Basili, Victor R.} } @conference {16421, title = {GoGoBot: group collaboration, multi-agent modeling, and robots}, booktitle = {Proceedings of the 7th international joint conference on Autonomous agents and multiagent systems: demo papers}, series = {AAMAS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {1715 - 1716}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {Multi-agent simulation is a powerful technique used to encode real-world simple rules in virtual agents and then simulate their interactions [1]. Participatory simulations are similar to multi-agent simulation except individuals play the role of virtual agents, sometimes in combination with these virtual agents [2]. Finally, the bifocal modeling framework has enabled the examination of agents embodied in physical entities using sensors and actuators [3]. All three of these technologies are concerned with the creation, manipulation, and development of agents in one form or another. Thus combining these three disparate systems in to one unified platform would be useful. Multi-agent simulation platforms, participatory simulations, and bifocal modeling have all been demonstrated separately in the past. However many extant systems are difficult if not impossible to integrate.}, keywords = {multi-agent simulation, participatory simulation, ROBOTICS}, url = {http://dl.acm.org/citation.cfm?id=1402744.1402780}, author = {Rand, William and Blikstein,Paulo and Wilensky,Uri} } @conference {12245, title = {Growth of the flickr social network}, booktitle = {Proceedings of the first workshop on Online social networks}, series = {WOSN {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {25 - 30}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online social networking sites like MySpace, Orkut, and Flickr are among the most popular sites on the Web and continue to experience dramatic growth in their user population. The popularity of these sites offers a unique opportunity to study the dynamics of social networks at scale. Having a proper understanding of how online social networks grow can provide insights into the network structure, allow predictions of future growth, and enable simulation of systems on networks of arbitrary size. However, to date, most empirical studies have focused on static network snapshots rather than growth dynamics. In this paper, we collect and examine detailed growth data from the Flickr online social network, focusing on the ways in which new links are formed. Our study makes two contributions. First, we collect detailed data covering three months of growth, encompassing 950,143 new users and over 9.7 million new links, and we make this data available to the research community. Second, we use a first-principles approach to investigate the link formation process. In short, we find that links tend to be created by users who already have many links, that users tend to respond to incoming links by creating links back to the source, and that users link to other users who are already close in the network.}, keywords = {growth, measurement, social networks}, isbn = {978-1-60558-182-8}, doi = {10.1145/1397735.1397742}, url = {http://doi.acm.org/10.1145/1397735.1397742}, author = {Mislove,Alan and Koppula,Hema Swetha and Gummadi,Krishna P. and Druschel,Peter and Bhattacharjee, Bobby} } @conference {19450, title = {Hci for community and international development}, booktitle = {SIGCHI EA {\textquoteright}08}, series = {CHI EA {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {3909 - 3912}, publisher = {ACM}, organization = {ACM}, abstract = {This workshop explores the challenges in applying, extending and inventing appropriate methods and contributions of Human Computer Interaction (HCI) to International economic and community Development. We address interaction design for parts of the world that are often marginalized by the Global North as well as people in the Global North who are themselves similarly marginalized by poverty or other barriers. We hope to extend the boundaries of the field of Human Computer Interaction by spurring a discussion on how existing methods and practices can be adapted and modified, and how new practices can be developed, to deal with the unique challenges posed by these contexts.}, keywords = {community design, ict4d, information and communication technology, international development, participatory design, ucd4id, User centered design}, isbn = {978-1-60558-012-8}, url = {http://doi.acm.org/10.1145/1358628.1358954}, author = {Thomas, John and Dearden, Andy and Dray, Susan and Light, Ann and Best, Michael and Arkin, Nuray and Maunder, Andrew and Kam, Mathew and Marshini Chetty and Sambasivan, Nithya and Buckhalter, Celeste and Krishnan, Gaurishankar} } @article {16844, title = {Hierarchical infrastructure for internet mapping services}, journal = {Geospatial Services and Applications for the Internet}, year = {2008}, month = {2008///}, pages = {1 - 30}, doi = {10.1007/978-0-387-74674-6_1}, author = {Brabec,F. and Samet, Hanan} } @article {14970, title = {High Performance Computing Algorithms for Land Cover}, year = {2008}, month = {2008///}, institution = {CiteSeerX}, abstract = {Global and regional land cover studies require the ability to apply complex models on selected subsets of large amounts of multi-sensor and multi-temporal data sets that have been derived from raw instrument measurements using widely accepted pre-processing algorithms. The computational and storage requirements of most such studies far exceed what is possible on a single workstation environment. We have been pursuing a new approach that couples scalable and open distributed heterogeneous hardware with the development of high performance software for processing, indexing, and organizing remotely sensed data. Hierarchical data management tools are used to ingest raw data, create metadata, and organize the archived data so as to automatically achieve computational load balancing among the available nodes and minimize I/O overheads. We illustrate our approach with four specific examples. The first is the development of the first fast operational scheme for the atmospheric correction of Landsat TM scenes, while the second example focuses on image segmentation using a novel hierarchical connected components algorithm. Retrieval of global BRDF (Bidirectional Reflectance Distribution Function) in the red and near infrared wavelengths using four years (1983 to 1986) of Pathfinder AVHRR Land (PAL) data set is the focus of our third example. The fourth example is the development of a hierarchical data organization scheme that allows on-demand processing and retrieval of regional and global AVHRR data sets. Our results show that substantial improvements in computational times can be achieved by using the high performance computing technology.}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.58.4213}, author = {Dynamics Using Remote and Satya Kalluri and Bader,David A. and John Townshend and JaJa, Joseph F. and Zengyan Zhang and Fallah-adl,Hassan} } @article {18492, title = {Hosting virtual networks on commodity hardware}, volume = {GT-CS-07-10}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {This paper describes Trellis, a software platform for hostingmultiple virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topol- ogy, control protocols, and forwarding tables, which low- ers the barrier for deploying custom services on an isolated, reconfigurable, and programmable network, while amor- tizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed vir- tual networks. We describe the design and implementation, of Trellis, including kernel-level performance optimizations, and evaluate its supported packet-forwarding rates against other virtualization technologies. We are in the process of upgrading the VINI facility to use Trellis. We also plan to release Trellis as part of MyVINI, a standalone software dis- tribution that allows researchers and application developers to deploy their own virtual network hosting platforms. }, author = {Bhatia,S. and Motiwala,M. and Muhlbauer,W. and Valancius,V. and Bavier,A. and Feamster, Nick and Peterson,L. and Rexford,J.} } @conference {12240, title = {Integrating categorical resource types into a P2P desktop grid system}, booktitle = {Grid Computing, 2008 9th IEEE/ACM International Conference on}, year = {2008}, month = {2008/10/29/1}, pages = {284 - 291}, abstract = {We describe and evaluate a set of protocols that implement a distributed, decentralized desktop grid. Incoming jobs are matched with system nodes through proximity in an N-dimensional resource space. This work improves on prior work by (1) efficiently accommodating node and job characterizations that include both continuous and categorical resource types, and (2) scaling gracefully to large system sizes even with highly non-uniform distributions of job and node types. We use extensive simulation results to show that the resulting system handles both continuous and categorical constraints efficiently, and that the new scalability techniques are effective.}, keywords = {computing;peer-to-peer, computing;protocols;, computing;protocols;scalability, desktop, Grid, grid;distributed, grid;peer-to-peer, N-dimensional, resource, space;P2P, system;categorical, technique;grid, types;decentralized}, doi = {10.1109/GRID.2008.4662810}, author = {Kim,Jik-Soo and Nam,Beomseok and Marsh,M. and Keleher,P. and Bhattacharjee, Bobby and Sussman, Alan} } @article {17250, title = {Interactive Entity Resolution in Relational Data: A Visual Analytic Tool and Its Evaluation}, journal = {IEEE Transactions on Visualization and Computer Graphics}, volume = {14}, year = {2008}, month = {2008/10//Sept}, pages = {999 - 1014}, abstract = {Databases often contain uncertain and imprecise references to real-world entities. Entity resolution, the process of reconciling multiple references to underlying real-world entities, is an important data cleaning process required before accurate visualization or analysis of the data is possible. In many cases, in addition to noisy data describing entities, there is data describing the relationships among the entities. This relational data is important during the entity resolution process; it is useful both for the algorithms which determine likely database references to be resolved and for visual analytic tools which support the entity resolution process. In this paper, we introduce a novel user interface, D-Dupe, for interactive entity resolution in relational data. D-Dupe effectively combines relational entity resolution algorithms with a novel network visualization that enables users to make use of an entity{\textquoteright}s relational context for making resolution decisions. Since resolution decisions often are interdependent, D-Dupe facilitates understanding this complex process through animations which highlight combined inferences and a history mechanism which allows users to inspect chains of resolution decisions. An empirical study with 12 users confirmed the benefits of the relational context visualization on the performance of entity resolution tasks in relational data in terms of time as well as users{\textquoteright} confidence and satisfaction.}, keywords = {algorithms, Computer Graphics, D-Dupe, data visualisation, database management systems, Databases, Factual, graphical user interface, Graphical user interfaces, human-centered computing, Image Interpretation, Computer-Assisted, Information Storage and Retrieval, Information Visualization, interactive entity resolution, relational context visualization, Relational databases, relational entity resolution algorithm, User interfaces, user-centered design, User-Computer Interface, visual analytic tool}, isbn = {1077-2626}, doi = {10.1109/TVCG.2008.55}, author = {Kang,Hyunmo and Getoor, Lise and Shneiderman, Ben and Bilgic,M. and Licamele,L.} } @inbook {13024, title = {The Lattice Project: a Grid research and production environment combining multiple Grid computing models}, booktitle = {Distributed \& Grid Computing {\textemdash} Science Made Transparent for Everyone. Principles, Applications and Supporting CommunitiesDistributed \& Grid Computing {\textemdash} Science Made Transparent for Everyone. Principles, Applications and Supporting Communities}, year = {2008}, month = {2008///}, pages = {2 - 13}, publisher = {Rechenkraft.net}, organization = {Rechenkraft.net}, address = {Marburg}, author = {Bazinet,A. L and Cummings, Michael P.}, editor = {Weber,MHW} } @conference {14454, title = {Leveraging social context for searching social media}, booktitle = {Proceedings of the 2008 ACM workshop on Search in social media}, series = {SSM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {91 - 94}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The ability to utilize and benefit from today{\textquoteright}s explosion of social media sites depends on providing tools that allow users to productively participate. In order to participate, users must be able to find resources (both people and information) that they find valuable. Here, we argue that in order to do this effectively, we should make use of a user{\textquoteright}s "social context". A user{\textquoteright}s social context includes both their personal social context (their friends and the communities to which they belong) and their community social context (their role and identity in different communities).}, keywords = {social context, social media, social search}, isbn = {978-1-60558-258-0}, doi = {10.1145/1458583.1458602}, url = {http://doi.acm.org/10.1145/1458583.1458602}, author = {Smith,Marc and Barash,Vladimir and Getoor, Lise and Lauw,Hady W.} } @conference {12244, title = {Matchmaking and implementation issues for a P2P desktop grid}, booktitle = {Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on}, year = {2008}, month = {2008/04//}, pages = {1 - 5}, abstract = {We present some recent and ongoing work in our decentralized desktop computing grid project. Specifically, we discuss matching jobs with compute nodes in a peer-to-peer grid of heterogeneous platforms, and the implementation of our algorithms in a concrete system.}, keywords = {computing, computing;, computing;peer-to-peer, desktop, grid;decentralized, grid;grid, grid;peer-to-peer, P2P}, doi = {10.1109/IPDPS.2008.4536388}, author = {Marsh,M. and Kim,Jik-Soo and Nam,Beomseok and Jaehwan Lee and Ratanasanya,S. and Bhattacharjee, Bobby and Keleher,P. and Richardson,D. and Wellnitz,D.} } @article {14569, title = {Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development}, journal = {Development}, volume = {135}, year = {2008}, month = {2008///}, pages = {2729 - 2738}, abstract = {CTCF is a multifunctional nuclear factor involved in epigenetic regulation. Despite recent advances that include the systematic discovery of CTCF-binding sites throughout the mammalian genome, the in vivo roles of CTCF in adult tissues and during embryonic development are largely unknown. Using transgenic RNAi, we depleted maternal stores of CTCF from growing mouse oocytes, and identified hundreds of misregulated genes. Moreover, our analysis suggests that CTCF predominantly activates or derepresses transcription in oocytes. CTCF depletion causes meiotic defects in the egg, and mitotic defects in the embryo that are accompanied by defects in zygotic gene expression, and culminate in apoptosis. Maternal pronuclear transfer and CTCF mRNA microinjection experiments indicate that CTCF is a mammalian maternal effect gene, and that persistent transcriptional defects rather than persistent chromosomal defects perturb early embryonic development. This is the first study detailing a global and essential role for CTCF in mouse oocytes and preimplantation embryos.}, doi = {10.1242/dev.024539}, url = {http://dev.biologists.org/content/135/16/2729.abstract}, author = {Wan,Le-Ben and Pan,Hua and Hannenhalli, Sridhar and Cheng,Yong and Ma,Jun and Fedoriw,Andrew and Lobanenkov,Victor and Latham,Keith E. and Schultz,Richard M. and Bartolomei,Marisa S.} } @article {12147, title = {Measures and Risk Indicators for Early Insight into Software Safety. Development of Fault-Tolerant Systems}, year = {2008}, month = {2008/10//}, institution = {ABERDEEN TEST CENTER MD}, abstract = {Software contributes an ever-increasing level of functionality and control in today{\textquoteright}s systems. This increased use of software can dramatically increase the complexity and time needed to evaluate the safety of a system. Although the actual system safety cannot be verified during its development, measures can reveal early insights into potential safety problems and risks. An approach for developing early software safety measures is presented in this article. The approach and the example software measures presented are based on experience working with the safety engineering group on a large Department of Defense program.}, keywords = {*SOFTWARE ENGINEERING, *SYSTEM SAFETY, COMPUTER PROGRAMMING AND SOFTWARE, fault tolerant computing, INDICATORS, measurement, REPRINTS, risk, SAFETY ENGINEERING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA487120}, author = {Basili, Victor R. and Marotta,Frank and Dangle,Kathleen and Esker,Linda and Rus,Ioana} } @conference {14229, title = {Measuring 1st order stretchwith a single filter}, booktitle = {IEEE International Conference on Acoustics, Speech and Signal Processing, 2008. ICASSP 2008}, year = {2008}, month = {2008/04/31/March}, pages = {909 - 912}, publisher = {IEEE}, organization = {IEEE}, abstract = {We analytically develop a filter that is able to measure the linear stretch of the transformation around a point, and present results of applying it to real signals. We show that this method is a real-time alternative solution for measuring local signal transformations. Experimentally, this method can accurately measure stretch, however, it is sensitive to shift.}, keywords = {Cepstral analysis, Educational institutions, filter, filtering theory, Fourier transforms, Frequency domain analysis, Frequency estimation, Gabor filters, Image analysis, IMAGE PROCESSING, linear stretch measurement, local signal transformation measurement, Nonlinear filters, Phase estimation, Signal analysis, Speech processing}, isbn = {978-1-4244-1483-3}, doi = {10.1109/ICASSP.2008.4517758}, author = {Bitsakos,K. and Domke, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {12360, title = {Memory-constrained block processing for dsp software optimization}, journal = {Journal of Signal Processing Systems}, volume = {50}, year = {2008}, month = {2008///}, pages = {163 - 177}, author = {Ko,M. Y and Shen,C. C and Bhattacharyya, Shuvra S.} } @conference {18775, title = {Methods to directly measure the trapping potential in optical tweezers}, year = {2008}, month = {2008///}, pages = {70380V{\textendash}1 - 70380V{\textendash}1}, abstract = {Techniques to measure the trapping force in an optical tweezers without any prior assumptions about the trapshape have been developed. The response of a trapped micro or nanoparticle to a step input is measured and then used to calculate the trapping force experienced by the particle as a function of it{\textquoteright}s position in the trap. This method will provide new insight into the trapping behavior of nanoparticles, which are more weakly bound than microparticles and thereby explore larger regions of the trapping potential due to Brownian motion. Langevin dynamics simulations are presented to model the system and are used to demonstrate this technique. Preliminary experimental results are then presented to validate the simulations. Finally, the measured trapping forces, from simulations and laboratory experiments, are integrated to recover the trapping potential. }, url = {http://144.206.159.178/FT/CONF/16419087/16419102.pdf}, author = {Balijepalli,A. and LeBrun,T. W. and Gorman,J. J. and Gupta,S.K.} } @conference {12247, title = {Motivating participation in internet routing overlays}, booktitle = {Proceedings of the 3rd international workshop on Economics of networked systems}, series = {NetEcon {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {91 - 96}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {PeerWise is an Internet routing overlay that reduces end-to-end latencies by allowing peers to forward through a relay instead of connecting directly to their destinations. Fundamental to PeerWise is the notion of peering agreements between two peers, wherein they agree to forward for one another. In this paper, we consider the problem of motivating users to establish and maintain peerings in a completely decentralized, scalable manner. We show that routing overlays present unique challenges and goals. For instance, since participants can always "fall back" on standard Internet routing, we must encourage users to stay in the system and maintain long-lived peering agreements. To address these challenges, we propose two mechanisms: First, we use Service Level Agreements (SLAs) to expressively negotiate peers{\textquoteright} demands and the recourses they will take when SLAs are violated. Second, we propose a mechanism to address SLA violations that differs from the standard notion of punishment via service degradation. Our simulation results demonstrate that our mechanism causes peers to avoid SLA violators in favor of long-lived peerings. Lastly, we discuss potential, emergent behaviors in a selfish routing overlay.}, keywords = {incentives, internet routing overlays, service-level agreements}, isbn = {978-1-60558-179-8}, doi = {10.1145/1403027.1403048}, url = {http://doi.acm.org/10.1145/1403027.1403048}, author = {Levin,Dave and Baden,Randolph and Lumezanu,Cristian and Spring, Neil and Bhattacharjee, Bobby} } @conference {12556, title = {Multi-biometric cohort analysis for biometric fusion}, booktitle = {Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on}, year = {2008}, month = {2008/04/31/4}, pages = {5224 - 5227}, abstract = {Biometric matching decisions have traditionally been made based solely on a score that represents the similarity of the query biometric to the enrolled biometric(s) of the claimed identity. Fusion schemes have been proposed to benefit from the availability of multiple biometric samples (e.g., multiple samples of the same fingerprint) or multiple different biometrics (e.g., face and fingerprint). These commonly adopted fusion approaches rarely make use of the large number of non-matching biometric samples available in the database in the form of other enrolled identities or training data. In this paper, we study the impact of combining this information with the existing fusion methodologies in a cohort analysis framework. Experimental results are provided to show the usefulness of such a cohort-based fusion of face and fingerprint biometrics.}, keywords = {(access, analysis;biometrics, biometric, biometrics;fingerprint, biometrics;multi-biometric, cohort, control);face, data;, decisions;face, fusion;biometric, identification;security, MATCHING, of, recognition;fingerprint}, doi = {10.1109/ICASSP.2008.4518837}, author = {Aggarwal,G. and Ratha,N. K and Bolle, R.M. and Chellapa, Rama} } @article {18707, title = {Mutations in the Hydrophobic Core of Ubiquitin Differentially Affect Its Recognition by Receptor Proteins}, journal = {Journal of Molecular Biology}, volume = {375}, year = {2008}, month = {2008/01/25/}, pages = {979 - 996}, abstract = {Ubiquitin (Ub) is one of the most highly conserved signaling proteins in eukaryotes. In carrying out its myriad functions, Ub conjugated to substrate proteins interacts with dozens of receptor proteins that link the Ub signal to various biological outcomes. Here we report mutations in conserved residues of Ub{\textquoteright}s hydrophobic core that have surprisingly potent and specific effects on molecular recognition. Mutant Ubs bind tightly to the Ub-associated domain of the receptor proteins Rad23 and hHR23A but fail to bind the Ub-interacting motif present in the receptors Rpn10 and S5a. Moreover, chains assembled on target substrates with mutant Ubs are unable to support substrate degradation by the proteasome in vitro or sustain viability of yeast cells. The mutations have relatively little effect on Ub{\textquoteright}s overall structure but reduce its rigidity and cause a slight displacement of the C-terminal β-sheet, thereby compromising association with Ub-interacting motif but not with Ub-associated domains. These studies emphasize an unexpected role for Ub{\textquoteright}s core in molecular recognition and suggest that the diversity of protein{\textendash}protein interactions in which Ub engages placed enormous constraints on its evolvability.}, keywords = {hydrophobic core mutation, molecular recognition, proteasomal degradation, ubiquitin, ubiquitin receptors}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2007.11.016}, url = {http://www.sciencedirect.com/science/article/pii/S0022283607014763}, author = {Haririnia,Aydin and Verma,Rati and Purohit,Nisha and Twarog,Michael Z. and Deshaies,Raymond J. and Bolon,Dan and Fushman, David} } @article {17303, title = {NASDAQ Velocity and Forces: An Interactive Visualization of Activity and Change}, journal = {Journal of Universal Computer Science}, volume = {14}, year = {2008}, month = {2008///}, pages = {1391 - 1410}, author = {Dao,H.T. and Bazinet,A. and Berthier,R. and Shneiderman, Ben} } @conference {13389, title = {Network-Aware Join Processing in Global-Scale Database Federations}, booktitle = {IEEE 24th International Conference on Data Engineering, 2008. ICDE 2008}, year = {2008}, month = {2008/04/07/12}, pages = {586 - 595}, publisher = {IEEE}, organization = {IEEE}, abstract = {We introduce join scheduling algorithms that employ a balanced network utilization metric to optimize the use of all network paths in a global-scale database federation. This metric allows algorithms to exploit excess capacity in the network, while avoiding narrow, long-haul paths. We give a two- approximate, polynomial-time algorithm for serial (left-deep) join schedules. We also present extensions to this algorithm that explore parallel schedules, reduce resource usage, and define tradeoffs between computation and network utilization. We evaluate these techniques within the SkyQuery federation of Astronomy databases using spatial-join queries submitted by SkyQuery{\textquoteright}s users. Experiments show that our algorithms realize near-optimal network utilization with minor computational overhead.}, keywords = {Astronomy, Computer networks, Concurrent computing, global-scale database federations, join scheduling algorithms, network utilization, network-aware join processing, parallel schedules, polynomial-time algorithm, Polynomials, Processor scheduling, Query processing, reduce resource usage, Scheduling algorithm, Spatial databases, spatial-join queries, Telecommunication traffic, Throughput}, isbn = {978-1-4244-1836-7}, doi = {10.1109/ICDE.2008.4497467}, author = {Xiaodan Wang and Burns,R. and Terzis,A. and Deshpande, Amol} } @article {12900, title = {New records of phytoplankton for Bangladesh. 2. Cryptophyceae and Synurophyceae}, journal = {Bangladesh Journal of Botany}, volume = {36}, year = {2008}, month = {2008/11/05/}, abstract = {This study presents two species of Rhodomonas, four species of Chroomonas, six species of Cryptomonas and Cryptochrysis minor, Cyanomonas coeruleus, Chrysodidymus synuroideus and Mallomonas akrokomos. These species have been reported from some ponds of Mathbaria in Pirojpur and Bakerganj of Barisal district in Bangladesh.}, isbn = {0253-5416}, doi = {10.3329/bjb.v36i1.1549}, url = {http://www.banglajol.info/bd/index.php/BJB/article/viewArticle/1549}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12902, title = {New records of phytoplankton for Bangladesh. 5. Euglena, Euglenocapsa}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {15}, year = {2008}, month = {2008/06/16/}, abstract = {This study presents 20 taxa of the genus Euglena and one species of the rare euglenoid genus Euglenocapsa. All these taxa are reported for the first time from some pond ecosystems of Mathbaria in Pirojpur and Bakerganj of Barisal districts of Bangladesh.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v15i1.910}, url = {http://www.banglajol.info/index.php/BJPT/article/viewArticle/910}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12899, title = {New records of phytoplankton for Bangladesh. 7. Phacus spp.}, journal = {Bangladesh Journal of Botany}, volume = {37}, year = {2008}, month = {2008/11/05/}, abstract = {Thirteen species of Phacus hitherto not reported from Bangladesh have been described and illustrated. Freshwater ponds at southern districts of Pirojpur and Barisal revealed these presence of the species.}, isbn = {0253-5416}, doi = {10.3329/bjb.v37i1.1564}, url = {http://www.banglajol.info/bd/index.php/BJB/article/viewArticle/1564}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12897, title = {New records of phytoplankton for Bangladesh. 8. Trachelomonas Ehr. (Euglenophyceae)}, journal = {Bangladesh Journal of Botany}, volume = {37}, year = {2008}, month = {2008/12/19/}, abstract = {Investigation of pelagic plankton communities from some freshwater ponds of Pirojpur and Barisal districts revealed the presence of 17 species under the genus Trachelomonas Ehr. for the first time in Bangladesh.}, isbn = {0253-5416}, doi = {10.3329/bjb.v37i2.1719}, url = {http://www.banglajol.info/bd/index.php/BJB/article/viewArticle/1719}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @conference {12548, title = {A Non-generative Approach for Face Recognition Across Aging}, booktitle = {Biometrics: Theory, Applications and Systems, 2008. BTAS 2008. 2nd IEEE International Conference on}, year = {2008}, month = {2008/10//undefin}, pages = {1 - 6}, abstract = {Human faces undergo a lot of change in appearance as they age. Though facial aging has been studied for decades, it is only recently that attempts have been made to address the problem from a computational point of view. Most of these early efforts follow a simulation approach in which matching is performed by synthesizing face images at the target age. Given the innumerable different ways in which a face can potentially age, the synthesized aged image may not be similar to the actual aged image. In this paper, we bypass the synthesis step and directly analyze the drifts of facial features with aging from a purely matching perspective. Our analysis is based on the observation that facial appearance changes in a coherent manner as people age. We provide measures to capture this coherency in feature drifts. Illustrations and experimental results show the efficacy of such an approach for matching faces across age progression.}, keywords = {appearance;nongenerative, approach;face, Face, image, matching;, recognition;facial, recognition;image, synthesis;face}, doi = {10.1109/BTAS.2008.4699331}, author = {Biswas,S. and Aggarwal,G. and Ramanathan,N. and Chellapa, Rama} } @conference {12195, title = {One-handed touchscreen input for legacy applications}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {1399 - 1408}, author = {Karlson,A.K. and Bederson, Benjamin B.} } @article {18503, title = {Packets with provenance}, volume = {GT-CS-08-02}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {Traffic classification and distinction allows network operators to provision resources, enforce trust, control unwanted traffic, and traceback unwanted traffic to its source. Today{\textquoteright}s classification mechanisms rely primarily on IP addresses and port numbers; unfortunately, these fields are often too coarse and ephemeral, and moreover, they do not reflect traffic{\textquoteright}s provenance, associated trust, or relationship to other processes or hosts. This paper presents the design, analysis, user-space implementation, and evaluation of Pedigree, which consists of two components: a trusted tagger that resides on hosts and tags packets with information about their provenance (i.e., identity and history of potential input from hosts and resources for the process that generated them), and an arbiter, which decides what to do with the traffic that carries certain tags. Pedigree allows operators to write traffic classification policies with expressive semantics that reflect properties of the actual process that generated the traffic. Beyond offering new function and flexibility in traffic classification, Pedigree represents a new and interesting point in the design space between filtering and capabilities, and it allows network operators to leverage host-based trust models to decide treatment of network traffic.}, url = {http://hdl.handle.net/1853/25467}, author = {Ramachandran,A. and Bhandankar,K. and Tariq,M.B. and Feamster, Nick} } @conference {18593, title = {Photo-based authentication using social networks}, booktitle = {Proceedings of the first workshop on Online social networks}, series = {WOSN {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {55 - 60}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present Lineup, a system that uses the social network graph in Facebook and auxiliary information (e.g., "tagged" user photos) to build a photo-based Web site authentication framework. Lineup{\textquoteright}s underlying mechanism leverages the concept of CAPTCHAs, programs that are designed to distinguish bots from human users. Lineup extends this functionality to help a Web site ascertain a user{\textquoteright}s identity or membership in a certain group (e.g., an interest group, invitees to a certain event) in order to infer some level of trust. Lineup works by presenting a user with photographs and asking the user to identify subjects in the photo whom a user with the appropriate identity or group membership should know. We present the design and implementation for Lineup, describe a preliminary prototype implementation, and discuss Lineup{\textquoteright}s security properties, including possible guarantees and threats.}, keywords = {social networks, trust}, isbn = {978-1-60558-182-8}, doi = {10.1145/1397735.1397748}, url = {http://doi.acm.org/10.1145/1397735.1397748}, author = {Yardi,Sarita and Feamster, Nick and Bruckman,Amy} } @article {12109, title = {A pilot study to compare programming effort for two parallel programming models}, journal = {Journal of Systems and Software}, volume = {81}, year = {2008}, month = {2008/11//}, pages = {1920 - 1930}, abstract = {ContextWriting software for the current generation of parallel systems requires significant programmer effort, and the community is seeking alternatives that reduce effort while still achieving good performance. Objective Measure the effect of parallel programming models (message-passing vs. PRAM-like) on programmer effort. Design, setting, and subjects One group of subjects implemented sparse-matrix dense-vector multiplication using message-passing (MPI), and a second group solved the same problem using a PRAM-like model (XMTC). The subjects were students in two graduate-level classes: one class was taught MPI and the other was taught XMTC. Main outcome measures Development time, program correctness. Results Mean XMTC development time was 4.8\&$\#$xa0;h less than mean MPI development time (95\% confidence interval, 2.0{\textendash}7.7), a 46\% reduction. XMTC programs were more likely to be correct, but the difference in correctness rates was not statistically significant (p\&$\#$xa0;=\&$\#$xa0;.16). Conclusions XMTC solutions for this particular problem required less effort than MPI equivalents, but further studies are necessary which examine different types of problems and different levels of programmer experience. }, keywords = {effort, empirical study, Message-passing, MPI, parallel programming, PRAM, XMT}, isbn = {0164-1212}, doi = {10.1016/j.jss.2007.12.798}, url = {http://www.sciencedirect.com/science/article/pii/S0164121208000125}, author = {Hochstein, Lorin and Basili, Victor R. and Vishkin, Uzi and Gilbert,John} } @conference {12173, title = {Readability of scanned books in digital libraries}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {705 - 714}, author = {Quinn,A.J. and Hu,C. and Arisaka,T. and Rose,A. and Bederson, Benjamin B.} } @article {13016, title = {Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence}, journal = {Syst Biol}, volume = {57}, year = {2008}, month = {2008/12//}, pages = {920 - 938}, abstract = {This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations{\textendash}first codon positions encoding leucine and arginine, which were also compositionally heterogeneous{\textendash}yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned{\textendash}fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II.}, doi = {10.1080/10635150802570791}, author = {Regier,J. C and Shultz,J. W and Ganley,A. R.D and Hussey,A. and Shi,D. and Ball,B. and Zwick,A. and Stajich,J. E and Cummings, Michael P. and Martin,J. W and Cunningham,CW} } @article {12180, title = {A review of overview+ detail, zooming, and focus+ context interfaces}, journal = {ACM Computing Surveys (CSUR)}, volume = {41}, year = {2008}, month = {2008///}, pages = {1 - 31}, author = {Cockburn,A. and Karlson,A. and Bederson, Benjamin B.} } @article {14077, title = {Role of transposable elements in trypanosomatids}, journal = {Microbes and Infection}, volume = {10}, year = {2008}, month = {2008/05//}, pages = {575 - 581}, abstract = {Transposable elements constitute 2-5\% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.}, keywords = {Cellular function, Domestication, Evolution, Gene expression, Leishmania, Regulation of mRNA stability, Retroposon, Transposable element, Trypanosoma}, isbn = {1286-4579}, doi = {16/j.micinf.2008.02.009}, url = {http://www.sciencedirect.com/science/article/pii/S1286457908000464}, author = {Bringaud,Fr{\'e}d{\'e}ric and Ghedin,Elodie and El-Sayed, Najib M. and Papadopoulou,Barbara} } @article {12241, title = {A scalable key management and clustering scheme for wireless ad hoc and sensor networks}, journal = {Future Generation Computer Systems}, volume = {24}, year = {2008}, month = {2008/10//}, pages = {860 - 869}, abstract = {This paper describes a scalable key management and clustering scheme for secure group communications in ad hoc and sensor networks. The scalability problem is solved by partitioning the communicating devices into subgroups, with a leader in each subgroup, and further organizing the subgroups into hierarchies. Each level of the hierarchy is called a tier or layer. Key generation, distribution, and actual data transmissions follow the hierarchy. The distributed, efficient clustering approach (DECA) provides robust clustering to form subgroups, and analytical and simulation results demonstrate that DECA is energy-efficient and resilient against node mobility. Comparing with most other schemes, our approach is extremely scalable and efficient, provides more security guarantees, and is selective, adaptive and robust.}, keywords = {ad hoc networks, clustering, Group communications, Key management, sensor networks}, isbn = {0167-739X}, doi = {10.1016/j.future.2008.03.007}, url = {http://www.sciencedirect.com/science/article/pii/S0167739X08000782}, author = {Li,Jason H. and Bhattacharjee, Bobby and Yu,Miao and Levy,Renato} } @article {14853, title = {Searching the world{\textquoteright}s herbaria: A system for visual identification of plant species}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {116 - 129}, abstract = {We describe a working computer vision system that aids in the identification of plant species. A user photographs an isolated leaf on a blank background, and the system extracts the leaf shape and matches it to the shape of leaves of known species. In a few seconds, the system displays the top matching species, along with textual descriptions and additional images. This system is currently in use by botanists at the Smithsonian Institution National Museum of Natural History. The primary contributions of this paper are: a description of a working computer vision system and its user interface for an important new application area; the introduction of three new datasets containing thousands of single leaf images, each labeled by species and verified by botanists at the US National Herbarium; recognition results for two of the three leaf datasets; and descriptions throughout of practical lessons learned in constructing this system.}, doi = {10.1007/978-3-540-88693-8_9}, author = {Belhumeur,P. and Chen,D. and Feiner,S. and Jacobs, David W. and Kress,W. and Ling,H. and Lopez,I. and Ramamoorthi,R. and Sheorey,S. and White,S.} } @article {14098, title = {Sequence diversity and evolution of multigene families in Trypanosoma cruzi}, journal = {Molecular and Biochemical Parasitology}, volume = {157}, year = {2008}, month = {2008/01//}, pages = {65 - 72}, abstract = {Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome.}, keywords = {Amastin, Gene conversion, Genetic diversity, Multigene families, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/j.molbiopara.2007.10.002}, url = {http://www.sciencedirect.com/science/article/pii/S0166685107002769}, author = {Cerqueira,Gustavo C. and Bartholomeu,Daniella C. and DaRocha,Wanderson D. and Hou,Lihua and Freitas-Silva,Danielle M. and Machado,Carlos Renato and El-Sayed, Najib M. and Teixeira,Santuza M.R.} } @article {14574, title = {Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure}, journal = {Circulation: Cardiovascular Genetics}, volume = {1}, year = {2008}, month = {2008/12/01/}, pages = {117 - 125}, abstract = {Background{\textemdash} We report the first comprehensive analysis of gene expression differences by sex and age in left ventricular samples from 102 patients with dilated cardiomyopathy.Methods and Results{\textemdash} Gene expression data (HG-U133A gene chip, Affymetrix) were analyzed from 30 females and 72 males from 3 separate centers. More than 1800 genes displayed sexual dimorphism in the heart (adjusted P value <0.05). A significant number of these genes were highly represented in gene ontology pathways involved in ion transport and G-protein-coupled receptor signaling. Localization of these genes revealed enrichment on both the sex chromosomes as well as chromosomes 3, 4, and 14. The second goal of this study was to determine the effect of age on gene expression. Within the female cohort, >140 genes were differentially expressed in the <55 years age group compared with the >55 years age group. These genes were highly represented in gene ontology pathways involved in DNA damage. In contrast, zero genes in the male cohort <55 years met statistical significance when compared with the >55 years age group.Conclusions{\textemdash} Gene expression in dilated cardiomyopathy displayed evidence of sexual dimorphism similar to other somatic tissues and age dimorphism within the female cohort.}, doi = {10.1161/CIRCGENETICS.108.802652}, url = {http://circgenetics.ahajournals.org/content/1/2/117.abstract}, author = {Fermin,David R. and Barac,Ana and Lee,Sangjin and Polster,Sean P. and Hannenhalli, Sridhar and Bergemann,Tracy L. and Grindle,Suzanne and Dyke,David B. and Pagani,Francis and Miller,Leslie W. and Tan,Sarah and dos Remedios,Cris and Cappola,Thomas P. and Margulies,Kenneth B. and Hall,Jennifer L.} } @article {14433, title = {Structural Sampling for Statistical Software Testing}, journal = {Probabilistic, Logical and Relational Learning-A Further Synthesis}, year = {2008}, month = {2008///}, abstract = {Structural Statistical Software Testing exploits the control flow graph of the program being tested to construct test cases. While test cases can easily be extracted from {em feasible paths} in the control flow graph, that is, paths which are actually exerted for some values of the program input, the feasible path region is a tiny fraction of the graph paths (less than $10^{-5}]$ for medium size programs). The S4T algorithm presented in this paper aims to address this limitation; as an Active Relational Learning Algorithm, it uses the few feasible paths initially available to sample new feasible paths. The difficulty comes from the non-Markovian nature of the feasible path concept, due to the long-range dependencies between the nodes in the control flow graph. Experimental validation on real-world and artificial problems demonstrates significant improvements compared to the state of the art.}, author = {Baskiotis,N. and Sebag,M. and De Raedt,L. and Dietterich,T. and Getoor, Lise and Kersting,K. and Muggleton,S. H} } @conference {18777, title = {A Survey of the Virtual Environments-based Assembly Training Applications}, year = {2008}, month = {2008///}, abstract = {The advent of virtual environments is presenting new ways of trainingtomorrow{\textquoteright}s workforce. Virtual environments offer numerous benefits in training applications. First, virtual environments allow extensive user interactions in a very convenient and natural manner. This interaction is greatly beneficial for increasing the user{\textquoteright}s retention of spatial information compared to text-based or video-based instructions that are non-interactive in nature. Second, virtual environments provide users with a 3D immersive experience. This feature helps users gain a better understanding of spatial relationships compared to 2D displays. Third, virtual environments support multi-media instructions. One can watch standard videos, view 3D animations, view text instructions, listen to audio instructions, and interact with 3D objects in the scene. This paper describes representative research and associated systems that use of virtual environments in assembly training applications. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.151.2892\&rep=rep1\&type=pdf}, author = {Gupta,S.K. and Anand,D. K. and Brough,J. E. and Kavetsky,R. A. and Schwartz,M. and Thakur,A.} } @conference {18867, title = {Towards Design and Fabrication of a Miniature MRI-Compatible Robot for Applications in Neurosurgery}, year = {2008}, month = {2008///}, pages = {747 - 754}, publisher = {ASME}, organization = {ASME}, abstract = {Brain tumors are among the most feared complications of cancer and they occur in 20{\textendash}40\% of adult cancer patients. Despite numerous advances in treatment, the prognosis for these patients is poor, with a median survival of 4{\textendash}8 months. The primary reasons for poor survival rate are the lack of good continuous imaging modality for intraoperative intracranial procedures and the inability to remove the complete tumor tissue due to its placement in the brain and the corresponding space constraints to reach it. Intraoperative magnetic resonance imaging (MRI) supplements the surgeon{\textquoteright}s visual and tactile senses in a way that no other imaging device can achieve resulting in less trauma to surrounding healthy brain tissue during surgery. To minimize the trauma to surrounding healthy brain tissue, it would be beneficial to operate through a narrow surgical corridor dissected by the neurosurgeon. Facilitating tumor removal by accessing regions outside the direct {\textquotedblleft}line-of-sight{\textquotedblright} of the neurosurgical corridor will require a highly dexterous, small cross section, and MRI-compatible robot. Developing such a robot is extremely challenging task. In this paper we report a preliminary design of 6-DOF robot for possible application in neurosurgery. The robot actuators and body parts are constructed from MRI compatible materials. The current prototype is 0.36{\textquotedblright} in diameter and weighs only 0.0289 N (2.95 grams). The device was actuated using Flexinol{\textregistered} which is a shape memory alloy manufactured by Dynalloy, Inc. The end-effector forces ranged from 12 mN to 50 mN depending on the robot configuration. The end-effector force to robot weight ratio varied from 0.41 to 1.73. During trials the robot motion was repeatable and the range of motion of the robot was about 90 degrees for the end-effector when one side shape memory alloy (SMA) channel was actuated. The actuation time from the start to finish was about 2.5 s.}, isbn = {978-0-7918-4326-0}, doi = {10.1115/DETC2008-49587}, url = {http://link.aip.org/link/ASMECP/v2008/i43260/p747/s1\&Agg=doi}, author = {Pappafotis,Nicholas and Bejgerowski,Wojciech and Gullapalli,Rao and Simard,J. Marc and Gupta, Satyandra K. and Desai,Jaydev P.} } @article {12243, title = {Trade-offs in matching jobs and balancing load for distributed desktop grids}, journal = {Future Generation Computer Systems}, volume = {24}, year = {2008}, month = {2008/05//}, pages = {415 - 424}, abstract = {Desktop grids~can achieve tremendous computing power at low cost through opportunistic sharing of resources. However, traditional client{\textendash}server Grid architectures do not deal with all types of failures, and do not always cope well with very dynamic environments. This paper describes the design of a desktop grid implemented over a modified Peer-to-Peer (P2P) architecture. The underlying P2P system is decentralized and inherently adaptable, giving the Grid robustness, scalability, and the ability to cope with dynamic environments, while still efficiently mapping application instances to available resources throughout the system.We use simulation to compare three different types of matching algorithms under differing workloads. Overall, the P2P approach produces significantly lower wait times than prior approaches, while adapting efficiently to the dynamic environment. }, keywords = {Desktop grid, load balancing, Matchmaking, peer-to-peer computing, Resource discovery}, isbn = {0167-739X}, doi = {10.1016/j.future.2007.07.007}, url = {http://www.sciencedirect.com/science/article/pii/S0167739X07001240}, author = {Kim,Jik-Soo and Nam,Beomseok and Keleher,Peter and Marsh,Michael and Bhattacharjee, Bobby and Sussman, Alan} } @conference {18608, title = {Trellis: a platform for building flexible, fast virtual networks on commodity hardware}, booktitle = {Proceedings of the 2008 ACM CoNEXT Conference}, series = {CoNEXT {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {72:1{\textendash}72:6 - 72:1{\textendash}72:6}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe Trellis, a platform for hosting virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topology, control protocols, and forwarding tables, while amortizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed virtual networks. We describe the design and implementation of Trellis and evaluate its packet-forwarding rates relative to other virtualization technologies and native kernel forwarding performance.}, isbn = {978-1-60558-210-8}, doi = {10.1145/1544012.1544084}, url = {http://doi.acm.org/10.1145/1544012.1544084}, author = {Bhatia,Sapan and Motiwala,Murtaza and Muhlbauer,Wolfgang and Mundada,Yogesh and Valancius,Vytautas and Bavier,Andy and Feamster, Nick and Peterson,Larry and Rexford,Jennifer} } @article {18609, title = {UFO: a resilient layered routing architecture}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {38}, year = {2008}, month = {2008/09//}, pages = {59 - 62}, abstract = {Conventional wisdom has held that routing protocols cannot achieve both scalability and high availability. Despite scaling relatively well, today{\textquoteright}s Internet routing system does not react quickly to changing network conditions (e.g., link failures or excessive congestion). Overlay networks, on the other hand, can respond quickly to changing network conditions, but their reliance on aggressive probing does not scale to large topologies. The paper presents a layered routing architecture called UFO (Underlay Fused with Overlays), which achieves the best of both worlds by having the "underlay" provide explicit notification about network conditions to help improve the efficiency and scalability of routing overlays.}, keywords = {network monitoring, overlay networks, routing architecture}, isbn = {0146-4833}, doi = {10.1145/1452335.1452344}, url = {http://doi.acm.org/10.1145/1452335.1452344}, author = {Zhu,Yaping and Bavier,Andy and Feamster, Nick and Rangarajan,Sampath and Rexford,Jennifer} } @article {18448, title = {Understanding the High-Performance-Computing Community: A Software Engineer{\textquoteright}s Perspective}, journal = {Software, IEEE}, volume = {25}, year = {2008}, month = {2008/08//july}, pages = {29 - 36}, abstract = {Computational scientists developing software for HPC systems face unique software engineering issues. Attempts to transfer SE technologies to this domain must take these issues into account.}, keywords = {community;software, computational, engineering;, engineering;software, Science, software;high-performance-computing}, isbn = {0740-7459}, doi = {10.1109/MS.2008.103}, author = {Basili, Victor R. and Carver, J. C and Cruzes, D. and Hochstein, L. M and Hollingsworth, Jeffrey K and Shull, F. and Zelkowitz, Marvin V} } @article {12242, title = {A Unified Framework for Multipath Routing for Unicast and Multicast Traffic}, journal = {Networking, IEEE/ACM Transactions on}, volume = {16}, year = {2008}, month = {2008/10//}, pages = {1038 - 1051}, abstract = {We study the problem of load balancing the traffic from a set of unicast and multicast sessions. The problem is formulated as an optimization problem. However, we assume that the gradient of the network cost function is not available and needs to be estimated. Multiple paths are provided between a source and a destination using application-layer overlay. We propose a novel algorithm that is based on what is known as simultaneous perturbation stochastic approximation and utilizes only noisy measurements collected and reported to the sources, using an overlay architecture. We consider three network models that reflect different sets of assumptions regarding multicast capabilities of the network. Using an analytical model we first prove the almost sure convergence of the algorithm to a corresponding optimal solution under each network model considered in this paper with decreasing step sizes. Then, we establish the weak convergence (or convergence in distribution) with a fixed step size. In addition, we investigate the benefits acquired from implementing additional multicast capabilities by studying the relative performance of our algorithm under the three network models.}, keywords = {application-layer, approximation;unicast, balancing;multicast, channels;stochastic, communication;multipath, cost, function;optimization, network, overlay;load, perturbation, problem;simultaneous, processes;telecommunication, routing;network, routing;telecommunication, Stochastic, traffic;, traffic;multicast, traffic;multipath}, isbn = {1063-6692}, doi = {10.1109/TNET.2007.909686}, author = {Guven,T. and La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @conference {12263, title = {Accountability as a service}, booktitle = {Proceedings of the 3rd USENIX workshop on Steps to reducing unwanted traffic on the internet}, series = {SRUTI{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {5:1{\textendash}5:6 - 5:1{\textendash}5:6}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {We propose that accountability be a first-class network service, independent of addressing and routing. We design a scheme for allowing accountability services, rather than connectivity-providing ISPs, to vouch for traffic, allowing victims to report abuse, filter abusive traffic, and isolate malicious senders. We discuss how accountability services may evolve, how they may facilitate new applications, and the implications of shifting the burden of network policing to a dedicated service.}, url = {http://dl.acm.org/citation.cfm?id=1361436.1361441}, author = {Bender,Adam and Spring, Neil and Levin,Dave and Bhattacharjee, Bobby} } @article {18734, title = {Algorithms for on-line monitoring of micro spheres in an optical tweezers-based assembly cell}, journal = {Journal of Computing and Information Science in Engineering}, volume = {7}, year = {2007}, month = {2007///}, pages = {330 - 330}, abstract = {Optical tweezers have emerged as a powerful tool for microand nanomanipulation. Using optical tweezers to perform auto- mated assembly requires on-line monitoring of components in the assembly workspace. This paper presents algorithms for estimat- ing positions and orientations of microscale and nanoscale com- ponents in the 3-Dimensional assembly workspace. Algorithms presented in this paper use images obtained by optical section microscopy. The images are first segmented to locate areas of in- terest and then image gradient information from the areas of in- terest is used to generate probable locations and orientations of components in the XY-plane. Finally, signature curves are com- puted and utilized to obtain component locations and orienta- tions in 3-D space. We have tested these algorithms with silica micro-spheres as well as metallic nanowires. We believe that the algorithms described in this paper will provide the foundation for realizing automated assembly operations in optical tweezers- based assembly cells. }, author = {Peng,T. and Balijepalli,A. and Gupta,S.K. and LeBrun,T.} } @article {13421, title = {Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids}, journal = {Protein Engineering Design and SelectionProtein Engineering, Design and Selection}, volume = {20}, year = {2007}, month = {2007/07/01/}, pages = {347 - 351}, abstract = {Here, we present the AA-QSPR Db (Amino Acid Quantitative Structure Property Relationship Database): a novel, freely available web-resource of data pertaining to amino acids, both engineered and naturally occurring. In addition to presenting fundamental molecular descriptors of size, charge and hydrophobicity, it also includes online visualization tools for users to perform instant, interactive analyses of amino acid sub-sets in which they are interested. The database has been designed with extensible markup language technology to provide a flexible structure, suitable for future development. In addition to providing easy access for queries by external computers, it also offers a user-friendly web-based interface that facilitates human interactions (submission, storage and retrieval of amino acid data) and an associated e-forum that encourages users to question and discuss current and future database contents.}, keywords = {Amino acids, database, QSPR, XML}, isbn = {1741-0126, 1741-0134}, doi = {10.1093/protein/gzm027}, url = {http://peds.oxfordjournals.org/content/20/7/347}, author = {Lu,Yi and Bulka,Blazej and desJardins, Marie and Freeland,Stephen J} } @conference {15460, title = {Automated gui testing guided by usage profiles}, booktitle = {Proceedings of the twenty-second IEEE/ACM international conference on Automated software engineering}, series = {ASE {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {333 - 342}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Most software developed in recent years has a graphical userinterface (GUI). The only way for the end-user to interact with the software application is through the GUI. Hence, acceptance and system testing of the software requires GUI testing. This paper presents a new technique for testing of GUI applications. Information on the actual usage of the application, in the form of "usage profiles," is used to ensure that a new version of the application will function correctly. Usage profiles, sequences of events that end-users execute on a GUI, are used to develop a probabilistic usage model of the application. An algorithm uses the model to generate test cases that represent events the user is most likely to execute. Reverse engineering methods are used to extract the underlying structure of the application. An empirical study on four open source GUI applications reveals that test suites generated from the probabilistic model are 0.2-22\% of the size of test suites produced directly from usage profiles. Furthermore, the test suites generated from the model detect more faults per test case than those detected directly from the usage profiles, and detect faults not detected by the original profiles}, keywords = {event-driven software, GUI testing, usage profiles}, isbn = {978-1-59593-882-4}, doi = {10.1145/1321631.1321681}, url = {http://doi.acm.org/10.1145/1321631.1321681}, author = {Brooks,Penelope A. and Memon, Atif M.} } @article {16862, title = {Autonomic computing}, journal = {IEEE internet computing}, volume = {11}, year = {2007}, month = {2007///}, pages = {52 - 59}, author = {Brabec,F. and Samet, Hanan} } @conference {12258, title = {Backbone construction in selfish wireless networks}, booktitle = {Proceedings of the 2007 ACM SIGMETRICS international conference on Measurement and modeling of computer systems}, series = {SIGMETRICS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {121 - 132}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a protocol to construct routing backbones in wireless networks composed of selfish participants. Backbones are inherently cooperative, so constructing them in selfish environments is particularly difficult; participants want a backbone to exist (soothers relay their packets) but do not want to join the backbone (so they do not have to relay packets for others). We model the wireless backbone as a public good and use impatience as an incentive for cooperation. To determine if and when to donate to this public good, each participant calculates how patient it should be in obtaining the public good. We quantify patience using the Volunteer{\textquoteright}s Timing Dilemma (VTD), which we extend to general multihop network settings. Using our generalized VTD analysis, each node individually computes as its dominant strategy the amount of time to wait before joining the backbone. We evaluate our protocol using both simulations and an implementation. Our results show that, even though participants in our system deliberately wait before volunteering, a backbone is formed quickly. Further, the quality of the backbone (such as the size and resulting network lifetime) is comparable to that of existing backbone protocols that assume altruistic behavior.}, keywords = {incentives, public good, selfish network, volunteer{\textquoteright}s dilemma, wireless backbone}, isbn = {978-1-59593-639-4}, doi = {10.1145/1254882.1254896}, url = {http://doi.acm.org/10.1145/1254882.1254896}, author = {Lee,Seungjoon and Levin,Dave and Gopalakrishnan,Vijay and Bhattacharjee, Bobby} } @article {16076, title = {BELIV{\textquoteright}06: beyond time and errors: novel evaluation methods for information visualization}, journal = {interactions}, volume = {14}, year = {2007}, month = {2007/05//}, pages = {59 - 60}, isbn = {1072-5520}, doi = {10.1145/1242421.1242460}, url = {http://doi.acm.org/10.1145/1242421.1242460}, author = {Bertini,Enrico and Plaisant, Catherine and Santucci,Giuseppe} } @article {12345, title = {Beyond single-appearance schedules: Efficient DSP software synthesis using nested procedure calls}, journal = {ACM Transactions on Embedded Computing Systems (TECS)}, volume = {6}, year = {2007}, month = {2007///}, pages = {14{\textendash}es - 14{\textendash}es}, author = {Ko,M. Y and Murthy,P. K and Bhattacharyya, Shuvra S.} } @article {12257, title = {Boycotting and extorting nodes in an internetwork}, journal = {NetE-con+ IBC}, year = {2007}, month = {2007///}, author = {Levin,D. and Bender,A. and Lumezanu,C. and Spring, Neil and Bhattacharjee, Bobby} } @article {12215, title = {Capture, annotate, browse, find, share: novel interfaces for personal photo management}, journal = {International Journal of Human-] Computer Interaction}, volume = {23}, year = {2007}, month = {2007///}, pages = {315 - 337}, author = {Kang,H. and Bederson, Benjamin B. and Suh,B.} } @article {14556, title = {Cell breathing in wireless LANs: Algorithms and evaluation}, journal = {IEEE Transactions on Mobile Computing}, volume = {6}, year = {2007}, month = {2007///}, pages = {164 - 178}, author = {Hajiaghayi, Mohammad T. and Mirrokni,S. V. and Saberi,A. and Bahl,P. and Jain,K. and Qiu,L.} } @conference {13926, title = {Children{\textquoteright}s interests and concerns when using the international children{\textquoteright}s digital library: a four-country case study}, booktitle = {Proceedings of the 7th ACM/IEEE-CS joint conference on Digital libraries}, year = {2007}, month = {2007///}, pages = {167 - 176}, author = {Druin, Allison and Weeks,A. and Massey,S. and Bederson, Benjamin B.} } @article {12260, title = {Chit-based access control}, year = {2007}, month = {2007///}, institution = {Technical Report CS-TR-4878, University of Maryland at College Park}, author = {Keleher,P. J and Spring, Neil and Bhattacharjee, Bobby} } @article {15156, title = {Chosen-ciphertext security from identity-based encryption}, journal = {SIAM Journal on Computing}, volume = {36}, year = {2007}, month = {2007///}, pages = {1301 - 1328}, abstract = {We propose simple and efficient CCA-secure public-key encryption schemes (i.e., schemessecure against adaptive chosen-ciphertext attacks) based on any identity-based encryption (IBE) scheme. Our constructions have ramifications of both theoretical and practical interest. First, our schemes give a new paradigm for achieving CCA-security; this paradigm avoids {\textquotedblleft}proofs of well-formedness{\textquotedblright} that have been shown to underlie previous constructions. Second, instantiating our construction using known IBE constructions we obtain CCA-secure encryption schemes whose performance is competitive with the most efficient CCA-secure schemes to date. Our techniques extend naturally to give an efficient method for securing IBE schemes (even hierarchical ones) against adaptive chosen-ciphertext attacks. Coupled with previous work, this gives the first efficient constructions of CCA-secure IBE schemes. }, author = {Boneh,D. and Canetti,R. and Halevi,S. and Katz, Jonathan} } @article {16861, title = {Client-Based Spatial Browsing on the World Wide Web}, journal = {IEEE Internet Computing}, volume = {11}, year = {2007}, month = {2007///}, pages = {52 - 59}, abstract = {Being able to visualize both spatial and nonspatial data is becoming increasingly important to today{\textquoteright}s Internet users. Spatial data viewers and query tools can aid in visualization, but they should also let users access data instantly and with minimal effort. The authors explore new ways to allow visualization of data stored in a central server database on a simple client. They also consider usage scenarios in which transferring the whole database to the client for processing isn{\textquoteright}t feasible due to the amount of data on the server, insufficient computing power on the client, and a slow link between the two.}, keywords = {client-server spatial browsing, geographic information systems (GIS), Spatial databases, web access, web-based mapping}, isbn = {1089-7801}, author = {Brabec,Frantisek and Samet, Hanan} } @article {14103, title = {Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei}, journal = {Parasitology research}, volume = {100}, year = {2007}, month = {2007///}, pages = {887 - 892}, author = {Djikeng,A. and Raverdy,S. and Foster, Jeffrey S. and Bartholomeu,D. and Zhang,Y. and El-Sayed, Najib M. and Carlow,C.} } @article {14365, title = {Collective entity resolution in relational data}, journal = {ACM Trans. Knowl. Discov. Data}, volume = {1}, year = {2007}, month = {2007/03//}, abstract = {Many databases contain uncertain and imprecise references to real-world entities. The absence of identifiers for the underlying entities often results in a database which contains multiple references to the same entity. This can lead not only to data redundancy, but also inaccuracies in query processing and knowledge extraction. These problems can be alleviated through the use of entity resolution. Entity resolution involves discovering the underlying entities and mapping each database reference to these entities. Traditionally, entities are resolved using pairwise similarity over the attributes of references. However, there is often additional relational information in the data. Specifically, references to different entities may cooccur. In these cases, collective entity resolution, in which entities for cooccurring references are determined jointly rather than independently, can improve entity resolution accuracy. We propose a novel relational clustering algorithm that uses both attribute and relational information for determining the underlying domain entities, and we give an efficient implementation. We investigate the impact that different relational similarity measures have on entity resolution quality. We evaluate our collective entity resolution algorithm on multiple real-world databases. We show that it improves entity resolution performance over both attribute-based baselines and over algorithms that consider relational information but do not resolve entities collectively. In addition, we perform detailed experiments on synthetically generated data to identify data characteristics that favor collective relational resolution over purely attribute-based algorithms.}, keywords = {data cleaning, entity resolution, graph clustering, record linkage}, isbn = {1556-4681}, doi = {10.1145/1217299.1217304}, url = {http://doi.acm.org/10.1145/1217299.1217304}, author = {Bhattacharya,Indrajit and Getoor, Lise} } @conference {14388, title = {Combining Collective Classification and Link Prediction}, booktitle = {Data Mining Workshops, 2007. ICDM Workshops 2007. Seventh IEEE International Conference on}, year = {2007}, month = {2007/10//}, pages = {381 - 386}, abstract = {The problems of object classification (labeling the nodes of a graph) and link prediction (predicting the links in a graph) have been largely studied independently. Commonly, object classification is performed assuming a complete set of known links and link prediction is done assuming a fully observed set of node attributes. In most real world domains, however, attributes and links are often missing or incorrect. Object classification is not provided with all the links relevant to correct classification and link prediction is not provided all the labels needed for accurate link prediction. In this paper, we propose an approach that addresses these two problems by interleaving object classification and link prediction in a collective algorithm. We investigate empirically the conditions under which an integrated approach to object classification and link prediction improves performance, and find that performance improves over a wide range of network types, and algorithm settings.}, keywords = {algorithm;link, classification;, classification;graph, collective, prediction;object, theory;pattern}, doi = {10.1109/ICDMW.2007.35}, author = {Bilgic,M. and Namata,G.M. and Getoor, Lise} } @conference {14207, title = {Combining motion from texture and lines for visual navigation}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems, 2007. IROS 2007}, year = {2007}, month = {2007/11/29/Oct. }, pages = {232 - 239}, publisher = {IEEE}, organization = {IEEE}, abstract = {Two novel methods for computing 3D structure information from video for a piecewise planar scene are presented. The first method is based on a new line constraint, which clearly separates the estimation of distance from the estimation of slant. The second method exploits the concepts of phase correlation to compute from the change of image frequencies of a textured plane, distance and slant information. The two different estimates together with structure estimates from classical image motion are combined and integrated over time using an extended Kalman filter. The estimation of the scene structure is demonstrated experimentally in a motion control algorithm that allows the robot to move along a corridor. We demonstrate the efficacy of each individual method and their combination and show that the method allows for visual navigation in textured as well as un-textured environments.}, keywords = {3D structure information, CAMERAS, Computer vision, extended Kalman filter, Frequency, image frequencies, Image motion analysis, Image texture, Kalman filters, Layout, motion control, Motion estimation, Navigation, Optical computing, phase correlation, piecewise planar scene, Robustness, Simultaneous localization and mapping, Speech processing, textured plane, video signal processing, visual navigation}, isbn = {978-1-4244-0912-9}, doi = {10.1109/IROS.2007.4399568}, author = {Bitsakos,K. and Li Yi and Ferm{\"u}ller, Cornelia} } @conference {12351, title = {Compact, low power wireless sensor network system for line crossing recognition}, booktitle = {Circuits and Systems, 2007. ISCAS 2007. IEEE International Symposium on}, year = {2007}, month = {2007///}, pages = {2506 - 2509}, author = {Shen,C. C and Kupershtok,R. and Yang,B. and Vanin,F. M and Shao,X. and Sheth,D. and Goldsman,N. and Balzano,Q. and Bhattacharyya, Shuvra S.} } @conference {12252, title = {Creating a Robust Desktop Grid using Peer-to-Peer Services}, booktitle = {Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International}, year = {2007}, month = {2007/03//}, pages = {1 - 7}, abstract = {The goal of the work described in this paper is to design and build a scalable infrastructure for executing grid applications on a widely distributed set of resources. Such grid infrastructure must be decentralized, robust, highly available, and scalable, while efficiently mapping application instances to available resources in the system. However, current desktop grid computing platforms are typically based on a client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. Fortunately, these problems can be addressed through the capabilities promised by new techniques and approaches in peer-to-peer (P2P) systems. By employing P2P services, our system allows users to submit jobs to be run in the system and to run jobs submitted by other users on any resources available in the system, essentially allowing a group of users to form an ad-hoc set of shared resources. The initial target application areas for the desktop grid system are in astronomy and space science simulation and data analysis.}, keywords = {allocation;, architecture;load, balancing;peer-to-peer, client-server, computing;peer-to-peer, computing;resource, desktop, grid;scalable, infrastructure;client-server, system;robust, systems;grid}, doi = {10.1109/IPDPS.2007.370505}, author = {Kim,J.-S. and Nam,B. and Marsh,M. and Keleher,P. and Bhattacharjee, Bobby and Richardson,D. and Wellnitz,D. and Sussman, Alan} } @article {13361, title = {Data Management in the Worldwide Sensor Web}, journal = {IEEE Pervasive Computing}, volume = {6}, year = {2007}, month = {2007///}, pages = {30 - 40}, abstract = {Advances in hardware and miniaturization technologies have led to a rapid increase in the number of large-scale sensor network deployments around the world, bringing us closer to the vision of a worldwide sensor web. Exploiting the sensor web to its full potential, however, raises several hard data management challenges. Addressing these challenges requires a concerted multidisciplinary effort encompassing many computer science fields. This article outlines some of the key data management challenges of a worldwide sensor web. It also presents recent advances in data management research that aim to address these challenges. Hopefully, the scientific, ubiquitous computing, and sensor network communities will adopt some of these solutions for managing their data. The article also attempts to bring many of the remaining open issues to the attention of the database community. This article is part of a special issue on Building a Sensor-Rich World.}, keywords = {data modeling, data streams, data uncertainty, distributed systems, interoperability, sensor networks}, isbn = {1536-1268}, author = {Balazinska,Magdalena and Deshpande, Amol and Franklin,Michael J. and Gibbons,Phillip B. and Gray,Jim and Hansen,Mark and Liebhold,Michael and Nath,Suman and Szalay,Alexander and Tao,Vincent} } @article {12326, title = {Dataflow-based mapping of computer vision algorithms onto FPGAs}, journal = {EURASIP Journal on Embedded Systems}, volume = {2007}, year = {2007}, month = {2007///}, pages = {29 - 29}, author = {Sen,M. and Corretjer,I. and Haim,F. and Saha,S. and Schlessman,J. and Lv,T. and Bhattacharyya, Shuvra S. and Wolf,W.} } @booklet {19446, title = {Description of Computer Science Higher Education in Sub-Saharan Africa: Initial Explorations}, year = {2007}, month = {2007///}, abstract = {Many countries in Sub-Saharan Africa (SSA) are in need oftechnology innovators who are equipped to leverage technologies in locally relevant domains such as health, government and education. To create skilled graduates who can build and shape locally relevant technologies, higher education institutes in Africa must have Computer Science (CS) education programs that meet local needs, for example, to satisfy the demand for entrepreneurs to build industry and strengthen an economy. This paper characterizes the current state of CS education in SSA in order to identify opportunities for addressing education challenges and to make suggestions that may improve the Information and Communication Technology (ICT) infrastructure in this region. We present the results of a survey of CS educators in SSA institutions of higher education, which was aimed at exploring the issues they face. In addition to the continued chronic under-funding of SSA education, we found that universities in SSA have smaller departments, less focus on Human Computer Interaction (HCI) and offer a variety of courses aside from undergraduate Bachelors degrees. We discuss directions to improve CS curricula through investing in locally tailored courses and changing perceptions of the value of SSA CS higher education programs, standards and educators. Further, we reflect on the challenges of conducting research on SSA. We conclude that further research in this area is needed to build on the ideas we offer here to continue to strengthen CS higher education in SSA. }, keywords = {Sub-Saharan Africa, Undergraduate computing education}, doi = {Technical Report}, url = {https://smartech.gatech.edu/handle/1853/20060}, author = {Marshini Chetty and Buckhalter, Celeste and Best, Michael L. and Grinter, Rebecca E. and Guzdial, Mark} } @article {18756, title = {Development of in-mold assembly process for realizing mesoscale revolute joints}, journal = {Transactions of North American Manufacturing Research Institution of SME}, volume = {35}, year = {2007}, month = {2007///}, abstract = {In-mold Assembly process at the mesoscalepresents several manufacturing challenges. Results reported in this paper demonstrate the technical feasibility of creating rigid body mesoscale revolute joints using In-Mold Assembly process. The following new results are reported in this paper. First, we describe a mold design with varying cavity shape to perform In-Mold Assembly. This mold design uses an accurate mold piece positioning method to avoid damage to delicate mesoscale parts during the cavity change step. Second, we describe a mold insert fabrication process for making mold inserts with the desired surface characteristics for mesoscale molding. Finally, we describe methods to limit the adhesion at the interfaces and hence create articulated revolute joint. Using the advances reported in this paper we have successfully molded a mesoscale revolute joint. To the best of our knowledge, this is the first demonstration of In-Mold Assembly process using a varying cavity shape mold to create a mesoscale revolute joint. }, url = {ftp://ftp.eng.umd.edu/:/home/glue/s/k/skgupta/pub/Publication/NAMRC07_Ananthanarayanan_draft.pdf}, author = {Ananthanarayanan,A. and Gupta,S.K. and Bruck,H. A. and Yu,Z. and Rajurkar,K. P.} } @article {12261, title = {Distributed ranked search}, journal = {High Performance Computing{\textendash}HiPC 2007}, year = {2007}, month = {2007///}, pages = {7 - 20}, abstract = {P2P deployments are a natural infrastructure for building distributed search networks. Proposed systems support locating and retrieving all results, but lack the information necessary to rank them. Users, however, are primarily interested in the most relevant results, not necessarily all possible results.Using random sampling, we extend a class of well-known information retrieval ranking algorithms such that they can be applied in this decentralized setting. We analyze the overhead of our approach, and quantify how our system scales with increasing number of documents, system size, document to node mapping (uniform versus non-uniform), and types of queries (rare versus popular terms). Our analysis and simulations show that a) these extensions are efficient, and scale with little overhead to large systems, and b) the accuracy of the results obtained using distributed ranking is comparable to that of a centralized implementation. }, author = {Gopalakrishnan,V. and Morselli,R. and Bhattacharjee, Bobby and Keleher,P. and Srinivasan, Aravind} } @inbook {17584, title = {Distributed Ranked Search}, booktitle = {High Performance Computing {\textendash} HiPC 2007High Performance Computing {\textendash} HiPC 2007}, series = {Lecture Notes in Computer Science}, volume = {4873}, year = {2007}, month = {2007///}, pages = {7 - 20}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {P2P deployments are a natural infrastructure for building distributed search networks. Proposed systems support locating and retrieving all results, but lack the information necessary to rank them. Users, however, are primarily interested in the most relevant results, not necessarily all possible results. Using random sampling, we extend a class of well-known information retrieval ranking algorithms such that they can be applied in this decentralized setting. We analyze the overhead of our approach, and quantify how our system scales with increasing number of documents, system size, document to node mapping (uniform versus non-uniform), and types of queries (rare versus popular terms). Our analysis and simulations show that a) these extensions are efficient, and scale with little overhead to large systems, and b) the accuracy of the results obtained using distributed ranking is comparable to that of a centralized implementation.}, isbn = {978-3-540-77219-4}, url = {http://dx.doi.org/10.1007/978-3-540-77220-0_6}, author = {Gopalakrishnan,Vijay and Morselli,Ruggero and Bhattacharjee, Bobby and Keleher,Pete and Srinivasan, Aravind}, editor = {Aluru,Srinivas and Parashar,Manish and Badrinath,Ramamurthy and Prasanna,Viktor} } @article {16257, title = {Draft Genome of the Filarial Nematode Parasite Brugia Malayi}, journal = {Science}, volume = {317}, year = {2007}, month = {2007/09/21/}, pages = {1756 - 1760}, abstract = {Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the \~{}90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict \~{}11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during \~{}350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1145406}, url = {http://www.sciencemag.org/content/317/5845/1756}, author = {Ghedin,Elodie and Wang,Shiliang and Spiro,David and Caler,Elisabet and Zhao,Qi and Crabtree,Jonathan and Allen,Jonathan E and Delcher,Arthur L. and Guiliano,David B and Miranda-Saavedra,Diego and Angiuoli,Samuel V and Creasy,Todd and Amedeo,Paolo and Haas,Brian and El-Sayed, Najib M. and Wortman,Jennifer R. and Feldblyum,Tamara and Tallon,Luke and Schatz,Michael and Shumway,Martin and Koo,Hean and Salzberg,Steven L. and Schobel,Seth and Pertea,Mihaela and Pop, Mihai and White,Owen and Barton,Geoffrey J and Carlow,Clotilde K. S and Crawford,Michael J and Daub,Jennifer and Dimmic,Matthew W and Estes,Chris F and Foster,Jeremy M and Ganatra,Mehul and Gregory,William F and Johnson,Nicholas M and Jin,Jinming and Komuniecki,Richard and Korf,Ian and Kumar,Sanjay and Laney,Sandra and Li,Ben-Wen and Li,Wen and Lindblom,Tim H and Lustigman,Sara and Ma,Dong and Maina,Claude V and Martin,David M. A and McCarter,James P and McReynolds,Larry and Mitreva,Makedonka and Nutman,Thomas B and Parkinson,John and Peregr{\'\i}n-Alvarez,Jos{\'e} M and Poole,Catherine and Ren,Qinghu and Saunders,Lori and Sluder,Ann E and Smith,Katherine and Stanke,Mario and Unnasch,Thomas R and Ware,Jenna and Wei,Aguan D and Weil,Gary and Williams,Deryck J and Zhang,Yinhua and Williams,Steven A and Fraser-Liggett,Claire and Slatko,Barton and Blaxter,Mark L and Scott,Alan L} } @article {12186, title = {EcoLens: Integration and interactive visualization of ecological datasets}, journal = {Ecological Informatics}, volume = {2}, year = {2007}, month = {2007/01/01/}, pages = {61 - 69}, abstract = {Complex multi-dimensional datasets are now pervasive in science and elsewhere in society. Better interactive tools are needed for visual data exploration so that patterns in such data may be easily discovered, data can be proofread, and subsets of data can be chosen for algorithmic analysis. In particular, synthetic research such as ecological interaction research demands effective ways to examine multiple datasets. This paper describes our integration of hundreds of food-web datasets into a common platform, and the visualization software, EcoLens, we developed for exploring this information. This publicly-available application and integrated dataset have been useful for our research predicting large complex food webs, and EcoLens is favorably reviewed by other researchers. Many habitats are not well represented in our large database. We confirm earlier results about the small size and lack of taxonomic resolution in early food webs but find that they and a non-food-web source provide trophic information about a large number of taxa absent from more modern studies. Corroboration of Tuesday Lake trophic links across studies is usually possible, but lack of links among congeners may have several explanations. While EcoLens does not provide all kinds of analytical support, its label- and item-based approach is effective at addressing concerns about the comparability and taxonomic resolution of food-web data.}, keywords = {Data integration, Food webs, Taxonomy, Visualization}, isbn = {1574-9541}, doi = {10.1016/j.ecoinf.2007.03.005}, url = {http://www.sciencedirect.com/science/article/pii/S1574954107000118}, author = {Parr,Cynthia Sims and Lee,Bongshin and Bederson, Benjamin B.} } @conference {12588, title = {Efficient Indexing For Articulation Invariant Shape Matching And Retrieval}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {Most shape matching methods are either fast but too simplistic to give the desired performance or promising as far as performance is concerned but computationally demanding. In this paper, we present a very simple and efficient approach that not only performs almost as good as many state-of-the-art techniques but also scales up to large databases. In the proposed approach, each shape is indexed based on a variety of simple and easily computable features which are invariant to articulations and rigid transformations. The features characterize pairwise geometric relationships between interest points on the shape, thereby providing robustness to the approach. Shapes are retrieved using an efficient scheme which does not involve costly operations like shape-wise alignment or establishing correspondences. Even for a moderate size database of 1000 shapes, the retrieval process is several times faster than most techniques with similar performance. Extensive experimental results are presented to illustrate the advantages of our approach as compared to the best in the field.}, keywords = {alignment;image, articulation, geometric, invariant, matching;image, matching;indexing;invariant, relationships;shape-wise, retrieval;indexing;, retrieval;pairwise, SHAPE}, doi = {10.1109/CVPR.2007.383227}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @article {17591, title = {Efficient lookup on unstructured topologies}, journal = {IEEE Journal on Selected Areas in Communications}, volume = {25}, year = {2007}, month = {2007/01//}, pages = {62 - 72}, abstract = {We present LMS, a protocol for efficient lookup on unstructured networks. Our protocol uses a virtual namespace without imposing specific topologies. It is more efficient than existing lookup protocols for unstructured networks, and thus is an attractive alternative for applications in which the topology cannot be structured as a Distributed Hash Table (DHT). We present analytic bounds for the worst-case performance of LMS. Through detailed simulations (with up to 100,000 nodes), we show that the actual performance on realistic topologies is significantly better. We also show in both simulations and a complete implementation (which includes over five hundred nodes) that our protocol is inherently robust against multiple node failures and can adapt its replication strategy to optimize searches according to a specific heuristic. Moreover, the simulation demonstrates the resilience of LMS to high node turnover rates, and that it can easily adapt to orders of magnitude changes in network size. The overhead incurred by LMS is small, and its performance approaches that of DHTs on networks of similar size}, keywords = {Computer science, DHT, distributed algorithms, Distributed computing, distributed hash table, Least squares approximation, LMS, local minima search, lookup protocol, Network topology, node failures, Peer to peer computing, Performance analysis, Protocols, replication strategy, Resilience, Robustness, table lookup, telecommunication network topology, unstructured network topology}, isbn = {0733-8716}, doi = {10.1109/JSAC.2007.07007}, author = {Morselli,R. and Bhattacharjee, Bobby and Marsh,M.A. and Srinivasan, Aravind} } @article {12346, title = {Efficient parallel memory organization for turbo decoders}, journal = {Red}, volume = {5}, year = {2007}, month = {2007///}, author = {Salmela,P. and Gu,R. and Bhattacharyya, Shuvra S. and Takala,J.} } @article {12357, title = {Efficient simulation of critical synchronous dataflow graphs}, journal = {ACM Transactions on Design Automation of Electronic Systems (TODAES)}, volume = {12}, year = {2007}, month = {2007///}, pages = {1 - 28}, author = {Hsu,C. J and Ko,M. Y and Bhattacharyya, Shuvra S. and Ramasubbu,S. and Pino,J. L} } @article {12130, title = {Empirical studies to build a science of computer science}, journal = {Communications of the ACM}, volume = {50}, year = {2007}, month = {2007/11//}, pages = {33 - 37}, abstract = {We learn to develop software by building, testing, and evolving models.}, isbn = {0001-0782}, doi = {10.1145/1297797.1297819}, url = {http://doi.acm.org/10.1145/1297797.1297819}, author = {Basili, Victor R. and Zelkowitz, Marvin V} } @conference {12330, title = {Energy-aware data compression for wireless sensor networks}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007///}, pages = {II{\textendash}45 - II{\textendash}45}, author = {Puthenpurayil,S. and Gu,R. and Bhattacharyya, Shuvra S.} } @conference {12382, title = {An energy-driven design methodology for distributing DSP applications across wireless sensor networks}, booktitle = {Proceedings of RTSS}, year = {2007}, month = {2007///}, pages = {214 - 226}, author = {Shen,C. C and Plishker,W. and Bhattacharyya, Shuvra S. and Goldsman,N.} } @article {12118, title = {An Environment of Conducting Families of Software Engineering Experiments}, year = {2007}, month = {2007/05//}, institution = {University of Maryland, College Park}, abstract = {The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. This paper describes an environment that simplifies the process of collecting, managing and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages on programmer productivity at multiple universities across the United States.}, keywords = {collecting data, managing data, parallel programming languages, sanitizing data, software engineering experiments, universities}, url = {http://drum.lib.umd.edu/handle/1903/7545}, author = {Hochstein, Lorin and Nakamura,Taiga and Shull, Forrest and Zazworka, Nico and Voelp,Martin and Zelkowitz, Marvin V and Basili, Victor R.} } @article {16261, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007/11/08/}, pages = {203 - 218}, abstract = {Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.}, isbn = {0028-0836}, doi = {10.1038/nature06341}, url = {http://www.nature.com/nature/journal/v450/n7167/full/nature06341.html}, author = {Clark,Andrew G. and Eisen,Michael B. and Smith,Douglas R. and Bergman,Casey M. and Oliver,Brian and Markow,Therese A. and Kaufman,Thomas C. and Kellis,Manolis and Gelbart,William and Iyer,Venky N. and Pollard,Daniel A. and Sackton,Timothy B. and Larracuente,Amanda M. and Singh,Nadia D. and Abad,Jose P. and Abt,Dawn N. and Adryan,Boris and Aguade,Montserrat and Akashi,Hiroshi and Anderson,Wyatt W. and Aquadro,Charles F. and Ardell,David H. and Arguello,Roman and Artieri,Carlo G. and Barbash,Daniel A. and Barker,Daniel and Barsanti,Paolo and Batterham,Phil and Batzoglou,Serafim and Begun,Dave and Bhutkar,Arjun and Blanco,Enrico and Bosak,Stephanie A. and Bradley,Robert K. and Brand,Adrianne D. and Brent,Michael R. and Brooks,Angela N. and Brown,Randall H. and Butlin,Roger K. and Caggese,Corrado and Calvi,Brian R. and Carvalho,A. Bernardo de and Caspi,Anat and Castrezana,Sergio and Celniker,Susan E. and Chang,Jean L. and Chapple,Charles and Chatterji,Sourav and Chinwalla,Asif and Civetta,Alberto and Clifton,Sandra W. and Comeron,Josep M. and Costello,James C. and Coyne,Jerry A. and Daub,Jennifer and David,Robert G. and Delcher,Arthur L. and Delehaunty,Kim and Do,Chuong B. and Ebling,Heather and Edwards,Kevin and Eickbush,Thomas and Evans,Jay D. and Filipski,Alan and Findei|[szlig]|,Sven and Freyhult,Eva and Fulton,Lucinda and Fulton,Robert and Garcia,Ana C. L. and Gardiner,Anastasia and Garfield,David A. and Garvin,Barry E. and Gibson,Greg and Gilbert,Don and Gnerre,Sante and Godfrey,Jennifer and Good,Robert and Gotea,Valer and Gravely,Brenton and Greenberg,Anthony J. and Griffiths-Jones,Sam and Gross,Samuel and Guigo,Roderic and Gustafson,Erik A. and Haerty,Wilfried and Hahn,Matthew W. and Halligan,Daniel L. and Halpern,Aaron L. and Halter,Gillian M. and Han,Mira V. and Heger,Andreas and Hillier,LaDeana and Hinrichs,Angie S. and Holmes,Ian and Hoskins,Roger A. and Hubisz,Melissa J. and Hultmark,Dan and Huntley,Melanie A. and Jaffe,David B. and Jagadeeshan,Santosh and Jeck,William R. and Johnson,Justin and Jones,Corbin D. and Jordan,William C. and Karpen,Gary H. and Kataoka,Eiko and Keightley,Peter D. and Kheradpour,Pouya and Kirkness,Ewen F. and Koerich,Leonardo B. and Kristiansen,Karsten and Kudrna,Dave and Kulathinal,Rob J. and Kumar,Sudhir and Kwok,Roberta and Lander,Eric and Langley,Charles H. and Lapoint,Richard and Lazzaro,Brian P. and Lee,So-Jeong and Levesque,Lisa and Li,Ruiqiang and Lin,Chiao-Feng and Lin,Michael F. and Lindblad-Toh,Kerstin and Llopart,Ana and Long,Manyuan and Low,Lloyd and Lozovsky,Elena and Lu,Jian and Luo,Meizhong and Machado,Carlos A. and Makalowski,Wojciech and Marzo,Mar and Matsuda,Muneo and Matzkin,Luciano and McAllister,Bryant and McBride,Carolyn S. and McKernan,Brendan and McKernan,Kevin and Mendez-Lago,Maria and Minx,Patrick and Mollenhauer,Michael U. and Montooth,Kristi and Mount, Stephen M. and Mu,Xu and Myers,Eugene and Negre,Barbara and Newfeld,Stuart and Nielsen,Rasmus and Noor,Mohamed A. F. and O{\textquoteright}Grady,Patrick and Pachter,Lior and Papaceit,Montserrat and Parisi,Matthew J. and Parisi,Michael and Parts,Leopold and Pedersen,Jakob S. and Pesole,Graziano and Phillippy,Adam M and Ponting,Chris P. and Pop, Mihai and Porcelli,Damiano and Powell,Jeffrey R. and Prohaska,Sonja and Pruitt,Kim and Puig,Marta and Quesneville,Hadi and Ram,Kristipati Ravi and Rand,David and Rasmussen,Matthew D. and Reed,Laura K. and Reenan,Robert and Reily,Amy and Remington,Karin A. and Rieger,Tania T. and Ritchie,Michael G. and Robin,Charles and Rogers,Yu-Hui and Rohde,Claudia and Rozas,Julio and Rubenfield,Marc J. and Ruiz,Alfredo and Russo,Susan and Salzberg,Steven L. and Sanchez-Gracia,Alejandro and Saranga,David J. and Sato,Hajime and Schaeffer,Stephen W. and Schatz,Michael C and Schlenke,Todd and Schwartz,Russell and Segarra,Carmen and Singh,Rama S. and Sirot,Laura and Sirota,Marina and Sisneros,Nicholas B. and Smith,Chris D. and Smith,Temple F. and Spieth,John and Stage,Deborah E. and Stark,Alexander and Stephan,Wolfgang and Strausberg,Robert L. and Strempel,Sebastian and Sturgill,David and Sutton,Granger and Sutton,Granger G. and Tao,Wei and Teichmann,Sarah and Tobari,Yoshiko N. and Tomimura,Yoshihiko and Tsolas,Jason M. and Valente,Vera L. S. and Venter,Eli and Venter,J. Craig and Vicario,Saverio and Vieira,Filipe G. and Vilella,Albert J. and Villasante,Alfredo and Walenz,Brian and Wang,Jun and Wasserman,Marvin and Watts,Thomas and Wilson,Derek and Wilson,Richard K. and Wing,Rod A. and Wolfner,Mariana F. and Wong,Alex and Wong,Gane Ka-Shu and Wu,Chung-I and Wu,Gabriel and Yamamoto,Daisuke and Yang,Hsiao-Pei and Yang,Shiaw-Pyng and Yorke,James A. and Yoshida,Kiyohito and Zdobnov,Evgeny and Zhang,Peili and Zhang,Yu and Zimin,Aleksey V. and Baldwin,Jennifer and Abdouelleil,Amr and Abdulkadir,Jamal and Abebe,Adal and Abera,Brikti and Abreu,Justin and Acer,St Christophe and Aftuck,Lynne and Alexander,Allen and An,Peter and Anderson,Erica and Anderson,Scott and Arachi,Harindra and Azer,Marc and Bachantsang,Pasang and Barry,Andrew and Bayul,Tashi and Berlin,Aaron and Bessette,Daniel and Bloom,Toby and Blye,Jason and Boguslavskiy,Leonid and Bonnet,Claude and Boukhgalter,Boris and Bourzgui,Imane and Brown,Adam and Cahill,Patrick and Channer,Sheridon and Cheshatsang,Yama and Chuda,Lisa and Citroen,Mieke and Collymore,Alville and Cooke,Patrick and Costello,Maura and D{\textquoteright}Aco,Katie and Daza,Riza and Haan,Georgius De and DeGray,Stuart and DeMaso,Christina and Dhargay,Norbu and Dooley,Kimberly and Dooley,Erin and Doricent,Missole and Dorje,Passang and Dorjee,Kunsang and Dupes,Alan and Elong,Richard and Falk,Jill and Farina,Abderrahim and Faro,Susan and Ferguson,Diallo and Fisher,Sheila and Foley,Chelsea D. and Franke,Alicia and Friedrich,Dennis and Gadbois,Loryn and Gearin,Gary and Gearin,Christina R. and Giannoukos,Georgia and Goode,Tina and Graham,Joseph and Grandbois,Edward and Grewal,Sharleen and Gyaltsen,Kunsang and Hafez,Nabil and Hagos,Birhane and Hall,Jennifer and Henson,Charlotte and Hollinger,Andrew and Honan,Tracey and Huard,Monika D. and Hughes,Leanne and Hurhula,Brian and Husby,M Erii and Kamat,Asha and Kanga,Ben and Kashin,Seva and Khazanovich,Dmitry and Kisner,Peter and Lance,Krista and Lara,Marcia and Lee,William and Lennon,Niall and Letendre,Frances and LeVine,Rosie and Lipovsky,Alex and Liu,Xiaohong and Liu,Jinlei and Liu,Shangtao and Lokyitsang,Tashi and Lokyitsang,Yeshi and Lubonja,Rakela and Lui,Annie and MacDonald,Pen and Magnisalis,Vasilia and Maru,Kebede and Matthews,Charles and McCusker,William and McDonough,Susan and Mehta,Teena and Meldrim,James and Meneus,Louis and Mihai,Oana and Mihalev,Atanas and Mihova,Tanya and Mittelman,Rachel and Mlenga,Valentine and Montmayeur,Anna and Mulrain,Leonidas and Navidi,Adam and Naylor,Jerome and Negash,Tamrat and Nguyen,Thu and Nguyen,Nga and Nicol,Robert and Norbu,Choe and Norbu,Nyima and Novod,Nathaniel and O{\textquoteright}Neill,Barry and Osman,Sahal and Markiewicz,Eva and Oyono,Otero L. and Patti,Christopher and Phunkhang,Pema and Pierre,Fritz and Priest,Margaret and Raghuraman,Sujaa and Rege,Filip and Reyes,Rebecca and Rise,Cecil and Rogov,Peter and Ross,Keenan and Ryan,Elizabeth and Settipalli,Sampath and Shea,Terry and Sherpa,Ngawang and Shi,Lu and Shih,Diana and Sparrow,Todd and Spaulding,Jessica and Stalker,John and Stange-Thomann,Nicole and Stavropoulos,Sharon and Stone,Catherine and Strader,Christopher and Tesfaye,Senait and Thomson,Talene and Thoulutsang,Yama and Thoulutsang,Dawa and Topham,Kerri and Topping,Ira and Tsamla,Tsamla and Vassiliev,Helen and Vo,Andy and Wangchuk,Tsering and Wangdi,Tsering and Weiand,Michael and Wilkinson,Jane and Wilson,Adam and Yadav,Shailendra and Young,Geneva and Yu,Qing and Zembek,Lisa and Zhong,Danni and Zimmer,Andrew and Zwirko,Zac and Jaffe,David B. and Alvarez,Pablo and Brockman,Will and Butler,Jonathan and Chin,CheeWhye and Gnerre,Sante and Grabherr,Manfred and Kleber,Michael and Mauceli,Evan and MacCallum,Iain} } @article {19072, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007}, pages = {203 - 218}, author = {Clark, A.G. and Eisen,M. B and Smith,D. R and Bergman, C.M. and Oliver, B. and Markow, T.A. and Kaufman, T.C. and Kellis, M. and Gelbart, W. and Iyer, V.N. and others} } @article {16408, title = {Examining Group Behavior and Collaboration using ABM and Robots}, journal = {Proc. of Agent}, year = {2007}, month = {2007///}, abstract = {Agent-based modeling has been extensively used by scientists to study complex systems.Participatory simulations are similar to agent-based models except that humans play the role of the virtual agents. The Bifocal modeling approach uses sensors to gather data about the real-world phenomena being modeled and uses that information to affect the model. In this work, we are interested in automatically extracting, analyzing and modeling group behaviors in problem solving. Combining these three systems into one unified platform would be useful for those purposes, since it would facilitate a synthesis of their main affordances: understanding the role of locality, mapping human action to emergent behaviors, and controlling embedded physical objects in noisy environments while receiving sensory feedback. We will demonstrate a technological platform based on the NetLogo/HubNet architecture that supports simulated agents, participatory agents and physical agents. We place this platform within a more general framework that we call Human, Embedded and Virtual agents in Mediation (HEV-M). We have run several studies using an instantiation of this platform that consists of a robot-car with four users who navigate a maze. We believe that this tool has potential for three main reasons (1) it facilitates logging of participant{\textquoteright}s actions, so as to identify patterns, (2) it offers researchers in the field of computer-supported collaborative learning an easy-to-use tool to design engaging collaborative learning activities and, (3) it foregrounds the role of individual actions within the accomplishment of a collective goal, highlighting the connections between simple individual actions and the resultant macroscopic behaviors of the system. }, author = {Blikstein,P. and Rand, William and Wilensky,Uri} } @article {12134, title = {Experimenting with software testbeds for evaluating new technologies}, journal = {Empirical Software Engineering}, volume = {12}, year = {2007}, month = {2007///}, pages = {417 - 444}, abstract = {The evolution of a new technology depends upon a good theoretical basis for developing the technology, as well as upon its experimental validation. In order to provide for this experimentation, we have investigated the creation of a software testbed and the feasibility of using the same testbed for experimenting with a broad set of technologies. The testbed is a set of programs, data, and supporting documentation that allows researchers to test their new technology on a standard software platform. An important component of this testbed is the Unified Model of Dependability (UMD), which was used to elicit dependability requirements for the testbed software. With a collection of seeded faults and known issues of the target system, we are able to determine if a new technology is adept at uncovering defects or providing other aids proposed by its developers. In this paper, we present the Tactical Separation Assisted Flight Environment (TSAFE) testbed environment for which we modeled and evaluated dependability requirements and defined faults to be seeded for experimentation. We describe two completed experiments that we conducted on the testbed. The first experiment studies a technology that identifies architectural violations and evaluates its ability to detect the violations. The second experiment studies model checking as part of design for verification. We conclude by describing ongoing experimental work studying testing, using the same testbed. Our conclusion is that even though these three experiments are very different in terms of the studied technology, using and re-using the same testbed is beneficial and cost effective.}, doi = {10.1007/s10664-006-9034-0}, author = {Lindvall,M. and Rus,I. and Donzelli,P. and Memon, Atif M. and Zelkowitz, Marvin V and Betin-Can,A. and Bultan,T. and Ackermann,C. and Anders,B. and Asgari, S. and Basili, Victor R.} } @conference {12249, title = {Exploiting approximate transitivity of trust}, booktitle = {Broadband Communications, Networks and Systems, 2007. BROADNETS 2007. Fourth International Conference on}, year = {2007}, month = {2007/09//}, pages = {515 - 524}, abstract = {Social networks, of which webs of trust are a particular type, have been shown to be effective ways of moving information with minimal external configuration, setup, or management. For applications requiring information assurance, a web of trust is an appealing system architecture, since trust is an inherent component of both the network design and assurance. The trust in a typical web of trust is not transitive, however, making the construction of an application with strong assurance difficult or impossible. Instead, in this paper we examine a notion of weak assurance that can be provided by a web of trust, and might be $\#$x201C;good enough $\#$x201D; for many applications. As a motivating example, and to provide a more concrete basis for exposition, we present KeyChains, a peer-to-peer system that operates over a distributed web of trust to provide fully decentralized public key publishing and retrieval. In addition to weak assurance guarantees, KeyChains also provides an audit trail for public keys retrieved. Our analysis and simulations show that the resulting system is both efficient and secure.}, doi = {10.1109/BROADNETS.2007.4550477}, author = {Morselli,Ruggero and Bhattacharjee, Bobby and Katz, Jonathan and Marsh,Michael} } @article {15606, title = {A fast implementation of the ISODATA clustering algorithm}, journal = {International Journal of Computational Geometry and Applications}, volume = {17}, year = {2007}, month = {2007///}, pages = {71 - 103}, abstract = {Clustering is central to many image processing and remote sensing applications. isodatais one of the most popular and widely used clustering methods in geoscience applications, but it can run slowly, particularly with large data sets. We present a more efficient approach to isodata clustering, which achieves better running times by storing the points in a kd-tree and through a modification of the way in which the algorithm estimates the dispersion of each cluster. We also present an approximate version of the algorithm which allows the user to further improve the running time, at the expense of lower fidelity in computing the nearest cluster center to each point. We provide both theoretical and empirical justification that our modified approach produces clusterings that are very similar to those produced by the standard isodata approach. We also provide empirical studies on both synthetic data and remotely sensed Landsat and MODIS images that show that our approach has significantly lower running times. }, author = {Memarsadeghi,N. and Mount, Dave and Netanyahu,N. S and Le Moigne,J. and de Berg,M.} } @article {14581, title = {GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo}, journal = {Development}, volume = {134}, year = {2007}, month = {2007/01/01/}, pages = {189 - 198}, abstract = {In vitro studies have suggested that members of the GATA and Nkx transcription factor families physically interact, and synergistically activate pulmonary epithelial- and cardiac-gene promoters. However, the relevance of this synergy has not been demonstrated in vivo. We show that Gata6-Titf1 (Gata6-Nkx2.1) double heterozygous (G6-Nkx DH) embryos and mice have severe defects in pulmonary epithelial differentiation and distal airway development, as well as reduced phospholipid production. The defects in G6-Nkx DH embryos and mice are similar to those observed in human neonates with respiratory distress syndromes, including bronchopulmonary dysplasia, and differential gene expression analysis reveals essential developmental pathways requiring synergistic regulation by both Gata6 and Titf1 (Nkx2.1). These studies indicate that Gata6 and Nkx2.1 act in a synergistic manner to direct pulmonary epithelial differentiation and development in vivo, providing direct evidence that interactions between these two transcription factor families are crucial for the development of the tissues in which they are co-expressed.}, doi = {10.1242/dev.02720}, url = {http://dev.biologists.org/content/134/1/189.abstract}, author = {Zhang,Yuzhen and Rath,Nibedita and Hannenhalli, Sridhar and Wang,Zhishan and Cappola,Thomas and Kimura,Shioko and Atochina-Vasserman,Elena and Lu,Min Min and Beers,Michael F. and Morrisey,Edward E.} } @article {15279, title = {Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {13}, year = {2007}, month = {2007/05//}, pages = {713 - 718}, abstract = {Although linked, these viruses are distinct from earlier outbreak strains., To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.}, isbn = {1080-6040}, doi = {10.3201/eid1305.070013}, author = {Salzberg,Steven L. and Kingsford, Carl and Cattoli,Giovanni and Spiro,David J. and Janies,Daniel A. and Aly,Mona Mehrez and Brown,Ian H. and Couacy-Hymann,Emmanuel and De Mia,Gian Mario and Dung,Do Huu and Guercio,Annalisa and Joannis,Tony and Ali,Ali Safar Maken and Osmani,Azizullah and Padalino,Iolanda and Saad,Magdi D. and Savi{\'c},Vladimir and Sengamalay,Naomi A. and Yingst,Samuel and Zaborsky,Jennifer and Zorman-Rojs,Olga and Ghedin,Elodie and Capua,Ilaria} } @article {14618, title = {Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007/11/20/}, pages = {R247 - R247}, abstract = {The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by sleep:wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances.}, isbn = {1465-6906}, doi = {10.1186/gb-2007-8-11-r247}, url = {http://genomebiology.com/2007/8/11/R247}, author = {Yang,Shuzhang and Wang,Kai and Valladares,Otto and Hannenhalli, Sridhar and Bucan,Maja} } @article {18847, title = {Geometrical algorithms for automated design of side actions in injection moulding of complex parts}, journal = {Computer-Aided Design}, volume = {39}, year = {2007}, month = {2007/10//}, pages = {882 - 897}, abstract = {This paper describes algorithms for generating shapes of side actions to minimize a customizable injection moulding cost function. Given a set of undercut facets on a polyhedral part and the main mold opening directions, our approach works in the following manner: first, we compute candidate retraction space for every undercut facet. This space represents the set of candidate translation vectors that can be used by the side action to completely disengage from the undercut facet. As the next step, we generate a discrete set of feasible, nondominated retractions. Then we group the undercut facets into undercut regions by performing state space search over such retractions. This search step is performed by minimizing the given moulding cost function. After identifying the undercut regions, we generate the shapes of individual side actions. We believe that the results presented in this paper will provide the foundations for developing fully automated software for designing side actions.}, keywords = {Configuration spaces, Geometrical reasoning, Mould design}, isbn = {0010-4485}, doi = {10.1016/j.cad.2007.05.014}, url = {http://www.sciencedirect.com/science/article/pii/S0010448507001339}, author = {Banerjee,Ashis Gopal and Gupta, Satyandra K.} } @conference {12136, title = {Get Your Experience Factory Ready for the Next Decade{\textendash}Ten Years after "How to Build and Run One"}, booktitle = {Companion to the proceedings of the 29th International Conference on Software Engineering}, series = {ICSE COMPANION {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {167 - 168}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {This one-day tutorial aims at industry practitioners, managers and developers alike, who want to learn more about how to successfully design, implement and run an Experience Factory, to systematically build up and manage the experience of an organization. State-of- the art methods and techniques on how to initially set-up or to further develop and improve an organization{\textquoteright}s Experience Factory are discussed. Participants should come from organizations (not only from the software domain) that are interested in implementing an Experience Factory to help effectively support improvement activities (such as TQM, ISO 9000, CMMI, SPICE, or TSP) to gain competitive advantages.}, isbn = {0-7695-2892-9}, doi = {10.1109/ICSECOMPANION.2007.41}, url = {http://dx.doi.org/10.1109/ICSECOMPANION.2007.41}, author = {Basili, Victor R. and Bomarius,Frank and Feldmann,Raimund L.} } @article {13002, title = {Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services}, journal = {Future Generation Comp Syst}, volume = {23}, year = {2007}, month = {2007///}, pages = {517 - 522}, abstract = {The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering the barriers to writing Grid services. The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed.}, author = {Bazinet,A. L and Myers,D. S and Fuetsch,J. and Cummings, Michael P.} } @article {12579, title = {Guest Editorial: Special Issue on Human Detection and Recognition}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {2}, year = {2007}, month = {2007/09//}, pages = {489 - 490}, abstract = {The 12 regular papers and three correspondences in this special issue focus on human detection and recognition. The papers represent gait, face (3-D, 2-D, video), iris, palmprint, cardiac sounds, and vulnerability of biometrics and protection against the spoof attacks.}, isbn = {1556-6013}, doi = {10.1109/TIFS.2007.905740}, author = {Bhanu, B. and Ratha,N. K and Kumar, V. and Chellapa, Rama and Bigun, J.} } @article {13437, title = {Heuristic Search and Information Visualization Methods for School Redistricting}, journal = {AI Magazine}, volume = {28}, year = {2007}, month = {2007/09/15/}, pages = {59 - 59}, abstract = {We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives, such as school capacity, busing costs, and socioeconomic distribution, must be considered. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different trade-offs in the decision space. We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans.}, isbn = {0738-4602}, doi = {10.1609/aimag.v28i3.2055}, url = {https://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/2055}, author = {desJardins, Marie and Bulka,Blazej and Carr,Ryan and Jordan,Eric and Rheingans,Penny} } @conference {18573, title = {Holding the Internet Accountable}, booktitle = {Proc. 6th ACM Workshop on Hot Topics in Networks (Hotnets-VI)}, year = {2007}, month = {2007/11/01/}, abstract = {Today{\textquoteright}s IP network layer provides little to no protection against misconfiguration or malice. Despite some progress in improving the robustness and security of the IP layer, misconfigurations and attacks still occur frequently. We show how a network layer that provides accountability, i.e., the ability to associate each action with the responsible entity, provides a firm foundation for defenses against misconfiguration and malice. We present the design of a network layer that incorporates accountability called AIP (Accountable Internet Protocol) and show how its features{\textemdash}notably, its use of self-certifying addresses{\textemdash} can improve both source accountability (the ability to trace actions to a particular end host and stop that host from misbehaving) and control-plane accountability (the ability to pinpoint and prevent attacks on routing).}, url = {http://repository.cmu.edu/compsci/66}, author = {Andersen,David and Balakrishnan,Hari and Feamster, Nick and Koponen,Teemu and Moon,Daekyong and Shenker,Scott} } @inbook {17208, title = {Human Values for Shaping the Made World}, booktitle = {Human-Computer Interaction {\textendash} INTERACT 2007Human-Computer Interaction {\textendash} INTERACT 2007}, series = {Lecture Notes in Computer Science}, volume = {4662}, year = {2007}, month = {2007///}, pages = {1 - 1}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Interface design principles have been effective in shaping new desktop applications, web-based resources, and mobile devices. Usability and sociability promote successful online communities and social network services. The contributions of human-computer interaction researchers have been effective in raising the quality of design of many products and services. As our influence grows, we can play an even more profound role in guaranteeing that enduring human values are embedded in the next generation of technology. This talk identifies which goals are realistic, such as universality, responsibility, trust, empathy, and privacy, and how we might ensure that they become part of future services and systems.}, isbn = {978-3-540-74794-9}, url = {http://dx.doi.org/10.1007/978-3-540-74796-3_1}, author = {Shneiderman, Ben}, editor = {Baranauskas,C{\'e}cilia and Palanque,Philippe and Abascal,Julio and Barbosa,Simone} } @article {12573, title = {Hybrid Detectors for Subpixel Targets}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {29}, year = {2007}, month = {2007/11//}, pages = {1891 - 1903}, abstract = {Subpixel detection is a challenging problem in hyperspectral imagery analysis. Since the target size is smaller than the size of a pixel, detection algorithms must rely solely on spectral information. A number of different algorithms have been developed over the years to accomplish this task, but most detectors have taken either a purely statistical or a physics-based approach to the problem. We present two new hybrid detectors that take advantage of these approaches by modeling the background using both physics and statistics. Results demonstrate improved performance over the well-known AMSD and ACE subpixel algorithms in experiments that include multiple targets, images, and area types - especially when dealing with weak targets in complex backgrounds.}, keywords = {ACE subpixel algorithm;AMSD subpixel algorithm;hybrid detectors;hyperspectral imagery analysis;physics;statistics;subpixel target detection;subspace detection;object detection;spectral analysis;statistical analysis;target tracking;Algorithms;Artificial In, Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer-Assisted;, Computer-Assisted;Models, Computer-Assisted;Pattern Recognition, Statistical;Image Enhancement;Image Interpretation, Statistical;Numerical Analysis}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.1104}, author = {Broadwater, J. and Chellapa, Rama} } @article {18576, title = {Implications of Autonomy for the Expressiveness of Policy Routing}, journal = {Networking, IEEE/ACM Transactions on}, volume = {15}, year = {2007}, month = {2007/12//}, pages = {1266 - 1279}, abstract = {Thousands of competing autonomous systems must cooperate with each other to provide global Internet connectivity. Each autonomous system (AS) encodes various economic, business, and performance decisions in its routing policy. The current interdomain routing system enables each AS to express policy using rankings that determine how each router in the AS chooses among different routes to a destination, and filters that determine which routes are hidden from each neighboring AS. Because the Internet is composed of many independent, competing networks, the interdomain routing system should provide autonomy, allowing network operators to set their rankings independently, and to have no constraints on allowed filters. This paper studies routing protocol stability under these conditions. We first demonstrate that ldquonext-hop rankings,rdquo commonly used in practice, may not ensure routing stability. We then prove that, when providers can set rankings and filters autonomously, guaranteeing that the routing system will converge to a stable path assignment imposes strong restrictions on the rankings ASes are allowed to choose. We discuss the implications of these results for the future of interdomain routing.}, keywords = {autonomous systems, global Internet connectivity, interdomain routing system, Internet, next-hop rankings, routing protocol, routing protocols, routing stability, stable path assignment}, isbn = {1063-6692}, doi = {10.1109/TNET.2007.896531}, author = {Feamster, Nick and Johari,R. and Balakrishnan,H.} } @article {18851, title = {Incorporating manufacturability considerations during design of injection molded multi-material objects}, journal = {Research in Engineering Design}, volume = {17}, year = {2007}, month = {2007///}, pages = {207 - 231}, abstract = {The presence of an already molded component during the second and subsequent molding stages makes multi-material injection molding different from traditional injection molding process. Therefore, designing multi-material molded objects requires addressing many additional manufacturability considerations. In this paper, we first present an approach to systematically identifying potential manufacturability problems that are unique to the multi-material molding processes and design rules to avoid these problems. Then we present a comprehensive manufacturability analysis approach that incorporates both the traditional single material molding rules as well as the specific rules that have been identified for multi-material molding. Our analysis shows that sometimes the traditional rules need to be suppressed or modified. Lastly, for each of the new manufacturability problem, this paper describes algorithms for automatically detecting potential occurrences and generating redesign suggestions. These algorithms have been implemented in a computer-aided manufacturability analysis system. The approach presented in this paper is applicable to multi-shot and over molding processes. We expect that the manufacturability analysis techniques presented in this paper will help in decreasing the product development time for the injection molded multi-material objects.}, keywords = {engineering}, isbn = {0934-9839}, doi = {10.1007/s00163-007-0027-9}, url = {http://www.springerlink.com/content/c35337h3r5129525/abstract/}, author = {Banerjee,Ashis and Li,Xuejun and Fowler,Greg and Gupta, Satyandra K.} } @conference {16424, title = {Just a cog in the machine: participatory robotics as a tool for understanding collaborative learning and decision-making}, booktitle = {Proceedings of the 8th iternational conference on Computer supported collaborative learning}, series = {CSCL{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {84 - 86}, publisher = {International Society of the Learning Sciences}, organization = {International Society of the Learning Sciences}, abstract = {We will demonstrate the integration of a software-based multi-agent modeling platform with a participatory simulation environment and a real-time control system for a physical robotic agent. Both real and virtual participants will be able to act collaboratively in a simulation that will control a physical agent. The backbone of this demonstration is a widely used, freely available, mature modeling platform (NetLogo). We posit that this technological platform can be of use for researchers interested in investigating collaborative learning and decision-making, as well as to design collaborative learning activities. We will present preliminary findings from pilot studies with the tool.}, isbn = {978-0-6151-5436-7}, url = {http://dl.acm.org/citation.cfm?id=1599600.1599614}, author = {Blikstein,Paulo and Rand, William and Wilensky,Uri} } @conference {12581, title = {Kernel fully constrained least squares abundance estimates}, booktitle = {Geoscience and Remote Sensing Symposium, 2007. IGARSS 2007. IEEE International}, year = {2007}, month = {2007/07//}, pages = {4041 - 4044}, abstract = {A critical step for fitting a linear mixing model to hyperspectral imagery is the estimation of the abundances. The abundances are the percentage of each end member within a given pixel; therefore, they should be non-negative and sum to one. With the advent of kernel based algorithms for hyperspectral imagery, kernel based abundance estimates have become necessary. This paper presents such an algorithm that estimates the abundances in the kernel feature space while maintaining the non-negativity and sum-to-one constraints. The usefulness of the algorithm is shown using the AVIRIS Cuprite, Nevada image.}, keywords = {abundance, algorithm;kernel, analysis;, AVIRIS, based, constrained, constraint;feature, constraint;spectral, estimates;linear, extraction;geophysical, feature, fully, image;hyperspectral, imagery;kernel, least, mixing, model;nonnegativity, processing;geophysical, processing;multidimensional, processing;spectral, signal, space;kernel, squares, techniques;image, unmixing;sum-to-one}, doi = {10.1109/IGARSS.2007.4423736}, author = {Broadwater, J. and Chellapa, Rama and Banerjee, A. and Burlina, P.} } @conference {12254, title = {Large-scale byzantine fault tolerance: safe but not always live}, booktitle = {Proceedings of the 3rd workshop on on Hot Topics in System Dependability}, series = {HotDep{\textquoteright}07}, year = {2007}, month = {2007///}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {The overall correctness of large-scale systems composed of many groups of replicas executing BFT protocols scales poorly with the number of groups. This is because the probability of at least one group being compromised (more than 1/3 faulty replicas) increases rapidly as the number of groups increases. In this paper we address this problem with a simple modification to Castro and Liskov{\textquoteright}s BFT replication that allows for arbitrary choice of n (number of replicas) and f (failure threshold). The price to pay is a more restrictive liveness requirement, and we present the design of a large-scale BFT replicated system that obviates this problem.}, url = {http://dl.acm.org/citation.cfm?id=1323140.1323157}, author = {Rodrigues,Rodrigo and Kouznetsov,Petr and Bhattacharjee, Bobby} } @conference {18000, title = {Layout-Accurate Design and Implementation of a High-Throughput Interconnection Network for Single-Chip Parallel Processing}, booktitle = {High-Performance Interconnects, 2007. HOTI 2007. 15th Annual IEEE Symposium on}, year = {2007}, month = {2007/08//}, pages = {21 - 28}, abstract = {A mesh of trees (MoT) on-chip interconnection network has been proposed recently to provide high throughput between memory units and processors for single-chip parallel processing (Balkan et al., 2006). In this paper, we report our findings in bringing this concept to silicon. Specifically, we conduct cycle-accurate Verilog simulations to verify the analytical results claimed in (Balkan et al., 2006). We synthesize and obtain the layout of the MoT interconnection networks of various sizes. To further improve throughput, we investigate different arbitration primitives to handle load and store, the two most common memory operations. We also study the use of pipeline registers in large networks when there are long wires. Simulation based on full network layout demonstrates that significant throughput improvement can be achieved over the original proposed MoT interconnection network. The importance of this work lies in its validation of performance features of the MoT interconnection network, as they were previously shown to be competitive with traditional network solutions. The MoT network is currently used in an eXplicit multi-threading (XMT) on-chip parallel processor, which is engineered to support parallel programming. In that context, a 32-terminal MoT network could support up to 512 on-chip XMT processors. Our 8-terminal network that could serve 8 processor clusters (or 128 total processors), was also accepted recently for fabrication.}, keywords = {description, design;mesh, interconnection, languages;multi-threading;multiprocessor, MoT, multi-threading;layout-accurate, network;on-chip, network;Verilog, networks;parallel, of, on-chip, Parallel, processing;, processing;hardware, processor;parallel, processors;on-chip, programming;pipeline, registers;single-chip, simulations;eXplicit, TREES, XMT}, doi = {10.1109/HOTI.2007.11}, author = {Balkan,A.O. and Horak,M.N. and Gang Qu and Vishkin, Uzi} } @article {13452, title = {Local strategy learning in networked multi-agent team formation}, journal = {Autonomous Agents and Multi-Agent Systems}, volume = {15}, year = {2007}, month = {2007///}, pages = {29 - 45}, abstract = {Networked multi-agent systems are comprised of many autonomous yet interdependent agents situated in a virtual social network. Two examples of such systems are supply chain networks and sensor networks. A common challenge in many networked multi-agent systems is decentralized team formation among the spatially and logically extended agents. Even in cooperative multi-agent systems, efficient team formation is made difficult by the limited local information available to the individual agents. We present a model of distributed multi-agent team formation in networked multi-agent systems, describe a policy learning framework for joining teams based on local information, and give empirical results on improving team formation performance. In particular, we show that local policy learning from limited information leads to a significant increase in organizational team formation performance compared to a random policy.}, isbn = {1387-2532}, url = {http://dx.doi.org/10.1007/s10458-006-0007-x}, author = {Bulka,Blazej and Gaston,Matthew and desJardins, Marie} } @conference {12343, title = {Low-overhead run-time scheduling for fine-grained acceleration of signal processing systems}, booktitle = {Signal Processing Systems, 2007 IEEE Workshop on}, year = {2007}, month = {2007///}, pages = {457 - 462}, author = {Boutellier,J. and Bhattacharyya, Shuvra S. and Silv{\'e}n,O.} } @conference {12256, title = {Measurement and analysis of online social networks}, booktitle = {Proceedings of the 7th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {29 - 42}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online social networking sites like Orkut, YouTube, and Flickr are among the most popular sites on the Internet. Users of these sites form a social network, which provides a powerful means of sharing, organizing, and finding content and contacts. The popularity of these sites provides an opportunity to study the characteristics of online social network graphs at large scale. Understanding these graphs is important, both to improve current systems and to design new applications of online social networks. This paper presents a large-scale measurement study and analysis of the structure of multiple online social networks. We examine data gathered from four popular online social networks: Flickr, YouTube, LiveJournal, and Orkut. We crawled the publicly accessible user links on each site, obtaining a large portion of each social network{\textquoteright}s graph. Our data set contains over 11.3 million users and 328 million links. We believe that this is the first study to examine multiple online social networks at scale. Our results confirm the power-law, small-world, and scale-free properties of online social networks. We observe that the indegree of user nodes tends to match the outdegree; that the networks contain a densely connected core of high-degree nodes; and that this core links small groups of strongly clustered, low-degree nodes at the fringes of the network. Finally, we discuss the implications of these structural properties for the design of social network based systems.}, keywords = {analysis, measurement, social networks}, isbn = {978-1-59593-908-1}, doi = {10.1145/1298306.1298311}, url = {http://doi.acm.org/10.1145/1298306.1298311}, author = {Mislove,Alan and Marcon,Massimiliano and Gummadi,Krishna P. and Druschel,Peter and Bhattacharjee, Bobby} } @conference {19036, title = {Multi-Dimensional Range Query over Encrypted Data}, year = {2007}, month = {2007}, pages = {350 - 364}, abstract = {We design an encryption scheme called multi-dimensional range query over encrypted data (MRQED), to address the privacy concerns related to the sharing of network audit logs and various other applications. Our scheme allows a network gateway to encrypt summaries of network flows before submitting them to an untrusted repository. When network intrusions are suspected, an authority can release a key to an auditor, allowing the auditor to decrypt flows whose attributes (e.g., source and destination addresses, port numbers, etc.) fall within specific ranges. However, the privacy of all irrelevant flows are still preserved. We formally define the security for MRQED and prove the security of our construction under the decision bilinear Diffie-Hellman and decision linear assumptions in certain bilinear groups. We study the practical performance of our construction in the context of network audit logs. Apart from network audit logs, our scheme also has interesting applications for financial audit logs, medical privacy, untrusted remote storage, etc. In particular, we show that MRQED implies a solution to its dual problem, which enables investors to trade stocks through a broker in a privacy-preserving manner.}, keywords = {auditing, cryptography, data privacy, decision bilinear Diffie-Hellman, decision linear assumptions, encrypted data, multi-dimensional range query, network audit logs, network gateway, network intrusions}, author = {Elaine Shi and Bethencourt, J. and Chan, T.-H.H. and Song, Dawn and Perrig, A.} } @article {14711, title = {Mutatis Mutandis: Safe and predictable dynamic software updating}, journal = {ACM Trans. Program. Lang. Syst.}, volume = {29}, year = {2007}, month = {2007/08//}, abstract = {This article presents Proteus, a core calculus that models dynamic software updating, a service for fixing bugs and adding features to a running program. Proteus permits a program{\textquoteright}s type structure to change dynamically but guarantees the updated program remains type-correct by ensuring a property we call con-freeness. We show how con-freeness can be enforced dynamically, and how it can be approximated via a novel static analysis. This analysis can be used to assess the implications of a program{\textquoteright}s structure on future updates in order to make update success more predictable. We have implemented Proteus for C, and briefly discuss our implementation which we have tested on several well-known programs.}, keywords = {capability, dynamic software updating, proteus, Type inference, updateability analysis}, isbn = {0164-0925}, doi = {10.1145/1255450.1255455}, url = {http://doi.acm.org/10.1145/1255450.1255455}, author = {Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Sewell,Peter and Neamtiu,Iulian} } @article {16077, title = {NetLens: Iterative Exploration of Content-Actor Network Data}, journal = {Information VisualizationInformation Visualization}, volume = {6}, year = {2007}, month = {2007/03/20/}, pages = {18 - 31}, abstract = {Networks have remained a challenge for information retrieval and visualization because of the rich set of tasks that users want to accomplish. This paper offers an abstract Content-Actor network data model, a classification of tasks, and a tool to support them. The NetLens interface was designed around the abstract Content-Actor network data model to allow users to pose a series of elementary queries and iteratively refine visual overviews and sorted lists. This enables the support of complex queries that are traditionally hard to specify. NetLens is general and scalable in that it applies to any data set that can be represented with our abstract data model. This paper describes the use of NetLens with a subset of the ACM Digital Library consisting of about 4000 papers from the CHI conference written by about 6000 authors, and reports on a usability study with nine participants.}, keywords = {content-actor network data, digital library, incremental data exploration, iterative query refinement, User interfaces}, isbn = {1473-8716, 1473-8724}, doi = {10.1057/palgrave.ivs.9500143}, url = {http://ivi.sagepub.com/content/6/1/18}, author = {Kang,Hyunmo and Plaisant, Catherine and Lee,Bongshin and Bederson, Benjamin B.} } @article {12214, title = {NetLens: iterative exploration of content-actor network data}, journal = {Information Visualization}, volume = {6}, year = {2007}, month = {2007///}, pages = {18 - 31}, author = {Kang,H. and Plaisant, Catherine and Lee,B. and Bederson, Benjamin B.} } @article {12918, title = {New records of phytoplankton for Bangladesh. 3. Volvocales}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {14}, year = {2007}, month = {2007/12/01/}, abstract = {This study presents 21 species of Chlamydomonas, four species of Carteria, two species of each of Nephroselmis, Pyramidomonas and Scherffelia, and Collodictyon triciliatum, Polytoma minus, Tetrachloridium ? allorgei and Tetraselmis cordiformis. These species have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal districts in Bangladesh.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v14i1.518}, url = {http://www.banglajol.info/bd/index.php/BJPT/article/viewArticle/518}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasmin,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {12917, title = {New records of phytoplankton for Bangladesh. 4. Chlorococcales}, journal = {Bangladesh Journal of Plant Taxonomy}, volume = {14}, year = {2007}, month = {2007/12/02/}, abstract = {This study presents three species from each of Schroederia, Monoraphidium and Ankistrodesmus, two species and one variety of Dictyosphaerium, two varieties of Pediastrum, and Tetraedron arthrodesmiforme var. contorta, Chlorotetraedron polymorphum, Myrmecia aquatica, Oocystis tainoensis, Nephrocytium spirale, Kirchneriella irregularis, Coelastrum indicum and Scenedesmus similagineus. These taxa have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal Districts in Bangladesh.}, isbn = {1028-2092}, doi = {10.3329/bjpt.v14i2.528}, url = {http://www.banglajol.info/bd/index.php/BJPT/article/viewArticle/528}, author = {Khondker,Moniruzzaman and Bhuiyan,Rauf Ahmed and Yeasim,Jenat and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @article {14919, title = {Object recognition using linear subspaces}, volume = {EP20010117763}, year = {2007}, month = {2007/01/17/}, abstract = {Abstract of EP1204069A method for choosing an image from a plurality of three-dimensional models which is most similar to an input image is provided. The method includes the steps of: (a) providing a database of the plurality of three-dimensional models; (b) providing an input image; (c) positioning each three-dimensional model relative to the input image; (d) for each three-dimensional model, determining a rendered image that is most similar to the input image by: (d)(i) computing a linear subspace that describes an approximation to the set of all possible rendered images that each three-dimensional model can produce under all possible lighting conditions where each point in the linear subspace represents a possible image; and one of(d)(ii) finding the point on the linear subspace that is closest to the input image or finding a rendered image in a subset of the linear subspace obtained by projecting the set of images that are generated by positive lights onto the linear subspace; (e) computing a measure of similarly between the input image and each rendered image; and (f) selecting the three-dimensional model corresponding to the rendered image whose measure of similarity is most similar to the input image. Step (d) is preferably repeated for each of a red, green, and blue color component for each three-dimensional model. The linear subspace is preferably either four-dimensional or nine-dimensional.}, url = {http://www.freepatentsonline.com/EP1204069.html}, author = {Jacobs, David W. and Basri,Ronen The Weizmann Institute}, editor = {NEC Laboratories America, Inc. (4 Independence Way, Princeton, New Jersey 08540, US)} } @article {14474, title = {Online collective entity resolution}, journal = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {22}, year = {2007}, month = {2007///}, pages = {1606 - 1606}, abstract = {Entity resolution is a critical component of data integration where the goal is to reconcile database references correspond- ing to the same real-world entities. Given the abundance of publicly available databases that have unresolved entities, we motivate the problem of quick and accurate resolution for an- swering queries over such {\textquoteleft}unclean{\textquoteright} databases. Since collec- tive entity resolution approaches {\textemdash} where related references are resolved jointly {\textemdash} have been shown to be more accu- rate than independent attribute-based resolution, we focus on adapting collective resolution for answering queries. We pro- pose a two-stage collective resolution strategy for processing queries. We then show how it can be performed on-the-fly by adaptively extracting and resolving those database references that are the most helpful for resolving the query. We validate our approach on two large real-world publication databases where we show the usefulness of collective resolution and at the same time demonstrate the need for adaptive strategies for query processing. We then show how the same queries can be answered in real time using our adaptive approach while pre- serving the gains of collective resolution. This work extends work presented in (Bhattacharya, Licamele, \& Getoor 2006).}, author = {Bhattacharya,I. and Getoor, Lise} } @article {12352, title = {Parameterized Looped Schedules for Compact Representation of Execution Sequences in DSP Hardware and Software Implementation}, journal = {IEEE Transactions on Signal Processing}, volume = {55}, year = {2007}, month = {2007/06//}, pages = {3126 - 3138}, abstract = {In this paper, we present a technique for compact representation of execution sequences in terms of efficient looping constructs. Here, by a looping construct, we mean a compact way of specifying a finite repetition of a set of execution primitives. Such compaction, which can be viewed as a form of hierarchical run-length encoding (RLE), has application in many very large scale integration (VLSI) signal processing contexts, including efficient control generation for Kahn processes on field-programmable gate arrays (FPGAs), and software synthesis for static dataflow models of computation. In this paper, we significantly generalize previous models for loop-based code compaction of digital signal processing (DSP) programs to yield a configurable code compression methodology that exhibits a broad range of achievable tradeoffs. Specifically, we formally develop and apply to DSP hardware and software synthesis a parameterizable loop scheduling approach with compact format, dynamic reconfigurability, and low-overhead decompression}, keywords = {Application software, array signal processing, code compression methodology, compact representation, Compaction, data compression, Design automation, Digital signal processing, digital signal processing chips, DSP, DSP hardware, embedded systems, Encoding, Field programmable gate arrays, field-programmable gate arrays (FPGAs), FPGA, Hardware, hierarchical runlength encoding, high-level synthesis, Kahn process, loop-based code compaction, looping construct, parameterized loop schedules, program compilers, reconfigurable design, runlength codes, scheduling, Signal generators, Signal processing, Signal synthesis, software engineering, software implementation, static dataflow models, Very large scale integration, VLSI}, isbn = {1053-587X}, doi = {10.1109/TSP.2007.893964}, author = {Ming-Yung Ko and Zissulescu,C. and Puthenpurayil,S. and Bhattacharyya, Shuvra S. and Kienhuis,B. and Deprettere,E. F} } @article {14871, title = {Photometric stereo with general, unknown lighting}, journal = {International Journal of Computer Vision}, volume = {72}, year = {2007}, month = {2007///}, pages = {239 - 257}, abstract = {Work on photometric stereo has shown how to recover the shape and reflectance properties of an object using multiple images taken with a fixed viewpoint and variable lighting conditions. This work has primarily relied on known lighting conditions or the presence of a single point source of light in each image. In this paper we show how to perform photometric stereo assuming that all lights in a scene are distant from the object but otherwise unconstrained. Lighting in each image may be an unknown and may include arbitrary combination of diffuse, point and extended sources. Our work is based on recent results showing that for Lambertian objects, general lighting conditions can be represented using low order spherical harmonics. Using this representation we can recover shape by performing a simple optimization in a low-dimensional space. We also analyze the shape ambiguities that arise in such a representation. We demonstrate our method by reconstructing the shape of objects from images obtained under a variety of lightings. We further compare the reconstructed shapes against shapes obtained with a laser scanner.}, doi = {10.1007/s11263-006-8815-7}, author = {Basri,R. and Jacobs, David W. and Kemelmacher,I.} } @article {12362, title = {Probabilistic design of multimedia embedded systems}, journal = {ACM Transactions on Embedded Computing Systems (TECS)}, volume = {6}, year = {2007}, month = {2007///}, pages = {15{\textendash}es - 15{\textendash}es}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @conference {18688, title = {Profiling Attacker Behavior Following SSH Compromises}, year = {2007}, month = {2007/06//}, pages = {119 - 124}, abstract = {This practical experience report presents the results of an experiment aimed at building a profile of attacker behavior following a remote compromise. For this experiment, we utilized four Linux honeypot computers running SSH with easily guessable passwords. During the course of our research, we also determined the most commonly attempted usernames and passwords, the average number of attempted logins per day, and the ratio of failed to successful attempts. To build a profile of attacker behavior, we looked for specific actions taken by the attacker and the order in which they occurred. These actions were: checking the configuration, changing the password, downloading a file, installing/running rogue code, and changing the system configuration.}, keywords = {Linux, Linux honeypot computers, profiling attacker behavior, remote compromise, rogue code, security of data, SSH compromises, system configuration}, doi = {10.1109/DSN.2007.76}, author = {Ramsbrock,D. and Berthier,R. and Michel Cukier} } @inbook {18418, title = {Protocols in the use of empirical software engineering artifacts}, booktitle = {Empirical Software EngineeringEmpirical Software Engineering}, volume = {12}, year = {2007}, month = {2007///}, pages = {107 - 119}, publisher = {Springer}, organization = {Springer}, abstract = {If empirical software engineering is to grow as a valid scientific endeavor, the ability to acquire, use, share, and compare data collected from a variety of sources must be encouraged. This is necessary to validate the formal models being developed within computer science. However, within the empirical software engineering community this has not been easily accomplished. This paper analyses experiences from a number of projects, and defines the issues, which include the following: (1) How should data, testbeds, and artifacts be shared? (2) What limits should be placed on who can use them and how? How does one limit potential misuse? (3) What is the appropriate way to credit the organization and individual that spent the effort collecting the data, developing the testbed, and building the artifact? (4) Once shared, who owns the evolved asset? As a solution to these issues, the paper proposes a framework for an empirical software engineering artifact agreement. Such an agreement is intended to address the needs for both creator and user of such artifacts and should foster a market in making available and using such artifacts. If this framework for sharing software engineering artifacts is commonly accepted, it should encourage artifact owners to make the artifacts accessible to others (gaining credit is more likely and misuse is less likely). It may be easier for other researchers to request artifacts since there will be a well-defined protocol for how to deal with relevant matters.}, author = {Basili, Victor R. and Zelkowitz, Marvin V and Sj{\o}berg,D. I.K and Johnson,P. and Cowling,A. J} } @conference {12411, title = {PUTOP: turning predominant senses into a topic model for word sense disambiguation}, booktitle = {Proceedings of the 4th International Workshop on Semantic Evaluations}, series = {SemEval {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {277 - 281}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We extend on McCarthy et al.{\textquoteright}s predominant sense method to create an unsupervised method of word sense disambiguation that uses automatically derived topics using Latent Dirichlet allocation. Using topic-specific synset similarity measures, we create predictions for each word in each document using only word frequency information. It is hoped that this procedure can improve upon the method for larger numbers of topics by providing more relevant training corpora for the individual topics. This method is evaluated on SemEval-2007 Task 1 and Task 17.}, url = {http://dl.acm.org/citation.cfm?id=1621474.1621534}, author = {Jordan Boyd-Graber and Blei,David} } @article {13400, title = {Report on the Fourth International Workshop on Data Management for Sensor Networks (DMSN 2007)}, journal = {SIGMOD Rec.}, volume = {36}, year = {2007}, month = {2007/12//}, pages = {53 - 55}, abstract = {Sensor networks enable an unprecedented level of access to the physical world, and hold tremendous potential to revolutionize many application domains. Research on sensor networks spans many areas of computer science, and there are now major conferences, e.g., IPSN and SenSys, devoted to sensor networks. However, there is no focused forum for discussion of early and innovative work on data management in sensor networks. The International Workshop on Data Management for Sensor Networks (DMSN), inaugurated in 2004, aims to fill this significant gap in the database and sensor network communities.}, isbn = {0163-5808}, doi = {10.1145/1361348.1361362}, url = {http://doi.acm.org/10.1145/1361348.1361362}, author = {Balazinska,Magdalena and Deshpande, Amol and Labrinidis,Alexandros and Luo,Qiong and Madden,Samuel and Yang,Jun} } @conference {12250, title = {Robust Routing with Unknown Traffic Matrices}, booktitle = {INFOCOM 2007. 26th IEEE International Conference on Computer Communications. IEEE}, year = {2007}, month = {2007/05//}, pages = {2436 - 2440}, abstract = {In this paper, we present an algorithm for intra-domain traffic engineering. We assume that the traffic matrix, which specifies traffic load between every source-destination pair in the network, is unknown and varies with time, but that always lies inside an explicitly defined region. Our goal is to compute a fixed robust routing with best worst case performance for all traffic matrices inside the bounding region. We formulate this problem as a semi-infinite programming problem. Then, we focus on a special case with practical merits, where (1) the traffic matrix region is assumed to be a polytope specified by a finite set of linear inequalities, and (2) our objective is to find the routing that minimizes the maximum link utilization. Under these assumptions, the problem can be formulated as a polynomial size linear programming (LP) problem with finite number of constraints. We further consider two specific set of constraints for the traffic matrix region. The first set is based on the hose model and limits the total traffic rate of network point of presence (PoP) nodes. The second set is based on the pipe model and limits the traffic between source-destination pairs. We study the effectiveness of each set of constraints using extensive simulations.}, keywords = {engineering;linear, inequalities;maximum, intradomain, linear, link, matrices;linear, matrix, network, nodes;polynomial, of, point, presence, problem;traffic, Programming, programming;semiinfinite, programming;telecommunication, region;unknown, routing;telecommunication, size, traffic, traffic;, utilization;network}, doi = {10.1109/INFCOM.2007.296}, author = {Tabatabaee,V. and Kashyap,A. and Bhattacharjee, Bobby and La,R.J. and Shayman,M.A.} } @article {12255, title = {SAAR: A shared control plane for overlay multicast}, journal = {Proceedings of 4th USENIX Symposium on Networked Systems Design \& Implementation}, year = {2007}, month = {2007///}, pages = {57 - 72}, abstract = {Many cooperative overlay multicast systems of diverse designs have been implemented and deployed. In this paper, we explore a new architecture for overlay multicast: we factor out the control plane into a separate overlay that provides a single primitive: a configurable anycast for peer selection. This separation of control and data overlays has several advantages. Data overlays can be optimized for efficient content delivery, while the control overlay can be optimized for flexible and efficient peer selection. Several data channels can share a control plane for fast switching among content channels, which is particularly important for IPTV. And, the control overlay can be reused in multicast systems with different data plane organizations.We designed and evaluated a decentralized control overlay for endsystem multicast. The overlay proactively aggregates system state and implements a powerful anycast primitive for peer selection. We demonstrate that SAAR{\textquoteright}s efficiency in locating peers reduces channel switching time, improves the quality of content delivery, and reduces overhead, even under dynamic conditions and at scale. An experimental evaluation demonstrates that the system can efficiently support single-tree, multi-tree and block-based multicast systems. }, author = {Nandi,A. and Ganjam,A. and Druschel,P. and Ng,T. S.E and Stoica,I. and Zhang,H. and Bhattacharjee, Bobby} } @article {14099, title = {Schistosoma mansoni genome: Closing in on a final gene set}, journal = {Experimental Parasitology}, volume = {117}, year = {2007}, month = {2007/11//}, pages = {225 - 228}, abstract = {The Schistosoma mansoni genome sequencing consortium has recently released the latest versions of the genome assembly as well as an automated preliminary gene structure annotation. The combined datasets constitute a vast resource for researchers to exploit in a variety of post-genomic studies with an emphasis of transcriptomic and proteomic tools. Here we present an innovative method used for combining diverse sources of evidence including ab initio gene predictions, protein and transcript sequence homologies, and cross-genome sequence homologies between S. mansoni and Schistosoma japonicum to define a comprehensive list of protein-coding genes.}, keywords = {Annotation, Gene finding, Genome, Schistosoma mansoni}, isbn = {0014-4894}, doi = {16/j.exppara.2007.06.005}, url = {http://www.sciencedirect.com/science/article/pii/S0014489407001683}, author = {Haas,Brian J. and Berriman,Matthew and Hirai,Hirohisa and Cerqueira,Gustavo G. and LoVerde,Philip T. and El-Sayed, Najib M.} } @article {12248, title = {A Secure DHT via the Pigeonhole Principle}, journal = {Technical Reports of the Computer Science Department, CS-TR-4884}, year = {2007}, month = {2007/09/24/}, abstract = {The standard Byzantine attack model assumes no more than some fixedfraction of the participants are faulty. This assumption does not accurately apply to peer-to-peer settings, where Sybil attacks and botnets are realistic threats. We propose an attack model that permits an arbitrary number of malicious nodes under the assumption that each node can be classified based on some of its attributes, such as autonomous system number or operating system, and that the number of classes with malicious nodes is bounded (e.g., an attacker may exploit at most a few operating systems at a time). In this model, we present a secure DHT, evilTwin, which replaces a single, large DHT with sufficiently many smaller instances such that it is impossible for an adversary to corrupt every instance. Our system ensures high availability and low-latency lookups, is easy to implement, does not require a complex Byzantine agreement protocol, and its proof of security is a straightforward application of the pigeonhole principle. The cost of security comes in the form of increased storage and bandwidth overhead; we show how to reduce these costs by replicating data and adaptively querying participants who historically perform well. We use implementation and simulation to show that evilTwin imposes a relatively small additional cost compared to conventional DHTs. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/7136}, author = {Baden,Randy and Bender,Adam and Levin,Dave and Sherwood,Rob and Spring, Neil and Bhattacharjee, Bobby} } @article {12262, title = {Secure lookup without (constrained) flooding}, journal = {WRAITS 2007}, year = {2007}, month = {2007///}, author = {Bhattacharjee, Bobby and Rodrigues,R. and Kouznetsov,P.} } @article {15471, title = {Semantics-Preserving Design of Embedded Control Software from Synchronous Models}, journal = {Software Engineering, IEEE Transactions on}, volume = {33}, year = {2007}, month = {2007/08//}, pages = {497 - 509}, abstract = {The design of embedded controllers is experiencing a growth in complexity as embedded systems increase their functionality while they become ubiquitous in electronic appliances, cars, airplanes, etc. As requirements become more challenging, mathematical models gain importance for mastering complexity. Among the different computational models proposed, synchronous models have proved to be the most widely used for control dominated applications. While synchronous models simplify the way of dealing with concurrency by decoupling functional and timing aspects, their software implementation on multitasking and multiprocessor platforms is far from straightforward, because of the asynchronous nature of most industrial software platforms. Known solutions in the literature either restrict the solution space or focus on special cases. We present a method for preserving the synchronous semantics through buffer-based intertask communication mechanisms, grounded on an abstraction of the target platform. This allows us to deal with any task set and, most importantly, being independent of the implementation, to explore the design space effectively.}, keywords = {embedded control software, embedded systems, multiprocessing programs, multiprocessor, multitasking, semantics-preserving design, software engineering, software implementation, systems analysis}, isbn = {0098-5589}, doi = {10.1109/TSE.2007.70718}, author = {Mangeruca,L. and Baleani,M. and Ferrari,A. and Sangiovanni-Vincentelli,A.} } @article {12196, title = {Semi-automatic photo annotation strategies using event based clustering and clothing based person recognition}, journal = {Interacting with Computers}, volume = {19}, year = {2007}, month = {2007///}, pages = {524 - 544}, author = {Suh,B. and Bederson, Benjamin B.} } @conference {17780, title = {Sentiment analysis: Adjectives and adverbs are better than adjectives alone}, booktitle = {Proceedings of the International Conference on Weblogs and Social Media (ICWSM)}, year = {2007}, month = {2007///}, abstract = {Most past work on determining the strength of subjective expres-sions within a sentence or a document use specific parts of speech such as adjectives, verbs and nouns. To date, there is almost no work on the use of adverbs in sentiment analysis, nor has there been any work on the use of adverb-adjective combinations (AACs). We propose an AAC-based sentiment analysis technique that uses a lin- guistic analysis of adverbs of degree. We define a set of general axioms (based on a classification of adverbs of degree into five cat- egories) that all adverb scoring techniques must satisfy. Instead of aggregating scores of both adverbs and adjectives using simple scor- ing functions, we propose an axiomatic treatment of AACs based on the linguistic classification of adverbs. Three specific AAC scor- ing methods that satisfy the axioms are presented. We describe the results of experiments on an annotated set of 200 news articles (an- notated by 10 students) and compare our algorithms with some exist- ing sentiment analysis algorithms. We show that our results lead to higher accuracy based on Pearson correlation with human subjects. }, author = {Benamara,F. and Cesarano,C. and Picariello, A. and Reforgiato,D. and V.S. Subrahmanian} } @conference {17360, title = {Similarity-Based Forecasting with Simultaneous Previews: A River Plot Interface for Time Series Forecasting}, booktitle = {Information Visualization, 2007. IV {\textquoteright}07. 11th International Conference}, year = {2007}, month = {2007/07/04/6}, pages = {191 - 196}, publisher = {IEEE}, organization = {IEEE}, abstract = {Time-series forecasting has a large number of applications. Users with a partial time series for auctions, new stock offerings, or industrial processes desire estimates of the future behavior. We present a data driven forecasting method and interface called similarity-based forecasting (SBF). A pattern matching search in an historical time series dataset produces a subset of curves similar to the partial time series. The forecast is displayed graphically as a river plot showing statistical information about the SBF subset. A forecasting preview interface allows users to interactively explore alternative pattern matching parameters and see multiple forecasts simultaneously. User testing with 8 users demonstrated advantages and led to improvements.}, keywords = {data driven forecasting method, data visualisation, Data visualization, Economic forecasting, forecasting preview interface, Graphical user interfaces, historical time series dataset, Laboratories, new stock offerings, partial time series, pattern matching, pattern matching search, Predictive models, river plot interface, Rivers, similarity-based forecasting, Smoothing methods, Technological innovation, Testing, time series, time series forecasting, Weather forecasting}, isbn = {0-7695-2900-3}, doi = {10.1109/IV.2007.101}, author = {Buono,P. and Plaisant, Catherine and Simeone,A. and Aris,A. and Shneiderman, Ben and Shmueli,G. and Jank,W.} } @article {19503, title = {Stochastic Communication: A New Paradigm for Fault-Tolerant Networks-on-Chip}, journal = {VLSI Design}, volume = {2007}, year = {2007}, month = {2007/04/22/}, abstract = {As CMOS technology scales down into the deep-submicron (DSM) domain, the costs of design and verification for Systems-on-Chip (SoCs) are rapidly increasing. Relaxing the requirement of 100\&$\#$x0025; correctness for devices and interconnects drastically reduces the costs of design but, at the same time, requires SoCs to be designed with some degree of system-level fault-tolerance. Towards this end, this paper introduces a novel communication paradigm for SoCs, called stochastic communication. This scheme separates communication from computation by allowing the on-chip interconnect to be designed as a reusable IP and also provides a built-in tolerance to DSM failures, without a significant performance penalty. By using this communication scheme, a large percentage of data upsets, packet losses due to buffers overflow, and severe levels of synchronization failures can be tolerated, while providing high levels of performance.}, isbn = {1065-514X}, url = {http://www.hindawi.com/journals/vlsi/2007/095348/abs/}, author = {Bogdan, Paul and Dumitra\&$\#$351 and Tudor and Marculescu, Radu} } @article {13922, title = {Supporting elementary-age children{\textquoteright}s searching and browsing: Design and evaluation using the international children{\textquoteright}s digital library}, journal = {Journal of the American Society for Information Science and Technology}, volume = {58}, year = {2007}, month = {2007///}, pages = {1618 - 1630}, author = {Hutchinson,H.B. and Druin, Allison and Bederson, Benjamin B.} } @conference {12589, title = {Symmetric Objects are Hardly Ambiguous}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 7}, abstract = {Given any two images taken under different illumination conditions, there always exist a physically realizable object which is consistent with both the images even if the lighting in each scene is constrained to be a known point light source at infinity. In this paper, we show that images are much less ambiguous for the class of bilaterally symmetric Lambertian objects. In fact, the set of such objects can be partitioned into equivalence classes such that it is always possible to distinguish between two objects belonging to different equivalence classes using just one image per object. The conditions required for two objects to belong to the same equivalence class are very restrictive, thereby leading to the conclusion that images of symmetric objects are hardly ambiguous. The observation leads to an illumination-invariant matching algorithm to compare images of bilaterally symmetric Lambertian objects. Experiments on real data are performed to show the implications of the theoretical result even when the symmetry and Lambertian assumptions are not strictly satisfied.}, keywords = {algorithm;symmetric, bilaterally, images;image, Lambertian, MATCHING, matching;, objects, objects;illumination-invariant, objects;symmetric, symmetric}, doi = {10.1109/CVPR.2007.383289}, author = {Aggarwal,G. and Biswas,S. and Chellapa, Rama} } @conference {12368, title = {A taxonomy for medical image registration acceleration techniques}, booktitle = {Life Science Systems and Applications Workshop, 2007. LISA 2007. IEEE/NIH}, year = {2007}, month = {2007///}, pages = {160 - 163}, author = {Plishker,W. and Dandekar,O. and Bhattacharyya, Shuvra S. and Shekhar,R.} } @conference {15500, title = {Test suite prioritization by interaction coverage}, booktitle = {Workshop on Domain specific approaches to software test automation: in conjunction with the 6th ESEC/FSE joint meeting}, series = {DOSTA {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1 - 7}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Event-driven software (EDS) is a widely used class of software that takes sequences of events as input, changes state, and outputs new event sequences. Managing the size of tests suites for EDS is difficult as the number of event combinations and sequences grow exponentially with the number of events. We propose a new testing technique that extends software interaction testing. Traditional software interaction testing systematically examines all t-way interactions of parameters for a program. This paper extends the notion to t-way interactions over sequences of events. The technique applies to many classes of software; we focus on that of EDS. As a proof-of-concept, we prioritize existing test suites for four GUI-based programs by t-way interaction coverage. We compare the rate of fault detection with that of several other prioritization criteria. Results show that prioritization by interaction coverage has the fastest rate of fault detection in half of our experiments, making the most impact when tests have high interaction coverage.}, keywords = {t-way interaction coverage, combinatorial interaction testing, covering arrays, event driven software, test suite prioritization}, isbn = {978-1-59593-726-1}, doi = {10.1145/1294921.1294922}, url = {http://doi.acm.org/10.1145/1294921.1294922}, author = {Bryce,Ren{\'e}e C. and Memon, Atif M.} } @conference {12212, title = {Thumbspace: Generalized one-handed input for touchscreen-based mobile devices}, booktitle = {Proceedings of the 11th IFIP TC 13 international conference on Human-computer interaction}, year = {2007}, month = {2007///}, pages = {324 - 338}, author = {Karlson,A.K. and Bederson, Benjamin B.} } @conference {12395, title = {A topic model for word sense disambiguation}, booktitle = {Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL)}, year = {2007}, month = {2007///}, pages = {1024 - 1033}, author = {Jordan Boyd-Graber and Blei,D. and Zhu,X.} } @conference {12331, title = {Towards a heterogeneous medical image registration acceleration platform}, booktitle = {Biomedical Circuits and Systems Conference, 2007. BIOCAS 2007. IEEE}, year = {2007}, month = {2007///}, pages = {231 - 234}, author = {Plishker,W. and Dandekar,O. and Bhattacharyya, Shuvra S. and Shekhar,R.} } @article {18869, title = {Towards the development of a virtual environment-based training system for mechanical assembly operations}, journal = {Virtual Reality}, volume = {11}, year = {2007}, month = {2007///}, pages = {189 - 206}, abstract = {In this paper, we discuss the development of Virtual Training Studio (VTS), a virtual environment-based training system that allows training supervisors to create training instructions and allows trainees to learn assembly operations in a virtual environment. Our system is mainly focused on the cognitive side of training so that trainees can learn to recognize parts, remember assembly sequences, and correctly orient the parts during assembly operations. Our system enables users to train using the following three training modes: (1) Interactive Simulation, (2) 3D Animation, and (3) Video. Implementing these training modes required us to develop several new system features. This paper presents an overview of the VTS system and describes a few main features of the system. We also report user test results that show how people train using our system. The user test results indicate that the system is able to support a wide variety of training preferences and works well to support training for assembly operations.}, keywords = {Computer science}, isbn = {1359-4338}, doi = {10.1007/s10055-007-0076-4}, url = {http://www.springerlink.com/content/g7760422m13l83x1/abstract/}, author = {Brough,John and Schwartz,Maxim and Gupta, Satyandra K. and Anand,Davinder and Kavetsky,Robert and Pettersen,Ralph} } @article {17893, title = {Using Content-Addressable Networks for Load Balancing in Desktop Grids}, volume = {UMIACS-TR-2007-16}, year = {2007}, month = {2007/03/29/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Desktop grids combine Peer-to-Peer and Grid computing techniques to improvethe robustness, reliability and scalability of job execution infrastructures. However, efficiently matching incoming jobs to available system resources and achieving good load balance in a fully decentralized and heterogeneous computing environment is a challenging problem. In this paper, we extend our prior work with a new decentralized algorithm for maintaining approximate global load information, and a job pushing mechanism that uses the global information to push jobs towards underutilized portions of the system. The resulting system more effectively balances load and improves overall system throughput. Through a comparative analysis of experimental results across different system configurations and job profiles, performed via simulation, we show that our system can reliably execute Grid applications on a distributed set of resources both with low cost and with good load balance. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/4355}, author = {Kim,Jik-Soo and Keleher,Peter and Marsh,Michael and Bhattacharjee, Bobby and Sussman, Alan} } @conference {18766, title = {Using virtual demonstrations for creating multi-media training instructions}, year = {2007}, month = {2007///}, abstract = {Often generating training instructions for virtual environments is a long and tedious process. In thispaper, we discuss the development of a virtual environment (VE) instruction generating tool called Virtual Author which is the main component of the Virtual Training Studio (VTS). VTS is a virtual environment-based training system that provides instructors with a tool to create training instructions and allows trainees to learn assembly operations in a personal virtual environment. The Virtual Author tool is designed to allow an instructor to perform virtual demonstrations using CAD models in the virtual environment in order to quickly generate VE-based training instructions for use in VTS. This paper describes the algorithms used to carry out motion smoothening of instructor{\textquoteright}s actions, automated text instruction generation based on part and assembly motions, and extraction of alignment constraints from 3D CAD models to support instruction generation. We also present examples to illustrate how the use of the Virtual Author tool leads to a significant reduction in the training instruction generation time. }, url = {http://www.cadanda.com/CAD_4_1-4__11.PDF}, author = {Schwartz,M. and Gupta,S.K. and Anand,D. K. and Brough,J. E. and Kavetsky,R.} } @article {14572, title = {Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes}, journal = {Virology}, volume = {365}, year = {2007}, month = {2007/08/15/}, pages = {60 - 69}, abstract = {Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5{\textquoteright}-(T/C)CCTT-3{\textquoteright}. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13~bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.}, keywords = {Annotation of topoisomerase sites, Sequence specific recognition, Topoisomerase IB, Variola virus}, isbn = {0042-6822}, doi = {16/j.virol.2007.02.037}, url = {http://www.sciencedirect.com/science/article/pii/S0042682207001225}, author = {Minkah,Nana and Hwang,Young and Perry,Kay and Van Duyne,Gregory D. and Hendrickson,Robert and Lefkowitz,Elliot J. and Hannenhalli, Sridhar and Bushman,Frederic D.} } @conference {14405, title = {Visual Mining of Multi-Modal Social Networks at Different Abstraction Levels}, booktitle = {Information Visualization, 2007. IV {\textquoteright}07. 11th International Conference}, year = {2007}, month = {2007/07//}, pages = {672 - 679}, abstract = {Social networks continue to become more and more feature rich. Using local and global structural properties and descriptive attributes are necessary for more sophisticated social network analysis and support for visual mining tasks. While a number of visualization tools for social network applications have been developed, most of them are limited to uni-modal graph representations. Some of the tools support a wide range of visualization options, including interactive views. Others have better support for calculating structural graph properties such as the density of the graph or deploying traditional statistical social network analysis. We present Invenio, a new tool for visual mining of socials. Invenio integrates a wide range of interactive visualization options from Prefuse, with graph mining algorithm support from JUNG. While the integration expands the breadth of functionality within the core engine of the tool, our goal is to interactively explore multi-modal, multi-relational social networks. Invenio also supports construction of views using both database operations and basic graph mining operations.}, keywords = {computing;, database;interactive, graph, management, mining;data, network;structural, property;visual, sciences, social, systems;graph, systems;social, theory;interactive, visualisation;database, visualization;multimodal}, doi = {10.1109/IV.2007.126}, author = {Singh,L. and Beard,M. and Getoor, Lise and Blake,M.B.} } @article {14475, title = {Voila: Efficient feature-value acquisition for classification}, journal = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {22}, year = {2007}, month = {2007///}, pages = {1225 - 1225}, abstract = {We address the problem of efficient feature-value acquisi- tion for classification in domains in which there are varying costs associated with both feature acquisition and misclassi- fication. The objective is to minimize the sum of the infor- mation acquisition cost and misclassification cost. Any de- cision theoretic strategy tackling this problem needs to com- pute value of information for sets of features. Having cal- culated this information, different acquisition strategies are possible (acquiring one feature at time, acquiring features in sets, etc.). However, because the value of information cal- culation for arbitrary subsets of features is computationally intractable, most traditional approaches have been greedy, computing values of features one at a time. We make the problem of value of information calculation tractable in prac- tice by introducing a novel data structure called the Value of Information Lattice (VOILA). VOILA exploits dependencies between missing features and makes sharing of information value computations between different feature subsets possi- ble. To the best of our knowledge, performance differences between greedy acquisition, acquiring features in sets, and a mixed strategy have not been investigated empirically in the past, due to inherit intractability of the problem. With the help of VOILA, we are able to evaluate these strategies on five real world datasets under various cost assumptions. We show that VOILA reduces computation time dramatically. We also show that the mixed strategy outperforms both greedy acqui- sition and acquisition in sets.}, author = {Bilgic,M. and Getoor, Lise} } @article {16492, title = {Adaptive pull-based policies for wide area data delivery}, journal = {ACM Transactions on Database Systems (TODS)}, volume = {31}, year = {2006}, month = {2006///}, pages = {631 - 671}, author = {Bright,L. and Gal,A. and Raschid, Louiqa} } @conference {12617, title = {An Adaptive Threshold Method for Hyperspectral Target Detection}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {In this paper, we present a new approach to automatically determine a detector threshold. This research problem is especially important in hyperspectral target detection as targets are typically very similar to the background. While a number of methods exist to determine the threshold, these methods require either large amounts of data or make simplifying assumptions about the background distribution. We use a method called inverse blind importance sampling which requires few samples and makes no a-priori assumptions about the background statistics. Results show the promise of this algorithm to determine thresholds for fixed false alarm densities in hyperspectral detectors}, keywords = {adaptive, blind, detection;, detection;inverse, importance, method;background, processing;importance, sampling;geophysical, sampling;object, signal, statistics;hyperspectral, target, threshold}, doi = {10.1109/ICASSP.2006.1661497}, author = {Broadwater, J. and Chellapa, Rama} } @article {12396, title = {Adding dense, weighted connections to wordnet}, journal = {Proceedings of the Third International WordNet Conference}, year = {2006}, month = {2006///}, pages = {29 - 36}, abstract = {WORDNET, a ubiquitous tool for natural language processing, suffers from sparsity of connectionsbetween its component concepts (synsets). Through the use of human annotators, a subset of the connections between 1000 hand-chosen synsets was assigned a value of {\textquotedblleft}evocation{\textquotedblright} representing how much the first concept brings to mind the second. These data, along with existing similarity measures, constitute the basis of a method for predicting evocation between previously unrated pairs. }, author = {Jordan Boyd-Graber and Fellbaum,C. and Osherson,D. and Schapire,R.} } @conference {18758, title = {Algorithms for on-line monitoring of components in an optical tweezers-based assembly cell}, year = {2006}, month = {2006///}, pages = {1 - 13}, abstract = {Optical tweezers have emerged as a powerful tool for microand nanomanipulation. Using optical tweezers to perform auto- mated assembly requires on-line monitoring of components in the assembly workspace. This paper presents algorithms for estimat- ing positions and orientations of microscale and nanoscale com- ponents in the 3-Dimensional assembly workspace. Algorithms presented in this paper use images obtained by optical section microscopy. The images are first segmented to locate areas of in- terest and then image gradient information from the areas of in- terest is used to generate probable locations and orientations of components in the XY-plane. Finally, signature curves are com- puted and utilized to obtain component locations and orienta- tions in 3-D space. We have tested these algorithms with silica micro-spheres as well as metallic nanowires. We believe that the algorithms described in this paper will provide the foundation for realizing automated assembly operations in optical tweezers- based assembly cells. }, url = {http://www.glue.umd.edu/~skgupta/Publication/CIE06_Peng1.pdf}, author = {Peng,T. and Balijepalli,A. and Gupta,S.K. and LeBrun,T. W.} } @article {19020, title = {Anonymous multi-attribute encryption with range query and conditional decryption}, year = {2006}, month = {2006}, institution = {Carnegie Mellon University}, abstract = {We introduce the concept of Anonymous Multi-Attribute Encryption with Range Query and Con-ditional Decryption (AMERQCD). In AMERQCD, a plaintext is encrypted under a point in multi- dimensional space. To a computationally bounded adversary, the ciphertext hides both the plaintext and the point under which it is encrypted. In a range query, a master key owner releases the decryp- tion key for an arbitrary hyper-rectangle in space, thus allowing decryption of ciphertexts previ- ously encrypted under any point within the hyper-rectangle. However, a computationally bounded adversary cannot learn any information on ciphertexts outside the range covered by the decryption key (except the fact that they do not lie within this range). We give an efficient construction based on the Decision Bilinear Diffie-Hellman (D-BDH) and Decision Linear (D-Linear) assumption. }, isbn = {CMU-CS-06-135}, doi = {Technical Report}, url = {http://reports-archive.adm.cs.cmu.edu/anon/anon/home/ftp/2006/CMU-CS-06-135.pdf}, author = {Bethencourt, J. and Chan, H. and Perrig, A. and Elaine Shi and Song,D.} } @conference {18767, title = {Bio-inspired, Modular, and Multifunctional Thermal and Impact Protected (TIPed) Embedded Sensing Controls Actuation Power Element (ESCAPE) Structures}, year = {2006}, month = {2006///}, abstract = {There is a great deal of interest in creating new structural concepts, such as snake robots, from analogousbiological systems. These biological systems are typically composed of materials that serve multiple functions. For example, the skin of a snake is a system consisting of a soft, hyperelastic covering, with nerves providing thermal and pressure sensitivity, and a hard, scaly coating to resist wear and tear from hard particles such as sand. Therefore, bio-inspired structures can also be composed of multifunctional materials. There are currently many approaches to fabricating bio-inspired structures with conventional materials. These concepts typically utilize a system-of-systems design approach where the structure will be composed of a structural framework, an actuation system, a power source for the actuation system, controllers, and external sensors. The drawbacks to these structures include the need to assemble all of the components, interfaces between components that can compromise reliability, constraints on scaling down the structure, and very high power consumption and power generation requirements. These problems have been addressed by developing a new scalable approach to creating multifunctional materials for bio-inspired structures where the controllers, actuators, and sensors are integrated into a modular, multifunctional structure. This approach is facilitated by using multi-material multi-stage molding processes with fully embedded electronic systems, and has resulted in new Thermal and Impact Protected (TIPed) Embedded Sensing Controls Actuation Power Element (ESCAPE) Structures for compact and rugged robotic applications. }, url = {http://sem-proceedings.com/06s/sem.org-2006-SEM-Ann-Conf-s89p07-Bio-inspired-Modular-Multifunctional-Thermal-Impact-Protected-TIPed.pdf}, author = {Gyger Jr,L. S. and Spranklin,B. W. and Gupta,S.K. and Bruck,H. A.} } @conference {12264, title = {CAM04-6: Single-Path Routing of Time-varying Traffic}, booktitle = {Global Telecommunications Conference, 2006. GLOBECOM {\textquoteright}06. IEEE}, year = {2006}, month = {2006/12/27/1}, pages = {1 - 6}, abstract = {We consider the problem of finding a single-path intra-domain routing for time-varying traffic. We characterize the traffic variations by a finite set of traffic profiles with given non-zero fractions of occurrence. Our goal is to optimize the average performance over all of these traffic profiles. We solve the optimal multi-path version of this problem using linear programming and develop heuristic single-path solutions using randomized rounding and iterated rounding. We analyze our single-path heuristic (finding the optimal single-path routing is NP-hard), and prove that the randomized rounding algorithm has a worst case performance bound of O(log(KN)/log(log(KN))) compared to the optimal multi-path routing with a high probability, where K is the number of traffic profiles, and N the number of nodes in the network. Further, our simulations show the iterated rounding heuristics perform close to the optimal multi-path routing on a wide range of measured ISP topologies, in both the average and the worst-case. Overall, these results are extremely positive since they show that in a wide-range of practical situations, it is not necessary to deploy multi-path routing; instead, an appropriately computed single-path routing is sufficient to provide good performance.}, keywords = {algorithm;linear, algorithm;time-varying, algorithms;telecommunication, bound;IP, case, complexity;iterative, intra-domain, IP, methods;linear, multipath, network, network;ISP, networks;Internet;computational, optimal, performance, problem;heuristic, profile;worst, programming;optimal, programming;probability;randomised, rounding, routing;iterated, routing;probability;randomized, routing;telecommunication, single-path, topology;NP-hard, topology;telecommunication, traffic, traffic;}, doi = {10.1109/GLOCOM.2006.29}, author = {Kashyap,A. and Bhattacharjee, Bobby and La,R. and Shayman,M. and Tabatabaee,V.} } @conference {13894, title = {A case study of tangible flags: a collaborative technology to enhance field trips}, booktitle = {Proceedings of the 2006 conference on Interaction design and children}, year = {2006}, month = {2006///}, pages = {1 - 8}, author = {Chipman,G. and Druin, Allison and Beer,D. and Fails,J. A and Guha,M.L. and Simms,S.} } @article {17544, title = {A client-driven approach for channel management in wireless LANs}, journal = {IEEE Infocom}, volume = {6}, year = {2006}, month = {2006///}, abstract = {We propose an efficient client-based approach for channel man-agement (channel assignment and load balancing) in 802.11-based WLANs that lead to better usage of the wireless spectrum. This approach is based on a {\textquotedblleft}conflict set coloring{\textquotedblright} formulation that jointly performs load balancing along with channel assignment. Such a formulation has a number of advantages. First, it explicitly captures interference effects at clients. Next, it intrinsically ex- poses opportunities for better channel re-use. Finally, algorithms based on this formulation do not depend on specific physical RF models and hence can be applied efficiently to a wide-range of in- building as well as outdoor scenarios. We have performed extensive packet-level simulations and mea- surements on a deployed wireless testbed of 70 APs to validate the performance of our proposed algorithms. We show that in addi- tion to single network scenarios, the conflict set coloring formu- lation is well suited for channel assignment where multiple wire- less networks share and contend for spectrum in the same physical space. Our results over a wide range of both simulated topologies and in-building testbed experiments indicate that our approach improves application level performance at the clients by upto three times (and atleast 50\%) in comparison to current best-known tech- niques. }, author = {Mishra,A. and Brik,V. and Banerjee,S. and Srinivasan, Aravind and Arbaugh, William A.} } @article {17574, title = {Client-driven channel management for wireless LANs}, journal = {SIGMOBILE Mob. Comput. Commun. Rev.}, volume = {10}, year = {2006}, month = {2006/10//}, pages = {8 - 10}, abstract = {With the explosive growth in the density of 802.11 access points (APs) in the form of hotspots and public/home access networks, coordinating the shared use of spectrum has become an important problem. The irregular coverage topologies present in WLANs due to the vagaries of the indoor RF environment make the channel assignment algorithms in cellular networks inapplicable [1, 2].}, isbn = {1559-1662}, doi = {10.1145/1215976.1215981}, url = {http://doi.acm.org/10.1145/1215976.1215981}, author = {Mishra,Arunesh and Brik,Vladimir and Banerjee,Suman and Srinivasan, Aravind and Arbaugh, William A.} } @conference {12347, title = {A Communication Interface for Multiprocessor Signal Processing Systems}, booktitle = {Proceedings of the 2006 IEEE/ACM/IFIP Workshop on Embedded Systems for Real Time Multimedia}, year = {2006}, month = {2006/10//}, pages = {127 - 132}, publisher = {IEEE}, organization = {IEEE}, abstract = {Parallelization of embedded software is often desirable for power/performance-related considerations for computation-intensive applications that frequently occur in the signal-processing domain. Although hardware support for parallel computation is increasingly available in embedded processing platforms, there is a distinct lack of effective software support. One of the most widely known efforts in support of parallel software is the message passing interface (MPI). However, MPI suffers from several drawbacks with regards to customization to specialized parallel processing contexts, and performance degradation for communication-intensive applications. In this paper, we propose a new interface, the signal passing interface (SPI), that is targeted toward signal processing applications and addresses the limitations of MPI for this important domain of embedded software by integrating relevant properties of MPI and coarse-grain dataflow modeling. SPI is much easier and more intuitive to use, and due to its careful specialization, more performance-efficient for the targeted application domain. We present our preliminary version of SPI, along with experiments using SPI on a practical face detection system that demonstrate the capabilities of SPI}, keywords = {application program interfaces, Application software, coarse-grain dataflow modeling, Computer applications, Concurrent computing, Context, data flow graphs, Embedded computing, Embedded software, face detection system, Hardware, Message passing, message passing interface, MPI, Multiprocessing systems, multiprocessor signal processing system, PARALLEL PROCESSING, signal passing interface, Signal processing, SPI}, isbn = {0-7803-9783-5}, doi = {10.1109/ESTMED.2006.321285}, author = {Sankalita Saha and Bhattacharyya, Shuvra S. and Wayne Wolf} } @article {18971, title = {Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis}, journal = {BMC Genomics}, volume = {7}, year = {2006}, month = {2006/12/28/}, pages = {327 - 327}, abstract = {Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST) libraries. We employed the Program to Assemble Spliced Alignments (PASA) to identify and analyze alternatively spliced isoforms in both species.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-7-327}, url = {http://www.biomedcentral.com/1471-2164/7/327/abstract}, author = {Campbell,Matthew A. and Haas,Brian J. and Hamilton,John P. and Mount, Stephen M. and Buell,C. Robin} } @conference {12316, title = {Compression techniques for minimum energy consumption}, booktitle = {25th Army Science Conference}, year = {2006}, month = {2006///}, author = {Puthenpurayil,S. and Gu,R. and Bhattacharyya, Shuvra S.} } @conference {12376, title = {Configuration and representation of large-scale dataflow graphs using the dataflow interchange format}, booktitle = {Proceedings of the IEEE Workshop on Signal Processing Systems, Banff, Canada}, year = {2006}, month = {2006///}, pages = {10 - 15}, author = {Corretjer,I. and Hsu,C. and Bhattacharyya, Shuvra S.} } @inbook {14601, title = {Conservation Patterns in cis-Elements Reveal Compensatory Mutations}, booktitle = {Comparative GenomicsComparative Genomics}, series = {Lecture Notes in Computer Science}, volume = {4205}, year = {2006}, month = {2006///}, pages = {186 - 199}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Transcriptional regulation critically depends on proper interactions between transcription factors (TF) and their cognate DNA binding sites or cis elements. A better understanding and modelling of the TF-DNA interaction is an important area of research. The Positional Weight Matrix (PWM) is the most common model of TF-DNA binding and it presumes that the nucleotide preferences at individual positions within the binding site are independent. However, studies have shown that this independence assumption does not always hold. If the nucleotide preference at one position depends on the nucleotide at another position, a chance mutation at one position should exert selection pressures at the other position. By comparing the patterns of evolutionary conservation at individual positions within cis elements, here we show that positional dependence within binding sites is highly prevalent. We also show that dependent positions are more likely to be functional, as evidenced by a higher information content and higher conservation. We discuss two examples{\textemdash}Elk-1 and SAP-1 where the inferred compensatory mutation is consistent with known TF-DNA crystal structure.}, isbn = {978-3-540-44529-6}, url = {http://dx.doi.org/10.1007/11864127_15}, author = {Evans,Perry and Donahue,Greg and Hannenhalli, Sridhar}, editor = {Bourque,Guillaume and El-Mabrouk,Nadia} } @article {12378, title = {Contention-conscious transaction ordering in multiprocessor DSP systems}, journal = {IEEE Transactions on Signal Processing}, volume = {54}, year = {2006}, month = {2006/02//}, pages = {556 - 569}, abstract = {This paper explores the problem of efficiently ordering interprocessor communication (IPC) operations in statically scheduled multiprocessors for iterative dataflow graphs. In most digital signal processing (DSP) applications, the throughput of the system is significantly affected by communication costs. By explicitly modeling these costs within an effective graph-theoretic analysis framework, we show that ordered transaction schedules can significantly outperform self-timed schedules even when synchronization costs are low. However, we also show that when communication latencies are nonnegligible, finding an optimal transaction order given a static schedule is an NP-complete problem, and that this intractability holds both under iterative and noniterative execution. We develop new heuristics for finding efficient transaction orders, and perform an extensive experimental comparison to gauge the performance of these heuristics.}, keywords = {contention-conscious transaction ordering, Costs, data flow graphs, Dataflow, Delay, Digital signal processing, digital signal processing chips, Embedded system, graph-theoretic analysis, Instruments, Internet telephony, interprocessor communication, iterative dataflow graphs, iterative methods, Message passing, multiprocessor, multiprocessor DSP systems, NP-complete problem, Processor scheduling, scheduling, Signal processing, synchronization, Throughput}, isbn = {1053-587X}, doi = {10.1109/TSP.2005.861074}, author = {Khandelia,M. and Bambha,N. K and Bhattacharyya, Shuvra S.} } @article {12268, title = {Cooperative peer groups in NICE}, journal = {Computer Networks}, volume = {50}, year = {2006}, month = {2006/03/15/}, pages = {523 - 544}, abstract = {We present a distributed scheme for trust inference in peer-to-peer networks. Our work is in the context of the NICE system, which is a platform for implementing cooperative applications over the Internet. We describe a technique for efficiently storing user reputation information in a completely decentralized manner, and show how this information can be used to efficiently identify non-cooperative users in NICE. We present a simulation-based study of our algorithms, in which we show our scheme scales to thousands of users using modest amounts of storage, processing, and bandwidth at any individual node. Lastly we show that our scheme is robust and can form cooperative groups in systems where the vast majority of users are malicious.}, keywords = {distributed algorithms, P2P, Reputation base trust}, isbn = {1389-1286}, doi = {10.1016/j.comnet.2005.07.012}, url = {http://www.sciencedirect.com/science/article/pii/S1389128605002185}, author = {Sherwood,Rob and Lee,Seungjoon and Bhattacharjee, Bobby} } @inbook {13751, title = {Cross-Language Access to Recorded Speech in the MALACH Project}, booktitle = {Text, Speech and DialogueText, Speech and Dialogue}, series = {Lecture Notes in Computer Science}, volume = {2448}, year = {2006}, month = {2006///}, pages = {197 - 212}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The MALACH project seeks to help users find information in a vast multilingual collections of untranscribed oral history interviews. This paper introduces the goals of the project and focuses on supporting access by users who are unfamiliar with the interview language. It begins with a review of the state of the art in crosslanguage speech retrieval; approaches that will be investigated in the project are then described. Czech was selected as the first non-English language to be supported, so results of an initial experiment with Czech/English cross-language retrieval are reported.}, isbn = {978-3-540-44129-8}, url = {http://dx.doi.org/10.1007/3-540-46154-X_8}, author = {Oard, Douglas and Demner-Fushman,Dina and Haji{\v c},Jan and Ramabhadran,Bhuvana and Gustman,Samuel and Byrne,William and Soergel,Dagobert and Dorr, Bonnie J and Resnik, Philip and Picheny,Michael}, editor = {Sojka,Petr and Kopecek,Ivan and Pala,Karel} } @article {17837, title = {Data redistribution and remote method invocation for coupled components}, journal = {Journal of Parallel and Distributed Computing}, volume = {66}, year = {2006}, month = {2006/07//}, pages = {931 - 946}, abstract = {With the increasing availability of high-performance massively parallel computer systems, the prevalence of sophisticated scientific simulation has grown rapidly. The complexity of the scientific models being simulated has also evolved, leading to a variety of coupled multi-physics simulation codes. Such cooperating parallel programs require fundamentally new interaction capabilities, to efficiently exchange parallel data structures and collectively invoke methods across programs. So-called {\textquotedblleft} M {\texttimes} N {\textquotedblright} research, as part of the common component architecture (CCA) effort, addresses these special and challenging needs, to provide generalized interfaces and tools that support flexible parallel data redistribution and parallel remote method invocation. Using this technology, distinct simulation codes with disparate distributed data decompositions can work together to achieve greater scientific discoveries.}, keywords = {Common component architecture, Model coupling, Parallel data redistribution, Parallel remote method invocation}, isbn = {0743-7315}, doi = {10.1016/j.jpdc.2005.12.009}, url = {http://www.sciencedirect.com/science/article/pii/S0743731506000700}, author = {Bertrand,Felipe and Bramley,Randall and Bernholdt,David E. and Kohl,James A. and Sussman, Alan and Larson,Jay W. and Damevski,Kostadin B.} } @conference {12317, title = {Dataflow transformations in high-level DSP system design}, booktitle = {Proceedings of the International Symposium on System-on-Chip, Tampere, Finland}, year = {2006}, month = {2006///}, pages = {131 - 136}, author = {Saha,S. and Puthenpurayil,S. and Bhattacharyya, Shuvra S.} } @conference {14498, title = {D-Dupe: An Interactive Tool for Entity Resolution in Social Networks}, booktitle = {Visual Analytics Science And Technology, 2006 IEEE Symposium On}, year = {2006}, month = {2006/11/31/2}, pages = {43 - 50}, abstract = {Visualizing and analyzing social networks is a challenging problem that has been receiving growing attention. An important first step, before analysis can begin, is ensuring that the data is accurate. A common data quality problem is that the data may inadvertently contain several distinct references to the same underlying entity; the process of reconciling these references is called entity-resolution. D-Dupe is an interactive tool that combines data mining algorithms for entity resolution with a task-specific network visualization. Users cope with complexity of cleaning large networks by focusing on a small subnetwork containing a potential duplicate pair. The subnetwork highlights relationships in the social network, making the common relationships easy to visually identify. D-Dupe users resolve ambiguities either by merging nodes or by marking them distinct. The entity resolution process is iterative: as pairs of nodes are resolved, additional duplicates may be revealed; therefore, resolution decisions are often chained together. We give examples of how users can flexibly apply sequences of actions to produce a high quality entity resolution result. We illustrate and evaluate the benefits of D-Dupe on three bibliographic collections. Two of the datasets had already been cleaned, and therefore should not have contained duplicates; despite this fact, many duplicates were rapidly identified using D-Dupe{\textquoteright}s unique combination of entity resolution algorithms within a task-specific visual interface}, keywords = {algorithm;data, analysis;social, computing;user, D-Dupe, interactive, interface;data, interfaces;, mining, mining;interactive, network, problem;entity, QUALITY, resolution;entity-resolution;social, sciences, systems;social, tool;data, visual, visualization;task-specific}, doi = {10.1109/VAST.2006.261429}, author = {Bilgic,M. and Licamele,L. and Getoor, Lise and Shneiderman, Ben} } @conference {12271, title = {Decentralized message ordering for publish/subscribe systems}, booktitle = {Proceedings of the ACM/IFIP/USENIX 2006 International Conference on Middleware}, series = {Middleware {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {162 - 179}, publisher = {Springer-Verlag New York, Inc.}, organization = {Springer-Verlag New York, Inc.}, address = {New York, NY, USA}, abstract = {We describe a method to order messages across groups in a publish/subscribe system without centralized control or large vector timestamps. We show that our scheme is practical---little state is required; that it is scalable---the maximum message load is limited by receivers; and that it performs well---the paths messages traverse to be ordered are not made much longer than necessary. Our insight is that only messages to groups that overlap in membership can be observed to arrive out of order: sequencing messages to these groups is sufficient to provide a consistent order, and when publishers subscribe to the groups to which they send, this message order is a causal order.}, url = {http://dl.acm.org/citation.cfm?id=1515984.1515997}, author = {Lumezanu,Cristian and Spring, Neil and Bhattacharjee, Bobby} } @article {14210, title = {Depth estimation using the compound eye of dipteran flies}, journal = {Biological Cybernetics}, volume = {95}, year = {2006}, month = {2006///}, pages = {487 - 501}, abstract = {In the neural superposition eye of a dipteran fly every ommatidium has eight photoreceptors, each associated with a rhabdomere, two central and six peripheral, which altogether result in seven functional light guides. Groups of eight rhabdomeres in neighboring ommatidia have largely overlapping fields of view. Based on the hypothesis that the light signals collected by these rhabdomeres can be used individually, we investigated the feasibility of estimating 3D scene information. According to Pick (Biol Cybern 26:215{\textendash}224, 1977) the visual axes of these rhabdomeres are not parallel, but converge to a point 3{\textendash}6 mm in front of the cornea. Such a structure theoretically could estimate depth in a very simple way by assuming that locally the image intensity is well approximated by a linear function of the spatial coordinates. Using the measurements of Pick (Biol Cybern 26:215{\textendash}224, 1977) we performed simulation experiments to find whether this is practically possible. Our results indicate that depth estimation at small distances (up to about 1.5{\textendash}2 cm) is reasonably accurate. This would allow the insect to obtain at least an ordinal spatial layout of its operational space when walking.}, isbn = {0340-1200}, url = {http://dx.doi.org/10.1007/s00422-006-0097-1}, author = {Bitsakos,Konstantinos and Ferm{\"u}ller, Cornelia} } @conference {12277, title = {Distributing Google}, booktitle = {Data Engineering Workshops, 2006. Proceedings. 22nd International Conference on}, year = {2006}, month = {2006///}, pages = {33 - 33}, abstract = {We consider the problem of wide-area large-scale text search over a peer-to-peer infrastructure. A wide-area search infrastructure with billions of documents and millions of search terms presents unique challenges in terms of the amount of state that must be maintained and updated. Distributing such a system would require tens of thousands of hosts leading to the usual problems associated with node failures, churn and data migration. Localities inherent in query patterns will cause load imbalances and hot spots that can severely impair performance. In this paper, we describe an architecture for constructing a scalable search infrastructure that is designed to cope with the challenges of scale described above. Our architecture consists of a data store layer which is used to reliably store and recompute indexes over a slow timescale and a caching layer that is used to respond to most queries. Our primary insight is that the problem of efficiently retrieving a small number of relevant results must be decoupled from the problem of reliably storing potentially huge indexes. Relevant results can be quickly retrieved from caches of ranked results, which can be replicated based upon query load. An entirely different set of mechanisms, such as encoded storage and/or data partitioning, should be used to store large indexes reliably. These indexes should only be used to compute results when there is a miss in the cache.}, doi = {10.1109/ICDEW.2006.49}, author = {Gopalakrishnan,V. and Bhattacharjee, Bobby and Keleher,P.} } @article {12930, title = {Effect of transport at ambient temperature on detection and isolation of Vibrio cholerae from environmental samples}, journal = {Applied and environmental microbiology}, volume = {72}, year = {2006}, month = {2006///}, pages = {2185 - 2190}, abstract = {It has long been assumed that prolonged holding of environmental samples at the ambient air temperature prior to bacteriological analysis is detrimental to isolation and detection of Vibrio cholerae, the causative agent of pandemic cholera. The present study was aimed at understanding the effect of transporting environmental samples at the ambient air temperature on isolation and enumeration of V. cholerae. For water and plankton samples held at ambient temperatures ranging from 31{\textdegree}C to 35{\textdegree}C for 20 h, the total counts did not increase significantly but the number of culturable V. cholerae increased significantly compared to samples processed within 1 h of collection, as measured by culture, acridine orange direct count, direct fluorescent-antibody-direct viable count (DFA-DVC), and multiplex PCR analyses. For total coliform counts, total bacterial counts, and DFA-DVC counts, the numbers did not increase significantly, but the culturable plate counts for V. cholerae increased significantly after samples were held at the ambient temperature during transport to the laboratory for analysis. An increase in the recovery of V. cholerae O1 and improved detection of V. cholerae O1 rfb and ctxA also occurred when samples were enriched after they were kept for 20 h at the ambient temperature during transport. Improved detection and isolation of toxigenic V. cholerae from freshwater ecosystems can be achieved by holding samples at the ambient temperature, an observation that has significant implications for tracking this pathogen in diverse aquatic environments.}, author = {Alam,M. and Sadique,A. and Bhuiyan,N. A. and Nair,G. B. and Siddique,A. K. and Sack,D. A. and Ahsan,S. and Huq,A. and Sack,R. B. and Rita R Colwell and others} } @article {15744, title = {Efficient Circuits for Exact-Universal Computation with Qudits}, journal = {Quantum Information and Computation}, volume = {6}, year = {2006}, month = {2006///}, pages = {436 - 454}, author = {Brennen,Gavin K. and Bullock,Stephen S. and O{\textquoteright}Leary, Dianne P.} } @conference {12348, title = {Efficient simulation of critical synchronous dataflow graphs}, booktitle = {Proceedings of the 43rd annual Design Automation Conference}, year = {2006}, month = {2006///}, pages = {893 - 898}, author = {Hsu,C. J and Ramasubbu,S. and Ko,M. Y and Pino,J. L and Bhattacharyya, Shuvra S.} } @article {12373, title = {Efficient techniques for clustering and scheduling onto embedded multiprocessors}, journal = {IEEE Transactions on Parallel and Distributed Systems}, year = {2006}, month = {2006///}, pages = {667 - 680}, author = {Kianzad,V. and Bhattacharyya, Shuvra S.} } @conference {12115, title = {An empirical study to compare two parallel programming models}, booktitle = {Proceedings of the eighteenth annual ACM symposium on Parallelism in algorithms and architectures}, series = {SPAA {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {114 - 114}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {While there are strong beliefs within the community about whether one particular parallel programming model is easier to use than another, there has been little research to analyze these claims empirically. Currently, the most popular paradigm is message-passing, as implemented by the MPI library [1]. However, MPI is considered to be difficult for developing programs, because it forces the programmer to work at a very low level of abstraction. One alternative parallel programming model is the PRAM model, which supports fine-grained parallelism and has a substantial history of algorithmic theory [2]. It is not possible to program current parallel machines using the PRAM model because modern architectures are not designed to support such a model efficiently. However, current trends towards multicore chips suggest that large-scale, fine-grained uniform-memory access parallel machines may soon be feasible. XMT-C is an extension of the C language that supports parallel directives to provide a PRAM-like model to the programmer. A prototype compiler exists that generates code which runs on a simulator for an XMT architecture [3].To better understand how much benefit a PRAM-like model could provide over a message-passing model, we conducted a feasibility study in an academic setting to compare the effort required to solve a particular problem. The questions under study were: can we measure the effort in developing a program using these two programming models and can we differentiate the amount of effort for each model?.The subjects participating in the study were divided up into two groups. One group solved a problem using the MPI library in either C,C++, or Fortran, and the other group solved the problem using XMT-C. The task was to write a function to multiply a sparse matrix with a dense vector. To obtain subjects, we leveraged existing graduate-level parallel programming courses at two different universities: University of California, Santa Barbara (UCSB), and University of Maryland (UMD). At UCSB, the students solved the problem in MPI, and at UMD, the students solved the same problem in XMT-C. The focus of the UCSB class was on developing parallel programs to run on the current generation of architectures, and the students were taught MPI, as well as other models. The focus of the UMD class was parallel algorithms in the PRAM model, and the students were taught XMT-C. The students were assigned to treatment groups by class. The study was integrated into each class, as the problem was a required assignment in each class.Subjects kept track of their effort with a self-reported effort log. We also collected automatic effort data by instrumenting the compilers, which recorded data at each compile. We computed three effort measures: self-reported, instrumented, and combined. Self-reported effort measures are based entirely on effort logs, instrumented effort measures are based entirely on timestamps from the instrumented compilers, and combined effort measures are based on compiler timestamps when the subject is working on the instrumented machine, and self-reported effort when the subject is working off the instrumented machine.The results of this preliminary study answer both of our questions in the positive. In this case, on average, students required less effort to solve the problem using XMT-C compared to MPI. The reduction in mean effort was approximately 50\% for all three measures, which was statistically significant at the level of p < .05 using a t-test.This study demonstrates that the effect of programming model on effort can be directly measured through empirical studies with human subjects. While no single study can conclusively demonstrate the advantage of one programming model over another, a series of studies examining different models and different problems can provide insights into the relative strengths of parallel programming models in different contexts. The study described above is one of a series of such studies that we are currently conducting.}, keywords = {effort, empirical study, HPC, Message-passing, MPI, parallel programming, PRAM, Productivity, XMT}, isbn = {1-59593-452-9}, doi = {10.1145/1148109.1148127}, url = {http://doi.acm.org/10.1145/1148109.1148127}, author = {Hochstein, Lorin and Basili, Victor R.} } @article {12355, title = {Energy-efficient embedded software implementation on multiprocessor system-on-chip with multiple voltages}, journal = {ACM Transactions on Embedded Computing Systems (TECS)}, volume = {5}, year = {2006}, month = {2006///}, pages = {321 - 341}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @inbook {14424, title = {Entity Resolution in Graphs}, booktitle = {Mining Graph DataMining Graph Data}, year = {2006}, month = {2006/04/10/}, pages = {311 - 344}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, abstract = {This chapter contains sections titled:Introduction Related Work Motivating Example for Graph-Based Entity Resolution Graph-Based Entity Resolution: Problem Formulation Similarity Measures for Entity Resolution Graph-Based Clustering for Entity Resolution Experimental Evaluation Conclusion References }, keywords = {entity resolution in graphs, graph-based clustering for entity resolution, graph-based entity resolution problem}, isbn = {9780470073049}, url = {http://onlinelibrary.wiley.com/doi/10.1002/9780470073049.ch13/summary}, author = {Bhattacharya,Indrajit and Getoor, Lise}, editor = {Cook,Diane J. and Holder,Lawrence B.} } @conference {13165, title = {Estimation of Anthropomeasures from a Single Calibrated Camera}, booktitle = {Automatic Face and Gesture Recognition, 2006. FGR 2006. 7th International Conference on}, year = {2006}, month = {2006/04//}, pages = {499 - 504}, abstract = {We are interested in the recovery of anthropometric dimensions of the human body from calibrated monocular sequences, and their use in multi-target tracking across multiple cameras and identification of individual people. In this paper, we focus on two specific anthropomeasures that are relatively easy to estimate from low-resolution images: stature and shoulder breadth. Precise average estimates are obtained for each anthropomeasure by combining measurements from multiple frames in the sequence. Our contribution is two-fold: (i) a novel technique for automatic and passive estimation of shoulder breadth, that is based on modelling the shoulders as an ellipse, and (U) a novel method for increasing the accuracy of the mean estimates of both anthropomeasures. The latter is based on the observation that major sources of error in the measurements are landmark localization the 2D image and 3D modelling error, and that both of these are correlated with gait phase and body orientation with respect to the camera. Consequently, estimation error can be significantly reduced via appropriate selection or control of these two variables}, keywords = {anthropomeasures, calibrated, camera;anthropometry;error, estimation;error, estimation;gait, identification;image, phase;image, recovery;image, resolution;image, resolution;monocular, restoration;image, sensors;image, sequences;, sequences;single, statistics;image}, doi = {10.1109/FGR.2006.37}, author = {BenAbdelkader,C. and Davis, Larry S.} } @article {14068, title = {Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements}, journal = {Molecular and Biochemical Parasitology}, volume = {145}, year = {2006}, month = {2006/02//}, pages = {158 - 170}, abstract = {The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5{\textquoteright}-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.}, keywords = {Degenerate retroelement, Evolution, Ingi, L1Tc, Leishmania major, Non-LTR retrotransposon, Retroposon, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/j.molbiopara.2005.09.017}, url = {http://www.sciencedirect.com/science/article/pii/S0166685105002963}, author = {Bringaud,Fr{\'e}d{\'e}ric and Ghedin,Elodie and Blandin,Ga{\"e}lle and Bartholomeu,Daniella C. and Caler,Elisabet and Levin,Mariano J. and Baltz,Th{\'e}o and El-Sayed, Najib M.} } @conference {12182, title = {The evolution of the international children{\textquoteright}s digital library searching and browsing interface}, booktitle = {Proceedings of the 2006 conference on Interaction design and children}, year = {2006}, month = {2006///}, pages = {105 - 112}, author = {Hutchinson,H.B. and Bederson, Benjamin B. and Druin, Allison} } @article {12135, title = {Experiments to understand HPC time to development}, journal = {CTWatch Quarterly}, year = {2006}, month = {2006///}, abstract = {In order to understand how high performance computing (HPC) programs are developed, a series of experiments, using students in graduate level HPC classes, have been conducted at many universities in the US. In this paper we discuss the general process of conducting those experiments, give some of the early results of those experiments, and describe a web-based process we are developing that will allow us to run additional experiments at other universities and laboratories that will be easier to conduct and generate results that more accurately reflect the process of building HPC programs.}, keywords = {hackystat, HPC, publications-journals}, url = {http://csdl.ics.hawaii.edu/techreports/06-08/06-08.pdf}, author = {Hochstein, Lorin and Nakamura,Taiga and Basili, Victor R. and Asgari, Sima and Zelkowitz, Marvin V and Hollingsworth, Jeffrey K and Shull, Forrest and Carver,Jeffrey and Voelp,Martin and Zazworka, Nico and Johnson,Philip} } @conference {16085, title = {Exploring content-actor paired network data using iterative query refinement with NetLens}, booktitle = {Digital Libraries, 2006. JCDL {\textquoteright}06. Proceedings of the 6th ACM/IEEE-CS Joint Conference on}, year = {2006}, month = {2006/06//}, pages = {372 - 372}, abstract = {Networks have remained a challenge for information retrieval and visualization because of the rich set of tasks that users want to accomplish. This paper demonstrates a tool, NetLens, to explore a content-actor paired network data model. The NetLens interface was designed to allow users to pose a series of elementary queries and iteratively refine visual overviews and sorted lists. This enables the support of complex queries that are traditionally hard to specify in node-link visualizations. NetLens is general and scalable in that it applies to any dataset that can be represented with our abstract content-actor data model}, keywords = {data, interface, libraries;query, management, model;data, models;data, NetLens;content-actor, network, pair, processing;user, query, refinement;data, retrieval;iterative, systems;, visualisation;digital, visualization;information}, doi = {10.1145/1141753.1141868}, author = {Lee,Bongshin and Kang,Hyunmo and Plaisant, Catherine and Bederson, Benjamin B.} } @conference {12273, title = {Fair file swarming with FOX}, booktitle = {Proc. 5th IPTPS}, year = {2006}, month = {2006///}, abstract = {File swarming is a popular method of coordi-nated download by which peers obtain a file from an under- provisioned server. Critical problems arise within this domain when users act selfishly, yet most systems are built with altru- ism assumed. Working under the assumption that all peers are greedy, we introduce the Fair, Optimal eXchange (FOX) protocol. FOX, in addition to effective and robust application of the tit-for-tat incentive mechanism, provides theoretically optimal download times when everyone cooperates. Under our assumption of server and peer capabilities, we develop a strong threat model that provides peers with the incentives to not deviate from the protocol. From a theoretical perspective, we prove FOX{\textquoteright}s optimality and incentive properties, even when the network consists only of purely self-interested peers. We also discuss issues in implementing and deploying such a system, and address the cost of ensuring fairness in a domain where efficiency is so important. }, author = {Levin,D. and Sherwood,R. and Bhattacharjee, Bobby} } @conference {12278, title = {File System Support for Collaboration in theWide Area}, booktitle = {Distributed Computing Systems, 2006. ICDCS 2006. 26th IEEE International Conference on}, year = {2006}, month = {2006///}, pages = {26 - 26}, abstract = {We describe the design, implementation, and performance of MFS, a new file system designed to support efficient widearea collaboration. MFS is structured around the twin abstractions of lightweight sessions and snapshots, along with a highly configurable capability-based security architecture. Sessions simplify and clarify collaborative semantics. Snapshots allow atomic access to arbitrary collections of files, and allow sharing to be defined in a simple and expressive fashion. MFS $\#$146;s security architecture is a layered system that allows diverse usage scenarios. Pure capability-based access allows clients to access data without needing expensive public key or authentication servers, or complicated administration. However, MFS $\#$146;s capabilities can also be watermarked, allowing a range of services to be added on a per-mount basis, up to and including traditional user authentication based on passwords or public keys. Basing the system around the use of immutable snapshots enables the underlying system to use several performance optimizations aggressively. Performance results from our MFS prototype show that, far from adding overhead, the use of snapshots allows the system to perform comparably to NFS in the local-area case and significantly outperform existing systems in wide-area environments.}, doi = {10.1109/ICDCS.2006.41}, author = {Gaburici,V. and Keleher,P. and Bhattacharjee, Bobby} } @article {17161, title = {Find that photo!: interface strategies to annotate, browse, and share}, journal = {Communications of the ACM - Supporting exploratory search}, volume = {49}, year = {2006}, month = {2006/04//}, pages = {69 - 71}, isbn = {0001-0782}, doi = {10.1145/1121949.1121985}, url = {http://doi.acm.org/10.1145/1121949.1121985}, author = {Shneiderman, Ben and Bederson, Benjamin B. and Drucker,Steven M.} } @article {14909, title = {First Steps Toward an Electronic Field Guide for Plants}, journal = {Taxon}, volume = {55}, year = {2006}, month = {2006///}, pages = {597 - 610}, abstract = {this paper, we will describe our progress towards building a digital collection of the Smithsonian{\textquoteright}s type specimens, developing recognition algorithms that can match an image of a leaf to the species of plant from which it comes, and designing user interfaces for interacting with an electronic field guide. To start, we are developing a prototype electronic field guide for the flora of Plummers Island, a small, well-studied island in the Potomac River. This prototype system contains multiple images for each of about 130 species of plants on the island, and should soon grow to cover all 200+ species currently recorded (Shetler et al., 2005). Images of full specimens are available, as well as images of isolated leaves of each species. A zoomable user interface allows a user to browse these images, zooming in on ones of interest. Visual recognition algorithms assist a botanist in locating the specimens that are most relevant to identify the species of a plant. The system currently runs on a small hand-held computer. We will describe the components of this prototype, and also describe some of the future challenges we anticipate if we are to provide botanists in the field with all the resources that are now currently available in the world{\textquoteright}s museums and herbaria. Type Specimen Digital Collection The first challenge in producing our electronic field guide is to create a digital collection covering all of the Smithsonian{\textquoteright}s 85,000 vascular plant type specimens. For each type specimen, the database should eventually include systematically acquired high-resolution digital images of the specimen, textual descriptions, links to decision trees, images of live plants, and 3D models. Figure 1: On the left, our set-up at the Smithsonian for digitally photographing type specimens. On the...}, author = {Haibin,Gaurav Agarwal and Agarwal,Gaurav and Ling,Haibin and Jacobs, David W. and Shirdhonkar,Sameer and Kress,W. John and Russell,Rusty and Belhumeur,Peter and Dixit,An and Feiner,Steve and Mahajan,Dhruv and Sunkavalli,Kalyan and Ramamoorthi,Ravi and White,Sean} } @conference {18755, title = {A flexible system framework for a nanoassembly cell using optical tweezers}, year = {2006}, month = {2006///}, address = {Philadelphia, Pennsylvania, USA}, abstract = {The optical tweezers instrument is a unique tool fordirected assembly of nanocomponents. In order to function as a viable nanomanufacturing tool, a software architecture is needed to run the optical tweezers hardware, provide an effective user interface, and allow automated operation. A flexible software system framework is described to utilize the optical tweezers hardware to its full potential. Initially we lay out the requirements for the system framework and define the broad architectural choices made while implementing the different modules. Implementation details of key system modules are then described. The flexible nature of the architecture is demonstrated by showing how a simulation module can be seamlessly included into the framework to replace the optical tweezers hardware as necessary. Finally, we show some representative assembly operations to demonstrate the capabilities of the system. }, url = {http://terpconnect.umd.edu/~skgupta/Publication/CIE06_Balijepalli.pdf}, author = {Balijepalli,A. and LeBrun,T. W. and Gupta,S.K.} } @article {12160, title = {The Goal Question Metric Approach}, journal = {5th ACM-IEEE International Symposium on Empirical Software Engineering (ISESE{\textquoteright}06)}, year = {2006}, month = {2006///}, author = {Basili, Victor R. and Caldiera,G. and Rombach,H. D} } @conference {13436, title = {Heuristic search and information visualization methods for school redistricting}, booktitle = {Proceedings of the 18th conference on Innovative applications of artificial intelligence - Volume 2}, series = {IAAI{\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1774 - 1781}, publisher = {AAAI Press}, organization = {AAAI Press}, abstract = {We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives must be considered, such as school capacity, busing costs, and socioeconomic distribution. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different tradeoffs in the decision space.We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans. }, isbn = {978-1-57735-281-5}, url = {http://dl.acm.org/citation.cfm?id=1597122.1597136}, author = {desJardins, Marie and Bulka,Blazej and Carr,Ryan and Hunt,Andrew and Rathod,Priyang and Rheingans,Penny} } @article {19661, title = {How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior}, journal = {Proceedings of the IEEE}, volume = {94}, year = {2006}, month = {2006/07//}, pages = {1445 - 1463}, abstract = {Our understanding of social insect behavior has significantly influenced artificial intelligence (AI) and multirobot systems{\textquoteright} research (e.g., ant algorithms and swarm robotics). In this work, however, we focus on the opposite question: "How can multirobot systems research contribute to the understanding of social animal behavior?" As we show, we are able to contribute at several levels. First, using algorithms that originated in the robotics community, we can track animals under observation to provide essential quantitative data for animal behavior research. Second, by developing and applying algorithms originating in speech recognition and computer vision, we can automatically label the behavior of animals under observation. In some cases the automatic labeling is more accurate and consistent than manual behavior identification. Our ultimate goal, however, is to automatically create, from observation, executable models of behavior. An executable model is a control program for an agent that can run in simulation (or on a robot). The representation for these executable models is drawn from research in multirobot systems programming. In this paper we present the algorithms we have developed for tracking, recognizing, and learning models of social animal behavior, details of their implementation, and quantitative experimental results using them to study social insects}, keywords = {Acceleration, Animal behavior, ant movement tracking, Artificial intelligence, biology computing, Computer vision, control engineering computing, Insects, Intelligent robots, Labeling, monkey movement tracking, multi-robot systems, multirobot systems, robotics algorithms, Robotics and automation, social animal behavior, social animals, social insect behavior, Speech recognition, tracking}, isbn = {0018-9219}, author = {Balch, T. and Dellaert, F. and Feldman, A. and Guillory, A. and Isbell, C.L. and Zia Khan and Pratt, S.C. and Stein, A.N. and Wilde, H.} } @conference {12137, title = {Identifying domain-specific defect classes using inspections and change history}, booktitle = {Proceedings of the 2006 ACM/IEEE international symposium on Empirical software engineering}, series = {ISESE {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {346 - 355}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present an iterative, reading-based methodology for analyzing defects in source code when change history is available. Our bottom-up approach can be applied to build knowledge of recurring defects in a specific domain, even if other sources of defect data such as defect reports and change requests are unavailable, incomplete or at the wrong level of abstraction for the purposes of the defect analysis. After defining the methodology, we present the results of an empirical study where our method was applied to analyze defects in parallel programs which use the MPI (Message Passing Interface) library to express parallelism. This library is often used in the domain of high performance computing, where there is much discussion but little empirical data about the frequency and severity of defect types. Preliminary results indicate the methodology is feasible and can provide insights into the nature of real defects. We present the results, derived hypothesis, and lessons learned.}, keywords = {change history, code reading, domain specific defects, Inspection}, isbn = {1-59593-218-6}, doi = {10.1145/1159733.1159785}, url = {http://doi.acm.org/10.1145/1159733.1159785}, author = {Nakamura,Taiga and Hochstein, Lorin and Basili, Victor R.} } @article {18577, title = {In VINI veritas: realistic and controlled network experimentation}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {36}, year = {2006}, month = {2006/08//}, pages = {3 - 14}, abstract = {This paper describes VINI, a virtual network infrastructure that allows network researchers to evaluate their protocols and services in a realistic environment that also provides a high degree of control over network conditions. VINI allows researchers to deploy and evaluate their ideas with real routing software, traffic loads, and network events. To provide researchers flexibility in designing their experiments, VINI supports simultaneous experiments with arbitrary network topologies on a shared physical infrastructure. This paper tackles the following important design question: What set of concepts and techniques facilitate flexible, realistic, and controlled experimentation (e.g., multiple topologies and the ability to tweak routing algorithms) on a fixed physical infrastructure? We first present VINI{\textquoteright}s high-level design and the challenges of virtualizing a single network. We then present PL-VINI, an implementation of VINI on PlanetLab, running the "Internet In a Slice". Our evaluation of PL-VINI shows that it provides a realistic and controlled environment for evaluating new protocols and services.}, keywords = {architecture, experimentation, Internet, Routing, virtualization}, isbn = {0146-4833}, doi = {10.1145/1151659.1159916}, url = {http://doi.acm.org/10.1145/1151659.1159916}, author = {Bavier,Andy and Feamster, Nick and Huang,Mark and Peterson,Larry and Rexford,Jennifer} } @article {16091, title = {Interactive sonification for blind people exploration of geo-referenced data: comparison between a keyboard-exploration and a haptic-exploration interfaces}, journal = {Cognitive Processing}, volume = {7}, year = {2006}, month = {2006///}, pages = {178 - 179}, isbn = {1612-4782}, url = {http://dx.doi.org/10.1007/s10339-006-0137-8}, author = {Delogu,Franco and Belardinelli,Marta and Palmiero,Massimiliano and Pasqualotto,Emanuele and Zhao,Haixia and Plaisant, Catherine and Federici,Stefano} } @conference {12611, title = {Invariant Geometric Representation of 3D Point Clouds for Registration and Matching}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {1209 - 1212}, abstract = {Though implicit representations of surfaces have often been used for various computer graphics tasks like modeling and morphing of objects, it has rarely been used for registration and matching of 3D point clouds. Unlike in graphics, where the goal is precise reconstruction, we use isosurfaces to derive a smooth and approximate representation of the underlying point cloud which helps in generalization. Implicit surfaces are generated using a variational interpolation technique. Implicit function values on a set of concentric spheres around the 3D point cloud of object are used as features for matching. Geometric-invariance is achieved by decomposing implicit values based feature set into various spherical harmonics. The decomposition provides a compact representation of 3D point clouds while achieving rotation invariance}, keywords = {3D, cloud;computer, function, geometric, graphics;geophysical, graphics;image, Interpolation, matching;image, point, processing;image, reconstruction;image, registration;image, registration;implicit, representation;interpolation;, representation;variational, signal, technique;clouds;computer, value;invariant}, doi = {10.1109/ICIP.2006.312542}, author = {Biswas,S. and Aggarwal,G. and Chellapa, Rama} } @article {18013, title = {Issues in writing a parallel compiler starting from a serial compiler}, year = {2006}, month = {2006///}, institution = {draft. Technical report, University of Maryland Institute for Advanced Compuer Studies}, author = {Tzannes,A. and Barua,R. and Caragea,G. and Vishkin, Uzi} } @article {12269, title = {KeyChains: A Decentralized Public-Key Infrastructure}, journal = {Technical Reports from UMIACS, UMIACS-TR-2006-12}, year = {2006}, month = {2006/03/02/}, abstract = {A Certification Authority (CA) can be used to certify keys and build apublic-key infrastructure (PKI) when all users trust the same CA. A decentralized PKI trades off absolute assurance on keys for independence from central control and improved scalability and robustness. The PGP {\textquoteleft}{\textquoteleft}web of trust{\textquoteright}{\textquoteright} model has been suggested as a decentralized certification system, and has been used with great success for secure email. Although the PGP web of trust model allows anyone to issue certificates which can be used to form certificate chains, the discovery and construction of certificate chains relies on centralized keyservers to store certificates and respond to queries. In this paper, we design and implement KeyChains, a peer-to-peer system which incorporates a novel lookup mechanism specifically tailored to the task of generating and retrieving certificate chains in completely unstructured networks. By layering our system on top of the web of trust model, we thus obtain the first PKI which is truly decentralized in all respects. Our analysis and simulations show that the resulting system is both efficient and secure. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3332}, author = {Morselli,Ruggero and Bhattacharjee, Bobby and Katz, Jonathan and Marsh,Michael A} } @article {14354, title = {A latent dirichlet allocation model for entity resolution}, journal = {6th SIAM Conference on Data Mining (SDM), Bethesda, USA}, year = {2006}, month = {2006///}, abstract = {In this paper, we address the problem of entity resolution, where given many references to un-derlying objects, the task is to predict which references correspond to the same object. We propose a probabilistic model for collective entity resolution. Our approach differs from other recently pro- posed entity resolution approaches in that it is a) unsupervised, b) generative and c) introduces a hidden {\textquoteleft}group{\textquoteright} variable to capture collections of entities which are commonly observed together. The entity resolution decisions are not considered on an independent pairwise basis, but instead decisions are made collectively. We focus on how the use of relational links among the references can be exploited. We show how we can use Gibbs Sampling to infer the collaboration groups and the entities jointly from the observed co-author relationships among entity references and how this improves entity resolution performance. We demonstrate the utility of our approach on two real-world bibliographic datasets. In addition, we present preliminary results on characterizing conditions under which collaborative infor- mation is useful. }, author = {Bhattacharya,I. and Getoor, Lise} } @inbook {13825, title = {Machine Translation: Interlingual Methods}, booktitle = {Encyclopedia of Language \& Linguistics (Second Edition)Encyclopedia of Language \& Linguistics (Second Edition)}, year = {2006}, month = {2006///}, pages = {383 - 394}, publisher = {Elsevier}, organization = {Elsevier}, address = {Oxford}, abstract = {An interlingua is a notation for representing the content of a text that abstracts away from the characteristics of the language itself and focuses on the meaning (semantics) alone. Interlinguas are typically used as pivot representations in machine translation, allowing the contents of a source text to be generated in many different target languages. Because of the complexities involved, few interlinguas are more than demonstration prototypes, and only one has been used in a commercial MT system. In this article, we define the components of an interlingua and the principal issues faced by designers and builders of interlinguas and interlingua MT systems, illustrating with examples from operational systems and research prototypes. We discuss current efforts to annotate texts with interlingua-based information.}, keywords = {approximate interlingua, compositionality, conceptual knowledge, cross-language divergences, interlingua, interlingual speech translation, language-independent representation, lexical-conceptual structure, Machine translation, ontology, predicate-argument structure, semantic annotation, semantic frames, semantic zones, text-meaning representations, THEMATIC ROLES}, isbn = {978-0-08-044854-1}, url = {http://www.sciencedirect.com/science/article/pii/B0080448542009391}, author = {Dorr, Bonnie J and Hovy,E. and Levin,L.}, editor = {Editor-in-Chief:~~ Keith Brown} } @conference {17285, title = {Making a difference: integrating socially relevant projects into HCI teaching}, booktitle = {CHI {\textquoteright}06 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {41 - 44}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Enriching courses on human-computer interaction with socially-relevant projects provides a compelling opportunity for students to improve their education and make socially beneficial contributions. By having clearly defined user communities outside the classroom, students have the chance to practice their interview, observation, and usability testing skills, while developing projects that continue beyond the semester. These projects often give students life-changing exposure to genuine needs and impressive results to include in their portfolio when seeking employment. Educators will present their strategies for arranging, supervising, and grading these projects. Students will describe their experience and how it influenced them.}, keywords = {education, making a difference, relevance, service learning, social impact, team projects}, isbn = {1-59593-298-4}, doi = {10.1145/1125451.1125463}, url = {http://doi.acm.org/10.1145/1125451.1125463}, author = {Shneiderman, Ben and Bishop,Ann and Friedman,Batya and Lazar,Jonathan and Marsden,Gary and Nass,Cliff} } @article {18860, title = {Manufacturing of multi-material compliant mechanisms using multi-material molding}, journal = {The International Journal of Advanced Manufacturing Technology}, volume = {30}, year = {2006}, month = {2006///}, pages = {1049 - 1075}, abstract = {Multi-material compliant mechanisms enable many new design possibilities. Significant progress has been made in the area of design and analysis of multi-material compliant mechanisms. What is now needed is a method to mass-produce such mechanisms economically. A feasible and practical way of producing such mechanisms is through multi-material molding. Devices based on compliant mechanisms usually consist of compliant joints. Compliant joints in turn are created by carefully engineering interfaces between a compliant and a rigid material. This paper presents an overview of multi-material molding technology and describes feasible mold designs for creating different types of compliant joints found in multi-material compliant mechanisms. It also describes guidelines essential to successfully utilizing the multi-material molding process for creating compliant mechanisms. Finally, practical applications for the use of multi-material molding to create compliant mechanisms are demonstrated.}, keywords = {engineering}, isbn = {0268-3768}, doi = {10.1007/s00170-005-0152-4}, url = {http://www.springerlink.com/content/djk6wq2213447pqn/abstract/}, author = {Gouker,Regina and Gupta, Satyandra K. and Bruck,Hugh and Holzschuh,Tobias} } @conference {12391, title = {Mapping Multimedia Applications Onto Configurable Hardware With Parameterized Cyclo-Static Dataflow Graphs}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {3}, year = {2006}, month = {2006/05//}, pages = {III - III}, abstract = {This paper develops methods for model-based design and implementation of image processing applications. We apply our previously developed meta-modeling technique of homogeneous parameterized dataflow (HPDF) (M. Sen et al., 2005) to the framework of cyclostatic dataflow (CSDF) (G. Bilsen et al., 1996), and demonstrate this integrated modeling methodology through hardware mapping of a gesture recognition application. We also provide a comparative study between HPDF/CSDF-based representation of the gesture recognition application, and a previously developed version based on applying HPDF in conjunction with conventional synchronous dataflow (SDF) semantics (M. Sen et al., 2005)}, keywords = {configurable hardware, Data communication, Gesture recognition, gesture recognition application, graph theory, hardware mapping, image processing applications, mapping multimedia applications, meta-modeling technique, model-based design, Multimedia communication, parameterized cyclo-static dataflow graphs}, doi = {10.1109/ICASSP.2006.1660838}, author = {Haim,F. and Sen,M. and Ko,Dong-Ik and Bhattacharyya, Shuvra S. and Wolf,W.} } @article {12266, title = {Matching Jobs to Resources in Distributed Desktop Grid Environments}, journal = {Technical Reports from UMIACS, UMIACS-TR-2006-15}, year = {2006}, month = {2006/04//}, abstract = {Desktop grids use opportunistic sharing to exploit large collectionsof personal computers and workstations across the Internet and can achieve tremendous computing power with low cost. However, current systems are typically based on a traditional client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. In this paper, we propose a decentralized, robust, highly available, and scalable infrastructure to match incoming jobs to available resources. The key idea behind our proposed system is to leverage information provided by an underlying peer-to-peer system to create a hierarchical Rendezvous Node Tree, which performs the matching efficiently. Our experimental results obtained via simulation show that we can effectively match jobs with varying levels of resource constraints to available nodes and maintain good load balance in a fully decentralized heterogeneous computational environment. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3669}, author = {Kim,Jik-Soo and Bhattacharjee, Bobby and Keleher, Peter J. and Sussman, Alan} } @article {19662, title = {MCMC Data Association and Sparse Factorization Updating for Real Time Multitarget Tracking with Merged and Multiple Measurements}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {28}, year = {2006}, month = {2006/12//}, pages = {1960 - 1972}, abstract = {In several multitarget tracking applications, a target may return more than one measurement per target and interacting targets may return multiple merged measurements between targets. Existing algorithms for tracking and data association, initially applied to radar tracking, do not adequately address these types of measurements. Here, we introduce a probabilistic model for interacting targets that addresses both types of measurements simultaneously. We provide an algorithm for approximate inference in this model using a Markov chain Monte Carlo (MCMC)-based auxiliary variable particle filter. We Rao-Blackwellize the Markov chain to eliminate sampling over the continuous state space of the targets. A major contribution of this work is the use of sparse least squares updating and downdating techniques, which significantly reduce the computational cost per iteration of the Markov chain. Also, when combined with a simple heuristic, they enable the algorithm to correctly focus computation on interacting targets. We include experimental results on a challenging simulation sequence. We test the accuracy of the algorithm using two sensor modalities, video, and laser range data. We also show the algorithm exhibits real time performance on a conventional PC}, keywords = {algorithms, approximate inference, Artificial intelligence, auxiliary variable particle filter, Computational efficiency, continuous state space, downdating, Image Enhancement, Image Interpretation, Computer-Assisted, Inference algorithms, Information Storage and Retrieval, laser range scanner, laser range scanner., Least squares approximation, least squares approximations, Least squares methods, linear least squares, Markov chain Monte Carlo, Markov processes, MCMC data association, merged measurements, Monte Carlo methods, Movement, multiple merged measurements, multitarget tracking, particle filter, particle filtering (numerical methods), Particle filters, Pattern Recognition, Automated, probabilistic model, QR factorization, Radar tracking, Rao-Blackwellized, real time multitarget tracking, Reproducibility of results, Sampling methods, Sensitivity and Specificity, sensor fusion, sparse factorization updating, sparse least squares, State-space methods, Subtraction Technique, target tracking, updating}, isbn = {0162-8828}, author = {Zia Khan and Balch, T. and Dellaert, F.} } @article {12274, title = {Measurement-based optimal routing on overlay architectures for unicast sessions}, journal = {Computer Networks}, volume = {50}, year = {2006}, month = {2006///}, pages = {1938 - 1951}, abstract = {We propose a measurement-based routing algorithm to load-balance intradomain traffic along multiple paths for multi-ple unicast sources. Multiple paths are established using overlay nodes. The distributed algorithm is derived from simul- taneous perturbation stochastic approximation (SPSA) and does not assume that the gradient of an analytical cost function is known. Instead, we rely on (potentially) noisy estimates from local measurements. Using the analytical model presented in the paper, we first show the almost sure convergence of the algorithm to the optimal solution under a decreas- ing step size policy (as with a standard SPSA model). Motivated by practical concerns, we next consider the constant step size case, for which we establish weak convergence. We provide simulation results to demonstrate the advantages of our proposed algorithm under various network scenarios, and also present a comparative study with MATE (an existing opti- mal routing algorithm) }, author = {La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @book {12356, title = {Memory management for synthesis of DSP software}, year = {2006}, month = {2006///}, publisher = {CRC}, organization = {CRC}, author = {Murthy,P. K and Bhattacharyya, Shuvra S.} } @conference {12325, title = {Memory-constrained block processing optimization for synthesis of DSP software}, booktitle = {Embedded Computer Systems: Architectures, Modeling and Simulation, 2006. IC-SAMOS 2006. International Conference on}, year = {2006}, month = {2006///}, pages = {137 - 143}, author = {Ko,M. Y and Shen,C. C and Bhattacharyya, Shuvra S.} } @article {18010, title = {Mesh-of-Trees and Alternative Interconnection Networks for Single Chip Parallel Processing (Extended Abstract)}, year = {2006}, month = {2006/06//}, abstract = {Many applications have stimulated the recent surge of interest single-chip parallel processing. In such machines, it is crucial to implement a high-throughput low-latency interconnection network to connect the on-chip components, especially the processing units and the memory units. In this paper, we propose a new mesh of trees (MoT) implementation of the interconnection network and evaluate it relative to metrics such as wire area, register count, total switch delay, maximum throughput, latency-throughput relation and delay effects of long wires. We show that on-chip interconnection networks can facilitate higher bandwidth between processors and shared first-level cache than previously considered possible. This has significant impact for chip multiprocessing. MoT is also compared, both analytically and experimentally, to some other traditional network topologies, such as hypercube, butterfly, fat trees and butterfly fat trees. When we evaluate a 64-terminal MoT network at 65nm technology, concrete results show that MoT provides higher throughput and lower latency especially when the input traffic (or the on-chip parallelism) is high, at the cost of larger area. A recurring problem in networking and communication is that of achieving good sustained throughput in contrast to just high theoretical peak performance that does not materialize for typical work loads. Our quantitative results demonstrate a clear advantage of the proposed MoT network in the context of single-chip parallel processing.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3678}, author = {Balkan,Aydin O. and Gang Qu and Vishkin, Uzi} } @article {16933, title = {A model for computer frustration: the role of instrumental and dispositional factors on incident, session, and post-session frustration and mood}, journal = {Computers in Human Behavior}, volume = {22}, year = {2006}, month = {2006/11//}, pages = {941 - 961}, abstract = {Frustration is almost universally accepted as the emotional outcome of a negative computing experience. Despite the wide use of the term, however, it has not been rigorously conceptualized as a factor in the study of the human{\textendash}computer interface. This project sets out to explicate frustration as a pre-emotional state generated by the user{\textquoteright}s appraisal of the interface as an impediment to goal attainment, and looks at how user characteristics, such as self-efficacy, relate to it. This project employed episode report methodology to capture data from 144 computer users{\textquoteright} reports of actual frustrating events as they took place. Diaries taken as users worked at their everyday tasks yield detailed data about the problems they encountered and included information about session length and an estimate of the time lost due to the experiences. Outcomes were measured as either situational or dispositional factors. Situational factors, having to do with specific events, predicted incident frustration. However, disposition variables, especially user self-efficacy, were much stronger, predicting incident and session frustration, and post-session mood. One surprising outcome was the failure of demographic variables as predictors of frustration.}, keywords = {Efficacy, Emotion, Frustration, Mood, problem solving, usability}, isbn = {0747-5632}, doi = {10.1016/j.chb.2004.03.015}, url = {http://www.sciencedirect.com/science/article/pii/S0747563204000615}, author = {Bessi{\`e}re,Katie and Newhagen,John E. and Robinson,John P. and Shneiderman, Ben} } @conference {12333, title = {Model-based mapping of image registration applications onto configurable hardware}, booktitle = {Signals, Systems and Computers, 2006. ACSSC{\textquoteright}06. Fortieth Asilomar Conference on}, year = {2006}, month = {2006///}, pages = {1453 - 1457}, author = {Hemaraj,Y. and Sen,M. and Shekhar,R. and Bhattacharyya, Shuvra S.} } @conference {17854, title = {Model-based OpenMP implementation of a 3D facial pose tracking system}, booktitle = {2006 International Conference on Parallel Processing Workshops, 2006. ICPP 2006 Workshops}, year = {2006}, month = {2006///}, pages = {8 pp.-73 - 8 pp.-73}, publisher = {IEEE}, organization = {IEEE}, abstract = {Most image processing applications are characterized by computation-intensive operations, and high memory and performance requirements. Parallelized implementation on shared-memory systems offer an attractive solution to this class of applications. However, we cannot thoroughly exploit the advantages of such architectures without proper modeling and analysis of the application. In this paper, we describe our implementation of a 3D facial pose tracking system using the OpenMP platform. Our implementation is based on a design methodology that uses coarse-grain dataflow graphs to model and schedule the application. We present our modeling approach, details of the implementation that we derived based on this modeling approach, and associated performance results. The parallelized implementation achieves significant speedup, and meets or exceeds the target frame rate under various configurations}, keywords = {3D facial pose tracking system, application modeling, application program interfaces, application scheduling, coarse-grain dataflow graphs, Concurrent computing, data flow graphs, Educational institutions, face recognition, IMAGE PROCESSING, image processing applications, Inference algorithms, Message passing, OpenMP platform, parallel implementation, PARALLEL PROCESSING, parallel programming, Particle tracking, Processor scheduling, SHAPE, shared memory systems, shared-memory systems, Solid modeling, tracking}, isbn = {0-7695-2637-3}, doi = {10.1109/ICPPW.2006.55}, author = {Saha,S. and Chung-Ching Shen and Chia-Jui Hsu and Aggarwal,G. and Veeraraghavan,A. and Sussman, Alan and Bhattacharyya, Shuvra S.} } @article {14081, title = {Molecular Characterization of Serine-, Alanine-, and Proline-Rich Proteins of Trypanosoma cruzi and Their Possible Role in Host Cell Infection}, journal = {Infect. Immun.}, volume = {74}, year = {2006}, month = {2006/03/01/}, pages = {1537 - 1546}, abstract = {We previously reported the isolation of a novel protein gene family, termed SAP (serine-, alanine-, and proline-rich protein), from Trypanosoma cruzi. Aided by the availability of the completed genome sequence of T. cruzi, we have now identified 39 full-length sequences of SAP, six pseudogenes and four partial genes. SAPs share a central domain of about 55 amino acids and can be divided into four groups based on their amino (N)- and carboxy (C)-terminal sequences. Some SAPs have conserved N- and C-terminal domains encoding a signal peptide and a glycosylphosphatidylinositol anchor addition site, respectively. Analysis of the expression of SAPs in metacyclic trypomastigotes by two-dimensional electrophoresis and immunoblotting revealed that they are likely to be posttranslationally modified in vivo. We have also demonstrated that some SAPs are shed into the extracellular medium. The recombinant SAP exhibited an adhesive capacity toward mammalian cells, where binding was dose dependent and saturable, indicating a possible ligand-receptor interaction. SAP triggered the host cell Ca2+ response required for parasite internalization. A cell invasion assay performed in the presence of SAP showed inhibition of internalization of the metacyclic forms of the CL strain. Taken together, these results show that SAP is involved in the invasion of mammalian cells by metacyclic trypomastigotes, and they confirm the hypothesis that infective trypomastigotes exploit an arsenal of surface glycoproteins and shed proteins to induce signaling events required for their internalization.}, doi = {

10.1128/IAI.74.3.1537-1546.2006

}, url = {http://iai.asm.org/cgi/content/abstract/74/3/1537}, author = {Baida,Renata C. P. and Santos,Marcia R. M. and Carmo,Mirian S. and Yoshida,Nobuko and Ferreira,Danielle and Ferreira,Alice Teixeira and El Sayed,Najib M. and Andersson,Bjorn and da Silveira,Jose Franco} } @conference {12616, title = {Motion Based Correspondence for 3D Tracking of Multiple Dim Objects}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {2}, year = {2006}, month = {2006/05//}, pages = {II - II}, abstract = {Tracking multiple objects in a video is a demanding task that is frequently encountered in several systems such as surveillance and motion analysis. Ability to track objects in 3D requires the use of multiple cameras. While tracking multiple objects using multiples video cameras, establishing correspondence between objects in the various cameras is a nontrivial task. Specifically, when the targets are dim or are very far away from the camera, appearance cannot be used in order to establish this correspondence. Here, we propose a technique to establish correspondence across cameras using the motion features extracted from the targets, even when the relative position of the cameras is unknown. Experimental results are provided for the problem of tracking multiple bees in natural flight using two cameras. The reconstructed 3D flight paths of the bees show some interesting flight patterns}, keywords = {3D, analysis;motion, analysis;video, based, cameras;feature, correspondence;motion, dim, extraction;image, extraction;multiple, features, MOTION, objects;video, processing;, signal, tracking;motion}, doi = {10.1109/ICASSP.2006.1660431}, author = {Veeraraghavan,A. and Srinivasan, M. and Chellapa, Rama and Baird, E. and Lamont, R.} } @article {14799, title = {A New Hardware Monitor Design to Measure Data Structure-Specific Cache Eviction Information}, journal = {International Journal of High Performance Computing Applications}, volume = {20}, year = {2006}, month = {2006///}, pages = {353 - 363}, abstract = {In this paper, we propose a hardware performance monitor that provides support not only for measuring cache misses and the addresses associated with them, but also for determining what data is being evicted from the cache when a miss occurs. We describe how to use this hardware support to efficiently determine the cache behavior of application data structures at the source code level. We also present the results of a simulation-based study of this technique, in which we examined the overhead, perturbation of results, and usefulness of collecting this information.}, doi = {10.1177/1094342006067470}, url = {http://hpc.sagepub.com/content/20/3/353.abstract}, author = {Buck, B. R and Hollingsworth, Jeffrey K} } @article {17309, title = {Nuclear Envelope Dystrophies Show a Transcriptional Fingerprint Suggesting Disruption of Rb{\textendash}MyoD Pathways in Muscle Regeneration}, journal = {BrainBrain}, volume = {129}, year = {2006}, month = {2006/04/01/}, pages = {996 - 1013}, abstract = {Mutations of lamin A/C (LMNA) cause a wide range of human disorders, including progeria, lipodystrophy, neuropathies and autosomal dominant Emery{\textendash}Dreifuss muscular dystrophy (EDMD). EDMD is also caused by X-linked recessive loss-of-function mutations of emerin, another component of the inner nuclear lamina that directly interacts with LMNA. One model for disease pathogenesis of LMNA and emerin mutations is cell-specific perturbations of the mRNA transcriptome in terminally differentiated cells. To test this model, we studied 125 human muscle biopsies from 13 diagnostic groups (125 U133A, 125 U133B microarrays), including EDMD patients with LMNA and emerin mutations. A Visual and Statistical Data Analyzer (VISDA) algorithm was used to statistically model cluster hierarchy, resulting in a tree of phenotypic classifications. Validations of the diagnostic tree included permutations of U133A and U133B arrays, and use of two probe set algorithms (MAS5.0 and MBEI). This showed that the two nuclear envelope defects (EDMD LMNA, EDMD emerin) were highly related disorders and were also related to fascioscapulohumeral muscular dystrophy (FSHD). FSHD has recently been hypothesized to involve abnormal interactions of chromatin with the nuclear envelope. To identify disease-specific transcripts for EDMD, we applied a leave-one-out (LOO) cross-validation approach using LMNA patient muscle as a test data set, with reverse transcription{\textendash}polymerase chain reaction (RT{\textendash}PCR) validations in both LMNA and emerin patient muscle. A high proportion of top-ranked and validated transcripts were components of the same transcriptional regulatory pathway involving Rb1 and MyoD during muscle regeneration (CRI-1, CREBBP, Nap1L1, ECREBBP/p300), where each was specifically upregulated in EDMD. Using a muscle regeneration time series (27 time points) we develop a transcriptional model for downstream consequences of LMNA and emerin mutations. We propose that key interactions between the nuclear envelope and Rb and MyoD fail in EDMD at the point of myoblast exit from the cell cycle, leading to poorly coordinated phosphorylation and acetylation steps. Our data is consistent with mutations of nuclear lamina components leading to destabilization of the transcriptome in differentiated cells.}, keywords = {EDMD = Emery{\textendash}Dreifuss muscular dystrophy, emerin, Emery-Dreifuss muscular dystrophy, FSHD = fascioscapulohumeral muscular dystrophy, IDG = individual discriminatory genes, JDG = jointly discriminatory genes, lamin A/C, LGMD = limb-girdle muscular dystrophy, LOO = leave-one-out, RT{\textendash}PCR = reverse transcription{\textendash}polymerase chain reaction; VISDA = Visual and Statistical Data Analyzer, Skeletal muscle, wFC = weighted Fisher criterion}, isbn = {0006-8950, 1460-2156}, doi = {10.1093/brain/awl023}, url = {http://brain.oxfordjournals.org/content/129/4/996}, author = {Bakay,Marina and Wang,Zuyi and Melcon,Gisela and Schiltz,Louis and Xuan,Jianhua and Zhao,Po and Sartorelli,Vittorio and Seo,Jinwook and Pegoraro,Elena and Angelini,Corrado and Shneiderman, Ben and Escolar,Diana and Chen,Yi-Wen and Winokur,Sara T and Pachman,Lauren M and Fan,Chenguang and Mandler,Raul and Nevo,Yoram and Gordon,Erynn and Zhu,Yitan and Dong,Yibin and Wang,Yue and Hoffman,Eric P} } @article {12150, title = {Observations about software development for high end computing}, journal = {CTWatch Quarterly}, volume = {2}, year = {2006}, month = {2006///}, pages = {33 - 38}, abstract = {In this paper, we have summarized our findings from a series of case studies conducted with ten ASC and MP Codes as a series of observations. Due to different environments in which each code is developed, some of the observations are consistent across code teams while others vary across code teams. Overall, we found high consistency among the ASC Codes and the MP Codes. Due to the different environments and foci of these projects, this result is both surprising and positive. In addition, despite the fact that a large majority of the developers on these teams have little or no formal training in software engineering, they have been able to make use of some basic software engineering principles. Further education and motivation could increase the use of these principles and further increase the quality of scientific and engineering software that has already demonstrated its value.Based on the positive results thus far, we have plans to conduct additional case studies to gather more data in support of or in contradiction to the observations presented in this paper. In future case studies, we will strive to investigate codes from additional domains, thereby allowing broader, more inclusive conclusions to be drawn. }, author = {Carver, J. C and Hochstein, L. M and Kendall,R. P and Nakamura, T. and Zelkowitz, Marvin V and Basili, Victor R. and Post,D. E} } @book {12929, title = {Oceans And Health: Pathogens In The Marine Environment}, year = {2006}, month = {2006///}, publisher = {Springer}, organization = {Springer}, abstract = {The release of non-disinfected wastewaters into the marine environment is a common worldwide practice, in under-developed as well as in highly developed countries. Consequently, the seas are constantly infused with wastewater bacteria, among them highly pathogenic ones. In view of the public health significance of this phenomenon, it is surprising how little is actually known concerning the fate of such bacteria once they enter the sea. While numerous studies have addressed the effects of various environmental parameters on colony formation, many of them actually ignore the fact that bacteria can retain viability and infectivity while losing colony-forming ability. Only in recent years have efforts also been directed at unraveling the mechanisms determining bacterial sensitivity or survival under these conditions. This, therefore, is one subject of Oceans and Health: Pathogens in the Marine Environment: the survival, infectivity, pathogenicity and viability of enteric bacteria in the sea. Chapters also detail the public health aspects of wastewater release, civil engineering and economic considerations, other sources of pathogens, and much more.}, keywords = {Electronic books, Marine microbiology, Medical / Epidemiology, Medical / Microbiology, Nature / Animals / Marine Life, Pathogenic microorganisms, Science / Environmental Science, Science / Life Sciences / Biology, Science / Life Sciences / Marine Biology, Science / Life Sciences / Microbiology, Seawater/ microbiology}, isbn = {9780387237084}, author = {Belkin,Shimshon and Rita R Colwell} } @article {12265, title = {OMNI: An efficient overlay multicast infrastructure for real-time applications}, journal = {Computer Networks}, volume = {50}, year = {2006}, month = {2006/04/13/}, pages = {826 - 841}, abstract = {We consider an overlay architecture (called OMNI) where service providers deploy a set of service nodes (called MSNs) in the network to efficiently implement media-streaming applications. These MSNs are organized into an overlay and act as application-layer multicast forwarding entities for a set of clients.We present a decentralized scheme that organizes the MSNs into an appropriate overlay structure that is particularly beneficial for real-time applications. We formulate our optimization criterion as a {\textquotedblleft}degree-constrained minimum average-latency problem{\textquotedblright} which is known to be NP-Hard. A key feature of this formulation is that it gives a dynamic priority to different MSNs based on the size of its service set. Our proposed approach iteratively modifies the overlay tree using localized transformations to adapt with changing distribution of MSNs and clients, as well as network conditions. We show that a centralized greedy approach to this problem does not perform quite as well, while our distributed iterative scheme efficiently converges to near-optimal solutions. }, keywords = {Application-layer multicast, Minimum latency problem, overlay multicast}, isbn = {1389-1286}, doi = {10.1016/j.comnet.2005.07.023}, url = {http://www.sciencedirect.com/science/article/pii/S1389128605002434}, author = {Banerjee,Suman and Kommareddy,Christopher and Kar,Koushik and Bhattacharjee, Bobby and Khuller, Samir} } @conference {12390, title = {Optimization of signal processing software for control system implementation}, booktitle = {Computer Aided Control System Design, 2006 IEEE International Conference on Control Applications, 2006 IEEE International Symposium on Intelligent Control, 2006 IEEE}, year = {2006}, month = {2006/10//}, pages = {1562 - 1567}, abstract = {Signal processing plays a fundamental role in the design of control systems $\#$x2014; the portion of a digitally-implemented control system between the sensor outputs and the actuator inputs is precisely a digital signal processor (DSP). Consequently, effective techniques for design and optimization of signal processing software are important in achieving efficient controller implementations. Motivated by these relationships, this paper reviews techniques for modeling signal processing functionality in a manner that exposes aspects of application structure that are useful for mapping the functionality into efficient implementations. The paper then introduces some representative techniques that operate on such models to systematically derive optimized implementations from them.}, doi = {10.1109/CACSD-CCA-ISIC.2006.4776874}, author = {Bhattacharyya, Shuvra S. and Levine,William S.} } @article {18408, title = {Optimization of structured programs}, journal = {Software: Practice and Experience}, volume = {4}, year = {2006}, month = {2006/10/27/}, pages = {51 - 57}, abstract = {The class of programs which do not contain goto statements has a structure which lends itself to optimization by an optimizer that is fast, efficient and relatively easy to program. The design of such an optimizer is described, along with some of the results obtained using this optimizer{\textemdash}one such result being that very little code optimization is achieved. The conjecture is made that this is true because gotoless programming languages lend themselves to more compact and concise object code at the source language level.}, keywords = {compiler, Nested control structures, Optimizer, structured programming}, isbn = {1097-024X}, doi = {10.1002/spe.4380040106}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.4380040106/abstract}, author = {Zelkowitz, Marvin V and Bail,William G} } @article {16243, title = {An optimized system for expression and purification of secreted bacterial proteins}, journal = {Protein Expression and Purification}, volume = {46}, year = {2006}, month = {2006/03//}, pages = {23 - 32}, abstract = {In this report, we describe an optimized system for the efficient overexpression, purification, and refolding of secreted bacterial proteins. Candidate secreted proteins were produced recombinantly in Escherichia coli as Tobacco Etch Virus protease-cleavable hexahistidine-c-myc eptiope fusion proteins. Without regard to their initial solubility, recombinant fusion proteins were extracted from whole cells with guanidium chloride, purified under denaturing conditions by immobilized metal affinity chromatography, and refolded by rapid dilution into a solution containing only Tris buffer and sodium chloride. Following concentration on the same resin under native conditions, each protein was eluted for further purification and/or characterization. Preliminary studies on a test set of 12 secreted proteins ranging in size from 13 to 130\&$\#$xa0;kDa yielded between 10 and 50\&$\#$xa0;mg of fusion protein per liter of induced culture at greater than 90\% purity, as judged by Coomassie-stained SDS{\textendash}PAGE. Of the nine proteins further purified, analytical gel filtration chromatography indicated that each was a monomer in solution and circular dichroism spectroscopy revealed that each had adopted a well-defined secondary structure. While there are many potential applications for this system, the results presented here suggest that it will be particularly useful for investigators employing structural approaches to understand protein function, as attested to by the crystal structures of three proteins purified using this methodology (B.V. Geisbrecht, B.Y. Hamaoka, B. Perman, A. Zemla, D.J. Leahy, J. Biol. Chem. 280 (2005) 17243{\textendash}17250).}, keywords = {Pathogens, Secreted proteins, Toxins, Virulence factors}, isbn = {1046-5928}, doi = {10.1016/j.pep.2005.09.003}, url = {http://www.sciencedirect.com/science/article/pii/S1046592805003128}, author = {Geisbrecht,Brian V. and Bouyain,Samuel and Pop, Mihai} } @article {15785, title = {Parallelism for quantum computation with qudits}, journal = {Physical Review APhys. Rev. A}, volume = {74}, year = {2006}, month = {2006///}, pages = {032334 - 032334}, abstract = {Robust quantum computation with d-level quantum systems (qudits) poses two requirements: fast, parallel quantum gates and high-fidelity two-qudit gates. We first describe how to implement parallel single-qudit operations. It is by now well known that any single-qudit unitary can be decomposed into a sequence of Givens rotations on two-dimensional subspaces of the qudit state space. Using a coupling graph to represent physically allowed couplings between pairs of qudit states, we then show that the logical depth (time) of the parallel gate sequence is equal to the height of an associated tree. The implementation of a given unitary can then optimize the tradeoff between gate time and resources used. These ideas are illustrated for qudits encoded in the ground hyperfine states of the alkali-metal atoms 87Rb and 133Cs. Second, we provide a protocol for implementing parallelized nonlocal two-qudit gates using the assistance of entangled qubit pairs. Using known protocols for qubit entanglement purification, this offers the possibility of high-fidelity two-qudit gates.}, doi = {10.1103/PhysRevA.74.032334}, url = {http://link.aps.org/doi/10.1103/PhysRevA.74.032334}, author = {O{\textquoteright}Leary,Dianne P. and Brennen,Gavin K. and Bullock,Stephen S.} } @conference {12083, title = {Partially overlapped channels not considered harmful}, booktitle = {Proceedings of the joint international conference on Measurement and modeling of computer systems}, year = {2006}, month = {2006///}, pages = {63 - 74}, author = {Mishra,A. and Shrivastava,V. and Banerjee,S. and Arbaugh, William A.} } @conference {12410, title = {Participatory design with proxies: developing a desktop-PDA system to support people with aphasia}, booktitle = {Proceedings of the SIGCHI conference on Human Factors in computing systems}, series = {CHI {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {151 - 160}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we describe the design and preliminary evaluation of a hybrid desktop-handheld system developed to support individuals with aphasia, a disorder which impairs the ability to speak, read, write, or understand language. The system allows its users to develop speech communication through images and sound on a desktop computer and download this speech to a mobile device that can then support communication outside the home. Using a desktop computer for input addresses some of this population{\textquoteright}s difficulties interacting with handheld devices, while the mobile device addresses stigma and portability issues. A modified participatory design approach was used in which proxies, that is, speech-language pathologists who work with aphasic individuals, assumed the role normally filled by users. This was done because of the difficulties in communicating with the target population and the high variability in aphasic disorders. In addition, the paper presents a case study of the proxy-use participatory design process that illustrates how different interview techniques resulted in different user feedback.}, keywords = {aphasia, assistive technology, multi-modal interfaces, participatory design}, isbn = {1-59593-372-7}, doi = {10.1145/1124772.1124797}, url = {http://doi.acm.org/10.1145/1124772.1124797}, author = {Jordan Boyd-Graber and Nikolova,Sonya S. and Moffatt,Karyn A. and Kin,Kenrick C. and Lee,Joshua Y. and Mackey,Lester W. and Tremaine,Marilyn M. and Klawe,Maria M.} } @conference {16429, title = {Participatory, embodied, multi-agent simulation}, booktitle = {Proceedings of the fifth international joint conference on Autonomous agents and multiagent systems}, series = {AAMAS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1457 - 1458}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We will demonstrate the integration of a software-based multi-agent modeling platform with a participatory simulation environment and real-time control over a physical agent (robot). Both real and virtual participants will be able to act as agents in a simulation that will control a physical agent. The backbone of this demonstration is a widely used, freely available, mature modeling platform known as NetLogo.}, keywords = {embedded agents, multi-agent simulation, participatory simulation, ROBOTICS, Sensors}, isbn = {1-59593-303-4}, doi = {10.1145/1160633.1160913}, url = {http://doi.acm.org/10.1145/1160633.1160913}, author = {Blikstein,Paulo and Rand, William and Wilensky,Uri} } @article {12161, title = {The past, present, and future of experimental software engineering}, journal = {Journal of the Brazilian Computer Society}, volume = {12}, year = {2006}, month = {2006/12//}, pages = {7 - 12}, abstract = {This paper gives a 40 year overview of the evolution of experimental software engineering, from the past to the future, from a personal perspective. My hypothesis is that my work followed the evolution of the field. I use my own experiences and thoughts as a barometer of how the field has changed and present some opinions about where we need to go.}, isbn = {0104-6500}, doi = {10.1007/BF03194492}, url = {http://www.scielo.br/scielo.php?pid=S0104-65002006000400002\&script=sci_arttext}, author = {Basili, Victor R.} } @article {14631, title = {Patterns of sequence conservation in presynaptic neural genes}, journal = {Genome Biology}, volume = {7}, year = {2006}, month = {2006/11/10/}, pages = {R105 - R105}, abstract = {The neuronal synapse is a fundamental functional unit in the central nervous system of animals. Because synaptic function is evolutionarily conserved, we reasoned that functional sequences of genes and related genomic elements known to play important roles in neurotransmitter release would also be conserved.}, isbn = {1465-6906}, doi = {10.1186/gb-2006-7-11-r105}, url = {http://genomebiology.com/2006/7/11/R105}, author = {Hadley,Dexter and Murphy,Tara and Valladares,Otto and Hannenhalli, Sridhar and Ungar,Lyle and Kim,Junhyong and Bu{\'c}an,Maja} } @article {12607, title = {Physics-Based Detectors Applied to Long-Wave Infrared Hyperspectral Data}, year = {2006}, month = {2006/11//}, institution = {CENTER FOR AUTOMATION RESEARCH, UNIVERSITY OF MARYLAND COLLEGE PARK}, abstract = {Long-wave infrared (LWIR) hyperspectral image (HSI) data presents an interesting challenge for automatic target detection algorithms. LWIR HSI data is useful for both day and night operations, but weak signatures like disturbed soil can be problematic for standard matched-filter techniques. In this paper, we augment the standard matched-filter techniques with physics-based information particular to HSI data. Our results show that these physics-based detectors provide improved detection performance with quick processing times.}, keywords = {*HYPERSPECTRAL IMAGERY, algorithms, AUTOMATIC, DETECTION, FAR INFRARED RADIATION, LOW STRENGTH, Matched filters, MILITARY OPERATIONS, NIGHT, OPTICS, SIGNATURES, SOILS, SPECTROMETERS, TARGET DETECTION}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA481339}, author = {Broadwater,Joshua and Chellapa, Rama} } @article {12270, title = {Postmodern internetwork architecture}, journal = {ITTC-FY2006-TR-45030-01, Information and Telecommunication Center, The University of Kansas}, year = {2006}, month = {2006/02//}, abstract = {Network-layer innovation has proven surprisingly difficult, in part because internetworking protocols ignore com-peting economic interests and because a few protocols dominate, enabling layer violations that entrench technologies. Many shortcomings of today{\textquoteright}s internetwork layer result from its inflexibility with respect to the policies of the stake- holders: users and service providers. The consequences of these failings are well-known: various hacks, layering violations, and overloadings are introduced to enforce policies and attempt to get the upper hand in various {\textquotedblleft}tus- sles{\textquotedblright}. The result is a network that is increasingly brittle, hostile to innovation, vulnerable to attack, and insensitive to concerns about accountability and privacy. Our project aims to design, implement, and evaluate through daily use a minimalist internetwork layer and aux- iliary functionality that anticipates tussles and allows them to be played out in policy space, as opposed to in the packet-forwarding path. We call our approach postmodern internetwork architecture, because it is a reaction against many established network layer design concepts. The overall goal of the project is to make a larger portion of the network design space accessible without sacrificing the economy of scale offered by the unified Internet. We will use the postmodern architecture to explore basic architectural questions. These include: {\textbullet} What mechanisms should be supported by the network such that any foreseeable policy requirement can be explicitly addressed? {\textbullet} To what extent can routing and forwarding be isolated from each other while maintaining an efficient and usable network? {\textbullet} What forms of identity should be visible within the network, and what forms of accountability do different identities enable? {\textbullet} What mechanisms are needed to enable efficient access to cross-layer information and mechanisms such that lower layers can express their characteristics and upper layers can exert control downward? We plan to build and evaluate a complete end-to-end networking layer to help us understand feasible solutions to these questions. The Internet has fulfilled the potential of a complete generation of networking research by producing a global platform for innovation, commerce, and democracy. Unfortunately, the Internet also amply demonstrates the com- plexity and architectural ugliness that ensue when competing interests vie for benefits beyond those envisioned in the original design. This project is about redesigning the waist of the architectural hourglass to foster innovation, enhance security and accountability, and accomodate competing interests. }, author = {Bhattacharjee, Bobby and Calvert,K. and Griffioen,J. and Spring, Neil and Sterbenz,J. P.G} } @article {18009, title = {Programmer{\textquoteright}s Manual for XMTC Language, XMTC Compiler and XMT Simulator}, journal = {Technical Reports from UMIACS, UMIACS-TR-2005-45}, year = {2006}, month = {2006/06//}, abstract = {Explicit Multi-Threading (XMT) is a computing framework developed at the University of Maryland as part of a PRAM-on-chip vision (http://www.umiacs.umd.edu/users/vishkin/XMT). Much in the same way that performance programming of standard computers relies on C language, XMT performance programming is done using an extension of C called XMTC. This manual presents the second generation of XMTCprogramming paradigm. It is intended to be used by an application programmer, who is new to XMTC. In the first part of this technical report (UMIACS-TR 2005-45 Part 1 of 2), we define and describe key concepts, list the limitations and restrictions, and give examples. The second part (UMIACS-TR 2005-45 Part 2 of 2) is a brief tutorial, and it demonstrates the basic programming concepts of XMTC language with examples and exercises. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3673}, author = {Balkan,Aydin O. and Vishkin, Uzi} } @article {16469, title = {Query planning in the presence of overlapping sources}, journal = {Advances in Database Technology-EDBT 2006}, year = {2006}, month = {2006///}, pages = {811 - 828}, author = {Bleiholder,J. and Khuller, Samir and Naumann,F. and Raschid, Louiqa and Wu,Y.} } @article {15245, title = {Query planning in the presence of overlapping sources}, journal = {Advances in Database Technology-EDBT 2006}, year = {2006}, month = {2006///}, pages = {811 - 828}, abstract = {Navigational queries on Web-accessible life science sources pose unique query optimization challenges. The objects in these sources are interconnected to objects in other sources, forming a large and complex graph, and there is an overlap of objects in the sources. Answering a query requires the traversal of multiple alternate paths through these sources. Each path can be associated with the benefit or the cardinality of the target object set (TOS) of objects reached in the result. There is also an evaluation cost of reaching the TOS.We present dual problems in selecting the best set of paths. The first problem is to select a set of paths that satisfy a constraint on the evaluation cost while maximizing the benefit (number of distinct objects in the TOS). The dual problem is to select a set of paths that satisfies a threshold of the TOS benefit with minimal evaluation cost. The two problems can be mapped to the budgeted maximum coverage problem and the maximal set cover with a threshold. To solve these problems, we explore several solutions including greedy heuristics, a randomized search, and a traditional IP/LP formulation with bounds. We perform experiments on a real-world graph of life sciences objects from NCBI and report on the computational overhead of our solutions and their performance compared to the optimal solution. }, doi = {10.1007/11687238_48}, author = {Bleiholder,J. and Khuller, Samir and Naumann,F. and Raschid, Louiqa and Wu,Y.} } @conference {14407, title = {Query-time entity resolution}, booktitle = {International conference on knowledge discovery and data mining}, year = {2006}, month = {2006///}, pages = {529 - 534}, abstract = {The goal of entity resolution is to reconcile database references corresponding to the same real-world entities. Given the abundance of publicly available databases where entities are not resolved, we motivate the problem of quickly processing queries that require resolved entities from such {\textquoteright}unclean{\textquoteright} databases. We propose a two-stage collective resolution strategy for processing queries. We then show how it can be performed on-the-fly by adaptively extracting and resolving those database references that are the most helpful for resolving the query. We validate our approach on two large real-world publication databases where we show the usefulness of collective resolution and at the same time demonstrate the need for adaptive strategies for query processing. We then show how the same queries can be answered in real time using our adaptive approach while preserving the gains of collective resolution.}, author = {BHATTACHARVA,I. and Getoor, Lise and Licamele,L.} } @article {12276, title = {Ranking search results in P2P systems}, journal = {Technical Report, CR-TR-4779, Department of Computer Science, University of Maryland}, year = {2006}, month = {2006///}, abstract = {P2P deployments are a natural infrastructure for buildingdistributed search networks. Proposed systems support locating and retrieving all results, but lack the information necessary to rank them. Users, however, are primarily interested in the most relevant, and not all possible results. Using random sampling, we extend a class of well- known information retrieval ranking algorithms such that they can be applied in this distributed setting. We analyze the overhead of our approach, and quantify exactly how our system scales with increasing number of documents, system size, document to node mapping (uniform versus non-uniform), and types of queries (rare versus popular terms). Our analysis and simulations show that a) these extensions are efficient, and can scale with little overhead to large systems, and b) the accuracy of the results ob- tained using distributed ranking is comparable to a cen- tralized implementation. }, author = {Gopalakrishnan,V. and Morselli,R. and Bhattacharjee, Bobby and Keleher,P. and Srinivasan, Aravind} } @article {17649, title = {Ranking search results in peer-to-peer systems}, journal = {Technical Reports from UMIACS}, year = {2006}, month = {2006///}, abstract = {P2P deployments are a natural infrastructure for building distributed search networks. Proposed systems support locating and retrieving all results, but lack the information necessary to rank them. Users, however, are primarily interested in the most relevant, and not all possible results. Using random sampling, we extend a class of well-known information retrieval ranking algorithms such that they can be applied in this distributed setting. We analyze the overhead of our approach, and quantify exactly how our system scales with increasing number of documents, system size, document to node mapping (uniform versus non-uniform), and types of queries (rare versus popular terms). Our analysis and simulations show that a) these extensions are efficient, and can scale with little overhead to large systems, and b) the accuracy of the results obtained using distributed ranking is comparable to a centralized implementation.}, author = {Gopalakrishnan,V. and Morselli,R. and Bhattacharjee, Bobby and Keleher,P. and Srinivasan, Aravind} } @book {13182, title = {Real-Time Distributed Algorithms for Visual and Battlefield Reasoning}, year = {2006}, month = {2006///}, publisher = {MARYLAND UNIV COLLEGE PARK OFFICE OF RESEARCH ADMINISTRATION AND ADVANCEMENT}, organization = {MARYLAND UNIV COLLEGE PARK OFFICE OF RESEARCH ADMINISTRATION AND ADVANCEMENT}, abstract = {Information is key to the success of the next generation battlefield. There is a critical need to determine, in real-time, what the enemy is doing, and to interpret that information in the context of past related events. In this project we examined two aspects of this issue: development of a high-level task definition language for tasking a network of sensors to carry out given objectives, and interpreting recounted events so that past related scenarios could be automatically identified from a case database.}, author = {Davis, Larry S. and Basili, Victor R. and V.S. Subrahmanian and Reggia, James A. and Aloimonos, J.} } @conference {12374, title = {Reconfigurable image registration on FPGA platforms}, booktitle = {Biomedical Circuits and Systems Conference, 2006. BioCAS 2006. IEEE}, year = {2006}, month = {2006///}, pages = {154 - 157}, author = {Sen,M. and Hemaraj,Y. and Bhattacharyya, Shuvra S. and Shekhar,R.} } @conference {19459, title = {Reflecting on Health: A System for Students to Monitor Diet and Exercise}, booktitle = {SIGCHI EA {\textquoteright}06}, series = {CHI EA {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1807 - 1812}, publisher = {ACM}, organization = {ACM}, abstract = {Using an iterative design process, we designed and evaluated a system for college students to encourage the development and maintenance of healthy diet and exercise habits. The system has three components: a camera phone application to support photographic diet and exercise journaling, an automatic workout tracking application for exercise machines in the gym, and a visualization application to support users as they reflect on their diet and exercise activities.}, keywords = {diet, exercise, journaling, mobile phone, Visualization}, isbn = {1-59593-298-4}, url = {http://doi.acm.org/10.1145/1125451.1125794}, author = {Brown, Brandon and Marshini Chetty and Grimes, Andrea and Harmon, Ellie} } @conference {12379, title = {Register File Partitioning with Constraint Programming}, booktitle = {System-on-Chip, 2006. International Symposium on}, year = {2006}, month = {2006///}, pages = {1 - 4}, author = {Salmela,P. and Shen,C. C and Bhattacharyya, Shuvra S. and Takala,J.} } @article {14394, title = {Relational clustering for entity resolution queries}, journal = {ICML 2006 Workshop on Statistical Relational Learning (SRL)}, year = {2006}, month = {2006///}, abstract = {The goal of entity resolution is to recon-cile database references corresponding to the same real-world entities. Given the abun- dance of publicly available databases where entities are not resolved, we motivate the problem of quickly processing queries that require resolved entities from such {\textquoteleft}unclean{\textquoteright} databases. We first propose a cut-based rela- tional clustering formulation for collective en- tity resolution. We then show how it can be performed on-the-fly by adaptively extract- ing and resolving those database references that are the most helpful for resolving the query. We validate our approach on two large real-world publication databases, where we show the usefulness of collective resolution and at the same time demonstrate the need for adaptive strategies for query processing. We then show how the same queries can be answered in real time using our adaptive ap- proach while preserving the gains of collective resolution. }, author = {Bhattacharya,I. and Licamele,L. and Getoor, Lise} } @conference {15150, title = {Reliable broadcast in radio networks: the bounded collision case}, booktitle = {Proceedings of the twenty-fifth annual ACM symposium on Principles of distributed computing}, series = {PODC {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {258 - 264}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We study the problem of achieving global broadcast in a radio network where a node can multicast messages to all of its neighbors (that is, nodes within some given distance r), and up to t nodes in any single neighborhood may be corrupted. Previous work assumes that corrupted nodes can neither cause collisions nor spoof addresses of honest nodes. In this work, we eliminate these assumptions and allow each faulty node to cause a (known) bounded number of collisions and spoof the addresses of arbitrary other nodes. We show that the maximum tolerable t in this case is identical to the maximum tolerable t when collisions and address spoofing are not allowed. Thus, by causing collisions and spoofing addresses an adversary may be able to degrade the efficiency of achieving broadcast, but it cannot affect the feasibility of this task.}, keywords = {broadcast, byzantine failure, Fault tolerance, radio networks}, isbn = {1-59593-384-0}, doi = {10.1145/1146381.1146420}, url = {http://doi.acm.org/10.1145/1146381.1146420}, author = {Koo,Chiu-Yuen and Bhandari,Vartika and Katz, Jonathan and Vaidya,Nitin H.} } @article {17650, title = {Resilient multicast using overlays}, journal = {IEEE/ACM Transactions on Networking}, volume = {14}, year = {2006}, month = {2006/04//}, pages = {237 - 248}, abstract = {We introduce Probabilistic Resilient Multicast (PRM): a multicast data recovery scheme that improves data delivery ratios while maintaining low end-to-end latencies. PRM has both a proactive and a reactive components; in this paper we describe how PRM can be used to improve the performance of application-layer multicast protocols especially when there are high packet losses and host failures. Through detailed analysis in this paper, we show that this loss recovery technique has efficient scaling properties-the overheads at each overlay node asymptotically decrease to zero with increasing group sizes. As a detailed case study, we show how PRM can be applied to the NICE application-layer multicast protocol. We present detailed simulations of the PRM-enhanced NICE protocol for 10 000 node Internet-like topologies. Simulations show that PRM achieves a high delivery ratio (>97\%) with a low latency bound (600 ms) for environments with high end-to-end network losses (1\%-5\%) and high topology change rates (5 changes per second) while incurring very low overheads (<5\%).}, keywords = {application-layer multicast protocols, Computer science, Data communication, Delay, Internet, Internet-like topologies, IP networks, loss recovery technique, Multicast, multicast data recovery scheme, Multicast protocols, Network topology, NETWORKS, overlays, Performance loss, probabilistic forwarding, probabilistic resilient multicast, Protocols, Resilience, Streaming media, telecommunication network topology, Terminology}, isbn = {1063-6692}, doi = {10.1109/TNET.2006.872579}, author = {Banerjee,S. and Lee,Seungjoon and Bhattacharjee, Bobby and Srinivasan, Aravind} } @conference {12275, title = {Resource Discovery Techniques in Distributed Desktop Grid Environments}, booktitle = {Proceedings of the 7th IEEE/ACM International Conference on Grid Computing}, series = {GRID {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {9 - 16}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {Desktop grids use opportunistic sharing to exploit large collections of personal computers and workstations across the Internet, achieving tremendous computing power at low cost. Traditional desktop grid systems are typically based on a client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. In this paper, we propose a decentralized, robust, highly available, and scalable infrastructure to match incoming jobs to available resources. Through a comparative analysis on the experimental results obtained via simulation of three different types of matchmaking algorithms under different workload scenarios, we show the trade-offs between effcient matchmaking and good load balancing in a fully decentralized, heterogeneous computational environment.}, isbn = {1-4244-0343-X}, doi = {10.1109/ICGRID.2006.310992}, url = {http://dx.doi.org/10.1109/ICGRID.2006.310992}, author = {Kim,Jik-Soo and Nam,Beomseok and Keleher,Peter and Marsh,Michael and Bhattacharjee, Bobby and Sussman, Alan} } @article {14641, title = {Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection}, journal = {PLoS PathogPLoS Pathog}, volume = {2}, year = {2006}, month = {2006/06/23/}, pages = {e60 - e60}, abstract = {Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I{\textendash}hypersensitive sites (i.e., +/- 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.}, doi = {10.1371/journal.ppat.0020060}, url = {UR - http://dx.plos.org/10.1371/journal.ppat.0020060,http://dx.plos.org/10.1371/journal.ppat.0020060}, author = {Lewinski,Mary K and Yamashita,Masahiro and Emerman,Michael and Ciuffi,Angela and Marshall,Heather and Crawford,Gregory and Collins,Francis and Shinn,Paul and Leipzig,Jeremy and Hannenhalli, Sridhar and Berry,Charles C and Ecker,Joseph R and Bushman,Frederic D.} } @article {18506, title = {Revisiting Internet addressing: Back to the future}, volume = {MIT-CSAIL-TR-2006-025}, year = {2006}, month = {2006///}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {IP prefixes undermine three goals of Internet routing:accurate reflection of network-layer reachability, secure routing messages, and effective traffic control. This pa- per presents Atomic IP (AIP), a simple change to Inter- net addressing (which in fact reverts to how addressing once worked), that allows Internet routing to achieve these goals. }, author = {Vutukuru,M. and Feamster, Nick and Walfish,M. and Balakrishnan,H. and Shenker,S.} } @article {15166, title = {Ring signatures: Stronger definitions, and constructions without random oracles}, journal = {Theory of Cryptography}, year = {2006}, month = {2006///}, pages = {60 - 79}, abstract = {Ring signatures, first introduced by Rivest, Shamir, and Tauman, enable a user to sign a message so that a ring of possible signers (of which the user is a member) is identified, without revealing exactly which member of that ring actually generated the signature. In contrast to group signatures, ring signatures are completely {\textquotedblleft}ad-hoc{\textquotedblright} and do not require any central authority or coordination among the various users (indeed, users do not even need to be aware of each other); furthermore, ring signature schemes grant users fine-grained control over the level of anonymity associated with any particular signature.This paper has two main areas of focus. First, we examine previous definitions of security for ring signature schemes and suggest that most of these prior definitions are too weak, in the sense that they do not take into account certain realistic attacks. We propose new definitions of anonymity and unforgeability which address these threats, and then give separation results proving that our new notions are strictly stronger than previous ones. Next, we show two constructions of ring signature schemes in the standard model: one based on generic assumptions which satisfies our strongest definitions of security, and a second, more efficient scheme achieving weaker security guarantees and more limited functionality. These are the first constructions of ring signature schemes that do not rely on random oracles or ideal ciphers. }, doi = {10.1007/11681878_4}, author = {Bender,A. and Katz, Jonathan and Morselli,R.} } @conference {12272, title = {A scalable key management and clustering scheme for ad hoc networks}, booktitle = {Proceedings of the 1st international conference on Scalable information systems}, series = {InfoScale {\textquoteright}06}, year = {2006}, month = {2006///}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a scalable key management and clustering scheme for secure group communications in ad hoc and sensor networks. The scalability problem is solved by partitioning the communicating devices into subgroups, with a leader in each subgroup, and further organizing the subgroups into hierarchies. Each level of the hierarchy is called a tier or layer. Key generation, distribution, and actual data transmissions follow the hierarchy. The Distributed, Efficient Clustering Approach (DECA) provides robust clustering to form subgroups, and analytical and simulation results demonstrate that DECA is energy-efficient and resilient against node mobility. Comparing with most other schemes, our approach is extremely scalable and efficient, provides more security guarantees, and is selective, adaptive and robust.}, isbn = {1-59593-428-6}, doi = {10.1145/1146847.1146875}, url = {http://doi.acm.org/10.1145/1146847.1146875}, author = {Li,Jason H. and Levy,Renato and Yu,Miao and Bhattacharjee, Bobby} } @article {14069, title = {Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: Sixteen new members and a novel subfamily}, journal = {Gene}, volume = {366}, year = {2006}, month = {2006/02/01/}, pages = {303 - 315}, abstract = {Nuclear receptors (NRs) are important transcriptional modulators in metazoans. Sixteen new NRs were identified in the Platyhelminth trematode, Schistosoma mansoni. Three were found to possess novel tandem DNA-binding domains that identify a new subfamily of NR. Two NRs are homologues of the thyroid hormone receptor that previously were thought to be restricted to chordates. This study brings the total number of identified NR in S. mansoni to 21. Phylogenetic and comparative genomic analyses demonstrate that S. mansoni NRs share an evolutionary lineage with that of arthropods and vertebrates. Phylogenic analysis shows that more than half of the S. mansoni nuclear receptors evolved from a second gene duplication. As the second gene duplication of NRs was thought to be specific to vertebrates, our data challenge the current theory of NR evolution.}, keywords = {Nuclear receptors, Schistosoma mansoni}, isbn = {0378-1119}, doi = {16/j.gene.2005.09.013}, url = {http://www.sciencedirect.com/science/article/pii/S0378111905005871}, author = {Wu,Wenjie and Niles,Edward G. and El-Sayed, Najib M. and Berriman,Matthew and LoVerde,Philip T.} } @book {15403, title = {The Science of Hysteresis: Mathematical modeling and applications}, year = {2006}, month = {2006///}, publisher = {Academic Press}, organization = {Academic Press}, keywords = {Business \& Economics / Economics / Microeconomics, Hysteresis, Magnetism, Science / Physics / Magnetism}, isbn = {9780123694317}, author = {Bertotti,Giorgio and Mayergoyz, Issak D} } @article {12926, title = {Seasonal Cholera Caused by Vibrio Cholerae Serogroups O1 and O139 in the Coastal Aquatic Environment of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {72}, year = {2006}, month = {2006/06/01/}, pages = {4096 - 4104}, abstract = {Since Vibrio cholerae O139 first appeared in 1992, both O1 El Tor and O139 have been recognized as the epidemic serogroups, although their geographic distribution, endemicity, and reservoir are not fully understood. To address this lack of information, a study of the epidemiology and ecology of V. cholerae O1 and O139 was carried out in two coastal areas, Bakerganj and Mathbaria, Bangladesh, where cholera occurs seasonally. The results of a biweekly clinical study (January 2004 to May 2005), employing culture methods, and of an ecological study (monthly in Bakerganj and biweekly in Mathbaria from March 2004 to May 2005), employing direct and enrichment culture, colony blot hybridization, and direct fluorescent-antibody methods, showed that cholera is endemic in both Bakerganj and Mathbaria and that V. cholerae O1, O139, and non-O1/non-O139 are autochthonous to the aquatic environment. Although V. cholerae O1 and O139 were isolated from both areas, most noteworthy was the isolation of V. cholerae O139 in March, July, and September 2004 in Mathbaria, where seasonal cholera was clinically linked only to V. cholerae O1. In Mathbaria, V. cholerae O139 emerged as the sole cause of a significant outbreak of cholera in March 2005. V. cholerae O1 reemerged clinically in April 2005 and established dominance over V. cholerae O139, continuing to cause cholera in Mathbaria. In conclusion, the epidemic potential and coastal aquatic reservoir for V. cholerae O139 have been demonstrated. Based on the results of this study, the coastal ecosystem of the Bay of Bengal is concluded to be a significant reservoir for the epidemic serogroups of V. cholerae.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00066-06}, url = {http://aem.asm.org/content/72/6/4096}, author = {Alam,Munirul and Hasan,Nur A. and Sadique,Abdus and Bhuiyan,N. A. and Ahmed,Kabir U. and Nusrin,Suraia and Nair,G. Balakrish and Siddique,A. K. and Sack,R. Bradley and Sack,David A. and Huq,Anwar and Rita R Colwell} } @article {14642, title = {Selection of Target Sites for Mobile DNA Integration in the Human Genome}, journal = {PLoS Comput BiolPLoS Comput Biol}, volume = {2}, year = {2006}, month = {2006/11/24/}, pages = {e157 - e157}, abstract = {DNA sequences from retroviruses, retrotransposons, DNA transposons, and parvoviruses can all become integrated into the human genome. Accumulation of such sequences accounts for at least 40\% of our genome today. These integrating elements are also of interest as gene-delivery vectors for human gene therapy. Here we present a comprehensive bioinformatic analysis of integration targeting by HIV, MLV, ASLV, SFV, L1, SB, and AAV. We used a mathematical method which allowed annotation of each base pair in the human genome for its likelihood of hosting an integration event by each type of element, taking advantage of more than 200 types of genomic annotation. This bioinformatic resource documents a wealth of new associations between genomic features and integration targeting. The study also revealed that the length of genomic intervals analyzed strongly affected the conclusions drawn{\textemdash}thus, answering the question {\textquotedblleft}What genomic features affect integration?{\textquotedblright} requires carefully specifying the length scale of interest.}, doi = {10.1371/journal.pcbi.0020157}, url = {UR - http://dx.plos.org/10.1371/journal.pcbi.0020157,http://dx.plos.org/10.1371/journal.pcbi.0020157}, author = {Berry,Charles and Hannenhalli, Sridhar and Leipzig,Jeremy and Bushman,Frederic D.} } @article {16084, title = {Shared family calendars: Promoting symmetry and accessibility}, journal = {ACM Trans. Comput.-Hum. Interact.}, volume = {13}, year = {2006}, month = {2006/09//}, pages = {313 - 346}, abstract = {We describe the design and use of a system facilitating the sharing of calendar information between remotely located, multi-generational family members. Most previous work in this area involves software enabling younger family members to monitor their parents. We have found, however, that older adults are equally if not more interested in the activities of younger family members. The major obstacle preventing them from participating in information sharing is the technology itself. Therefore, we developed a multi-layered interface approach that offers simple interaction to older users. In our system, users can choose to enter information into a computerized calendar or write it by hand on digital paper calendars. All of the information is automatically shared among everyone in the distributed family. By making the interface more accessible to older users, we promote symmetrical sharing of information among both older and younger family members. We present our participatory design process, describe the user interface, and report on an exploratory field study in three households of an extended family.}, keywords = {calendar, digital paper, elderly, family technology, Home, layered interface, privacy, universal usability}, isbn = {1073-0516}, doi = {10.1145/1183456.1183458}, url = {http://doi.acm.org/10.1145/1183456.1183458}, author = {Plaisant, Catherine and Clamage,Aaron and Hutchinson,Hilary Browne and Bederson, Benjamin B. and Druin, Allison} } @conference {18649, title = {A Statistical Analysis of Attack Data to Separate Attacks}, year = {2006}, month = {2006/06//}, pages = {383 - 392}, abstract = {This paper analyzes malicious activity collected from a test-bed, consisting of two target computers dedicated solely to the purpose of being attacked, over a 109 day time period. We separated port scans, ICMP scans, and vulnerability scans from the malicious activity. In the remaining attack data, over 78\% (i.e., 3,677 attacks) targeted port 445, which was then statistically analyzed. The goal was to find the characteristics that most efficiently separate the attacks. First, we separated the attacks by analyzing their messages. Then we separated the attacks by clustering characteristics using the K-Means algorithm. The comparison between the analysis of the messages and the outcome of the K-Means algorithm showed that 1) the mean of the distributions of packets, bytes and message lengths over time are poor characteristics to separate attacks and 2) the number of bytes, the mean of the distribution of bytes and message lengths as a function of the number packets are the best characteristics for separating attacks}, keywords = {attack data statistical analysis, attack separation, computer crime, Data analysis, data mining, ICMP scans, K-Means algorithm, pattern clustering, port scans, statistical analysis, vulnerability scans}, doi = {10.1109/DSN.2006.9}, author = {Michel Cukier and Berthier,R. and Panjwani,S. and Tan,S.} } @inbook {18806, title = {A Step Towards Automated Design of Side Actions in Injection Molding of Complex Parts}, booktitle = {Geometric Modeling and Processing - GMP 2006}, series = {Lecture Notes in Computer Science}, volume = {4077}, year = {2006}, month = {2006///}, pages = {500 - 513}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Side actions contribute to mold cost by resulting in an additional manufacturing and assembly cost as well as by increasing the molding cycle time. Therefore, generating shapes of side actions requires solving a complex geometric optimization problem. Different objective functions may be needed depending upon different molding scenarios (e.g., prototyping versus large production runs). Manually designing side actions is a challenging task and requires considerable expertise. Automated design of side actions will significantly reduce mold design lead times. This paper describes algorithms for generating shapes of side actions to minimize a customizable molding cost function.}, keywords = {Computer science}, isbn = {978-3-540-36711-6}, url = {http://www.springerlink.com/content/w7q3212607500635/abstract/}, author = {Banerjee,Ashis and Gupta, Satyandra K.}, editor = {Kim,Myung-Soo and Shimada,Kenji} } @book {12328, title = {System synthesis for optically-connected, multiprocessors on-chip}, year = {2006}, month = {2006///}, publisher = {Citeseer}, organization = {Citeseer}, author = {Bambha,N. K and Bhattacharyya, Shuvra S. and STUDIES,MARYLAND UNIV COLLEGE PARK INST FOR ADVANCED COMPUTER} } @conference {12181, title = {Target size study for one-handed thumb use on small touchscreen devices}, booktitle = {Proceedings of the 8th conference on Human-computer interaction with mobile devices and services}, year = {2006}, month = {2006///}, pages = {203 - 210}, author = {Parhi,P. and Karlson,A.K. and Bederson, Benjamin B.} } @article {17434, title = {Toward an enriched (and revitalized) sense of help: Summary of an ASIS\&T 2005 panel session}, journal = {Bulletin of the American Society for Information Science and Technology}, volume = {32}, year = {2006}, month = {2006/06/01/}, pages = {23 - 26}, isbn = {1550-8366}, doi = {10.1002/bult.2006.1720320509}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bult.2006.1720320509/abstract}, author = {Haas,Stephanie W and Denn,Sheila and Locke,David and Shneiderman, Ben and Brown,Laurie} } @article {16082, title = {TreePlus: Interactive Exploration of Networks with Enhanced Tree Layouts}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {12}, year = {2006}, month = {2006/12//nov}, pages = {1414 - 1426}, abstract = {Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food Webs, ontologies and social networks difficult to understand and interact with. We propose a new interactive visual analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus}, keywords = {Automated;Software;User-Computer Interface;, Biological;Pattern Recognition, data visualization;graph structure;graphical user interface;interactive visual analytics;occlusion;tree-style layout;data visualisation;graphical user interfaces;hidden feature removal;interactive systems;trees (mathematics);Algorithms;Computer Graphics;C}, isbn = {1077-2626}, doi = {10.1109/TVCG.2006.106}, author = {Lee,B. and Parr,C.S. and Plaisant, Catherine and Bederson, Benjamin B. and Veksler,V.D. and Gray,W.D. and Kotfila,C.} } @article {14079, title = {The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion}, journal = {Molecular biology and evolution}, volume = {23}, year = {2006}, month = {2006///}, pages = {411 - 411}, author = {Bringaud,F. and Bartholomeu,D. C and Blandin,G. and Delcher,A. and Baltz,T. and El-Sayed, Najib M. and Ghedin,E.} } @article {17518, title = {Using PlanetLab for network research}, journal = {ACM SIGOPS Operating Systems Review}, volume = {40}, year = {2006}, month = {2006/01/01/}, pages = {17 - 17}, isbn = {01635980}, doi = {10.1145/1113361.1113368}, url = {http://dl.acm.org/citation.cfm?id=1113368}, author = {Spring, Neil and Peterson,Larry and Bavier,Andy and Pait,Vivek} } @inbook {12638, title = {Video Mensuration Using a Stationary Camera}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3953}, year = {2006}, month = {2006///}, pages = {164 - 176}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents a method for video mensuration using a single stationary camera. The problem we address is simple, i.e., the mensuration of any arbitrary line segment on the reference plane using multiple frames with minimal calibration. Unlike previous solutions that are based on planar rectification, our approach is based on fitting the image of multiple concentric circles on the plane. Further, the proposed method aims to minimize the error in mensuration. Hence we can calculate the mensuration of the line segments not lying on the reference plane. Using an algorithm for detecting and tracking wheels of an automobile, we have implemented a fully automatic system for wheel base mensuration. The mensuration results are accurate enough that they can be used to determine the vehicle classes. Furthermore, we measure the line segment between any two points on the vehicle and plot them in top and side views.}, isbn = {978-3-540-33836-9}, url = {http://dx.doi.org/10.1007/11744078_13}, author = {Guo,Feng and Chellapa, Rama}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @article {13183, title = {View-invariant estimation of height and stride for gait recognition}, journal = {Biometric Authentication}, year = {2006}, month = {2006///}, pages = {155 - 167}, abstract = {We present a parametric method to automatically identify people in monocular low-resolution video by estimating the height and stride parameters of their walking gait. Stride parameters (stride length and cadence) are functions of body height, weight, and gender. Previous work has demonstrated effective use of these biometrics for identification and verification of people. In this paper, we show that performance is significantly improved by using height as an additional discriminant feature. Height is estimated by robustly segmenting the person from the background and fitting their apparent height to a time-dependent model. This method is correspondence-free and works with low-resolution images of people. It is also view-invariant, albeit performance is optimal in near fronto-parallel configurations. Identification accuracy is estimated at 47\% for fronto-parallel sequences of 41 people, and 65\% for non-fronto-parallel sequences of 17 people, compared with 18\% and 51\%, respectively, when only stride and cadence are used.}, author = {BenAbdelkader,C. and Cutler, R. and Davis, Larry S.} } @conference {13481, title = {Visualization Support for Fusing Relational, Spatio-Temporal Data: Building Career Histories}, booktitle = {Information Fusion, 2006 9th International Conference on}, year = {2006}, month = {2006/07//}, pages = {1 - 7}, publisher = {IEEE}, organization = {IEEE}, abstract = {Many real-world domains resist analysis because they are best characterized by a variety of data types, including relational, spatial, and temporal components. Examples of such domains include disease outbreaks, criminal networks, and the World-Wide Web. We present two types of visualizations based on physical metaphors that facilitate fusion, analysis, and deep understanding of relational, spatio-temporal data. The first visualization is based on the metaphor of fluid flow through elastic pipes, and the second on wave propagation. We discuss both types of visualizations in the context of fusing information about the activities of scientists over time with the goal of constructing career histories}, isbn = {1-4244-0953-5, 0-9721844-6-5}, doi = {10.1109/ICIF.2006.301772}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4086058}, author = {Blythe,Jim and Patwardhan,Mithila and Oates,Tim and desJardins, Marie and Rheingans,Penny} } @inbook {16090, title = {Visualizing Graphs as Trees: Plant a Seed and Watch it Grow}, booktitle = {Graph DrawingGraph Drawing}, series = {Lecture Notes in Computer Science}, volume = {3843}, year = {2006}, month = {2006///}, pages = {516 - 518}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {TreePlus is a graph browsing technique based on a tree-style layout. It shows the missing graph structure using interaction techniques and enables users to start with a specific node and incrementally explore the local structure of graphs. We believe that it supports particularly well tasks that require rapid reading of labels.}, isbn = {978-3-540-31425-7}, url = {http://dx.doi.org/10.1007/11618058_50}, author = {Lee,Bongshin and Parr,Cynthia and Plaisant, Catherine and Bederson, Benjamin B.}, editor = {Healy,Patrick and Nikolov,Nikola} } @article {19462, title = {VoIP deregulation in South Africa: Implications for underserviced areas}, journal = {Telecommunications Policy}, volume = {30}, year = {2006}, month = {2006/06//}, pages = {332 - 344}, abstract = {Several statutory restrictions have recently been lifted on the use of Voice over Internet Protocol (VoIP) in South Africa. Previously, VoIP could only be utilised by the incumbent telecommunications operator, Telkom, the Second National Operator (SNO) and under serviced area licensees (USALs). This means new opportunities and cost savings for both network service providers and consumers. However, in rural and remote regions, further liberalisation is required so that service providers can take advantage of wireless technologies to provide connectivity in these areas. This paper discusses the legislative environment in South Africa and around the world with respect to VoIP and Wireless Fidelity (WiFi). In addition, examples are provided of how these technologies have been combined to provide last mile solutions around the world and particularly in South Africa. The paper concludes that further liberalisation in the telecommunications environment in South Africa is required if the goal of providing affordable access in rural areas is to be attained. Specifically, it is recommended that wireless technologies be deregulated since the combination of VoIP and WiFi may benefit rural areas. Also, the paper finds that USALs may not be the right model for underserviced areas in South Africa. Lastly, it is apparent that applications drive development and dictate which technologies are relevant for rural areas.}, keywords = {South Africa, VoIP, WiFi}, isbn = {0308-5961}, url = {http://www.sciencedirect.com/science/article/pii/S0308596106000231}, author = {Marshini Chetty and Blake, Edwin and McPhie, Ewan} } @inbook {14276, title = {Wavelet-Based Super-Resolution Reconstruction: Theory and Algorithm}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3954}, year = {2006}, month = {2006///}, pages = {295 - 307}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present a theoretical analysis and a new algorithm for the problem of super-resolution imaging: the reconstruction of HR (high-resolution) images from a sequence of LR (low-resolution) images. Super-resolution imaging entails solutions to two problems. One is the alignment of image frames. The other is the reconstruction of a HR image from multiple aligned LR images. Our analysis of the latter problem reveals insights into the theoretical limits of super-resolution reconstruction. We find that at best we can reconstruct a HR image blurred by a specific low-pass filter. Based on the analysis we present a new wavelet-based iterative reconstruction algorithm which is very robust to noise. Furthermore, it has a computationally efficient built-in denoising scheme with a nearly optimal risk bound. Roughly speaking, our method could be described as a better-conditioned iterative back-projection scheme with a fast and optimal regularization criteria in each iteration step. Experiments with both simulated and real data demonstrate that our approach has significantly better performance than existing super-resolution methods. It has the ability to remove even large amounts of mixed noise without creating smoothing artifacts.}, isbn = {978-3-540-33838-3}, url = {http://dx.doi.org/10.1007/11744085_23}, author = {Hui Ji and Ferm{\"u}ller, Cornelia}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @inbook {12642, title = {What Is the Range of Surface Reconstructions from a Gradient Field?}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3951}, year = {2006}, month = {2006///}, pages = {578 - 591}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We propose a generalized equation to represent a continuum of surface reconstruction solutions of a given non-integrable gradient field. We show that common approaches such as Poisson solver and Frankot-Chellappa algorithm are special cases of this generalized equation. For a N {\texttimes} N pixel grid, the subspace of all integrable gradient fields is of dimension N 2 {\textendash} 1. Our framework can be applied to derive a range of meaningful surface reconstructions from this high dimensional space. The key observation is that the range of solutions is related to the degree of anisotropy in applying weights to the gradients in the integration process. While common approaches use isotropic weights, we show that by using a progression of spatially varying anisotropic weights, we can achieve significant improvement in reconstructions. We propose (a) α-surfaces using binary weights, where the parameter α allows trade off between smoothness and robustness, (b) M-estimators and edge preserving regularization using continuous weights and (c) Diffusion using affine transformation of gradients. We provide results on photometric stereo, compare with previous approaches and show that anisotropic treatment discounts noise while recovering salient features in reconstructions.}, isbn = {978-3-540-33832-1}, url = {http://dx.doi.org/10.1007/11744023_45}, author = {Agrawal,Amit and Raskar,Ramesh and Chellapa, Rama}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @article {16414, title = {Widgets, Planets, and Demons: the Case for the Integration of Human, Embedded, and Virtual Agents via Mediation}, journal = {Proceedings of Swarmfest}, year = {2006}, month = {2006///}, author = {Rand, William and Blikstein,P. and Wilensky,U.} } @inbook {12679, title = {3D Facial Pose Tracking in Uncalibrated Videos}, booktitle = {Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence}, series = {Lecture Notes in Computer Science}, volume = {3776}, year = {2005}, month = {2005///}, pages = {515 - 520}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents a method to recover the 3D configuration of a face in each frame of a video. The 3D configuration consists of the 3 translational parameters and the 3 orientation parameters which correspond to the yaw, pitch and roll of the face, which is important for applications like face modeling, recognition, expression analysis, etc. The approach combines the structural advantages of geometric modeling with the statistical advantages of a particle-filter based inference. The face is modeled as the curved surface of a cylinder which is free to translate and rotate arbitrarily. The geometric modeling takes care of pose and self-occlusion while the statistical modeling handles moderate occlusion and illumination variations. Experimental results on multiple datasets are provided to show the efficacy of the approach. The insensitivity of our approach to calibration parameters (focal length) is also shown.}, isbn = {978-3-540-30506-4}, url = {http://dx.doi.org/10.1007/11590316_81}, author = {Aggarwal,Gaurav and Veeraraghavan,Ashok and Chellapa, Rama}, editor = {Pal,Sankar and Bandyopadhyay,Sanghamitra and Biswas,Sambhunath} } @article {17683, title = {Algorithm 844: Computing sparse reduced-rank approximations to sparse matrices}, journal = {ACM Transactions on Mathematical Software-TOMS}, volume = {31}, year = {2005}, month = {2005///}, pages = {252 - 269}, author = {Berry,M. W and Pulatova,S. A and Stewart, G.W.} } @conference {12673, title = {An architectural level design methodology for embedded face detection}, booktitle = {Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis}, series = {CODES+ISSS {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {136 - 141}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Face detection and recognition research has attracted great attention in recent years. Automatic face detection has great potential in a large array of application areas, including banking and security system access control, video surveillance, and multimedia information retrieval. In this paper, we discuss an architectural level design methodology for implementation of an embedded face detection system on a reconfigurable system on chip. We present models for performance estimation and validate these models with experimental values obtained from implementing our system on an FPGA platform. This modeling approach is shown to be efficient, accurate, and intuitive for designers to work with. Using this approach, we present several design options that trade-off various architectural features.}, keywords = {design space exploration, Face detection, platforms, reconfigurable, system-level models}, isbn = {1-59593-161-9}, doi = {10.1145/1084834.1084872}, url = {http://doi.acm.org/10.1145/1084834.1084872}, author = {Kianzad,V. and Saha,S. and Schlessman,J. and Aggarwal,G. and Bhattacharyya, Shuvra S. and Wolf,W. and Chellapa, Rama} } @article {15718, title = {Asymptotically Optimal Quantum Circuits for d-Level Systems}, journal = {Physical Review LettersPhys. Rev. Lett.}, volume = {94}, year = {2005}, month = {2005/06/14/}, pages = {230502 - 230502}, abstract = {Scalability of a quantum computation requires that the information be processed on multiple subsystems. However, it is unclear how the complexity of a quantum algorithm, quantified by the number of entangling gates, depends on the subsystem size. We examine the quantum circuit complexity for exactly universal computation on many d-level systems (qudits). Both a lower bound and a constructive upper bound on the number of two-qudit gates result, proving a sharp asymptotic of Θ(d2n) gates. This closes the complexity question for all d-level systems (d finite). The optimal asymptotic applies to systems with locality constraints, e.g., nearest neighbor interactions.}, doi = {10.1103/PhysRevLett.94.230502}, url = {http://link.aps.org/doi/10.1103/PhysRevLett.94.230502}, author = {Bullock,Stephen S. and O{\textquoteright}Leary,Dianne P. and Brennen,Gavin K.} } @conference {12655, title = {Average relative radiance transform for subpixel detection}, booktitle = {Geoscience and Remote Sensing Symposium, 2005. IGARSS {\textquoteright}05. Proceedings. 2005 IEEE International}, volume = {5}, year = {2005}, month = {2005/07//}, pages = {3565 - 3568}, doi = {10.1109/IGARSS.2005.1526617}, author = {Broadwater, J. and Meth, R. and Chellapa, Rama} } @article {17002, title = {Building a Coherent Data Pipeline in Microarray Data Analyses: Optimization of Signal/Noise Ratios Using an Interactive Visualization Tool and a Novel Noise Filtering Method (2003)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Motivation: Sources of uncontrolled noise strongly influence data analysis in microarray studies, yet signal/noise ratios are rarely considered in microarray data analyses. We hypothesized that different research projects would have different sources and levels of confounding noise, and built an interactive visual analysis tool to test and define parameters in Affymetrix analyses that optimize the ratio of signal (desired biological variable) versus noise (confounding uncontrolled variables). Results: Five probe set algorithms were studied with and without statistical weighting of probe sets using Microarray Suite (MAS) 5.0 probe set detection p values. The signal/noise optimization method was tested in two large novel microarray datasets with different levels of confounding noise; a 105 sample U133A human muscle biopsy data set (11 groups) (extensive noise), and a 40 sample U74A inbred mouse lung data set (8 groups) (little noise). Success was measured using F-measure value of success of unsupervised clustering into appropriate biological groups (signal). We show that both probe set signal algorithm and probe set detection p-value weighting have a strong effect on signal/noise ratios, and that the different methods performed quite differently in the two data sets. Among the signal algorithms tested, dChip difference model with p-value weighting was the most consistent at maximizing the effect of the target biological variables on data interpretation of the two data sets. Availability: The Hierarchical Clustering Explorer 2.0 is [url=http://www.cs.umd.edu/hcil/hce/]available[/url] online and the improved version of the Hierarchical Clustering Explorer 2.0 with p-value weighting and Fmeasure is available upon request to the first author. Murine arrays (40 samples) are publicly available at the [url=http://microarray.cnmcresearch.org/pgadatatable.asp]PEPR resource.[/url] (Chen et al., 2004).}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6511}, author = {Seo,Jinwook and Bakay,Marina and Chen,Yi-Wen and Hilmer,Sara and Shneiderman, Ben and Hoffman,Eric P} } @conference {14460, title = {Capital and benefit in social networks}, booktitle = {Proceedings of the 3rd international workshop on Link discovery}, series = {LinkKDD {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {44 - 51}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Recently there has been a surge of interest in social networks. Email traffic, disease transmission, and criminal activity can all be modeled as social networks. In this paper, we introduce a particular form of social network which we call a friendship-event network. A friendship-event network describes two inter-related networks. One is a friendship network among a set of actors. The other is an event network that describes events, event organizers and event participants. Within these types of networks, we formulate the notion of capital based on the actor-organizer friendship relationship and the notion of benefit, based on event participation. We ground these definitions in a real-world example of academic collaboration networks, where the actors are researchers, the friendships are collaborations, the events are conferences, the organizers are program committee members and the participants are conference authors. We incorporate a temporal component by considering the notion of an event series. We explore the use of these measures on a data set describing three computer science conferences over the past ten years.}, isbn = {1-59593-215-1}, doi = {10.1145/1134271.1134278}, url = {http://doi.acm.org/10.1145/1134271.1134278}, author = {Licamele,Louis and Bilgic,Mustafa and Getoor, Lise and Roussopoulos, Nick} } @conference {12388, title = {CASPER: an integrated energy-driven approach for task graph scheduling on distributed embedded systems}, booktitle = {Application-Specific Systems, Architecture Processors, 2005. ASAP 2005. 16th IEEE International Conference on}, year = {2005}, month = {2005/07//}, pages = {191 - 197}, abstract = {For multiprocessor embedded systems, the dynamic voltage scaling (DVS) technique can be applied to scheduled applications for energy reduction. DVS utilizes slack in the schedule to slow down processes and save energy. Therefore, it is generally believed that the maximal energy saving is achieved on a schedule with the minimum makespan (maximal slack). Most current approaches treat task assignment, scheduling, and DVS separately. In this paper, we present a framework called CASPER (combined assignment, scheduling, and power-management) that challenges this common belief by integrating task scheduling and DVS under a single iterative optimization loop via genetic algorithm. We have conducted extensive experiments to validate the energy efficiency of CASPER. For homogeneous multiprocessor systems (in which all processors are of the same type), we consider a recently proposed slack distribution algorithm (PDP-SPM) by S. Hua and G. Qu (2005): applying PDP-SPM on the schedule with the minimal makespan gives an average of 53.8\% energy saving; CASPER finds schedules with slightly larger makespan but a 57.3\% energy saving, a 7.8\% improvement. For heterogeneous systems, we consider the power variation DVS (PV-DVS) algorithm by Schmitz et al. (2004), CASPER improves its energy efficiency by 8.2\%. Finally, our results also show that the proposed single loop CASPER framework saves 23.3\% more energy over GMA+EE-GLSA by Schmitz et al. (2002), the only other known integrated approach with a nested loop that combines scheduling and power management in the inner loop but leaves assignment in the outer loop.}, keywords = {CASPER, combined-assignment-scheduling-and-power-management, computational complexity, distributed system, dynamic voltage scaling, embedded systems, energy reduction, genetic algorithm, Genetic algorithms, graph theory, homogeneous multiprocessor system, maximal energy saving, Multiprocessing systems, multiprocessor embedded system, optimization loop, power management, power variation, Processor scheduling, slack distribution algorithm, task assignment, task graph scheduling}, doi = {10.1109/ASAP.2005.23}, author = {Kianzad,V. and Bhattacharyya, Shuvra S. and Gang Qu} } @conference {14777, title = {Combining self-reported and automatic data to improve programming effort measurement}, booktitle = {Proceedings of the 10th European software engineering conference held jointly with 13th ACM SIGSOFT international symposium on Foundations of software engineering}, series = {ESEC/FSE-13}, year = {2005}, month = {2005///}, pages = {356 - 365}, publisher = {ACM}, organization = {ACM}, address = {Lisbon, Portugal}, abstract = {Measuring effort accurately and consistently across subjects in a programming experiment can be a surprisingly difficult task. In particular, measures based on self-reported data may differ significantly from measures based on data which is recorded automatically from a subject{\textquoteright}s computing environment. Since self-reports can be unreliable, and not all activities can be captured automatically, a complete measure of programming effort should incorporate both classes of data. In this paper, we show how self-reported and automatic effort can be combined to perform validation and to measure total programming effort.}, keywords = {effort, experimentation, human factors, manual approaches, measurement, process metrics, verification}, isbn = {1-59593-014-0}, doi = {10.1145/1081706.1081762}, author = {Hochstein, Lorin and Basili, Victor R. and Zelkowitz, Marvin V and Hollingsworth, Jeffrey K and Carver, Jeff} } @article {14078, title = {Comparative Genomics of Trypanosomatid Parasitic Protozoa}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {404 - 409}, abstract = {A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that{\textemdash}along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions{\textemdash}have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.}, doi = {10.1126/science.1112181}, url = {http://www.sciencemag.org/content/309/5733/404.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Blandin,Ga{\"e}lle and Berriman,Matthew and Crabtree,Jonathan and Aggarwal,Gautam and Caler,Elisabet and Renauld,Hubert and Worthey,Elizabeth A. and Hertz-Fowler,Christiane and Ghedin,Elodie and Peacock,Christopher and Bartholomeu,Daniella C. and Haas,Brian J. and Tran,Anh-Nhi and Wortman,Jennifer R. and Alsmark,U. Cecilia M. and Angiuoli,Samuel and Anupama,Atashi and Badger,Jonathan and Bringaud,Frederic and Cadag,Eithon and Carlton,Jane M. and Cerqueira,Gustavo C. and Creasy,Todd and Delcher,Arthur L. and Djikeng,Appolinaire and Embley,T. Martin and Hauser,Christopher and Ivens,Alasdair C. and Kummerfeld,Sarah K. and Pereira-Leal,Jose B. and Nilsson,Daniel and Peterson,Jeremy and Salzberg,Steven L. and Shallom,Joshua and Silva,Joana C. and Sundaram,Jaideep and Westenberger,Scott and White,Owen and Melville,Sara E. and Donelson,John E. and Andersson,Bj{\"o}rn and Stuart,Kenneth D. and Hall,Neil} } @conference {12370, title = {Computer vision on FPGAs: Design methodology and its application to gesture recognition}, booktitle = {Computer Vision and Pattern Recognition-Workshops, 2005. CVPR Workshops. IEEE Computer Society Conference on}, year = {2005}, month = {2005///}, pages = {133 - 133}, author = {Sen,M. and Corretjer,I. and Haim,F. and Saha,S. and Bhattacharyya, Shuvra S. and Schlessman,J. and Wolf,W.} } @article {17030, title = {Content Index to Volume 18}, journal = {INTERNATIONAL JOURNAL OF HUMAN{\textendash}COMPUTER INTERACTION}, volume = {18}, year = {2005}, month = {2005///}, pages = {367 - 368}, author = {Kuniavsky,M. and Vaughan,M. and Bederson, Benjamin B. and Shneiderman, Ben and Rau,P.L.P. and from Menus,T. and Lane,D.M. and Napier,H.A. and Peres,S.C. and S{\'a}ndor,A.} } @conference {18496, title = {Correctness properties for Internet routing}, booktitle = {Allerton Conference on Communication, Control, and Computing}, year = {2005}, month = {2005///}, abstract = {This paper motivates and presents a correctness specifi-cation for Internet routing. This specification is based on three properties{\textemdash}route validity, path visibility, and safety. This specification may be of use to people de- veloping tools to check routing configurations, to people designing solutions to specific problems in the current sys- tem, and to designers of new protocols and routing archi- tectures, all of whom can benefit from knowing what it means for Internet routing to be {\textquotedblleft}correct{\textquotedblright}. }, author = {Feamster, Nick and Balakrishnan,H.} } @article {15738, title = {Criteria for exact qudit universality}, journal = {Physical Review APhys. Rev. A}, volume = {71}, year = {2005}, month = {2005/05/16/}, pages = {052318 - 052318}, abstract = {We describe criteria for implementation of quantum computation in qudits. A qudit is a d-dimensional system whose Hilbert space is spanned by states |0⟩, |1⟩, {\textellipsis}, |d-1⟩. An important earlier work [ A. Muthukrishnan and C.R. Stroud, Jr. Phys. Rev. A 62 052309 (2000)] describes how to exactly simulate an arbitrary unitary on multiple qudits using a 2d-1 parameter family of single qudit and two qudit gates. That technique is based on the spectral decomposition of unitaries. Here we generalize this argument to show that exact universality follows given a discrete set of single qudit Hamiltonians and one two-qudit Hamiltonian. The technique is related to the QR-matrix decomposition of numerical linear algebra. We consider a generic physical system in which the single qudit Hamiltonians are a small collection of Hjkx=ℏΩ(|k⟩⟨j|+|j⟩⟨k|) and Hjky=ℏΩ(i|k⟩⟨j|-i|j⟩⟨k|). A coupling graph results taking nodes 0, {\textellipsis}, d-1 and edges j<->k iff Hjkx,y are allowed Hamiltonians. One qudit exact universality follows iff this graph is connected, and complete universality results if the two-qudit Hamiltonian H=ℏΩ|d-1,d-1⟩⟨d-1,d-1| is also allowed. We discuss implementation in the eight dimensional ground electronic states of 87Rb and construct an optimal gate sequence using Raman laser pulses.}, doi = {10.1103/PhysRevA.71.052318}, url = {http://link.aps.org/doi/10.1103/PhysRevA.71.052318}, author = {Brennen,Gavin K. and O{\textquoteright}Leary,Dianne P. and Bullock,Stephen S.} } @conference {17853, title = {Data Redistribution and Remote Method Invocation in Parallel Component Architectures}, booktitle = {Parallel and Distributed Processing Symposium, International}, volume = {1}, year = {2005}, month = {2005///}, pages = {40b - 40b}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {With the increasing availability of high-performance massively parallel computer systems, the prevalence of sophisticated scientific simulation has grown rapidly. The complexity of the scientific models being simulated has also evolved, leading to a variety of coupled multi-physics simulation codes. Such cooperating parallel programs require fundamentally new interaction capabilities, to efficiently exchange parallel data structures and collectively invoke methods across programs. So-called "M?N" research, as part of the Common Component Architecture (CCA) effort, addresses these special and challenging needs, to provide generalized interfaces and tools that support flexible parallel data redistribution and parallel remote method invocation. Using this technology, distinct simulation codes with disparate distributed data decompositions can work together to achieve greater scientific discoveries.}, doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2005.159}, author = {Bertrand,Felipe and Bramley,Randall and Sussman, Alan and Bernholdt,David E. and Kohl,James A. and Larson,Jay W. and Damevski,Kostadin B.} } @conference {18561, title = {Detecting BGP configuration faults with static analysis}, booktitle = {Proceedings of the 2nd conference on Symposium on Networked Systems Design \& Implementation - Volume 2}, series = {NSDI{\textquoteright}05}, year = {2005}, month = {2005///}, pages = {43 - 56}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {The Internet is composed of many independent autonomous systems (ASes) that exchange reachability information to destinations using the Border Gateway Protocol (BGP). Network operators in each AS configure BGP routers to control the routes that are learned, selected, and announced to other routers. Faults in BGP configuration can cause forwarding loops, packet loss, and unintended paths between hosts, each of which constitutes a failure of the Internet routing infrastructure. This paper describes the design and implementation of rcc, the router configuration checker, a tool that finds faults in BGP configurations using static analysis. rcc detects faults by checking constraints that are based on a high-level correctness specification. rcc detects two broad classes of faults: route validity faults, where routers may learn routes that do not correspond to usable paths, and path visibility faults, where routers may fail to learn routes for paths that exist in the network. rcc enables network operators to test and debug configurations before deploying them in an operational network, improving on the status quo where most faults are detected only during operation. rcc has been downloaded by more than sixty-five network operators to date, some of whom have shared their configurations with us. We analyze network-wide configurations from 17 different ASes to detect a wide variety of faults and use these findings to motivate improvements to the Internet routing infrastructure.}, url = {http://dl.acm.org/citation.cfm?id=1251203.1251207}, author = {Feamster, Nick and Balakrishnan,Hari} } @article {17079, title = {Determining Causes and Severity of End-User Frustration (2002)}, year = {2005}, month = {2005///}, abstract = {While computers are beneficial to individuals and society, frequently, users encounter frustrating experiences when using computers. This study attempts to measure, through 111 participants, the frequency, cause, and the level of severity of frustrating experiences. The data showed that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47-53\% of time spent on a computer depending on the location and study method. After discarding extreme cases the time lost was still above 38\%. These disturbing results should be a basis for future study.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6493}, author = {Ceaparu,Irina and Lazar,Jonathan and Bessiere,Katie and Robinson,John and Shneiderman, Ben} } @conference {12279, title = {Differentiated traffic engineering for QoS provisioning}, booktitle = {INFOCOM 2005. 24th Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings IEEE}, volume = {4}, year = {2005}, month = {2005/03//}, pages = {2349 - 2359 vol. 4 - 2349 - 2359 vol. 4}, abstract = {We introduce a new approach for QoS provisioning in packet networks based on the notion of differentiated traffic engineering (DTE). We consider a single AS network capable of source based multi-path routing. We do not require sophisticated queuing or per-class scheduling at individual routers; instead, if a link is used to forward QoS sensitive packets, we maintain its utilization below a threshold. As a consequence, DTE eliminates the need for per-flow (IntServ) or per-class (DiffServ) packet processing tasks such as traffic classification, queueing, shaping, policing and scheduling in the core and hence poses a lower burden on the network management unit. Conversely, DTE utilizes network bandwidth much more efficiently than simple over-provisioning. In this paper, we propose a complete architecture and an algorithmic structure for DTE. We show that our scheme can be formulated as a non-convex optimization problem, and we present an optimal solution framework based on simulated annealing. We present a simulation-based performance evaluation of DTE, and compare our scheme to existing (gradient projection) methods.}, keywords = {based, Computer, differentiated, DiffServ, DTE;, engineering;, evaluation;, link;, links;, management;, multipath, network, networks;, nonconvex, of, optimisation;, OPTIMIZATION, packet, performance, problem;, provisioning;, QoS, QUALITY, routing;, service;, simulation-based, source, Telecommunication, traffic, traffic;}, doi = {10.1109/INFCOM.2005.1498521}, author = {Tabatabaee,V. and Bhattacharjee, Bobby and La,R.J. and Shayman,M.A.} } @conference {12342, title = {DSP address optimization using evolutionary algorithms}, booktitle = {Proceedings of the 2005 workshop on Software and compilers for embedded systems}, year = {2005}, month = {2005///}, pages = {91 - 98}, author = {Leventhal,S. and Yuan,L. and Bambha,N. K and Bhattacharyya, Shuvra S. and Qu,G.} } @conference {12334, title = {Dynamic configuration of dataflow graph topology for DSP system design}, booktitle = {Proc. of the Int. Conf. on Acoustics, Speech, and Signal Processing}, year = {2005}, month = {2005///}, pages = {69 - 72}, author = {Ko,D. I and Bhattacharyya, Shuvra S.} } @article {17114, title = {Dynamic Querying for Pattern Identification in Microarray and Genomic Data (2003)}, year = {2005}, month = {2005///}, abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool TimeSearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. TimeSearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. TimeSearcher can be used to search these data sets for candidate splicing signals.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6503}, author = {Hochheiser,Harry and Baehrecke,Eric H and Mount, Stephen M. and Shneiderman, Ben} } @conference {12283, title = {Efficient geographic routing in multihop wireless networks}, booktitle = {Proceedings of the 6th ACM international symposium on Mobile ad hoc networking and computing}, series = {MobiHoc {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {230 - 241}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose a new link metric called normalized advance (NADV) for geographic routing in multihop wireless networks. NADV selects neighbors with the optimal trade-off between proximity and link cost. Coupled with the local next hop decision in geographic routing, NADV enables an adaptive and efficient cost-aware routing strategy. Depending on the objective or message priority, applications can use the NADV framework to minimize various types of link cost.We present efficient methods for link cost estimation and perform detailed simulations in diverse scenarios. Our results show that NADV outperforms current schemes in many aspects: for example, in high noise environments with frequent packet losses, the use of NADV leads to 81\% higher delivery ratio. When compared to centralized routing under certain settings, geographic routing using NADV finds paths whose cost is close to the optimum.}, keywords = {Geographic routing, Link cost estimation, Routing metric, Wireless multihop networks}, isbn = {1-59593-004-3}, doi = {10.1145/1062689.1062720}, url = {http://doi.acm.org/10.1145/1062689.1062720}, author = {Lee,Seungjoon and Bhattacharjee, Bobby and Banerjee,Suman} } @conference {12282, title = {Efficient lookup on unstructured topologies}, booktitle = {Proceedings of the twenty-fourth annual ACM symposium on Principles of distributed computing}, series = {PODC {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {77 - 86}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present LMS, a protocol for efficient lookup on unstructured networks. Our protocol uses a virtual namespace without imposing specific topologies. It is more efficient than existing lookup protocols for unstructured networks, and thus is an attractive alternative for applications in which the topology cannot be structured as a Distributed Hash Table (DHT).We present analytic bounds for the worst-case performance of our protocol. Through detailed simulations (with up to 100,000 nodes), we show that the actual performance on realistic topologies is significantly better. We also show in both simulations and a complete implementation (which includes over five hundred nodes) that our protocol is inherently robust against multiple node failures and can adapt its replication strategy to optimize searches according to a specific heuristic. Moreover, the simulation demonstrates the resilience of LMS to high node turnover rates, and that it can easily adapt to orders of magnitude changes in network size. The overhead incurred by LMS is small, and its performance approaches that of DHTs on networks of similar size.}, keywords = {distributed algorithms, lookup protocols, peer-to-peer networks, random walks}, isbn = {1-58113-994-2}, doi = {10.1145/1073814.1073828}, url = {http://doi.acm.org/10.1145/1073814.1073828}, author = {Morselli,Ruggero and Bhattacharjee, Bobby and Srinivasan, Aravind and Marsh,Michael A} } @article {17592, title = {Efficient strategies for channel management in wireless lans}, journal = {UMD, CS Tech. Rep. CS-TR}, volume = {4729}, year = {2005}, month = {2005///}, abstract = {We define efficient algorithms for channel management (channelassignment and load balancing among APs) in 802.11-based WLANs that lead to better usage of the wireless spectrum. These algorithms (called CFAssign) are based on a {\textquotedblleft}conflict-free set coloring{\textquotedblright} for- mulation that jointly perform load balancing along with channel assignment. Such a formulation has a number of advantages. First, it explicitly captures interference effects at clients. Next, it intrinsi- cally exposes opportunities for better channel re-use. Finally, algo- rithms based on this formulation do not depend on specific physical RF models and hence can be applied efficiently to a wide-range of in-building as well as outdoor scenarios. We have performed extensive packet-level simulations and mea- surements on a deployed wireless testbed of 70 APs to validate the performance of our proposed algorithms. We show that in ad- dition to single network scenarios, CFAssign algorithms are well suited for channel assignment in scenarios where multiple wireless networks share the same physical space and contend for the same frequency spectrum. Our results over a wide range of scenarios indicate that CFAssign reduces the interference at clients by about 50-70\% in comparison to current best-known techniques. }, author = {Mishra,A. and Brik,V. and Banerjee,S. and Srinivasan, Aravind and Arbaugh, William A.} } @article {18545, title = {An empirical study of "bogon" route advertisements}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {35}, year = {2005}, month = {2005/01//}, pages = {63 - 70}, abstract = {An important factor in the robustness of the interdomain routing system is whether the routers in autonomous systems (ASes) filter routes for "bogon" address space---i.e., private address space and address space that has not been allocated by the Internet Assigned Numbers Authority (IANA). This paper presents an empirical study of bogon route announcements, as observed at eight vantage points on the Internet. On average, we observe several bogon routes leaked every few days; a small number of ASes also temporarily leak hundreds of bogon routes. About 40\% of these bogon routes are not withdrawn for at least a day. We observed 110 different ASes originating routes for bogon prefixes and a few ASes that were responsible for advertising a disproportionate number of these routes. We also find that some ASes that do filter unallocated prefixes continue to filter them for as long as five months after they have been allocated, mistakenly filtering valid routes. Both of these types of delinquencies have serious implications: the failure to filter valid prefixes can could make nefarious activities such as denial of service attacks difficult to trace; failure to update filters when new prefixes are allocated prevents legitimate routes from being globally visible.}, keywords = {anomalies, BGP, bogon prefixes}, isbn = {0146-4833}, doi = {10.1145/1052812.1052826}, url = {http://doi.acm.org/10.1145/1052812.1052826}, author = {Feamster, Nick and Jung,Jaeyeon and Balakrishnan,Hari} } @article {14503, title = {Entity resolution in graph data}, year = {2005}, month = {2005///}, institution = {Technical report, University of Maryland, College Park}, abstract = {The goal of entity resolution is to reconcile data references corresponding to the same realworld entity. Here we introduce the problem of entity resolution in graphs, where the nodes are the references in the data and the hyper-edges represent the relations that are observed to hold between the references. The goal then is to reconstruct a {\textquoteright}cleaned{\textquoteright} entity graph that captures the relations among the true underlying entities from the reference graph. This is an important first step in any graph mining process; mining an unresolved graph will be inefficient and result in inaccurate conclusions. We also motivate collective entity resolution in graphs where references sharing hyper-edges are resolved jointly, as opposed to independent pair-wise resolution of the references. We illustrate the problem of graph-based entity resolution in bibliographic datasets. We discuss several interesting issues such as mul- tiple entity types, local and global resolution and different kinds of graph-based evidence. We formulate the graph-based entity resolution problem as an unsupervised clustering task, where each cluster represents references that map to the same entity, and the similarity measure between two clusters incorporates the similarity of the references attributes and, more interestingly, the similarity between their relations. We explore two different measures of relational similarity. One approach, which we call {\textquoteright}edge detail similarity{\textquoteright}, explicitly com- pares the individual edges that each cluster participates in, but is expensive to compute. A less computationally intensive alternative is measuring {\textquoteright}neighborhood similarity{\textquoteright}, which only compares the multi-set of neighboring clusters for each cluster. We perform an extensive empirical evaluation of the two relational similarity measures for author resolution using co- author relations in two real bibliographic datasets. We show that both similarity measures improve performance over unsupervised algorithms that consider only reference attributes. We also describe an efficient implementation and show that these algorithms scale gracefully with increasing size of the data. }, author = {Bhattacharya,I. and Getoor, Lise} } @article {17135, title = {Envisioning help resources for the future information ecology: Toward an enriched sense of help}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {42}, year = {2005}, month = {2005/01/01/}, pages = {n/a-n/a - n/a-n/a}, isbn = {1550-8390}, doi = {10.1002/meet.14504201123}, url = {http://onlinelibrary.wiley.com/doi/10.1002/meet.14504201123/abstract}, author = {Haas,Stephanie W and Brown,Laurie and Denn,Sheila and Locke,David and Shneiderman, Ben} } @article {15441, title = {An evolutionary testbed for software technology evaluation}, journal = {Innovations in Systems and Software Engineering}, volume = {1}, year = {2005}, month = {2005///}, pages = {3 - 11}, abstract = {Empirical evidence and technology evaluation are needed to close the gap between the state of the art and the state of the practice in software engineering. However, there are difficulties associated with evaluating technologies based on empirical evidence: insufficient specification of context variables, cost of experimentation, and risks associated with trying out new technologies. In this paper, we propose the idea of an evolutionary testbed for addressing these problems. We demonstrate the utility of the testbed in empirical studies involving two different research technologies applied to the testbed, as well as the results of these studies. The work is part of NASArsquos High Dependability Computing Project (HDCP), in which we are evaluating a wide range of new technologies for improving the dependability of NASA mission-critical systems.}, doi = {10.1007/s11334-005-0007-z}, author = {Lindvall,M. and Rus,I. and Shull, F. and Zelkowitz, Marvin V and Donzelli,P. and Memon, Atif M. and Basili, Victor R. and Costa,P. and Tvedt,R. and Hochstein, L.} } @inbook {12132, title = {Evolving and packaging reading technologies}, booktitle = {Foundations of Empirical Software Engineering: The Legacy of Victor R. BasiliFoundations of Empirical Software Engineering: The Legacy of Victor R. Basili}, volume = {1}, year = {2005}, month = {2005///}, pages = {362 - 362}, publisher = {Springer}, organization = {Springer}, isbn = {9783540245476}, author = {Basili, Victor R.} } @article {16389, title = {EvoSTOC Contributions}, journal = {Applications of evolutionary computing: EvoWorkshops 2005, EvoBIO, EvoCOMNET, EvoHOT, EvoIASP, EvoMUSART, and EvoSTOC}, year = {2005}, month = {2005///}, author = {Merkle,D. and Middendorf,M. and Scheidler,A. and Avigad,G. and Moshaiov,A. and Brauner,N. and Parsopoulos,K.E. and Vrahatis,M.N. and Rand, William and Riolo,R} } @conference {12071, title = {Exploiting partially overlapping channels in wireless networks: Turning a peril into an advantage}, booktitle = {Proceedings of the 5th ACM SIGCOMM conference on Internet Measurement}, year = {2005}, month = {2005///}, pages = {29 - 29}, author = {Mishra,A. and Rozner,E. and Banerjee,S. and Arbaugh, William A.} } @inbook {12678, title = {Fusing Depth and Video Using Rao-Blackwellized Particle Filter}, booktitle = {Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence}, series = {Lecture Notes in Computer Science}, volume = {3776}, year = {2005}, month = {2005///}, pages = {521 - 526}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We address the problem of fusing sparse and noisy depth data obtained from a range finder with features obtained from intensity images to estimate ego-motion and refine 3D structure of a scene using a Rao-Blackwellized particle filter. For scenes with low depth variability, the algorithm shows an alternate way of performing Structure from Motion (SfM) starting with a flat depth map. Instead of using 3D depths, we formulate the problem using 2D image domain parallax and show that conditioned on non-linear motion parameters, the parallax magnitude with respect to the projection of the vanishing point forms a linear subsystem independent of camera motion and their distributions can be analytically integrated. Thus, the structure is obtained by estimating parallax with respect to the given depths using a Kalman filter and only the ego-motion is estimated using a particle filter. Hence, the required number of particles becomes independent of the number of feature points which is an improvement over previous algorithms. Experimental results on both synthetic and real data show the effectiveness of our approach.}, isbn = {978-3-540-30506-4}, url = {http://dx.doi.org/10.1007/11590316_82}, author = {Agrawal,Amit and Chellapa, Rama}, editor = {Pal,Sankar and Bandyopadhyay,Sanghamitra and Biswas,Sambhunath} } @conference {18394, title = {Generating testable hypotheses from tacit knowledge for high productivity computing}, booktitle = {Proceedings of the second international workshop on Software engineering for high performance computing system applications}, series = {SE-HPCS {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {17 - 21}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this research, we are developing our understanding of how the high performance computing community develops effective parallel implementations of programs by collecting the folklore within the community. We use this folklore as the basis for a series of experiments, which we expect, will validate or negate these assumptions.}, keywords = {folklore elicitation, high productivity development time experimental studies, hypothesis generation, tacit knowledge solicitation, testable hypotheses}, isbn = {1-59593-117-1}, doi = {10.1145/1145319.1145325}, url = {http://doi.acm.org/10.1145/1145319.1145325}, author = {Asgari, Sima and Hochstein, Lorin and Basili, Victor R. and Zelkowitz, Marvin V and Hollingsworth, Jeffrey K and Carver, Jeff and Shull, Forrest} } @article {14076, title = {The genetic map and comparative analysis with the physical map of Trypanosoma brucei}, journal = {Nucleic acids research}, volume = {33}, year = {2005}, month = {2005///}, pages = {6688 - 6688}, author = {MacLeod,A. and Tweedie,A. and McLellan,S. and Taylor,S. and Hall,N. and Berriman,M. and El-Sayed, Najib M. and Hope,M. and Turner,C. M.R and Tait,A.} } @article {14092, title = {The genome of the African trypanosome Trypanosoma brucei}, journal = {Science}, volume = {309}, year = {2005}, month = {2005///}, pages = {416 - 416}, author = {Berriman,M. and Ghedin,E. and Hertz-Fowler,C. and Blandin,G. and Renauld,H. and Bartholomeu,D. C and Lennard,N. J and Caler,E. and Hamlin,N. E and Haas,B. and others} } @article {19077, title = {The genome of the protist parasite Entamoeba histolytica}, journal = {Nature}, volume = {433}, year = {2005}, month = {2005}, pages = {865 - 868}, author = {Loftus,B. and Anderson,I. and Davies,R. and Alsmark,U. C.M and Samuelson,J. and Amedeo,P. and Roncaglia,P. and Berriman,M. and Hirt,R. P and Mann,B. J and others} } @article {16291, title = {The Genome Sequence of Trypanosoma Cruzi, Etiologic Agent of Chagas Disease}, journal = {ScienceScience}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {19073, title = {The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease}, journal = {Science}, volume = {309}, year = {2005}, month = {2005}, author = {El-Sayed, N.M. and Myler,P. J and Bartholomeu,D. C and Nilsson,D. and Aggarwal,G. and Tran,A. N and Ghedin,E. and Worthey,E. A and Delcher,A. L and Blandin,G. and others} } @article {14071, title = {The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {14616, title = {Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription}, journal = {Journal of VirologyJ. Virol.}, volume = {79}, year = {2005}, month = {2005/06/01/}, pages = {6610 - 6619}, abstract = {We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.}, isbn = {0022-538X, 1098-5514}, doi = {10.1128/JVI.79.11.6610-6619.2005}, url = {http://jvi.asm.org/content/79/11/6610}, author = {Lewinski,M. K and Bisgrove,D. and Shinn,P. and Chen,H. and Hoffmann,C. and Hannenhalli, Sridhar and Verdin,E. and Berry,C. C and Ecker,J. R and Bushman,F. D} } @article {14566, title = {Genome-wide analysis of retroviral DNA integration}, journal = {Nat Rev MicroNat Rev Micro}, volume = {3}, year = {2005}, month = {2005/11//}, pages = {848 - 858}, isbn = {1740-1526}, doi = {10.1038/nrmicro1263}, url = {http://dx.doi.org/10.1038/nrmicro1263}, author = {Bushman,Frederic and Lewinski,Mary and Ciuffi,Angela and Barr,Stephen and Leipzig,Jeremy and Hannenhalli, Sridhar and Hoffmann,Christian} } @conference {18571, title = {Geographic locality of IP prefixes}, booktitle = {Proceedings of the 5th ACM SIGCOMM conference on Internet Measurement}, series = {IMC {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {13 - 13}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Information about the geographic locality of IP prefixes can be useful for understanding the issues related to IP address allocation, aggregation, and BGP routing table growth. In this paper, we use traceroute data and geographic mappings of IP addresses to study the geographic properties of IP prefixes and their implications on Internet routing. We find that (1) IP prefixes may be too coarse-grained for expressing routing policies, (2) address allocation policies and the granularity of routing contribute significantly to routing table size, and (3) not considering the geographic diversity of contiguous prefixes may result in overestimating the opportunities for aggregation in the BGP routing table.}, url = {http://dl.acm.org/citation.cfm?id=1251086.1251099}, author = {Freedman,Michael J. and Vutukuru,Mythili and Feamster, Nick and Balakrishnan,Hari} } @article {17187, title = {Help! I{\textquoteright}m Lost: User Frustration in Web Navigation (2003)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Computers can be valuable tools, and networked resources via the Internet can be beneficial to many different populations and communities. Unfortunately, when people are unable to reach their task goals due to frustrating experiences, this can hinder the effectiveness of technology. This research summary provides information about the user frustration research that has been performed at the University of Maryland and Towson University. Causes of user frustration are discussed in this research summary, along with the surprising finding that nearly one-third to one-half of the time spent in front of the computer is wasted due to frustrating experiences. Furthermore, when interfaces are planned to be deceptive and confusing, this}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6508}, author = {Lazar,Jonathan and Bessiere,Katie and Ceaparu,Irina and Robinson,John and Shneiderman, Ben} } @article {13927, title = {How do I find blue books about dogs? The errors and frustrations of young digital library users}, journal = {Proceedings of HCII 2005}, year = {2005}, month = {2005///}, author = {Hutchinson,H. and Druin, Allison and Bederson, Benjamin B. and Reuter,K. and Rose,A. and Weeks,A. C} } @conference {11897, title = {Identifying and segmenting human-motion for mobile robot navigation using alignment errors}, booktitle = {12th International Conference on Advanced Robotics, 2005. ICAR {\textquoteright}05. Proceedings}, year = {2005}, month = {2005/07//}, pages = {398 - 403}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a new human-motion identification and segmentation algorithm, for mobile robot platforms. The algorithm is based on computing the alignment error between pairs of object images acquired from a moving platform. Pairs of images generating relatively small alignment errors are used to estimate the fundamental frequency of the object{\textquoteright}s motion. A decision criterion is then used to test the significance of the estimated frequency and to classify the object{\textquoteright}s motion. To verify the validity of the proposed approach, experimental results are shown on different classes of objects}, keywords = {Computer errors, Educational institutions, Frequency estimation, human-motion identification, human-motion segmentation, HUMANS, Image motion analysis, Image segmentation, mobile robot navigation, Mobile robots, Motion estimation, Navigation, Object detection, robot vision, SHAPE}, isbn = {0-7803-9178-0}, doi = {10.1109/ICAR.2005.1507441}, author = {Abd-Almageed, Wael and Burns,B. J and Davis, Larry S.} } @inbook {12677, title = {Image Sequence Stabilization, Mosaicking, and Superresolution}, booktitle = {Handbook of Image and Video Processing (Second Edition)Handbook of Image and Video Processing (Second Edition)}, year = {2005}, month = {2005///}, pages = {309-VII - 309-VII}, publisher = {Academic Press}, organization = {Academic Press}, address = {Burlington}, abstract = {A sequence of temporal images gathered from a single sensor adds a whole new dimension to two-dimensional (2D) image data. Availability of an image sequence permits the measurement of quantities such as subpixel intensities, camera motion and depth, and detection and tracking of moving objects. In turn, the processing of image sequences necessitates the development of sophisticated techniques to extract this information. With the recent availability of powerful yet inexpensive computers, data storage systems, and image acquisition devices, image sequence analysis has transitioned from an esoteric research domain to a practical area with significant commercial interest.}, isbn = {978-0-12-119792-6}, url = {http://www.sciencedirect.com/science/article/pii/B9780121197926500826}, author = {Chellapa, Rama and Srinivasan, S. and Aggarwal,G. and Veeraraghavan,A.}, editor = {Al Bovik} } @conference {18575, title = {Implications of autonomy for the expressiveness of policy routing}, booktitle = {Proceedings of the 2005 conference on Applications, technologies, architectures, and protocols for computer communications}, series = {SIGCOMM {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {25 - 36}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Thousands of competing autonomous systems must cooperate with each other to provide global Internet connectivity. Each autonomous system (AS) encodes various economic, business, and performance decisions in its routing policy. The current interdomain routing system enables each AS to express policy using rankings that determine how each router inthe AS chooses among different routes to a destination, and filters that determine which routes are hidden from each neighboring AS. Because the Internet is composed of many independent, competing networks, the interdomain routing system should provide autonomy, allowing network operators to set their rankings independently, and to have no constraints on allowed filters. This paper studies routing protocol stability under these conditions. We first demonstrate that certain rankings that are commonly used in practice may not ensure routing stability. We then prove that, when providers can set rankings and filters autonomously, guaranteeing that the routing system will converge to a stable path assignment essentially requires ASes to rank routes based on AS-path lengths. We discuss the implications of these results for the future of interdomain routing.}, keywords = {autonomy, BGP, Internet, policy, protocol, Routing, Safety, stability}, isbn = {1-59593-009-4}, doi = {10.1145/1080091.1080096}, url = {http://doi.acm.org/10.1145/1080091.1080096}, author = {Feamster, Nick and Johari,Ramesh and Balakrishnan,Hari} } @article {15180, title = {Improved efficiency for CCA-secure cryptosystems built using identity-based encryption}, journal = {Topics in Cryptology{\textendash}CT-RSA 2005}, year = {2005}, month = {2005///}, pages = {87 - 103}, abstract = {Recently, Canetti, Halevi, and Katz showed a general method for constructing CCA-secure encryption schemes from identity-based encryption schemes in the standard model. We improve the efficiency of their construction, and show two specific instantiations of our resulting scheme which offer the most efficient encryption (and, in one case, key generation) of any CCA-secure encryption scheme to date.}, doi = {10.1007/978-3-540-30574-3_8}, author = {Boneh,D. and Katz, Jonathan} } @article {17247, title = {Interactive Color Mosaic and Dendogram Displays for Signal/Noise Optimization in Microarray Data Analysis (2003)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Data analysis and visualization is strongly influenced by noise and noise filters. There are multiple sources of oisein microarray data analysis, but signal/noise ratios are rarely optimized, or even considered. Here, we report a noise analysis of a novel 13 million oligonucleotide dataset - 25 human U133A (~500,000 features) profiles of patient muscle biposies. We use our recently described interactive visualization tool, the Hierarchical Clustering Explorer (HCE) to systemically address the effect of different noise filters on resolution of arrays into orrectbiological groups (unsupervised clustering into three patient groups of known diagnosis). We varied probe set interpretation methods (MAS 5.0, RMA), resent callfilters, and clustering linkage methods, and investigated the results in HCE. HCE interactive features enabled us to quickly see the impact of these three variables. Dendrogram displays showed the clustering results systematically, and color mosaic displays provided a visual support for the results. We show that each of these three variables has a strong effect on unsupervised clustering. For this dataset, the strength of the biological variable was maximized, and noise minimized, using MAS 5.0, 10\% present call filter, and Average Group Linkage. We propose a general method of using interactive tools to identify the optimal signal/noise balance or the optimal combination of these three variables to maximize the effect of the desired biological variable on data interpretation.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6506}, author = {Seo,Jinwook and Bakay,Marina and Zhao,Po and Chen,Yi-Wen and Clarkson,Priscilla and Shneiderman, Ben and Hoffman,Eric P} } @article {17255, title = {Interactive pattern search in time series}, journal = {Proceedings of SPIE}, volume = {5669}, year = {2005}, month = {2005/03/11/}, pages = {175 - 186}, abstract = {The need for pattern discovery in long time series data led researchers to develop algorithms for similarity search. Most of the literature about time series focuses on algorithms that index time series and bring the data into the main storage, thus providing fast information retrieval on large time series. This paper reviews the state of the art in visualizing time series, and focuses on techniques that enable users to visually and interactively query time series. Then, it presents TimeSearcher 2, a tool that enables users to explore multidimensional data using synchronized tables and graphs with overview+detail, filter the time series data to reduce the scope of the search, select an existing pattern to find similar occurrences, and interactively adjust similarity parameters to narrow the result set. This tool is an extension of previous work, TimeSearcher 1, which uses graphical timeboxes to interactively query time series data.}, isbn = {0277786X}, doi = {doi:10.1117/12.587537}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/5669/1/175_1?isAuthorized=no}, author = {Buono,Paolo and Aris,Aleks and Plaisant, Catherine and Khella,Amir and Shneiderman, Ben} } @article {17256, title = {Interactive Pattern Search in Time Series (2004)}, year = {2005}, month = {2005///}, abstract = {The need for pattern discovery in long time series data led researchers to develop algorithms for similarity search. Most of the literature about time series focuses on algorithms that index time series and bring the data into the main storage, thus providing fast information retrieval on large time series. This paper reviews the state of the art in visualizing time series, and focuses on techniques that enable users to interactively query time series. Then it presents TimeSearcher 2, a tool that enables users to explore multidimensional data using coordinated tables and graphs with overview+detail, filter the time series data to reduce the scope of the search, select an existing pattern to find similar occurrences, and interactively adjust similarity parameters to narrow the result set. This tool is an extension of previous work, TimeSearcher 1, which uses graphical timeboxes to interactively query time series data.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6519}, author = {Buono,Paolo and Aris,Aleks and Plaisant, Catherine and Khella,Amir and Shneiderman, Ben} } @conference {13920, title = {The International Children{\textquoteright}s Digital Library: A Case Study in Designing for a MultiLingual}, booktitle = {Multi-Cultural, Multi-Generational Audience. Information Technology and Libraries}, year = {2005}, month = {2005///}, author = {Hutchinson,H.B. and Rose,A. and Bederson, Benjamin B. and Weeks,A. C and Druin, Allison} } @inbook {12141, title = {Iterative enhancement: a practical technique for software development}, booktitle = {Foundations of Empirical Software Engineering: The Legacy of Victor R. BasiliFoundations of Empirical Software Engineering: The Legacy of Victor R. Basili}, volume = {1}, year = {2005}, month = {2005///}, pages = {28 - 28}, isbn = {9783540245476}, author = {Basili, Victor R. and Turner,A. J} } @article {12369, title = {Joint application mapping/interconnect synthesis techniques for embedded chip-scale multiprocessors}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {16}, year = {2005}, month = {2005///}, pages = {99 - 112}, author = {Bambha,N. K and Bhattacharyya, Shuvra S.} } @article {14918, title = {Lambertian reflectance and linear subspaces}, volume = {:~09/705,507}, year = {2005}, month = {2005/02/08/}, abstract = {A method for choosing an image from a plurality of three-dimensional models which is most similar to an input image is provided. The method includes the steps of: (a) providing a database of the plurality of three-dimensional models; (b) providing an input image; (c) positioning each three-dimensional model relative to the input image; (d) for each three-dimensional model, determining a rendered image that is most similar to the input image by: (d)(i) computing a linear subspace that describes an approximation to the set of all possible rendered images that each three-dimensional model can produce under all possible lighting conditions where each point in the linear subspace represents a possible image; and one of (d)(ii) finding the point on the linear subspace that is closest to the input image or finding a rendered image in a subset of the linear subspace obtained by projecting the set of images that are generated by positive lights onto the linear subspace; (e) computing a...}, url = {http://www.google.com/patents?id=6hEWAAAAEBAJ}, author = {Jacobs, David W. and Basri,Ronen}, editor = {NEC Laboratories America, Inc.} } @conference {11900, title = {A learning automata based power management for ad-hoc networks}, booktitle = {2005 IEEE International Conference on Systems, Man and Cybernetics}, volume = {4}, year = {2005}, month = {2005/10//}, pages = {3569- 3573 Vol. 4 - 3569- 3573 Vol. 4}, publisher = {IEEE}, organization = {IEEE}, abstract = {Power management is a very important aspect of ad-hoc networks. It directly impacts the network throughput among other network metrics. On the other hand, transmission power management may result in disconnected networks and increased level of collisions. In this paper, we introduce a transmission power control based on stochastic learning automata (SLA) to modify the transmission power. Based on the level of successful transmissions and the level of packet retransmissions, the SLA will modify the transmission power level either by increasing it or decreasing it. The probabilistic nature of SLA makes it a useful choice for ad-hoc networks. Using the network simulator NS, we show that using SLA for transmission power will result in an increased system bandwidth and a decrease in the collision levels.}, keywords = {ad hoc networks, ad-hoc networks, Computer network management, Computer networks, Energy management, Engineering management, learning automata, network metrics, network simulator, packet retransmissions, power control, power system management, power transmission control, stochastic learning automata, stochastic learning automta, Stochastic processes, system bandwidth, Technology management, Throughput, transmission power control, transmission power level, transmission power management}, isbn = {0-7803-9298-1}, doi = {10.1109/ICSMC.2005.1571701}, author = {El-Osery,A. I and Baird,D. and Abd-Almageed, Wael} } @conference {12192, title = {Maintaining concentration to achieve task completion}, booktitle = {Proceedings of the 2005 conference on Designing for User eXperience}, year = {2005}, month = {2005///}, pages = {9 - 9}, author = {Shneiderman, Ben and Bederson, Benjamin B.} } @conference {17284, title = {Maintaining concentration to achieve task completion}, booktitle = {Proceedings of the 2005 conference on Designing for User eXperience}, series = {DUX {\textquoteright}05}, year = {2005}, month = {2005///}, publisher = {AIGA: American Institute of Graphic Arts}, organization = {AIGA: American Institute of Graphic Arts}, address = {New York, NY, USA}, abstract = {When faced with a challenging goal, knowledge workers need to concentrate on their tasks so that they move forward toward completion. Since frustrations, distractions, and interruptions can interfere with their smooth progress, design strategies should enable users to maintain concentration. This paper promotes awareness of this issue, reviews related work, and suggests three initial strategies: Reduce short-term and working memory load, provide information abundant interfaces, and increase automaticity.}, keywords = {avoid interruption, calm, flow, focus, goal attainment, interface design, maintain concentration, situation awareness, task completion}, isbn = {1-59593-250-X}, url = {http://dl.acm.org/citation.cfm?id=1138235.1138246}, author = {Shneiderman, Ben and Bederson, Benjamin B.} } @article {19663, title = {MCMC-based particle filtering for tracking a variable number of interacting targets}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {27}, year = {2005}, month = {2005/11//}, pages = {1805 - 1819}, abstract = {We describe a particle filter that effectively deals with interacting targets, targets that are influenced by the proximity and/or behavior of other targets. The particle filter includes a Markov random field (MRF) motion prior that helps maintain the identity of targets throughout an interaction, significantly reducing tracker failures. We show that this MRF prior can be easily implemented by including an additional interaction factor in the importance weights of the particle filter. However, the computational requirements of the resulting multitarget filter render it unusable for large numbers of targets. Consequently, we replace the traditional importance sampling step in the particle filter with a novel Markov chain Monte Carlo (MCMC) sampling step to obtain a more efficient MCMC-based multitarget filter. We also show how to extend this MCMC-based filter to address a variable number of interacting targets. Finally, we present both qualitative and quantitative experimental results, demonstrating that the resulting particle filters deal efficiently and effectively with complicated target interactions.}, keywords = {algorithms, Animals, Artificial intelligence, Computer simulation, Computer vision, Filtering, filtering theory, HUMANS, Image Enhancement, Image Interpretation, Computer-Assisted, Index Terms- Particle filters, Information Storage and Retrieval, Insects, interacting targets, Markov chain Monte Carlo sampling step, Markov chain Monte Carlo., Markov chains, Markov processes, Markov random field motion, Markov random fields, Models, Biological, Models, Statistical, Monte Carlo Method, Monte Carlo methods, MOTION, Movement, multitarget filter, multitarget tracking, particle filtering, Particle filters, Particle tracking, Pattern Recognition, Automated, Sampling methods, Subtraction Technique, target tracking, Video Recording}, isbn = {0162-8828}, author = {Zia Khan and Balch, T. and Dellaert, F.} } @conference {12280, title = {Measurement-based multipath multicast}, booktitle = {INFOCOM 2005. 24th Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings IEEE}, volume = {4}, year = {2005}, month = {2005/03//}, pages = {2803 - 2808 vol. 4 - 2803 - 2808 vol. 4}, abstract = {We propose a measurement-based routing algorithm to load balance intradomain traffic along multiple paths for multiple multicast sources. Multiple paths are established using application-layer overlaying. The proposed algorithm is able to converge under different network models, where each model reflects a different set of assumptions about the multicasting capabilities of the network. The algorithm is derived from simultaneous perturbation stochastic approximation and relies only on noisy estimates from measurements. Simulation results are presented to demonstrate the additional benefits obtained by incrementally increasing the multicasting capabilities.}, keywords = {algorithm;, allocation;, application-layer, approximation, approximation;, balance, communication;, Convergence, convergence;, intradomain, load, measurement-based, methods;, Multicast, multipath, network, numerical, of, overlaying;, perturbation, processes;, resource, Routing, routing;, source;, Stochastic, techniques;, Telecommunication, theory;, traffic;}, doi = {10.1109/INFCOM.2005.1498566}, author = {Guven,T. and La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @conference {18402, title = {Measuring productivity on high performance computers}, booktitle = {11th IEEE International Symposium on Software Metric}, year = {2005}, month = {2005///}, abstract = {In the high performance computing domain, the speed ofexecution of a program has typically been the primary performance metric. But productivity is also of concern to high performance computing developers. In this paper we will discuss the problems of defining and measuring productivity for these machines and we develop a model of productivity that includes both a performance component and a component that measures the development time of the program. We ran several experiments using students in high performance courses at several universities, and we report on those results with respect to our model of productivity. }, author = {Zelkowitz, Marvin V and Basili, Victor R. and Asgari, S. and Hochstein, L. and Hollingsworth, Jeffrey K and Nakamura, T.} } @conference {12108, title = {A metric space for productivity measurement in software development}, booktitle = {Proceedings of the second international workshop on Software engineering for high performance computing system applications}, series = {SE-HPCS {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {13 - 16}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We define a metric space to measure the contributions of individual programmers to a software development project. It allows us to measure the distance between the contributions of two different programmers as well as the absolute contribution of each individual programmer. Our metric is based on an action function that provides a picture of how one programmer{\textquoteright}s approach differs from another at each instance of time during the project. We apply our metric to data we collected from students taking a course in parallel programming. We display the pictures for two students who showed approximately equal contributions but who followed very different paths through the course.}, isbn = {1-59593-117-1}, doi = {10.1145/1145319.1145324}, url = {http://doi.acm.org/10.1145/1145319.1145324}, author = {Numrich,Robert W. and Hochstein, Lorin and Basili, Victor R.} } @article {12148, title = {Metrics of software architecture changes based on structural distance}, journal = {IEEE METRICS}, year = {2005}, month = {2005///}, pages = {8 - 8}, abstract = {Software architecture is an important form of abstrac-tion, representing the overall system structure and the re- lationship among components. When software is modified from one version to another, its architecture may change. Software modification involving architectural change is of- ten difficult when the change goes beyond the original ar- chitectural design, involving changes to the connectivity of multiple components. Existing research has looked at ar- chitectural change at the level of architecture metrics such as size, complexity, coupling and cohesion, which abstract a particular version of the software in isolation. In this pa- per, we argue that this level of abstraction is often too high to characterize some interesting aspects of the architectural change process, and propose an approach that takes into account the change in connectivity from version to version of individual components. In this approach, two endpoints of a major change are taken as reference points, and inter- mediate connectivity changes are examined relative to the endpoints. We define a distance measure between software structures using a graph kernel function, which is quite powerful as it is applicable to any software structure repre- sentable as a graph. Using this distance measure, we define a metric which models the architecture change as a transi- tion between two endpoints. In addition to theoretical anal- ysis of the approach, we present empirical results obtained by applying the approach to open-source software projects to evaluate its validity and usefulness. }, author = {Nakamura, T. and Basili, Victor R.} } @conference {12281, title = {Misbehaving TCP receivers can cause internet-wide congestion collapse}, booktitle = {Proceedings of the 12th ACM conference on Computer and communications security}, series = {CCS {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {383 - 392}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {An optimistic acknowledgment (opt-ack) is an acknowledgment sent by a misbehaving client for a data segment that it has not received. Whereas previous work has focused on opt-ack as a means to greedily improve end-to-end performance, we study opt-ack exclusively as a denial of service attack. Specifically, an attacker sends optimistic acknowledgments to many victims in parallel, thereby amplifying its effective bandwidth by a factor of 30 million (worst case). Thus, even a relatively modest attacker can totally saturate the paths from many victims back to the attacker. Worse, a distributed network of compromised machines ("zombies") attacking in parallel can exploit over-provisioning in the Internet to bring about wide-spread, sustained congestion collapse.We implement this attack both in simulation and in a wide-area network, and show it severity both in terms of number of packets and total traffic generated. We engineer and implement a novel solution that does not require client or network modifications allowing for practical deployment. Additionally, we demonstrate the solution{\textquoteright}s efficiency on a real network.}, keywords = {Congestion control, distributed denial of service}, isbn = {1-59593-226-7}, doi = {10.1145/1102120.1102170}, url = {http://doi.acm.org/10.1145/1102120.1102170}, author = {Sherwood,Rob and Bhattacharjee, Bobby and Braud,Ryan} } @conference {12394, title = {Modeling image processing systems with homogeneous parameterized dataflow graphs}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {5}, year = {2005}, month = {2005/03//}, pages = {v/133 - v/136 Vol. 5 - v/133 - v/136 Vol. 5}, abstract = {We describe a new dataflow model called homogeneous parameterized dataflow (HPDF). This form of dynamic dataflow graph takes advantage of the fact that in a large number of image processing applications, data production and consumption rates, though dynamic, are equal across graph edges for any particular iteration, which leads to a homogeneous rate of actor execution, even though data production and consumption values are dynamic and vary across graph edges. We discuss existing dataflow models and formulate in detail the HPDF model. We develop examples of applications that are described naturally in terms of HPDF semantics and present experimental results that demonstrate the efficacy of the HPDF approach.}, keywords = {data consumption, data flow graphs, data production, dynamic dataflow graph, graph edges, homogeneous parameterized dataflow graphs, IMAGE PROCESSING, image processing system modeling, iteration, iterative methods}, doi = {10.1109/ICASSP.2005.1416258}, author = {Sen,Mainak and Bhattacharyya, Shuvra S. and Lv,Tiehan and Wolf,W.} } @article {12350, title = {Modeling of block-based DSP systems}, journal = {The Journal of VLSI Signal Processing}, volume = {40}, year = {2005}, month = {2005///}, pages = {289 - 299}, author = {Ko,D. I and Bhattacharyya, Shuvra S.} } @inbook {12670, title = {Moving Object Detection and Compression in IR Sequences}, booktitle = {Computer Vision Beyond the Visible SpectrumComputer Vision Beyond the Visible Spectrum}, series = {Advances in Pattern Recognition}, year = {2005}, month = {2005///}, pages = {141 - 165}, publisher = {Springer London}, organization = {Springer London}, abstract = {We consider the problem of remote surveillance using infrared (IR) sensors. The aim is to use IR image sequences to detect moving objects (humans or vehicles), and to transmit a few {\textquotedblleft}best-view images{\textquotedblright} of every new object that is detected. Since the available bandwidth is usually low, if the object chip is big, it needs to be compressed before being transmitted. Due to low computational power of computing devices attached to the sensor, the algorithms should be computationally simple. We present two approaches for object detection {\textemdash} one which specifically solves the more difficult long-range object detection problem, and the other for objects at short range. For objects at short range, we also present techniques for selecting a single best-view object chip and computationally simple techniques for compressing it to very low bit rates due to the channel bandwidth constraint. A fast image chip compression scheme implemented in the wavelet domain by combining a non-iterative zerotree coding method with 2D-DPCM for both low-and high-frequency subbands is presented. Comparisons with some existing schemes are also included. The object detection and compression algorithms have been implemented in C/C++ and their performance has been evaluated using the Hitachi{\textquoteright}s SH4 platform with software simulation.}, isbn = {978-1-84628-065-8}, url = {http://dx.doi.org/10.1007/1-84628-065-6_5}, author = {Vaswani,Namrata and Agrawal,Amit and Qinfen Zheng and Chellapa, Rama}, editor = {Bhanu,Bir and Pavlidis,Ioannis} } @conference {19665, title = {Multitarget tracking with split and merged measurements}, booktitle = {IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2005. CVPR 2005}, volume = {1}, year = {2005}, month = {2005/06//}, pages = {605 - 610 vol. 1}, abstract = {In many multitarget tracking applications in computer vision, a detection algorithm provides locations of potential targets. Subsequently, the measurements are associated with previously estimated target trajectories in a data association step. The output of the detector is often imperfect and the detection data may include multiple, split measurements from a single target or a single merged measurement from several targets. To address this problem, we introduce a multiple hypothesis tracker for interacting targets that generate split and merged measurements. The tracker is based on an efficient Markov chain Monte Carlo (MCMC) based auxiliary variable particle filter. The particle filter is Rao-Blackwellized such that the continuous target state parameters are estimated analytically, and an MCMC sampler generates samples from the large discrete space of data associations. In addition, we include experimental results in a scenario where we track several interacting targets that generate these split and merged measurements.}, keywords = {Application software, Computer vision, Detection algorithms, Detectors, filtering theory, Markov chain Monte Carlo based auxiliary variable particle filter, Markov processes, merged measurements, Monte Carlo methods, multiple hypothesis tracker, multitarget tracking, parameter estimation, Particle filters, Particle tracking, Rao-Blackwellized filter, split measurements, target tracking, Trajectory}, author = {Zia Khan and Balch, T. and Dellaert, F.} } @conference {14710, title = {Mutatis mutandis: safe and predictable dynamic software updating}, booktitle = {Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {183 - 194}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Dynamic software updates can be used to fix bugs or add features to a running program without downtime. Essential for some applications and convenient for others, low-level dynamic updating has been used for many years. Perhaps surprisingly, there is little high-level understanding or language support to help programmers write dynamic updates effectively.To bridge this gap, we present Proteus, a core calculus for dynamic software updating in C-like languages that is flexible, safe, and predictable. Proteus supports dynamic updates to functions (even active ones), to named types and to data, allowing on-line evolution to match source-code evolution as we have observed it in practice. We ensure updates are type-safe by checking for a property we call "con-freeness" for updated types t at the point of update. This means that non-updated code will not use t concretely beyond that point (concrete usages are via explicit coercions) and thus t{\textquoteright}s representation can safely change. We show how con-freeness can be enforced dynamically for a particular program state. We additionally define a novel and efficient static updateability analysis to establish con-freeness statically, and can thus automatically infer program points at which all future (well-formed) updates will be type-safe. We have implemented our analysis for C and tested it on several well-known programs.}, keywords = {capability, dynamic software updating, proteus, Type inference, updateability analysis}, isbn = {1-58113-830-X}, doi = {10.1145/1040305.1040321}, url = {http://doi.acm.org/10.1145/1040305.1040321}, author = {Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Sewell,Peter and Neamtiu,Iulian} } @article {15329, title = {New experimental data of STBLI at DNS/LES accessible Reynolds numbers}, journal = {AIAA paper}, volume = {309}, year = {2005}, month = {2005///}, pages = {2005 - 2005}, author = {Bookey,P. and Wyckham,C. and Smits,A. J. and Martin, M.P} } @article {17313, title = {Ordered and Quantum Treemaps: Making Effective Use of 2D Space to Display Hierarchies (2001)}, year = {2005}, month = {2005///}, abstract = {Treemaps, a space- filling method of visualizing large hierarchical data sets, are receiving increasing attention. Several algorithms have been proposed to create more useful displays by controlling the aspect ratios of the rectangles that make up a treemap. While these algorithms do improve visibility of small items in a single layout, they introduce instability over time in the display of dynamically changing data, fail to preserve order of the underlying data, and create layouts that are difficult to visually search. In addition, continuous treemap algorithms are not suitable for displaying quantum-sized objects within them, such as images. This paper introduces several new treemap algorithms, which address these shortcomings. In addition, we show a new application of these treemaps, using them to present groups of images. The ordered treemap algorithms ensure that items near each other in the given order will be near each other in the treemap layout. Using experimental evidence from Monte Carlo trials, we show that compared to other layout algorithms ordered treemaps are more stable while maintaining relatively favorable aspect ratios of the constituent rectangles. A second test set uses stock market data. The quantum treemap algorithms modify the layout of the continuous treemap algorithms to generate rectangles that are integral multiples of an input object size. The quantum treemap algorithm has been applied to PhotoMesa, an application that supports browsing of large numbers of images.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6486}, author = {Bederson, Benjamin B. and Shneiderman, Ben and Wattenberg,Martin} } @article {19652, title = {An outdoor 3-D visual tracking system for the study of spatial navigation and memory in rhesus monkeys}, journal = {Behavior Research Methods}, volume = {37}, year = {2005}, month = {2005/08/01/}, pages = {453 - 463}, abstract = {Previous studies of the navigational abilities of nonhuman primates have largely been limited to what could be described by a human observer with a pen and paper. Consequently, we have developed a system that uses a pair of cameras to automatically obtain the three-dimensional trajectory of rhesus monkeys performing an outdoor spatial navigation and memory task. The system provides trajectories, path length, speed, and other variables that would be impossible for an unaided observer to note. From trajectory data, we computed and validated a path-length measurement. We use this measurement to compare the navigation abilities of several animals. In addition, we provide quantitative data on the accuracy of a method for automatic behavior detection. Currently, the system is being used to examine the sex differences in spatial navigation of rhesus monkeys. We expect that measures derived from the trajectory data will reveal strategies used by animals to solve spatial problems.}, keywords = {cognitive psychology}, isbn = {1554-351X, 1554-3528}, url = {http://link.springer.com/article/10.3758/BF03192714}, author = {Zia Khan and Herman, Rebecca A. and Wallen, Kim and Balch, Tucker} } @article {16398, title = {Path dependence and the validation of agent-based spatial models of land use}, journal = {International Journal of Geographical Information Science}, volume = {19}, year = {2005}, month = {2005///}, pages = {153 - 174}, abstract = {In this paper, we identify two distinct notions of accuracy of land?use models and highlight a tension between them. A model can have predictive accuracy: its predicted land?use pattern can be highly correlated with the actual land?use pattern. A model can also have process accuracy: the process by which locations or land?use patterns are determined can be consistent with real world processes. To balance these two potentially conflicting motivations, we introduce the concept of the invariant region, i.e., the area where land?use type is almost certain, and thus path independent; and the variant region, i.e., the area where land use depends on a particular series of events, and is thus path dependent. We demonstrate our methods using an agent?based land?use model and using multi?temporal land?use data collected for Washtenaw County, Michigan, USA. The results indicate that, using the methods we describe, researchers can improve their ability to communicate how well their model performs, the situations or instances in which it does not perform well, and the cases in which it is relatively unlikely to predict well because of either path dependence or stochastic uncertainty.}, isbn = {1365-8816}, doi = {10.1080/13658810410001713399}, url = {http://www.tandfonline.com/doi/abs/10.1080/13658810410001713399}, author = {Brown,Daniel G. and Page,Scott and Riolo,Rick and Zellner,Moira and Rand, William} } @inbook {12676, title = {Pattern Recognition in Video}, booktitle = {Pattern Recognition and Machine IntelligencePattern Recognition and Machine Intelligence}, series = {Lecture Notes in Computer Science}, volume = {3776}, year = {2005}, month = {2005///}, pages = {11 - 20}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Images constitute data that live in a very high dimensional space, typically of the order of hundred thousand dimensions. Drawing inferences from correlated data of such high dimensions often becomes intractable. Therefore traditionally several of these problems like face recognition, object recognition, scene understanding etc. have been approached using techniques in pattern recognition. Such methods in conjunction with methods for dimensionality reduction have been highly popular and successful in tackling several image processing tasks. Of late, the advent of cheap, high quality video cameras has generated new interests in extending still image-based recognition methodologies to video sequences. The added temporal dimension in these videos makes problems like face and gait-based human recognition, event detection, activity recognition addressable. Our research has focussed on solving several of these problems through a pattern recognition approach. Of course, in video streams patterns refer to both patterns in the spatial structure of image intensities around interest points and temporal patterns that arise either due to camera motion or object motion. In this paper, we discuss the applications of pattern recognition in video to problems like face and gait-based human recognition, behavior classification, activity recognition and activity based person identification.}, isbn = {978-3-540-30506-4}, url = {http://dx.doi.org/10.1007/11590316_2}, author = {Chellapa, Rama and Veeraraghavan,Ashok and Aggarwal,Gaurav}, editor = {Pal,Sankar and Bandyopadhyay,Sanghamitra and Biswas,Sambhunath} } @conference {12387, title = {Porting DSP applications across design tools using the dataflow interchange format}, booktitle = {Rapid System Prototyping, 2005. (RSP 2005). The 16th IEEE International Workshop on}, year = {2005}, month = {2005/06//}, pages = {40 - 46}, abstract = {Modeling DSP applications through coarse-grain dataflow graphs is popular in the DSP design community, and a growing set of rapid prototyping tools support such dataflow semantics. Since different tools may be suitable for different phases or generations of a design, it is often desirable to migrate a dataflow-based application model from one prototyping tool to another. Two critical problems in transferring dataflow-based designs across different prototyping tools are the lack of a vendor-independent language for DSP-oriented dataflow graphs, and the lack of an efficient porting methodology. In our previous work, the dataflow interchange format (DIF) (C. Hsu et al., 2004) has been developed as a standard language to specify mixed-grain dataflow models for DSP systems. This paper presents the augmentation of the DIF infrastructure with a systematic porting approach that integrates DIF tightly with the specific exporting and importing mechanisms that interface DIF to specific DSP design tools. In conjunction with this porting mechanism, this paper also introduces a novel language, called the actor interchange format (AIF), for transferring relevant information pertaining to DSP library components across different tools. Through a case study of a synthetic aperture radar application, we demonstrate the high degree of automation offered by our DIF-based porting approach.}, keywords = {actor interchange format, coarse-grain dataflow graph, data flow analysis, data flow graphs, dataflow interchange format, dataflow model, dataflow semantic, DSP application, DSP design tool, DSP library component, electronic data interchange, formal specification, rapid prototyping tool, Signal processing, software prototyping, Specification languages, vendor-independent language}, doi = {10.1109/RSP.2005.39}, author = {Hsu,C.-J. and Bhattacharyya, Shuvra S.} } @article {15791, title = {QR Factorizations Using a Restricted Set of Rotations}, journal = {Electronic Transactions on Numerical Analysis}, volume = {21}, year = {2005}, month = {2005///}, pages = {20 - 27}, url = {http://etna.mcs.kent.edu/vol.21.2005/pp20-27.dir/pp20-27.pdfhttp://etna.mcs.kent.edu/vol.21.2005/pp20-27.dir/pp20-27.pdf}, author = {O{\textquoteright}Leary, Dianne P. and Bullock,Stephen S.} } @conference {14462, title = {Relational clustering for multi-type entity resolution}, booktitle = {Proceedings of the 4th international workshop on Multi-relational mining}, series = {MRDM {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {3 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In many applications, there are a variety of ways of referring to the same underlying entity. Given a collection of references to entities, we would like to determine the set of true underlying entities and map the references to these entities. The references may be to entities of different types and more than one type of entity may need to be resolved at the same time. We propose similarity measures for clustering references taking into account the different relations that are observed among the typed references. We pose typed entity resolution in relational data as a clustering problem and present experimental results on real data showing improvements over attribute-based models when relations are leveraged.}, isbn = {1-59593-212-7}, doi = {10.1145/1090193.1090195}, url = {http://doi.acm.org/10.1145/1090193.1090195}, author = {Bhattacharya,Indrajit and Getoor, Lise} } @article {15088, title = {Secure remote authentication using biometric data}, journal = {Advances in Cryptology{\textendash}EUROCRYPT 2005}, year = {2005}, month = {2005///}, pages = {147 - 163}, abstract = {Biometric data offer a potential source of high-entropy, secret information that can be used in cryptographic protocols provided two issues are addressed: (1) biometric data are not uniformly distributed; and (2) they are not exactly reproducible. Recent work, most notably that of Dodis, Reyzin, and Smith, has shown how these obstacles may be overcome by allowing some auxiliary public information to be reliably sent from a server to the human user. Subsequent work of Boyen has shown how to extend these techniques, in the random oracle model, to enable unidirectional authentication from the user to the server without the assumption of a reliable communication channel.We show two efficient techniques enabling the use of biometric data to achieve mutual authentication or authenticated key exchange over a completely insecure (i.e., adversarially controlled) channel. In addition to achieving stronger security guarantees than the work of Boyen, we improve upon his solution in a number of other respects: we tolerate a broader class of errors and, in one case, improve upon the parameters of his solution and give a proof of security in the standard model. }, doi = {10.1007/11426639_9}, author = {Boyen,X. and Dodis,Y. and Katz, Jonathan and Ostrovsky,R. and Smith,A.} } @article {17368, title = {Social and Psychological Influences on Computer User Frustration (Newhagen book chapter, 2002)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {As computer usage has proliferated, so has user frustration. Even devoted and knowledgeable users encounter annoying delays, incomprehensible messages, incompatible files, and indecipherable menus. The frustration generated by these problems can be personally disturbing and socially disruptive. Psychological and social perspectives on frustration may clarify the relationships among variables such as personality types, cultural factors, goal attainment, workplace anger, and computer anxiety. These perspectives may also help designers, managers, and users understand the range of responses to frustration, which could lead to effective interventions such as redesign of software, improved training, better online help, user discipline, and even resetting of national research priorities.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6497}, author = {Bessiere,Katie and Ceaparu,Irina and Lazar,Jonathan and Robinson,John and Shneiderman, Ben} } @inbook {12155, title = {Software defect reduction top 10 list}, booktitle = {Foundations of empirical software engineering: the legacy of Victor R. Basili}, year = {2005}, month = {2005///}, pages = {426 - 426}, isbn = {9783540245476}, author = {Boehm,B. and Basili, Victor R.} } @conference {12375, title = {Software synthesis from the dataflow interchange format}, booktitle = {Proceedings of the 2005 workshop on Software and compilers for embedded systems}, year = {2005}, month = {2005///}, pages = {37 - 49}, author = {Hsu,C. J and Ko,M. Y and Bhattacharyya, Shuvra S.} } @article {16403, title = {Spatial process and data models: Toward integration of agent-based models and GIS}, journal = {Journal of Geographical Systems}, volume = {7}, year = {2005}, month = {2005///}, pages = {25 - 47}, abstract = {The use of object-orientation for both spatial data and spatial process models facilitates their integration, which can allow exploration and explanation of spatial-temporal phenomena. In order to better understand how tight coupling might proceed and to evaluate the possible functional and efficiency gains from such a tight coupling, we identify four key relationships affecting how geographic data (fields and objects) and agent-based process models can interact: identity, causal, temporal and topological. We discuss approaches to implementing tight integration, focusing on a middleware approach that links existing GIS and ABM development platforms, and illustrate the need and approaches with example agent-based models.}, doi = {10.1007/s10109-005-0148-5}, author = {Brown,D.G. and Riolo,R and Robinson,D.T. and North,M. and Rand, William} } @article {18600, title = {Stable Policy Routing with Provider Independence}, volume = {MIT-CSAIL-TR-2005-009}, year = {2005}, month = {2005/02/08/}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {Thousands of competing autonomous systems (ASes) mustcooperate with each other to provide global Internet connectivity.These ASes encode various economic, business,and performance decisions in their routing policies. The currentinterdomain routing system enables ASes to express policyusing rankings that determine how each router in an ASorders the different routes to a destination, and filters thatdetermine which routes are hidden from each neighboringAS. Since the Internet is composed of many independent,competing networks, the interdomain routing system shouldallow providers to set their rankings independently, and tohave no constraints on allowed filters. This paper studiesrouting protocol stability under these constraints. We firstdemonstrate that certain rankings that are commonly usedin practice may not ensure routing stability. We then provethat, with ranking independence and unrestricted filtering,guaranteeing that the routing system will converge to a stablepath assignment essentially requires ASes to rank routesbased on AS-path lengths. Finally, we discuss the implicationsof these results for the future of interdomain routing.}, url = {http://dspace.mit.edu/handle/1721.1/30522}, author = {Feamster, Nick and Johari,Ramesh and Balakrishnan,Hari} } @article {12284, title = {Stub Domain DDoS Detection}, year = {2005}, month = {2005///}, institution = {Technical Report of the Department of Computer Science, University of Maryland, College Park}, author = {Kommareddy,C. and Levin,D. and Bhattacharjee, Bobby and La,R.J. and Shayman,M.} } @article {15824, title = {Time reversal and n-qubit canonical decompositions}, journal = {Journal of Mathematical Physics}, volume = {46}, year = {2005}, month = {2005/05/17/}, pages = {062104-062104-19 - 062104-062104-19}, abstract = {On pure states of n quantum bits, the concurrence entanglement monotone returns the norm of the inner product of a pure state with its spin-flip. The monotone vanishes for n odd, but for n even there is an explicit formula for its value on mixed states, i.e., a closed-form expression computes the minimum over all ensemble decompositions of a given density. For n even a matrix decomposition ν = k1ak2 of the unitary group is explicitly computable and allows for study of the monotone{\textquoteright}s dynamics. The side factors k1 and k2 of this concurrence canonical decomposition (CCD) are concurrence symmetries, so the dynamics reduce to consideration of the a factor. This unitary a phases a basis of entangled states, and the concurrence dynamics of u are determined by these relative phases. In this work, we provide an explicit numerical algorithm computing ν = k1ak2 for n odd. Further, in the odd case we lift the monotone to a two-argument function. The concurrence capacity of ν according to the double argument lift may be nontrivial for n odd and reduces to the usual concurrence capacity in the literature for n even. The generalization may also be studied using the CCD, leading again to maximal capacity for most unitaries. The capacity of ν(x)I2 is at least that of ν, so odd-qubit capacities have implications for even-qubit entanglement. The generalizations require considering the spin-flip as a time reversal symmetry operator in Wigner{\textquoteright}s axiomatization, and the original Lie algebra homomorphism defining the CCD may be restated entirely in terms of this time reversal. The polar decomposition related to the CCD then writes any unitary evolution as the product of a time-symmetric and time-antisymmetric evolution with respect to the spin-flip. En route we observe a Kramers{\textquoteright} nondegeneracy: the existence of a nondegenerate eigenstate of any time reversal symmetric n-qubit Hamiltonian demands (i) n even and (ii) maximal concurrence of said eigenstate. We provide examples of how to apply this work to study the kinematics and dynamics of entanglement in spin chain Hamiltonians.}, isbn = {00222488}, doi = {doi:10.1063/1.1900293}, url = {http://jmp.aip.org/resource/1/jmapaq/v46/i6/p062104_s1}, author = {Bullock,Stephen S. and Brennen,Gavin K. and O{\textquoteright}Leary,Dianne P.} } @article {16412, title = {Toward a graphical ABM toolkit with GIS integration}, journal = {Proceedings of Agent2005}, year = {2005}, month = {2005///}, abstract = {Agent-based modeling (ABM) has proved useful in a number of fields. Many of theearly successes of ABM were due to its ability to represent the processes of a phenomenon. However, less emphasis has been placed in ABM on developing its ability to replicate spatial patterns of phenomena. In order to do that, more powerful spatial modeling techniques, like those within geographical information systems (GIS), are necessary. The integration of these two tool sets into a cohesive package would allow for elegant modeling of both process and pattern. One problem with an integrated toolkit is that most GIS users are not programmers, but most GIS users are familiar with the use of detailed graphical user interfaces (GUIs) in order to create complex visualizations of data. Thus providing a detailed GUI to access an integrated ABM-GIS toolkit would vastly expand the number of users for such a toolkit. This paper is a first step toward that goal. We first outline several design principles for an ABM-GIS toolkit and then describe a survey of extant toolkits (RepastPy, NetLogo, and MobiDyc) that were selected based on the design principles. The toolkits were surveyed to see how well they fulfill some of the design principles. This survey is not meant to be a comparative review of these toolkits but rather it was conducted to determine what useful design principles can be gathered from them that might inform a new {\textquotedblleft}ideal{\textquotedblright} ABM-GIS toolkit. Finally, the paper concludes with some design recommendations for such a toolkit. }, author = {Rand, William and Brown,D and Riolo,R and Robinson,D} } @article {14072, title = {Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock}, journal = {Environmental Microbiology}, volume = {7}, year = {2005}, month = {2005/06/01/}, pages = {789 - 797}, abstract = {Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85{\textdegree}C to 65{\textdegree}C and 95{\textdegree}C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95{\textdegree}C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an α subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65{\textdegree}C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18~kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2005.00751.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2005.00751.x/abstract}, author = {Boonyaratanakornkit,Boonchai B and Simpson,Anjana J. and Whitehead,Timothy A and Fraser,Claire M. and El-Sayed, Najib M. and Clark,Douglas S} } @conference {17444, title = {Turning information visualization innovations into commercial products: lessons to guide the next success}, booktitle = {IEEE Symposium on Information Visualization, 2005. INFOVIS 2005}, year = {2005}, month = {2005/10/23/25}, pages = {241 - 244}, publisher = {IEEE}, organization = {IEEE}, abstract = {As information visualization matures as an academic research field, commercial spinoffs are proliferating, but success stories are harder to find. This is the normal process of emergence for new technologies, but the panel organizers believe that there are certain strategies that facilitate success. To teach these lessons, we have invited several key figures who are seeking to commercialize information visualization tools. The panelists make short presentations, engage in a moderated discussion, and respond to audience questions.}, keywords = {Books, commercial development, commercial product, Computer interfaces, Computer science, data visualisation, Data visualization, Educational institutions, exploratory data analysis, information visualization innovation, information visualization tool, innovation management, Laboratories, Management training, new technology emergence, Technological innovation, technology transfer, Turning, User interfaces}, isbn = {0-7803-9464-X}, doi = {10.1109/INFVIS.2005.1532153}, author = {Shneiderman, Ben and Rao,R. and Andrews,K. and Ahlberg,C. and Brodbeck,D. and Jewitt,T. and Mackinlay,J.} } @conference {12657, title = {UMD Experiments with FRGC Data}, booktitle = {Computer Vision and Pattern Recognition - Workshops, 2005. CVPR Workshops. IEEE Computer Society Conference on}, year = {2005}, month = {2005/06//}, pages = {172 - 172}, abstract = {Although significant work has been done in the field of face recognition, the performance of state-of-the art face recognition algorithms is not good enough to be effective in operational systems. Though most algorithms work well for controlled images, they are quite susceptible to changes in illumination and pose. Face Recognition Grand Challenge (FRGC) is an effort to examine such issues to suitably guide future research in the area. This paper describes the efforts made at UMD in this direction. We present our results on several experiments suggested in FRGC. We believe that though pattern classification techniques play an extremely significant role in automatic face recognition under controlled conditions, physical modeling is required to generalize across varying situations. Accordingly, we describe a generative approach to recognize faces across varying illumination. Unlike most current methods, our method does not ignore shadows. Instead we use them to our benefit by modeling attached shadows in our formulation.}, doi = {10.1109/CVPR.2005.586}, author = {Aggarwal,G. and Biswas,S. and Chellapa, Rama} } @article {17913, title = {Unsupervised learning applied to progressive compression of time-dependent geometry}, journal = {Computers \& Graphics}, volume = {29}, year = {2005}, month = {2005/06//}, pages = {451 - 461}, abstract = {We propose a new approach to progressively compress time-dependent geometry. Our approach exploits correlations in motion vectors to achieve better compression. We use unsupervised learning techniques to detect good clusters of motion vectors. For each detected cluster, we build a hierarchy of motion vectors using pairwise agglomerative clustering, and succinctly encode the hierarchy using entropy encoding. We demonstrate our approach on a client{\textendash}server system that we have built for downloading time-dependent geometry.}, keywords = {Clustering algorithms, Distributed/network graphics, pattern recognition}, isbn = {0097-8493}, doi = {10.1016/j.cag.2005.03.021}, url = {http://www.sciencedirect.com/science/article/pii/S009784930500052X}, author = {Baby,Thomas and Kim,Youngmin and Varshney, Amitabh} } @article {17465, title = {User Frustration with Technology in the Workplace (2004)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {When hard to use computers cause users to become frustrated, it can affect workplace productivity, user mood, and interactions with other co-workers. Previous research has examined the frustration that graduate students and their families face in using computers. To learn more about the causes and effects of user frustration with computers in the workplace, we collected modified time diaries from 50 workplace users, who spent an average of 5.1 hours on the computer. In this experiment, users reported wasting on average, 42-43\% of their time on the computer due to frustrating experiences. The causes of the frustrating experiences, the time lost due to the frustrating experiences, and the effects of the frustrating experiences on the mood of the users are discussed in this paper. Implications for designers, managers, users, information technology staff, and policymakers are discussed.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6515}, author = {Lazar,Jonathan and Jones,Adam and Bessiere,Katie and Ceaparu,Irina and Shneiderman, Ben} } @conference {12166, title = {Using measurement to build core competencies in software}, booktitle = {Seminar sponsored by Data and Analysis Center for Software}, year = {2005}, month = {2005///}, author = {Basili, Victor R.} } @inbook {18924, title = {Web Service Composition with Volatile Information}, booktitle = {The Semantic Web {\textendash} ISWC 2005}, series = {Lecture Notes in Computer Science}, volume = {3729}, year = {2005}, month = {2005///}, pages = {52 - 66}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In many Web service composition problems, information may be needed from Web services during the composition process. Existing research on Web service composition (WSC) procedures has generally assumed that this information will not change. We describe two ways to take such WSC procedures and systematically modify them to deal with volatile information. The black-box approach requires no knowledge of the WSC procedure{\textquoteright}s internals: it places a wrapper around the WSC procedure to deal with volatile information. The gray-box approach requires partial information of those internals, in order to insert coding to perform certain bookkeeping operations. We show theoretically that both approaches work correctly. We present experimental results showing that the WSC procedures produced by the gray-box approach can run much faster than the ones produced by the black-box approach.}, keywords = {Computer science}, isbn = {978-3-540-29754-3}, url = {http://www.springerlink.com/content/y105x8464k54l760/abstract/}, author = {Au,Tsz-Chiu and Kuter,Ugur and Nau, Dana S.}, editor = {Gil,Yolanda and Motta,Enrico and Benjamins,V. and Musen,Mark} } @article {12097, title = {Weighted coloring based channel assignment for WLANs}, journal = {ACM SIGMOBILE Mobile Computing and Communications Review}, volume = {9}, year = {2005}, month = {2005///}, pages = {19 - 31}, author = {Mishra,A. and Banerjee,S. and Arbaugh, William A.} } @conference {19670, title = {What Are the Ants Doing? Vision-Based Tracking and Reconstruction of Control Programs}, booktitle = {Proceedings of the 2005 IEEE International Conference on Robotics and Automation, 2005. ICRA 2005}, year = {2005}, month = {2005/04//}, pages = {4182 - 4187}, abstract = {In this paper, we study the problem of going from a real-world, multi-agent system to the generation of control programs in an automatic fashion. In particular, a computer vision system is presented, capable of simultaneously tracking multiple agents, such as social insects. Moreover, the data obtained from this system is fed into a mode-reconstruction module that generates low-complexity control programs, i.e. strings of symbolic descriptions of control-interrupt pairs, consistent with the empirical data. The result is a mechanism for going from the real system to an executable implementation that can be used for controlling multiple mobile robots.}, keywords = {Animals, Automatic generation control, Biological information theory, Computer vision, Control systems, Mobile robots, Probability distribution, Robot control, target tracking, Trajectory}, author = {Egerstedt, M. and Balch, T. and Dellaert, F. and Delmotte, F. and Zia Khan} } @conference {12296, title = {Adaptive replication in peer-to-peer systems}, booktitle = {Distributed Computing Systems, 2004. Proceedings. 24th International Conference on}, year = {2004}, month = {2004///}, pages = {360 - 369}, abstract = {Peer-to-peer systems can be used to form a low-latency decentralized data delivery system. Structured peer-to-peer systems provide both low latency and excellent load balance with uniform query and data distributions. Under the more common skewed access distributions, however, individual nodes are easily overloaded, resulting in poor global performance and lost messages. This paper describes a lightweight, adaptive, and system-neutral replication protocol, called LAR, that maintains low access latencies and good load balance even under highly skewed demand. We apply LAR to Chord and show that it has lower overhead and better performance than existing replication strategies.}, keywords = {adaptive, allocation;, data, databases;, decentralized, delivery, distributed, LAR, low-latency, peer-to-peer, processing;, protocol;, replicated, replication, resource, strategies;, structured, system-neutral, system;, systems;}, doi = {10.1109/ICDCS.2004.1281601}, author = {Gopalakrishnan,V. and Silaghi,B. and Bhattacharjee, Bobby and Keleher,P.} } @article {14075, title = {Advances in schistosome genomics}, journal = {Trends in Parasitology}, volume = {20}, year = {2004}, month = {2004/04/01/}, pages = {154 - 157}, abstract = {In Spring 2004, the first draft of the 270~Mb genome of Schistosoma mansoni will be released. This sequence is based on the assembly and annotation of a >7.5-fold coverage, shotgun sequencing project. The key stages involved in the international collaborative efforts that have led to the generation of these sequencing data for the parasite S. mansoni are discussed here.}, isbn = {1471-4922}, doi = {16/j.pt.2004.02.002}, url = {http://www.sciencedirect.com/science/article/pii/S1471492204000480}, author = {El-Sayed, Najib M. and Bartholomeu,Daniella and Ivens,Alasdair and Johnston,David A. and LoVerde,Philip T.} } @article {16392, title = {Agent-based and analytical modeling to evaluate the effectiveness of greenbelts}, journal = {Environmental Modelling \& Software}, volume = {19}, year = {2004}, month = {2004/12//}, pages = {1097 - 1109}, abstract = {We present several models of residential development at the rural{\textendash}urban fringe to evaluate the effectiveness of a greenbelt located beside a developed area, for delaying development outside the greenbelt. First, we develop a mathematical model, under two assumptions about the distributions of service centers, that represents the trade-off between greenbelt placement and width, their effects on the rate of development beyond the greenbelt, and how these interact with spatial patterns of aesthetic quality and the locations of services. Next, we present three agent-based models (ABMs) that include agents with the potential for heterogeneous preferences and a landscape with the potential for heterogeneous attributes. Results from experiments run with a one-dimensional ABM agree with the starkest of the results from the mathematical model, strengthening the support for both models. Further, we present two different two-dimensional ABMs and conduct a series of experiments to supplement our mathematical analysis. These include examining the effects of heterogeneous agent preferences, multiple landscape patterns, incomplete or imperfect information available to agents, and a positive aesthetic quality impact of the greenbelt on neighboring locations. These results suggest how width and location of the greenbelt could help determine the effectiveness of greenbelts for slowing sprawl, but that these relationships are sensitive to the patterns of landscape aesthetic quality and assumptions about service center locations.}, keywords = {Agent-based modeling, Land-use change, Landscape ecology, Urban sprawl}, isbn = {1364-8152}, doi = {10.1016/j.envsoft.2003.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S1364815203002664}, author = {Brown,Daniel G. and Page,Scott E. and Riolo,Rick and Rand, William} } @article {12361, title = {Analysis of dataflow programs with interval-limited data-rates}, journal = {Computer Systems: Architectures, Modeling, and Simulation}, year = {2004}, month = {2004///}, pages = {507 - 518}, author = {Teich,J. and Bhattacharyya, Shuvra S.} } @article {13495, title = {An Appearance-based Approach for Consistent Labeling of Humans and Objects in Video}, journal = {Pattern Analysis and Applications}, year = {2004}, month = {2004/11//}, pages = {1433 - 7541}, abstract = {We present an approach for consistently labeling people and for detecting human-object interactions using mono-camera surveillance video. The approach is based on a robust appearance based correlogram model which is combined with histogram information to model color distributions of people and objects in the scene. The models are dynamically built from non-stationary objects which are the outputs of background subtraction, and are used to identify objects on a frame-by-frame basis. We are able to detect when people merge into groups and to segment them even during partial occlusion. We can also detect when a person deposits or removes an object. The models persist when a person or object leaves the scene and are used to identify them when they reappear. Experiments show that the models are able to accommodate perspective foreshortening that occurs with overhead camera angles, as well as partial occlusion. The results show that this is an effective approach able to provide important information to algorithms performing higher-level analysis such as activity recognition, where human-object interactions play an important role.}, author = {Balcells-Capellades,M. and DeMenthon,D. and David Doermann} } @conference {18017, title = {Arbitrate-and-move primitives for high throughput on-chip interconnection networks}, booktitle = {Circuits and Systems, 2004. ISCAS {\textquoteright}04. Proceedings of the 2004 International Symposium on}, volume = {2}, year = {2004}, month = {2004/05//}, pages = {II - 441-4 Vol.2 - II - 441-4 Vol.2}, abstract = {An n-leaf pipelined balanced binary tree is used for arbitration of order and movement of data from n input ports to one output port. A novel arbitrate-and-move primitive circuit for every node of the tree, which is based on a concept of reduced synchrony that benefits from attractive features of both asynchronous and synchronous designs, is presented. The design objective of the pipelined binary tree is to provide a key building block in a high-throughput mesh-of-trees interconnection network for Explicit Multi Threading (XMT) architecture, a recently introduced parallel computation framework. The proposed reduced synchrony circuit was compared with asynchronous and synchronous designs of arbitrate-and-move primitives. Simulations with 0.18 mu;m technology show that compared to an asynchronous design, the proposed reduced synchrony implementation achieves a higher throughput, up to 2 Giga-Requests per second on an 8-leaf binary tree. Our circuit also consumes less power than the synchronous design, and requires less silicon area than both the synchronous and asynchronous designs.}, keywords = {8, arbiter, arbitrate-and-move, architecture;, asynchronous, balanced, binary, circuit, circuit;, circuits;, consumption;, data, explicit, interconnection, interconnections;, leaf, mesh-of-trees, multi-threading;, Multithreading, n-leaf, network;, pipeline, pipelined, power, primitive, processing;, reduced, simulation;, structures;, synchronous, synchrony, system-on-chip;, tree, tree;}, doi = {10.1109/ISCAS.2004.1329303}, author = {Balkan,A.O. and Gang Qu and Vishkin, Uzi} } @article {14263, title = {The Argus eye: a new imaging system designed to facilitate robotic tasks of motion}, journal = {IEEE Robotics \& Automation Magazine}, volume = {11}, year = {2004}, month = {2004/12//}, pages = {31 - 38}, abstract = {This article describes an imaging system that has been designed to facilitate robotic tasks of motion. The system consists of a number of cameras in a network, arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and, consequently, the estimation of shape models from the individual cameras. The reason is, inherent ambiguities of confusion between translation and rotation disappear. Pairs of cameras may also be arranged in multiple stereo configurations, which provide additional advantages for segmentation. Algorithms for the calibration of the system and the three-dimensional (3-D) motion estimation are provided.}, keywords = {Argus eye, Calibration, CAMERAS, computational geometry, Design automation, Eyes, image formation, imaging system, Information geometry, Layout, Motion estimation, multiple stereo configurations, panoramic robots, robot vision, Robot vision systems, robotic motion tasks, Robotics and automation, SHAPE, shape model estimation, system calibration}, isbn = {1070-9932}, doi = {10.1109/MRA.2004.1371606}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia} } @article {14167, title = {The Argus eye, a new tool for robotics}, journal = {IEEE Robotics and Automation Magazine}, volume = {11}, year = {2004}, month = {2004///}, pages = {31 - 38}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {13508, title = {Automatic recognition of spontaneous speech for access to multilingual oral history archives}, journal = {IEEE Transactions on Speech and Audio Processing, Special Issue on Spontaneous Speech Processing}, volume = {12}, year = {2004}, month = {2004/07//}, pages = {420 - 435}, abstract = {The MALACH project has the goal of developing the technologies needed to facilitate access to large collections of spontaneous speech. Its aim is to dramatically improve the state of the art in key Automatic Speech Recognition (ASR), Natural Language Processing (NLP) technologies for use in large-scale retrieval systems. The project leverages a unique collection of oral history interviews with survivors of the Holocaust that has been assembled and extensively annotated by the Survivors of the Shoah Visual History Foundation. This paper describes the collection, 116,000 hours of interviews in 32 languages, and the way in which system requirements have been discerned through user studies. It discusses ASR methods for very difficult speech (heavily accented, emotional, and elderly spontaneous speech), including transcription to create training data and methods for language modeling and speaker adaptation. Results are presented for for English and Czech. NLP results are presented for named entity tagging, topic segmentation, and supervised topic classification, and the architecture of an integrated search system that uses these results is described.}, author = {Byrne,W. and David Doermann and Franz,M. and Gustman,S. and Hajic,J. and Oard, Douglas and Picheny,M. and Psutka,J. and Ramabhadran,B.} } @article {12349, title = {Buffer merging{\textemdash}a powerful technique for reducing memory requirements of synchronous dataflow specifications}, journal = {ACM Transactions on Design Automation of Electronic Systems (TODAES)}, volume = {9}, year = {2004}, month = {2004///}, pages = {212 - 237}, author = {Murthy,P. K and Bhattacharyya, Shuvra S.} } @article {13933, title = {Building KidPad: an application for children{\textquoteright}s collaborative storytelling}, journal = {Software: Practice and Experience}, volume = {34}, year = {2004}, month = {2004///}, pages = {895 - 914}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison} } @conference {12290, title = {The case for a multi-hop wireless local area network}, booktitle = {INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies}, volume = {2}, year = {2004}, month = {2004/03//}, pages = {894 - 905 vol.2 - 894 - 905 vol.2}, abstract = {We propose a multi-hop wireless LAN architecture and demonstrate its benefits to wireless clients. For this architecture, we define implementation paths that allow interoperation with existing wireless LANs which can lead to an incremental deployment of this system. We quantify the performance benefits of the proposed schemes through measurements in realistic wireless LAN environments. We also examine the performance of such multi-hop wireless LANs through detailed simulation studies. Our results show that these multi-hop extensions can significantly improve the wireless access experience (in terms of data throughput, latency, etc.) for clients who enable such mechanisms. More interestingly, when multi-hop extensions are enabled by some of the clients, it also positively impacts the performance at other clients that are completely unaware of these extensions.}, keywords = {access, access;, area, benefits;, client-server, clients;, interoperation;, LAN;, local, multihop, network;, networks;, performance, radio, systems;, wireless}, doi = {10.1109/INFCOM.2004.1356977}, author = {Lee,Seungjoon and Banerjee,S. and Bhattacharjee, Bobby} } @conference {18602, title = {The case for separating routing from routers}, booktitle = {Proceedings of the ACM SIGCOMM workshop on Future directions in network architecture}, series = {FDNA {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {5 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Over the past decade, the complexity of the Internet{\textquoteright}s routing infrastructure has increased dramatically. This complexity and the problems it causes stem not just from various new demands made of the routing infrastructure, but also from fundamental limitations in the ability of today{\textquoteright}s distributed infrastructure to scalably cope with new requirements.The limitations in today{\textquoteright}s routing system arise in large part from the fully distributed path-selection computation that the IP routers in an autonomous system (AS) must perform. To overcome this weakness, interdomain routing should be separated from today{\textquoteright}s IP routers, which should simply forward packets (for the most part). Instead, a separate Routing Control Platform (RCP) should select routes on behalf of the IP routers in each AS and exchange reachability information with other domains.Our position is that an approach like RCP is a good way of coping with complexity while being responsive to new demands and can lead to a routing system that is substantially easier to manage than today. We present a design overview of RCP based on three architectural principles path computation based on a consistent view of network state, controlled interactions between routing protocol layers, and expressive specification of routing policies and discuss the architectural strengths and weaknesses of our proposal.}, keywords = {BGP, interdomain routing, routing architecture}, isbn = {1-58113-942-X}, doi = {10.1145/1016707.1016709}, url = {http://doi.acm.org/10.1145/1016707.1016709}, author = {Feamster, Nick and Balakrishnan,Hari and Rexford,Jennifer and Shaikh,Aman and van der Merwe,Jacobus} } @article {12338, title = {The CBP Parameter: A Module Characterization Approach for DSP Software Optimization}, journal = {The Journal of VLSI Signal Processing}, volume = {38}, year = {2004}, month = {2004///}, pages = {131 - 146}, author = {Bhattacharyya, Shuvra S. and Murthy,P. K} } @conference {14774, title = {Challenges in Measuring HPCS Learner Productivity in an Age of Ubiquitous Computing: The HPCS Program}, booktitle = {In Proceedings of ICSE Workshop on High Productivity Computing. May 2004}, year = {2004}, month = {2004///}, author = {Asgari, S. and Basili, Victor R. and Carver, J. and Hochstein, L. and Hollingsworth, Jeffrey K and Zelkowitz, Marvin V} } @inbook {18696, title = {Characterization of the Overall Rotational Diffusion of a Protein From 15N Relaxation Measurements and Hydrodynamic Calculations}, booktitle = {Protein NMR Techniques}, series = {Methods in Molecular Biology}, volume = {278}, year = {2004}, month = {2004///}, pages = {139 - 159}, publisher = {Humana Press}, organization = {Humana Press}, abstract = {In this chapter, we discuss experimental and theoretical methods for characterizing the overall rotational diffusion of molecules in solution. The methods are illustrated for the B3 domain of protein G, a small protein with rotational anisotropy of D par / D perp = 1.4. The rotational diffusion tensor of the protein is determined directly from 15 N relaxation measurements. The experimental data are treated assuming various possible models for the overall tumbling: isotropic, axially symmetric, and fully anisotropic, and the results of these analyses are compared to determine an adequate diffusion model for the protein. These experimentally derived characteristics of the protein are compared with the results of theoretical calculations of the diffusion tensor using various hydrodynamic models, to find optimal models and parameter sets for theoretical predictions. We also derive model-free characteristics of internal backbone motions in the protein, to show that different models for the overall motion can result in significantly different pictures of motion. This emphasizes the necessity of accurately characterizing the overall tumbling of a molecule to determine its local dynamics.}, keywords = {Biomedical and Life Sciences}, isbn = {978-1-59259-809-0}, url = {http://www.springerlink.com/content/h6w35487x3q1g6x7/abstract/}, author = {Blake-Hall,Jennifer and Walker,Olivier and Fushman, David}, editor = {Downing,A. Kristina and Walker,John M.} } @conference {12358, title = {CHARMED: A multi-objective co-synthesis framework for multi-mode embedded systems}, booktitle = {Application-Specific Systems, Architectures and Processors, 2004. Proceedings. 15th IEEE International Conference on}, year = {2004}, month = {2004///}, pages = {28 - 40}, author = {Kianzad,V. and Bhattacharyya, Shuvra S.} } @conference {12341, title = {Compact procedural implementation in DSP software synthesis through recursive graph decomposition}, booktitle = {Software and compilers for embedded systems: 8th international workshop, SCOPES 2004, Amsterdam, The Netherlands, September 2-3, 2004: proceedings}, volume = {3199}, year = {2004}, month = {2004///}, pages = {47 - 47}, author = {Ko,M. Y and Murthy,P. K and Bhattacharyya, Shuvra S.} } @conference {14209, title = {Compound eye sensor for 3D ego motion estimation}, booktitle = {2004 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2004. (IROS 2004). Proceedings}, volume = {4}, year = {2004}, month = {2004/10/28/Sept.}, pages = {3712- 3717 vol.4 - 3712- 3717 vol.4}, publisher = {IEEE}, organization = {IEEE}, abstract = {We describe a compound eye vision sensor for 3D ego motion computation. Inspired by eyes of insects, we show that the compound eye sampling geometry is optimal for 3D camera motion estimation. This optimality allows us to estimate the 3D camera motion in a scene-independent and robust manner by utilizing linear equations. The mathematical model of the new sensor can be implemented in analog networks resulting in a compact computational sensor for instantaneous 3D ego motion measurements in full six degrees of freedom.}, keywords = {3D camera motion estimation, CAMERAS, compound eye vision sensor, Computer vision, Equations, Eyes, Geometry, Image sensors, Insects, linear equations, Motion estimation, robot vision, Robustness, sampling geometry, Sampling methods, Sensor phenomena and characterization}, isbn = {0-7803-8463-6}, doi = {10.1109/IROS.2004.1389992}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J. and Brajovic,V.} } @conference {12292, title = {A cooperative bulk transfer protocol}, booktitle = {IEEE Infocom}, year = {2004}, month = {2004///}, author = {Sherwood,R. and Braud,R. and Bhattacharjee, Bobby} } @conference {14807, title = {Data Centric Cache Measurement on the Intel ltanium 2 Processor}, booktitle = {Proceedings of the 2004 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {58{\textendash} - 58{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {Processor speed continues to increase faster than the speed of access to main memory, making effective use of memory caches more important. Information about an application{\'y}s interaction with the cache is therefore critical to performance tuning. To be most useful, tools that measure this information should relate it to the source code level data structures in an application. We describe how to gather such information by using hardware performance counters to sample cache miss addresses, and present a new tool named Cache Scope that does this using the Intel Itanium 2 performance monitors. We present experimental results concerning Cache Scope{\'y}s accuracy and perturbation of cache behavior. We also describe a case study of using Cache Scope to tune two applications, achieving 24\% and 19\% reductions in running time.}, isbn = {0-7695-2153-3}, doi = {http://dx.doi.org/10.1109/SC.2004.21}, url = {http://dx.doi.org/10.1109/SC.2004.21}, author = {Buck, Bryan R and Hollingsworth, Jeffrey K} } @article {14481, title = {Data sciences technology for homeland security information management and knowledge discovery}, journal = {Report of the DHS Workshop Data Sciences, Jointly Released by Sandia National Laboratories and Lawrence Livermore National Laboratory, Alexandria, Va}, year = {2004}, month = {2004///}, author = {Kolda,T. and Brown,D and Corones,J. and Critchlow,T. and Eliassi-Rad,T. and Getoor, Lise and Hendrickson,B. and Kumar, V. and Lambert,D. and Matarazzo,C.} } @article {12210, title = {DateLens: A fisheye calendar interface for PDAs}, journal = {ACM Transactions on Computer-Human Interaction (TOCHI)}, volume = {11}, year = {2004}, month = {2004///}, pages = {90 - 119}, author = {Bederson, Benjamin B. and Clamage,A. and Czerwinski,M.P. and Robertson,G.G.} } @article {14414, title = {Deduplication and group detection using links}, journal = {KDD workshop on link analysis and group detection}, year = {2004}, month = {2004///}, abstract = {Clustering is a fundamental problem in data mining. Tradi-tionally, clustering is done based on the similarity of the at- tribute values of the entities to be clustered. More recently, there has been greater interest in clustering relational and structured data. Often times this data is best described as a graph, in which there are both entities, described by a collec- tion of attributes, and links between entities, representing the relations between them. Clustering in these scenarios becomes more complex, as we should also take into account the similarity of the entity links when we are clustering. We propose novel distance measures for clustering linked data, and show how they can be used to solve two important data mining tasks, entity deduplication and group discovery. }, author = {Bhattacharya,I. and Getoor, Lise} } @article {17078, title = {Determining Causes and Severity of End-User Frustration}, journal = {International Journal of Human-Computer Interaction}, volume = {17}, year = {2004}, month = {2004///}, pages = {333 - 356}, abstract = {Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47\% to 53\% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38\%. These disturbing results should be a basis for future study.Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47\% to 53\% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38\%. These disturbing results should be a basis for future study. }, isbn = {1044-7318}, doi = {10.1207/s15327590ijhc1703_3}, url = {http://www.tandfonline.com/doi/abs/10.1207/s15327590ijhc1703_3}, author = {Ceaparu,Irina and Lazar,Jonathan and Bessiere,Katie and Robinson,John and Shneiderman, Ben} } @conference {19447, title = {Developing Locally Relevant Software Applications for Rural Areas: A South African Example}, booktitle = {SAICSIT {\textquoteright}04}, series = {SAICSIT {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {239 - 243}, publisher = {South African Institute for Computer Scientists and Information Technologists}, organization = {South African Institute for Computer Scientists and Information Technologists}, abstract = {The digital divide between rural and urban areas within developing countries is vast. We investigate how to address this divide by introducing Information and Communication Technologies (ICTs) into remote rural areas. Our aim is to discover how to create locally relevant software applications with appropriate content for these areas. We use a user centred design approach and a modified software development lifecyle that is participatory, iterative and cyclical. This process is based on principles from Participatory Design and Action Research. This paper presents our initial experience of developing a telemedicine application for a rural village in the Eastern Cape Province of South Africa using this process. We present an overview of the methodology, describe the software application we have developed and cite several challenges we have faced. Finally we conclude that an inter-organisational and inter-disciplinary approach is needed to develop software for remote areas.}, keywords = {action research, design, human factors, participatory design, telemedicine}, url = {http://dl.acm.org/citation.cfm?id=1035053.1035083}, author = {Marshini Chetty and Tucker, William and Blake, Edwin} } @article {12340, title = {DIF: An interchange format for dataflow-based design tools}, journal = {Computer Systems: Architectures, Modeling, and Simulation}, year = {2004}, month = {2004///}, pages = {3 - 32}, author = {Hsu,C. J and Keceli,F. and Ko,M. Y and Shahparnia,S. and Bhattacharyya, Shuvra S.} } @article {12681, title = {Dimensionality Estimation in Hyperspectral Imagery Using Minimum Description Length}, year = {2004}, month = {2004/12//}, institution = {MARYLAND UNIV COLLEGE PARK CENTER FOR AUTOMATION RESEARCH}, abstract = {Numerous algorithms have been developed for hyperspectral automatic target recognition (ATR) applications. Many of these algorithms require estimation of a background subspace. The estimation of the background subspace has been addressed using multiple methods. but most of these methods assume a-priori knowledge of the background dimensionality. In order to automate the estimation of the background subspace. we present an algorithm based on minimum description length (MDL) that can identify the background dimension. Results show that the MDL criterion estimates the proper dimension of the background for ATR applications.}, keywords = {*ALGORITHMS, *HYPERSPECTRAL IMAGERY, *TARGET DETECTION, *TARGET RECOGNITION, AUTOMATIC, BURIED OBJECTS, COMPONENT REPORTS, MINE DETECTION, NUMERICAL MATHEMATICS, SURFACE TARGETS., SYMPOSIA, TARGET DIRECTION, RANGE AND POSITION FINDING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA431643}, author = {Broadwater,Joshua B and Meth,Reuven and Chellapa, Rama} } @article {12285, title = {Efficient peer location on the Internet}, journal = {Computer Networks}, volume = {45}, year = {2004}, month = {2004/05/15/}, pages = {5 - 17}, abstract = {We consider the problem of locating nearby application peers over the Internet. We define a new peer-location scheme (called Tiers), that scales to large application peer groups. Tiers creates a hierarchy of peers, and provides an efficient and scalable solution to the peer-location problem. Tiers can be implemented entirely in the application-layer and does not require the deployment of either any additional measurement services, or well-known reference points in the network.We have evaluated the performance of Tiers through detailed experiments. Our results show that Tiers is able to locate the nearest peers quickly (<<1 s) and accurately on wide-area Internet-like topologies. We have also compared the performance of Tiers with two other schemes, Beaconing and Distributed Binning, both of which are known to have good performance. Both these techniques are reference-points based schemes and are efficient for overlays with a small number of peers (e.g. ⩽32). Our results show that Tiers significantly outperforms both these schemes. Tiers is particularly efficient for large overlay networks, has an order of magnitude lower control overhead for overlays with 512 peers and still achieves greater accuracy in locating the nearest peers. }, keywords = {Group communication, hierarchy, overlays, Peer location, triangle inequality}, isbn = {1389-1286}, doi = {10.1016/j.comnet.2004.02.005}, url = {http://www.sciencedirect.com/science/article/pii/S1389128604000271}, author = {Banerjee,Suman and Kommareddy,Chris and Bhattacharjee, Bobby} } @article {12297, title = {Efficient peer-to-peer namespace searches}, journal = {University of Maryland, College Park, MD, Tech. Rep. CSTR-4568}, year = {2004}, month = {2004///}, abstract = {In this paper we describe new methods for efficient and exact search (keyword and full-text) in distributed namespaces. Our methods can be used in conjunction with existing distributed lookup schemes, such as Distributed Hash Tables, and distributed directories. We describe how indexes for implementing distributed searches can be efficiently created, located, and stored. We describe techniques for creating approximate indexes that can be used to bound the space requirement at individual hosts; such techniques are particularly useful for full-text searches that may require a very large number of individual indexes to be created and maintained. Our methods use a new distributed data structure called the view tree. View trees can be used to efficiently cache and locate results from prior queries. We describe how view trees are created, and maintained. We present experimental results, using large namespaces and realistic data, showing that the techniques introduced in this paper can reduce search overheads (both network and processing costs) by more than an order of magnitude.}, author = {Gopalakrishnan,V. and Bhattacharjee, Bobby and Chawathe,S. and Keleher,P.} } @conference {12131, title = {Empirical-based estimation of the effect on software dependability of a technique for architecture conformance verification}, booktitle = {Proceedings of the ICSE 2004 Workshop on Architecting Dependable Systems, Edinburgh, UK}, year = {2004}, month = {2004///}, abstract = {The High Dependability Computing Program (HDCP)project is a NASA initiative for increasing dependability of software-based systems. It researches achieving high dependability by introducing new technologies. We focus on the evaluation of the effectiveness of technologies with respect to dependability. We employ empirical evaluation methods along with evaluation testbeds. In this paper, our technology evaluation approach is described. A testbed representative of air traffic control applications is used. An experiment to evaluate a technology to for identification of architectural violations is presented. }, author = {Asgari, S. and Basili, Victor R. and Costa,P. and Donzelli,P. and Hochstein, L. and Lindvall,M. and Rus,I. and Shull, F. and Tvedt,R. and Zelkowitz, Marvin V} } @conference {18759, title = {Enhancement of mechanical engineering curriculum to introduce manufacturing techniques and principles for bio-inspired product development}, year = {2004}, month = {2004///}, pages = {1 - 6}, url = {ftp://ftp.eng.umd.edu/:/home/glue/s/k/skgupta/backup/pub/Publication/IMECE04_Bruck.pdf}, author = {Bruck,H. A. and Gershon,A. L. and Gupta,S.K.} } @article {15384, title = {Finite-element computation of nonlinear magnetic diffusion and its effects when coupled to electrical, mechanical, and hydraulic systems}, journal = {Magnetics, IEEE Transactions on}, volume = {40}, year = {2004}, month = {2004/03//}, pages = {537 - 540}, abstract = {Finite elements are used to compute eddy currents and magnetic diffusion times in steel cylinders with nonlinear B{\textendash}H curves. Computations are made of diffusion times versus current in a typical axisymmetric magnetic actuator, showing good agreement with recently published approximate analytical formulas. The computed nonlinear diffusion times are then used to derive an equivalent resistor that is used in a model of an electrohydraulic system. The diffusion time causes delays in the coupled mechanical and hydraulic responses.}, keywords = {actuator;, actuators;, analysis;, axisymmetric, B-H, coupled, currents;, curves;, cylinders;, diffusion, diffusion;, eddy, electrical, electrohydraulic, electrohydraulics;, electromagnetic, element, equivalent, finite, finite-element, flux;, hydraulic, magnetic, mechanical, methods;, nonlinear, resistor;, responses;, steel, system;, systems;, times;, transducers;}, isbn = {0018-9464}, doi = {10.1109/TMAG.2004.824591}, author = {Brauer,J.R. and Mayergoyz, Issak D} } @article {13223, title = {Gait recognition using image self-similarity}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2004}, year = {2004}, month = {2004/01//}, pages = {572 - 585}, abstract = {Gait is one of the few biometrics that can be measured at a distance, and is hence useful for passive surveillance as well as biometric applications. Gait recognition research is still at its infancy, however, and we have yet to solve the fundamental issue of finding gait features which at once have suffcient discrimination power and can be extracted robustly and accurately from low-resolution video. This paper describes a novel gait recognition technique based on the image self-similarity of a walking person. We contend that the similarity plot encodes a projection of gait dynamics. It is also correspondence-free, robust to segmentation noise, and works well with low-resolution video. The method is tested on multiple data sets of varying sizes and degrees of diffculty. Performance is best for fronto-parallel viewpoints, whereby a recognition rate of 98\% is achieved for a data set of 6 people, and 70\% for a data set of 54 people.}, keywords = {behavioral biometrics, gait recognition, human identification at a distance, human movement analysis, pattern recognition}, isbn = {1110-8657}, doi = {10.1155/S1110865704309236}, url = {http://dx.doi.org/10.1155/S1110865704309236}, author = {BenAbdelkader,Chiraz and Cutler,Ross G. and Davis, Larry S.} } @conference {12293, title = {A game-theoretic framework for analyzing trust-inference protocols}, booktitle = {Workshop on Economics of Peer-to-Peer Systems}, year = {2004}, month = {2004///}, abstract = {We propose a novel game-theoretic framework foranalyzing the robustness of trust-inference protocols in the presence of adversarial (but rational) users. To the best of our knowledge, this is the first such framework which simultaneously (1) admits a rigor- ous and precise definition, thereby enabling formal proofs of security (in various adversarial settings) for specific trust-inference protocols; (2) is flexible enough to accommodate a full range of (realistic) ad- versarial behavior and network models; and (3) is ap- propriate for decentralized networks, and in particu- lar does not posit a trusted, centralized party with complete knowledge of the system history. We also show some preliminary results regarding the design of trust-inference protocols which can be rigorously proven secure within our model. In addition to establishing a solid foundation for future work, our framework also enables a rigorous and objective comparison among existing trust inference protocols. }, author = {Morselli,R. and Katz, Jonathan and Bhattacharjee, Bobby} } @conference {12287, title = {Hierarchical routing with soft-state replicas in TerraDir}, booktitle = {Parallel and Distributed Processing Symposium, 2004. Proceedings. 18th International}, year = {2004}, month = {2004/04//}, pages = {48 - 48}, abstract = {Summary form only given. Recent work on peer-to-peer systems has demonstrated the ability to deliver low latencies and good load balance when demand for data is relatively uniform. We describe an adaptive replication protocol that delivers low latencies, good load balance even when demand is heavily skewed. The protocol can withstand arbitrary and instantaneous changes in demand distribution. Our approach also addresses classical concerns related to topological constraints of asymmetrical namespaces, such as hierarchical bottlenecks in the context of hierarchical namespaces. The protocol replicates routing state in an ad-hoc manner based on profiled information, is lightweight, scalable, and requires no replica consistency guarantees.}, keywords = {ad-hoc, adaptive, allocation;, asymmetrical, balancing;, bottlenecks;, consistency, constraints;, delivering;, demand, distribution;, guarantees;, hierarchical, latency, load, low, namespaces;, peer-to-peer, protocol;, protocols;, replica, replicas;, replication, resource, routing;, soft-state, systems;, TerraDir;, topological}, doi = {10.1109/IPDPS.2004.1302967}, author = {Silaghi,B. and Gopalakrishnan,Vijay and Bhattacharjee, Bobby and Kelcher,P.} } @conference {12691, title = {A hybrid algorithm for subpixel detection in hyperspectral imagery}, booktitle = {Geoscience and Remote Sensing Symposium, 2004. IGARSS {\textquoteright}04. Proceedings. 2004 IEEE International}, volume = {3}, year = {2004}, month = {2004/09//}, pages = {1601 -1604 vol.3 - 1601 -1604 vol.3}, abstract = {Numerous subpixel detection algorithms utilizing structured backgrounds have been developed over the past few years. These range from detection schemes based on spectral unmixing to generalized likelihood ratio tests. Spectral unmixing algorithms such as the Fully Constrained Least Squares (FCLS) algorithm have the advantage of physically modeling the interactions of spectral signatures based on reflectance/emittance spectroscopy. Generalized likelihood ratio tests like the Adaptive Matched Subspace Detector (AMSD) have the advantage of identifying targets that are statistically different from the background. Therefore, a hybrid detector based on both AMSD and FCLS was developed to take advantage of each detector{\textquoteright}s strengths. Results demonstrate that the hybrid detector achieved the lowest false alarm rates while also producing meaningful abundance estimates}, keywords = {alarm, algorithm;abundance, algorithm;Fully, algorithm;hybrid, algorithm;statistical, AMSD;Adaptive, analysis;structured, approximations;maximum, backgrounds;subpixel, constrained, detection;alarm, detection;target, Detector;FCLS, detector;hyperspectral, estimation;, estimation;emittance, identification;adaptive, imagery;reflectance, least, likelihood, Matched, matching;least, processing;geophysical, rate;generalized, ratio, signal, signatures;spectral, spectra;false, spectra;spectral, squares, subspace, systems;geophysical, techniques;image, tests;hybrid, unmixing}, doi = {10.1109/IGARSS.2004.1370633}, author = {Broadwater, J. and Meth, R. and Chellapa, Rama} } @inbook {13787, title = {iCLEF 2003 at Maryland: Translation Selection and Document Selection}, booktitle = {Comparative Evaluation of Multilingual Information Access SystemsComparative Evaluation of Multilingual Information Access Systems}, series = {Lecture Notes in Computer Science}, volume = {3237}, year = {2004}, month = {2004///}, pages = {231 - 265}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Maryland performed two sets of experiments for the 2003 Cross-Language Evaluation Forum{\textquoteright}s interactive track, one focused on interactive selection of appropriate translations for query terms, the second focused on interactive selection of relevant documents. Translation selection was supported using possible synonyms discovered through back translation and two techniques for generating KeyWord In Context (KWIC) examples of usage. The results indicate that searchers typically achieved a similar search effectiveness using fewer query iterations when interactive translation selection was available. For document selection, a complete extract of the first 40 words of each news story was compared to a compressed extract generated using an automated parse-and-trim approach that approximates one way in which people can produce headlines. The results indicate that compressed {\textquotedblleft}headlines{\textquotedblright} result in faster assessment, but with a 20\% relative reduction in the F α = 0.8 search effectiveness measure.}, isbn = {978-3-540-24017-4}, url = {http://dx.doi.org/10.1007/978-3-540-30222-3_42}, author = {Dorr, Bonnie J and He,Daqing and Luo,Jun and Oard, Douglas and Schwartz,Richard and Wang,Jianqiang and Zajic, David}, editor = {Peters,Carol and Gonzalo,Julio and Braschler,Martin and Kluck,Michael} } @conference {17806, title = {Implementing stable semantics by linear programming}, booktitle = {Logic Programming and Non-Monotonic Reasoning, Proceedings of the Second International Workshop}, volume = {7}, year = {2004}, month = {2004///}, pages = {23 - 42}, author = {Bell,C. and Nerode,A. and Ng,R. T and V.S. Subrahmanian} } @conference {16887, title = {Importing abstract spatial data into the SAND database system}, booktitle = {Proceedings of the 2004 annual national conference on Digital government research}, series = {dg.o {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {62:1{\textendash}62:2 - 62:1{\textendash}62:2}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {The World Wide Web has opened ways to operate large applications by users with simple client platforms located half way around the world by connecting servers around the world together. We present a system that makes a centrally stored spatial database available to off-site users. Regardless of the specific platform available to a user, all they need to do is simply establish a link between their client and the server. Unlike well-known web-based services such as MapQuest [2] that rely on computational power of the server, our system distributes the workload among the client and the server in such a manner that the user will observe the system as being interactive, with minimal delay between the user action and appropriate response for most types of operations.}, url = {http://dl.acm.org/citation.cfm?id=1124191.1124253}, author = {Samet, Hanan and Brabec,Frantisek and Sankaranarayanan,Jagan} } @article {13227, title = {Improved Multiuser Detectors Employing Genetic Algorithms in a Space-Time Block Coded System, Yinggang Du and Kam Tai Chan}, journal = {Signal}, volume = {2004}, year = {2004}, month = {2004///}, pages = {640 - 648}, author = {Self-Similarity,G.R.U.I. and BenAbdelkader,C. and Cutler,R.G. and Davis, Larry S. and Local,F.R.U. and Global Features,J.H. and Yuen, P.C. and Lai,JH and Li,C.} } @article {14087, title = {The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei}, journal = {Molecular biology and evolution}, volume = {21}, year = {2004}, month = {2004///}, pages = {520 - 520}, author = {Bringaud,F. and Biteau,N. and Zuiderwijk,E. and Berriman,M. and El-Sayed, Najib M. and Ghedin,E. and Melville,S. E. and Hall,N. and Baltz,T.} } @article {17260, title = {Interactively Optimizing Signal-to-Noise Ratios in Expression Profiling: Project-Specific Algorithm Selection and Detection P-Value Weighting in Affymetrix Microarrays}, journal = {BioinformaticsBioinformatics}, volume = {20}, year = {2004}, month = {2004/11/01/}, pages = {2534 - 2544}, abstract = {Motivation: The most commonly utilized microarrays for mRNA profiling (Affymetrix) include {\textquoteleft}probe sets{\textquoteright} of a series of perfect match and mismatch probes (typically 22 oligonucleotides per probe set). There are an increasing number of reported {\textquoteleft}probe set algorithms{\textquoteright} that differ in their interpretation of a probe set to derive a single normalized {\textquoteleft}signal{\textquoteright} representative of expression of each mRNA. These algorithms are known to differ in accuracy and sensitivity, and optimization has been done using a small set of standardized control microarray data. We hypothesized that different mRNA profiling projects have varying sources and degrees of confounding noise, and that these should alter the choice of a specific probe set algorithm. Also, we hypothesized that use of the Microarray Suite (MAS) 5.0 probe set detection p-value as a weighting function would improve the performance of all probe set algorithms.Results: We built an interactive visual analysis software tool (HCE2W) to test and define parameters in Affymetrix analyses that optimize the ratio of signal (desired biological variable) versus noise (confounding uncontrolled variables). Five probe set algorithms were studied with and without statistical weighting of probe sets using the MAS 5.0 probe set detection p-values. The signal-to-noise ratio optimization method was tested in two large novel microarray datasets with different levels of confounding noise, a 105 sample U133A human muscle biopsy dataset (11 groups: mutation-defined, extensive noise), and a 40 sample U74A inbred mouse lung dataset (8 groups: little noise). Performance was measured by the ability of the specific probe set algorithm, with and without detection p-value weighting, to cluster samples into the appropriate biological groups (unsupervised agglomerative clustering with F-measure values). Of the total random sampling analyses, 50\% showed a highly statistically significant difference between probe set algorithms by ANOVA [F(4,10) > 14, p < 0.0001], with weighting by MAS 5.0 detection p-value showing significance in the mouse data by ANOVA [F(1,10) > 9, p < 0.013] and paired t-test [t(9) = -3.675, p = 0.005]. Probe set detection p-value weighting had the greatest positive effect on performance of dChip difference model, ProbeProfiler and RMA algorithms. Importantly, probe set algorithms did indeed perform differently depending on the specific project, most probably due to the degree of confounding noise. Our data indicate that significantly improved data analysis of mRNA profile projects can be achieved by optimizing the choice of probe set algorithm with the noise levels intrinsic to a project, with dChip difference model with MAS 5.0 detection p-value continuous weighting showing the best overall performance in both projects. Furthermore, both existing and newly developed probe set algorithms should incorporate a detection p-value weighting to improve performance. Availability: The Hierarchical Clustering Explorer 2.0 is available at http://www.cs.umd.edu/hcil/hce/. Murine arrays (40 samples) are publicly available at the PEPR resource (http://microarray.cnmcresearch.org/pgadatatable.asp; http://pepr.cnmcresearch.org; Chen et al., 2004). }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/bth280}, url = {http://bioinformatics.oxfordjournals.org/content/20/16/2534}, author = {Seo,Jinwook and Bakay,Marina and Chen,Yi-Wen and Hilmer,Sara and Shneiderman, Ben and Hoffman,Eric P} } @book {12353, title = {Interconnect Synthesis for Systems on Chip}, year = {2004}, month = {2004///}, publisher = {MARYLAND UNIV COLLEGE PARK DEPT OF ELECTRICAL AND COMPUTER ENGINEERING}, organization = {MARYLAND UNIV COLLEGE PARK DEPT OF ELECTRICAL AND COMPUTER ENGINEERING}, author = {Bhattacharyya, Shuvra S. and Bambha,N. K} } @conference {14464, title = {Iterative record linkage for cleaning and integration}, booktitle = {Proceedings of the 9th ACM SIGMOD workshop on Research issues in data mining and knowledge discovery}, series = {DMKD {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {11 - 18}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Record linkage, the problem of determining when two records refer to the same entity, has applications for both data cleaning (deduplication) and for integrating data from multiple sources. Traditional approaches use a similarity measure that compares tuples{\textquoteright} attribute values; tuples with similarity scores above a certain threshold are declared to be matches. While this method can perform quite well in many domains, particularly domains where there is not a large amount of noise in the data, in some domains looking only at tuple values is not enough. By also examining the context of the tuple, i.e. the other tuples to which it is linked, we can come up with a more accurate linkage decision. But this additional accuracy comes at a price. In order to correctly find all duplicates, we may need to make multiple passes over the data; as linkages are discovered, they may in turn allow us to discover additional linkages. We present results that illustrate the power and feasibility of making use of join information when comparing records.}, keywords = {clustering, deduplication, distance measure, record linkage}, isbn = {1-58113-908-X}, doi = {10.1145/1008694.1008697}, url = {http://doi.acm.org/10.1145/1008694.1008697}, author = {Bhattacharya,Indrajit and Getoor, Lise} } @conference {12367, title = {Java-through-c compilation: An enabling technology for java in embedded systems}, booktitle = {Proceedings of the conference on Design, automation and test in Europe-Volume 3}, year = {2004}, month = {2004///}, pages = {30161 - 30161}, author = {Varma,A. and Bhattacharyya, Shuvra S.} } @conference {14552, title = {Low-dimensional embedding with extra information}, booktitle = {Proceedings of the twentieth annual symposium on Computational geometry}, year = {2004}, month = {2004///}, pages = {320 - 329}, author = {Bǎdoiu,M. and Demaine,E. D and Hajiaghayi, Mohammad T. and Indyk,P.} } @article {18512, title = {Managing the 802.11 energy/performance tradeoff with machine learning}, volume = {MIT-CSAIL-TR-2004-068}, year = {2004}, month = {2004///}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {This paper addresses the problem of managing the tradeoff betweenenergy consumption and performance in wireless devices implementingthe IEEE 802.11 standard. To save energy, the 802.11 specificationproposes a power-saving mode (PSM), where a device can sleep to saveenergy, periodically waking up to receive packets from a neighbor(e.g., an access point) that may have buffered packets for thesleeping device. Previous work has shown that a fixed polling time forwaking up degrades the performance of Web transfers, because networkactivity is bursty and time-varying. We apply a new online machinelearning algorithm to this problem and show, using ns simulation andtrace analysis, that it is able to adapt well to network activity. Thelearning process makes no assumptions about the underlying networkactivity being stationary or even Markov. Our learning power-savingalgorithm, LPSM, guides the learning using a "loss function" thatcombines the increased latency from potentially sleeping too long andthe wasted use of energy in waking up too soon. In our nssimulations, LPSM saved 7\%-20\% more energy than 802.11 in power-savingmode, with an associated increase in average latency by a factor of1.02, and not more than 1.2. LPSM is straightforward to implementwithin the 802.11 PSM framework.}, url = {http://hdl.handle.net/1721.1/30499}, author = {Monteleoni,C. and Balakrishnan,H. and Feamster, Nick and Jaakkola,T.} } @inbook {19651, title = {An MCMC-Based Particle Filter for Tracking Multiple Interacting Targets}, booktitle = {Computer Vision - ECCV 2004}, series = {Lecture Notes in Computer Science}, year = {2004}, month = {2004/01/01/}, pages = {279 - 290}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We describe a Markov chain Monte Carlo based particle filter that effectively deals with interacting targets, i.e., targets that are influenced by the proximity and/or behavior of other targets. Such interactions cause problems for traditional approaches to the data association problem. In response, we developed a joint tracker that includes a more sophisticated motion model to maintain the identity of targets throughout an interaction, drastically reducing tracker failures. The paper presents two main contributions: (1) we show how a Markov random field (MRF) motion prior, built on the fly at each time step, can substantially improve tracking when targets interact, and (2) we show how this can be done efficiently using Markov chain Monte Carlo (MCMC) sampling. We prove that incorporating an MRF to model interactions is equivalent to adding an additional interaction factor to the importance weights in a joint particle filter. Since a joint particle filter suffers from exponential complexity in the number of tracked targets, we replace the traditional importance sampling step in the particle filter with an MCMC sampling step. The resulting filter deals efficiently and effectively with complicated interactions when targets approach each other. We present both qualitative and quantitative results to substantiate the claims made in the paper, including a large scale experiment on a video-sequence of over 10,000 frames in length.}, keywords = {Artificial Intelligence (incl. Robotics), Computer Graphics, Image Processing and Computer Vision, pattern recognition}, isbn = {978-3-540-21981-1, 978-3-540-24673-2}, url = {http://link.springer.com/chapter/10.1007/978-3-540-24673-2_23}, author = {Zia Khan and Balch, Tucker and Dellaert, Frank}, editor = {Pajdla, Tom{\'a}s and Matas, Ji{\v r}{\'\i}} } @conference {12291, title = {Measurement based optimal multi-path routing}, booktitle = {INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies}, volume = {1}, year = {2004}, month = {2004/03//}, pages = {187 - 196}, abstract = {We propose a new architecture for efficient network monitoring and measurements in a traditional IP network. This new architecture enables establishment of multiple paths (tunnels) between source-destination pairs without having to modify the underlying routing protocol(s). Based on the proposed architecture we propose a measurement-based multipath routing algorithm derived from simultaneous perturbation stochastic approximation. The proposed algorithm does not assume that the gradient of analytical cost function is known to the algorithm, but rather relies on noisy estimates from measurements. Using the analytical model presented in the paper we prove the convergence of the algorithm to the optimal solution. Simulation results are presented to demonstrate the advantages of the proposed algorithm under a variety of network scenarios. A comparative study with an existing optimal routing algorithm, MATE, is also provided}, keywords = {algorithm;network, approximation;routing, IP, measurement;network, monitoring;optimization;perturbation, multipath, network;measurement-based, networks;Internet;optimisation;routing, processes;, protocol;IP, protocols;stochastic, Routing, Stochastic}, doi = {10.1109/INFCOM.2004.1354493}, author = {Guven,T. and Kommareddy,C. and La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @conference {12286, title = {Multi-dimensional quorum sets for read-few write-many replica control protocols}, booktitle = {Cluster Computing and the Grid, 2004. CCGrid 2004. IEEE International Symposium on}, year = {2004}, month = {2004/04//}, pages = {355 - 362}, abstract = {We describe d-spaces, a replica control protocol defined in terms of quorum sets on multi-dimensional logical structures. Our work is motivated by asymmetrical access patterns, where the number of read accesses to data are dominant relative to update accesses, i.e. where the protocols should be read-few write-many. D-spaces are optimal with respect to quorum group sizes. The quality of the tradeoff between read efficiency and update availability is not matched by existing quorum protocols. We also propose a novel scheme for implementing d-spaces that combines caching and local information to provide a best-effort form of global views. This allows quorum reconfiguration to be lightweight without impacting access latencies, even when the rate of membership changes is very high.}, keywords = {accesses;, availability;, cache, caching;, Communication, complexity;, CONTROL, d-spaces;, distributed, efficiency;, lightweight, logical, multi-dimensional, processing;, protocols;, quorum, read, read-few, reconfiguration;, replica, sets;, storage;, structures;, update, write-many}, doi = {10.1109/CCGrid.2004.1336588}, author = {Silaghi,B. and Keleher,P. and Bhattacharjee, Bobby} } @article {14990, title = {Multiscale advanced raster map analysis system: definition, design and development}, journal = {Environmental and Ecological Statistics}, volume = {11}, year = {2004}, month = {2004///}, pages = {113 - 138}, abstract = {This paper brings together a multidisciplinary initiative to develop advanced statistical and computational techniques for analyzing, assessing, and extracting information from raster maps. This information will provide a rigorous foundation to address a wide range of applications including disease mapping, emerging infectious diseases, landscape ecological assessment, land cover trends and change detection, watershed assessment, and map accuracy assessment. It will develop an advanced map analysis system that integrates these techniques with an advanced visualization toolbox, and use the system to conduct large case studies using rich sets of raster data, primarily from remotely sensed imagery. As a result, it will be possible to study and evaluate raster maps of societal, ecological, and environmental variables to facilitate quantitative characterization and comparative analysis of geospatial trends, patterns, and phenomena. In addition to environmental and ecological studies, these techniques and tools can be used for policy decisions at national, state, and local levels, crisis management, and protection of infrastructure. Geospatial data form the foundation of an information-based society. Remote sensing has been a vastly under-utilized resource involving a multi-million dollar investment at the national levels. Even when utilized, the credibility has been at stake, largely because of lack of tools that can assess, visualize, and communicate accuracy and reliability in timely manner and at desired confidence levels. Consider an imminent 21st century scenario: What message does a multi-categorical map have about the large landscape it represents? And at what scale, and at what level of detail? Does the spatial pattern of the map reveal any societal, ecological, environmental condition of the landscape? And therefore can it be an indicator of change? How do you automate the assessment of the spatial structure and behavior of change to discover critical areas, hot spots, and their corridors? Is the map accurate? How accurate is it? How do you assess the accuracy of the map? How do we evaluate a temporal change map for change detection? What are the implications of the kind and amount of change and accuracy on what matters, whether climate change, carbon emission, water resources, urban sprawl, biodiversity, indicator species, human health, or early warning? And with what confidence? The proposed research initiative is expected to find answers to these questions and a few more that involve multi-categorical raster maps based on remote sensing and other geospatial data. It includes the development of techniques for map modeling and analysis using Markov Random Fields, geospatial statistics, accuracy assessment and change detection, upper echelons of surfaces, advanced computational techniques for geospatial data mining, and advanced visualization techniques.}, doi = {10.1023/B:EEST.0000027205.77490.8c}, author = {Patil,G. P. and Balbus,J. and Biging,G. and JaJa, Joseph F. and Myers,W. L. and Taillie,C.} } @article {12149, title = {New year{\textquoteright}s resolutions for software quality}, journal = {IEEE Software}, volume = {21}, year = {2004}, month = {2004///}, pages = {12 - 13}, abstract = {In the spirit of making resolutions for betterment in the New Year, ten distinguished individuals in the software quality field offer their recommendations on how organizations can improve software quality In the spirit of making resolutions for betterment in the New Year, ten distinguished individuals in the software quality field offer their recommendations on how organizations can improve software quality.}, author = {Basili, Victor R. and Boehm,B. and Davis,A. and Humphrey,W. S and Leveson,N. and Mead,N. R and Musa,J. D and Parnas,D. L and Pfleeger,S. L and Weyuker,E.} } @article {14590, title = {A Note on Efficient Computation of Haplotypes via Perfect Phylogeny}, journal = {Journal of Computational Biology}, volume = {11}, year = {2004}, month = {2004/10//}, pages = {858 - 866}, abstract = {The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is partly due to the observation that there are many regions on human genomic DNA where genetic recombination is rare (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. Gusfield{\textquoteright}s solution based on matroid theory was followed by direct θ(nm2 ) solutions that use simpler techniques (Bafna et al., 2003; Eskin et al., 2003), and also bound the number of solutions to the PPH problem. In this short note, we address two questions that were left open. First, can the algorithms of Bafna et al. (2003) and Eskin et al. (2003) be sped-up to O(nm + m2 ) time, which would imply an O(nm) time-bound for the PPH problem? Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes.We give reductions that suggests that the answer to both questions is "no." For the first problem, we show that computing the output of the first step (in either method) is equivalent to Boolean matrix multiplication. Therefore, the best bound we can presently achieve is O(nmω{\textendash}1), where ω <= 2.52 is the exponent of matrix multiplication. Thus, any linear time solution to the PPH problem likely requires a different approach. For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979).}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.2004.11.858}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2004.11.858}, author = {Bafna,Vineet and Gusfield,Dan and Hannenhalli, Sridhar and Yooseph,Shibu} } @article {12409, title = {Only in Europe?: The Economic and Military Foundations of European World Empires}, journal = {Typescript. Princeton University}, year = {2004}, month = {2004///}, author = {Jordan Boyd-Graber} } @article {12938, title = {Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh}, journal = {Canadian Journal of Microbiology}, volume = {50}, year = {2004}, month = {2004/10//}, pages = {827 - 834}, abstract = {A total of 1500 environmental strains of Vibrio parahaemolyticus, isolated from the aquatic environment of Bangladesh, were screened for the presence of a major V. parahaemolyticus virulence factor, the thermostable direct haemolysin (tdh) gene, by the colony blot hybridization method using a digoxigenin-labeled tdh gene probe. Of 1500 strains, 5 carried the tdh sequence, which was further confirmed by PCR using primers specific for the tdh gene. Examination by PCR confirmed that the 5 strains were V. parahamolyticus and lacked the thermostable direct haemolysin-related haemolysin (trh) gene, the alternative major virulence gene known to be absent in pandemic strains. All 5 strains gave positive Kanagawa phenomenon reaction with characteristic beta-haemolysis on Wagatsuma agar medium. Southern blot analysis of the HindIII-digested chromosomal DNA demonstrated, in all 5 strains, the presence of 2 tdh genes common to strains positive for Kanagawa phenomenon. However, the 5 strains were found to belong to 3 different serotypes (O3:K29, O4:K37, and O3:K6). The 2 with pandemic serotype O3:K6 gave positive results in group-specific PCR and ORF8 PCR assays, characteristics unique to the pandemic clone. Clonal variations among the 5 isolates were analyzed by comparing RAPD and ribotyping patterns. Results showed different patterns for the 3 serotypes, but the pattern was identical among the O3:K6 strains. This is the first report on the isolation of pandemic O3:K6 strains of V. parahaemolyticus from the aquatic environment of Bangladesh.}, url = {http://umd.library.ingentaconnect.com/content/nrc/cjm/2004/00000050/00000010/art00007}, author = {Islam,M. S. and Tasmin,Rizwana and Khan,Sirajul I. s l a m and Bakht,Habibul B. M. and Mahmood,Zahid H. a y a t and Rahman,M. Z. i a u r and Bhuiyan,Nurul A. m i n and Nishibuchi,Mitsuaki and Nair,G. B. a l a k r i s h and Sack,R. B. r a d l e y and Huq,Anwar and Rita R Colwell and Sack,David A.} } @conference {12170, title = {Pocket PhotoMesa: a Zoomable image browser for PDAs}, booktitle = {Proceedings of the 3rd international conference on Mobile and ubiquitous multimedia}, year = {2004}, month = {2004///}, pages = {19 - 24}, author = {Khella,A. and Bederson, Benjamin B.} } @conference {13919, title = {Preschool children{\textquoteright}s use of mouse buttons}, booktitle = {CHI{\textquoteright}04 extended abstracts on Human factors in computing systems}, year = {2004}, month = {2004///}, pages = {1411 - 1412}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison} } @conference {16493, title = {Querying Web-Accessible Life Science Sources: Which paths to choose?}, booktitle = {Proceedings of VLDB Workshop on Information Integration on the Web (IIWeb-2004)}, year = {2004}, month = {2004///}, pages = {83 - 83}, author = {Bleiholder,J. and Naumann,F. and Raschid, Louiqa and Vidal,M. E} } @conference {19649, title = {A Rao-Blackwellized particle filter for EigenTracking}, booktitle = {Proceedings of the 2004 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2004. CVPR 2004}, volume = {2}, year = {2004}, month = {2004/06//}, pages = {II - 980-II-986 Vol.2}, abstract = {Subspace representations have been a popular way to model appearance in computer vision. In Jepson and Black{\textquoteright}s influential paper on EigenTracking, they were successfully applied in tracking. For noisy targets, optimization-based algorithms (including EigenTracking) often fail catastrophically after losing track. Particle filters have recently emerged as a robust method for tracking in the presence of multi-modal distributions. To use subspace representations in a particle filter, the number of samples increases exponentially as the state vector includes the subspace coefficients. We introduce an efficient method for using subspace representations in a particle filter by applying Rao-Blackwellization to integrate out the subspace coefficients in the state vector. Fewer samples are needed since part of the posterior over the state vector is analytically calculated. We use probabilistic principal component analysis to obtain analytically tractable integrals. We show experimental results in a scenario in which we track a target in clutter.}, keywords = {analytically tractable integrals, Computer vision, EigenTracking, Filters, Gaussian processes, modal analysis, multi-modal distributions, NOISE, noisy targets, optimisation, optimization-based algorithms, Particle filters, Particle measurements, Particle tracking, Principal component analysis, probabilistic principal component analysis, Rao-Blackwellized particle filter, Robustness, SHAPE, State estimation, state vector, subspace coefficients, Subspace representations, target tracking, vectors}, author = {Zia Khan and Balch, T. and Dellaert, F.} } @article {14253, title = {Robotics \& Automation Magazine Vol. 11}, journal = {IEEE Robotics \& Automation Magazine}, year = {2004}, month = {2004///}, pages = {132 - 132}, author = {Aliaga, D.G. and Allen,PK and Archibald,JK and Argyros,AA and Arkin,RC and Baker,C. and Baker, P. and Beard,RW and Bicchi,A. and Birgmajer,B. and others} } @conference {12295, title = {Running on the bare metal with GeekOS}, booktitle = {Proceedings of the 35th SIGCSE technical symposium on Computer science education}, series = {SIGCSE {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {315 - 319}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Undergraduate operating systems courses are generally taught using one of two approaches: abstract or concrete. In the abstract approach, students learn the concepts underlying operating systems theory, and perhaps apply them using user-level threads in a host operating system. In the concrete approach, students apply concepts by working on a real operating system kernel. In the purest manifestation of the concrete approach, students implement operating system projects that run on real hardware.GeekOS is an instructional operating system kernel which runs on real hardware. It provides the minimum functionality needed to schedule threads and control essential devices on an x86 PC. On this foundation, we have developed projects in which students build processes, semaphores, a multilevel feedback scheduler, paged virtual memory, a filesystem, and inter-process communication. We use the Bochs emulator for ease of development and debugging. While this approach (tiny kernel run on an emulator) is not new, we believe GeekOS goes further towards the goal of combining realism and simplicity than previous systems have.}, keywords = {education, emulation, Hardware, Operating systems}, isbn = {1-58113-798-2}, doi = {10.1145/971300.971411}, url = {http://doi.acm.org/10.1145/971300.971411}, author = {Hovemeyer, David and Hollingsworth, Jeffrey K and Bhattacharjee, Bobby} } @conference {12298, title = {Scalable resilient media streaming}, booktitle = {Proceedings of the 14th international workshop on Network and operating systems support for digital audio and video}, series = {NOSSDAV {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {4 - 9}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a low-overhead media streaming system, called SRMS (Scalable Resilient Media Streaming) that can be used to scalably deliver streaming data to a large group of receivers. SRMS uses overlay multicast for data distribution. to a large group of users. SRMS leverages a probabilistic loss recovery technique to provide high data delivery guarantees even under large network losses and overlay node failures. The clients in the SRMS system are able to interoperate with existing media streaming servers that use RTP for data transport. One of the interesting features of SRMS is that it can simultaneously support clients with disparate access bandwidths. It enables the necessary bandwidth adaptations using standard Real-time Transport Protocol (RTP) mechanisms, e.g. RTP translators. We have implemented and evaluated the SRMS system in detail on an emulated network as well as on a wide-area testbed with up to 128 clients. Our results show that clients using SRMS achieve high (97\%) data delivery ratios with low overheads (<5\%) even for a very dynamic network (up to five membership changes per minute).}, keywords = {media streaming, Multicast, overlay network, Resilience}, isbn = {1-58113-801-6}, doi = {10.1145/1005847.1005851}, url = {http://doi.acm.org/10.1145/1005847.1005851}, author = {Banerjee,Suman and Lee,Seungjoon and Braud,Ryan and Bhattacharjee, Bobby and Srinivasan, Aravind} } @article {14256, title = {Self-Calibration from Image Derivatives}, journal = {International Journal of Computer Vision}, volume = {48}, year = {2004}, month = {2004///}, pages = {91 - 114}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia} } @article {14080, title = {Sequencing Strategies for Parasite Genomes}, journal = {METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-}, volume = {270}, year = {2004}, month = {2004///}, pages = {1 - 16}, author = {Bartholomeu,D. and El-Sayed, Najib M. and Melville,S. E.} } @article {17657, title = {SESSION 2: STREAMING}, journal = {Proceedings of the 14th International Workshop on Network and Operating Systems Support for Digital Audio and Video: NOSSDAV 2003: June 16-18, 2004, Cork, Ireland}, year = {2004}, month = {2004///}, pages = {3 - 3}, author = {Banerjee,S. and Lee,S. and Braud,R. and Bhattacharjee, Bobby and Srinivasan, Aravind and Chu,Y. and Zhang,H. and Sinha,R. and Papadopoulos,C. and Boustead,P. and others} } @article {12171, title = {SlideBar: Analysis of a linear input device}, journal = {Behaviour \& Information Technology}, volume = {23}, year = {2004}, month = {2004///}, pages = {1 - 9}, author = {Chipman,L.E. and Bederson, Benjamin B. and Golbeck,J.} } @conference {12288, title = {Slurpie: a cooperative bulk data transfer protocol}, booktitle = {INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies}, volume = {2}, year = {2004}, month = {2004/03//}, pages = {941 - 951 vol.2 - 941 - 951 vol.2}, abstract = {We present Slurpie: a peer-to-peer protocol for bulk data transfer. Slurpie is specifically designed to reduce client download times for large, popular files, and to reduce load on servers that serve these files. Slurpie employs a novel adaptive downloading strategy to increase client performance, and employs a randomized backoff strategy to precisely control load on the server. We describe a full implementation of the Slurpie protocol, and present results from both controlled local-area and wide-area testbeds. Our results show that Slurpie clients improve performance as the size of the network increases, and the server is completely insulated from large flash crowds entering the Slurpie network.}, keywords = {adaptive, bulk, client-server, clients;, computing;, cooperative, data, data;, downloading, network;, peer-to-peer, protocol;, protocols;, Slurpie, strategy;, systems;, transfer, transport}, doi = {10.1109/INFCOM.2004.1356981}, author = {Sherwood,R. and Braud,R. and Bhattacharjee, Bobby} } @inbook {17367, title = {Social and psychological influences on computer user frustration}, booktitle = {Media access: Social and psychological dimensions of new technology useMedia access: Social and psychological dimensions of new technology use}, year = {2004}, month = {2004///}, pages = {91 - 103}, author = {Bessiere,K. and Ceaparu,I. and Lazar,J. and Robinson,J. and Shneiderman, Ben} } @article {18490, title = {Some foundational problems in interdomain routing}, journal = {Proceedings of Third Workshop on Hot Topics in Networks (HotNets-III)}, year = {2004}, month = {2004///}, abstract = {The substantial complexity of interdomain routing in theInternet comes from the need to support flexible poli- cies while scaling to a large number of Autonomous Systems. Despite impressive progress in characterizing the various ills of the Border Gateway Protocol (BGP), many problems remain unsolved, and the behavior of the routing system is still poorly understood. This paper argues that we must understand interdomain routing in terms of: (1) intrinsic properties and design tradeoffs of policy-based routing, independent of the specific routing protocol and (2) properties that relate to artifacts in to- day{\textquoteright}s protocol. We pose open questions for the research community that, if answered, should help us understand why BGP{\textquoteright}s many problems are so difficult to fix. Un- derstanding the fundamental properties of interdomain routing will help us decide how to make progress, be it making backward-compatible modifications to BGP or designing a radically different protocol. }, author = {Feamster, Nick and Balakrishnan,H. and Rexford,J.} } @article {12157, title = {Spiral acquisition of software-intensive systems of systems}, journal = {CrossTalk}, year = {2004}, month = {2004///}, pages = {4 - 9}, author = {Boehm,B. and Brown,A. W and Basili, Victor R. and Turner,R.} } @article {12068, title = {Structure from motion of parallel lines}, journal = {Computer Vision-ECCV 2004}, year = {2004}, month = {2004///}, pages = {229 - 240}, author = {Baker, P. and Aloimonos, J.} } @conference {14761, title = {Studying code development for high performance computing: the HPCS program}, booktitle = {First International Workshop On Software Engineering for High Performance Computing System Applications}, year = {2004}, month = {2004///}, pages = {32 - 32}, author = {Carver, J. and Asgari, S. and Basili, Victor R. and Hochstein, L. and Hollingsworth, Jeffrey K and Shull, F. and Zelkowitz, Marvin V} } @conference {12393, title = {Systematic exploitation of data parallelism in hardware synthesis of DSP applications}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {5}, year = {2004}, month = {2004/05//}, pages = {V - 229-32 vol.5 - V - 229-32 vol.5}, abstract = {We describe an approach that we have explored for low-power synthesis and optimization of image, video, and digital signal processing (DSP) applications. In particular, we consider the systematic exploitation of data parallelism across the operations of an application dataflow graph when synthesizing a dedicated hardware implementation. Data parallelism occurs commonly in DSP applications, and provides flexible opportunities to increase throughput or lower power consumption. Exploiting this parallelism in a dedicated hardware implementation comes at the expense of increased resource requirements, which must be balanced carefully when applying the technique in a design tool. We propose a high level synthesis algorithm to determine the data parallelism factor for each computation, and, based on the area and performance trade-off curve, design an efficient hardware representation of the dataflow graph. For performance estimation, our approach uses a cyclostatic dataflow intermediate representation of the hardware structure under synthesis. We then apply an automatic hardware generation framework to build the actual circuit.}, keywords = {area-performance trade-off curve, automatic Verilog code generation, circuit optimisation, data flow graphs, data parallelism, dedicated hardware implementation synthesis, design tool, Digital signal processing, DSP applications, embedded systems, hardware description languages, hardware synthesis, high level synthesis, high level synthesis algorithm, IMAGE PROCESSING, PARALLEL PROCESSING, power consumption, Signal processing, synchronous dataflow graph, video processing}, doi = {10.1109/ICASSP.2004.1327089}, author = {Sen,M. and Bhattacharyya, Shuvra S.} } @conference {12354, title = {Systematic Integration of Parameterized Local Search Techniques in Evolutionary Algorithms}, booktitle = {Genetic and Evolutionary Computation{\textendash}GECCO 2004}, year = {2004}, month = {2004///}, pages = {383 - 384}, author = {Bambha,N. K and Bhattacharyya, Shuvra S. and Teich,J. and Zitzler,E.} } @article {12169, title = {Toolkit design for interactive structured graphics}, journal = {Software Engineering, IEEE Transactions on}, volume = {30}, year = {2004}, month = {2004///}, pages = {535 - 546}, author = {Bederson, Benjamin B. and Grosjean,J. and Meyer,J.} } @conference {12289, title = {Trust-preserving set operations}, booktitle = {INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies}, volume = {4}, year = {2004}, month = {2004/03//}, pages = {2231 - 2241 vol.4 - 2231 - 2241 vol.4}, abstract = {We describe a method for performing trust-preserving set operations by untrusted parties. Our motivation for this is the problem of securely reusing content-based search results in peer-to-peer networks. We model search results and indexes as data sets. Such sets have value for answering a new query only if they are trusted. In the absence of any system-wide security mechanism, a data set is trusted by a node a only if it was generated by some node which is trusted by a. Our main contributions are a formal definition of the problem as well as an efficient scheme that solves this problem by allowing untrusted peers to perform set operations on trusted data sets while also producing unforgeable proofs of correctness. This is accomplished by requiring trusted nodes to sign appropriately-defined digests of generated sets; each such digest consists of an RSA accumulator and a Bloom filter. The scheme is general, and has other applications as well. We give an analysis demonstrating the low overhead of the scheme, and we include experimental data which confirm the analysis.}, keywords = {accumulator;, Bloom, computing;, filter;, mechanism;, network;, operation;, peer-to-peer, RSA, Security, security;, set, system-wide, Telecommunication, theory;, trust-preserving}, doi = {10.1109/INFCOM.2004.1354646}, author = {Morselli,R. and Bhattacharjee, Bobby and Katz, Jonathan and Keleher,P.} } @conference {14461, title = {Unsupervised sense disambiguation using bilingual probabilistic models}, booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics}, series = {ACL {\textquoteright}04}, year = {2004}, month = {2004///}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We describe two probabilistic models for unsupervised word-sense disambiguation using parallel corpora. The first model, which we call the Sense model, builds on the work of Diab and Resnik (2002) that uses both parallel text and a sense inventory for the target language, and recasts their approach in a probabilistic framework. The second model, which we call the Concept model, is a hierarchical model that uses a concept latent variable to relate different language specific sense labels. We show that both models improve performance on the word sense disambiguation task over previous unsupervised approaches, with the Concept model showing the largest improvement. Furthermore, in learning the Concept model, as a by-product, we learn a sense inventory for the parallel language.}, doi = {10.3115/1218955.1218992}, url = {http://dx.doi.org/10.3115/1218955.1218992}, author = {Bhattacharya,Indrajit and Getoor, Lise and Bengio,Yoshua} } @inbook {12294, title = {Using Trust in Recommender Systems: An Experimental Analysis}, booktitle = {Trust ManagementTrust Management}, series = {Lecture Notes in Computer Science}, volume = {2995}, year = {2004}, month = {2004///}, pages = {221 - 235}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Recommender systems (RS) have been used for suggesting items (movies, books, songs, etc.) that users might like. RSs compute a user similarity between users and use it as a weight for the users{\textquoteright} ratings. However they have many weaknesses, such as sparseness, cold start and vulnerability to attacks. We assert that these weaknesses can be alleviated using a Trust-aware system that takes into account the {\textquotedblleft}web of trust{\textquotedblright} provided by every user. Specifically, we analyze data from the popular Internet web site epinions.com . The dataset consists of 49290 users who expressed reviews (with rating) on items and explicitly specified their web of trust, i.e. users whose reviews they have consistently found to be valuable. We show that any two users have usually few items rated in common. For this reason, the classic RS technique is often ineffective and is not able to compute a user similarity weight for many of the users. Instead exploiting the webs of trust, it is possible to propagate trust and infer an additional weight for other users. We show how this quantity can be computed against a larger number of users.}, keywords = {Computer, Science}, isbn = {978-3-540-21312-3}, url = {http://dx.doi.org/10.1007/978-3-540-24747-0_17}, author = {Massa,Paolo and Bhattacharjee, Bobby}, editor = {Jensen,Christian and Poslad,Stefan and Dimitrakos,Theo} } @article {18612, title = {Verifying the Correctness of Wide-Area Internet Routing}, volume = {MIT-CSAIL-TR-2004-031}, year = {2004}, month = {2004/05/17/}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {Several studies have shown that wide-area Internet routing is fragile, with failures occurring for a variety of reasons. Routing fragility is largely due to the flexible and powerful ways in which BGP can be configured to perform various tasks, which range from implementing the policies of commercial relationships to configuring backup paths. Configuring routers in an AS is like writing a distributed program, and BGP{\textquoteright}s flexible configuration and today{\textquoteright}s relatively low-level configuration languages make the process error-prone. The primary method used by operators to determine whether their complex configurations are correct is to try them out in operation.We believe that there is a need for a systematic approach to verifying router configurations before they are deployed. This paper develops a static analysis framework for configuration checking, and uses it in the design of rcc, a {\textquoteleft}{\textquoteleft}router configuration checker{\textquoteright}{\textquoteright}. rcc takes as input a set of router configurations and flags anomalies and errors, based on a set of well-defined correctness conditions. We have used rcc to check BGP configurations from 9 operational networks, testing nearly 700 real-world router configurations in the process. Every network we analyzed had configuration errors, some of which were potentially serious and had previously gone unnoticed. Our analysis framework and results also suggest ways in which BGP and configuration languages should be improved. rcc has also been downloaded by 30 network operators to date.}, url = {http://dspace.mit.edu/handle/1721.1/30471}, author = {Feamster, Nick and Balakrishnan,Hari} } @article {12936, title = {Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {70}, year = {2004}, month = {2004/12/01/}, pages = {7481 - 7486}, abstract = {In Argentina, as in other countries of Latin America, cholera has occurred in an epidemic pattern. Vibrio cholerae O1 is native to the aquatic environment, and it occurs in both culturable and viable but nonculturable (VNC) forms, the latter during interepidemic periods. This is the first report of the presence of VNC V. cholerae O1 in the estuarine and marine waters of the R{\'\i}o de la Plata and the Argentine shelf of the Atlantic Ocean, respectively. Employing immunofluorescence and PCR methods, we were able to detect reservoirs of V. cholerae O1 carrying the virulence-associated genes ctxA and tcpA. The VNC forms of V. cholerae O1 were identified in samples of water, phytoplankton, and zooplankton; the latter organisms were mainly the copepods Acartia tonsa, Diaptomus sp., Paracalanus crassirostris, and Paracalanus parvus. We found that under favorable conditions, the VNC form of V. cholerae can revert to the pathogenic, transmissible state. We concluded that V. cholerae O1 is a resident of Argentinean waters, as has been shown to be the case in other geographic regions of the world.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.70.12.7481-7486.2004}, url = {http://aem.asm.org/content/70/12/7481}, author = {Binsztein,Norma and Costagliola,Marcela C. and Pichel,Mariana and Jurquiza,Ver{\'o}nica and Ram{\'\i}rez,Fernando C. and Akselman,Rut and Vacchino,Marta and Huq,Anwarul and Rita R Colwell} } @article {17496, title = {Visualization and analysis of microarray and gene ontology data with treemaps}, journal = {BMC Bioinformatics}, volume = {5}, year = {2004}, month = {2004/06/28/}, pages = {84 - 84}, abstract = {The increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the challenge of integrating experimental results with information resources. The use of Gene Ontology enables researchers to summarize results of quantitative analyses in this framework, but the limitations of typical browser presentation restrict data access.}, isbn = {1471-2105}, doi = {10.1186/1471-2105-5-84}, url = {http://www.biomedcentral.com/1471-2105/5/84}, author = {Baehrecke,Eric H and Dang,Niem and Babaria,Ketan and Shneiderman, Ben} } @article {12189, title = {Visualizations for taxonomic and phylogenetic trees}, journal = {Bioinformatics}, volume = {20}, year = {2004}, month = {2004///}, pages = {2997 - 2997}, author = {Parr,C.S. and Lee,B. and Campbell,D. and Bederson, Benjamin B.} } @conference {13055, title = {Web search intent induction via automatic query reformulation}, booktitle = {Proceedings of HLT-NAACL 2004: Short Papers on XX}, year = {2004}, month = {2004///}, pages = {49 - 52}, author = {Daum{\'e}, Hal and Brill,E.} } @conference {15314, title = {What works better for question answering: Stemming or morphological query expansion}, booktitle = {Proceedings of the Information Retrieval for Question Answering (IR4QA) Workshop at SIGIR 2004}, year = {2004}, month = {2004///}, abstract = {How do different information retrieval techniques affect theperformance of document retrieval in the context of question answering? An exploration of this question is our overall re- search goal. In this paper, we specifically examine strategies for coping with morphological variation. This work quanti- tatively compares two different approaches to handling term variation: applying a stemming algorithm at indexing time, and performing morphological query expansion at retrieval time. We discovered that, compared to the no-stemming baseline, stemming results in lower recall, and morphologi- cal expansion yields higher recall. By separately weighting different term variants, we were able to achieve even higher recall, which opens the door to interesting question analy- sis algorithms for sophisticated query generation. Another significant contribution of our work is the development of a reusable question answering test collection to support our experiments. }, author = {Bilotti,M. W and Katz,B. and Jimmy Lin} } @conference {16901, title = {Accessing diverse geo-referenced data sources with the SAND spatial DBMS}, booktitle = {Proceedings of the 2003 annual national conference on Digital government research}, series = {dg.o {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {1 - 4}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {The Internet has become the most frequently accessed medium for obtaining various types of data. In particular, government agencies, academic institutions, and private enterprises have published gigabytes of geo-referenced data on the Web. However, to obtain geo-referenced data from the Web successfully, systems must be designed to be capable of understanding the data sets published in different data formats. Also, even if the data sets are available in a simple known format, they often have poorly defined structures. With these issues in mind, we have developed an Internet-enabled data collection and conversion utility that interfaces with our prototype spatial database system, SAND. Using this utility, data can be retrieved from many different sources on the Web and converted into a format understandable by the SAND spatial database management system. Our collection and conversion utility is able to import the most popular data formats; namely, ESRI Shapefiles, Microsoft Excel files, HTML files, and GML files. Data in unstructured formats are verified for correct selection of the data types and handling of missing tuples before the insertion operation into the database. Moreover, our utility makes it possible to download any nonspatial data set and combine it internally with a relevant spatial data set. These features are accessible through a spreadsheet-like interface for online editing and structuring of data.}, url = {http://dl.acm.org/citation.cfm?id=1123196.1123206}, author = {Sankaranarayanan,Jagan and Tanin,Egemen and Samet, Hanan and Brabec,Frantisek} } @article {13923, title = {Accuracy, Target Reentry and Fitts{\textquoteright} Law Performance of Preschool Children Using Mice}, journal = {University of Maryland Technical Report, HCIL-2003}, volume = {16}, year = {2003}, month = {2003///}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison and Guimbretiere,F.} } @article {18661, title = {AQuA: an adaptive architecture that provides dependable distributed objects}, journal = {Computers, IEEE Transactions on}, volume = {52}, year = {2003}, month = {2003/01//}, pages = {31 - 50}, abstract = {Building dependable distributed systems from commercial off-the-shelf components is of growing practical importance. For both cost and production reasons, there is interest in approaches and architectures that facilitate building such systems. The AQuA architecture is one such approach; its goal is to provide adaptive fault tolerance to CORBA applications by replicating objects. The AQuA architecture allows application programmers to request desired levels of dependability during applications{\textquoteright} runtimes. It provides fault tolerance mechanisms to ensure that a CORBA client can always obtain reliable services, even if the CORBA server object that provides the desired services suffers from crash failures and value faults. AQuA includes a replicated dependability manager that provides dependability management by configuring the system in response to applications{\textquoteright} requests and changes in system resources due to faults. It uses Maestro/Ensemble to provide group communication services. It contains a gateway to intercept standard CORBA IIOP messages to allow any standard CORBA application to use AQuA. It provides different types of replication schemes to forward messages reliably to the remote replicated objects. All of the replication schemes ensure strong, data consistency among replicas. This paper describes the AQuA architecture and presents, in detail, the active replication pass-first scheme. In addition, the interface to the dependability manager and the design of the dependability manager replication are also described. Finally, we describe performance measurements that were conducted for the active replication pass-first scheme, and we present results from our study of fault detection, recovery, and blocking times.}, keywords = {active replication pass-first scheme, adaptive architecture, adaptive fault tolerance, AQuA, CORBA, data consistency, data integrity, dependable distributed objects, distributed object management, performance measurements, quality of service, replicated dependability manager, replication schemes, software fault tolerance, system resources}, isbn = {0018-9340}, doi = {10.1109/TC.2003.1159752}, author = {Ren,Yansong and Bakken,D. E. and Courtney,T. and Michel Cukier and Karr,D. A. and Rubel,P. and Sabnis,C. and Sanders,W. H. and Schantz,R.E. and Seri,M.} } @article {12397, title = {Automatic classification of multi-word expressions in print dictionaries}, journal = {Lingvisticae Investigationes}, volume = {26}, year = {2003}, month = {2003/01/01/}, pages = {187 - 202}, abstract = {SummaryThis work demonstrates the assignment of multi-word expressions in print dictionaries to POS classes with minimal linguistic resources. In this application, 32,000 entries from the W{\"o}rterbuch der deutschen Idiomatik (H. Schemann 1993) were classified using an inductive description of POS sequences in conjunction with a Brill Tagger trained on manually tagged idiomatic entries. This process assigned categories to 86\% of entries with 88\% accuracy. This classification supplies a meaningful preprocessing step for further applications: the resulting POS-sequences for all idiomatic entries might be used for the automatic recognition of multi-word lexemes in unrestricted text.}, isbn = {03784169}, doi = {10.1075/li.26.2.03gey}, url = {http://umd.library.ingentaconnect.com/content/jbp/li/2003/00000026/00000002/art00002}, author = {Geyken,Alexander and Jordan Boyd-Graber} } @conference {14904, title = {Automatic thumbnail cropping and its effectiveness}, booktitle = {Proceedings of the 16th annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {95 - 104}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Thumbnail images provide users of image retrieval and browsing systems with a method for quickly scanning large numbers of images. Recognizing the objects in an image is important in many retrieval tasks, but thumbnails generated by shrinking the original image often render objects illegible. We study the ability of computer vision systems to detect key components of images so that automated cropping, prior to shrinking, can render objects more recognizable. We evaluate automatic cropping techniques 1) based on a general method that detects salient portions of images, and 2) based on automatic face detection. Our user study shows that these methods result in small thumbnails that are substantially more recognizable and easier to find in the context of visual search.}, keywords = {Face detection, image cropping, saliency map, thumbnail, usability study, visual search, zoomable user interfaces}, isbn = {1-58113-636-6}, doi = {10.1145/964696.964707}, url = {http://doi.acm.org/10.1145/964696.964707}, author = {Suh,Bongwon and Ling,Haibin and Bederson, Benjamin B. and Jacobs, David W.} } @conference {12191, title = {Automatic thumbnail cropping and its effectiveness}, booktitle = {Proceedings of the 16th annual ACM symposium on User interface software and technology}, year = {2003}, month = {2003///}, pages = {95 - 104}, author = {Suh,B. and Ling,H. and Bederson, Benjamin B. and Jacobs, David W.} } @conference {12076, title = {Bootstrapping security associations for routing in mobile ad-hoc networks}, booktitle = {IEEE Global Telecommunications Conference, 2003. GLOBECOM {\textquoteright}03}, volume = {3}, year = {2003}, month = {2003/12/01/5}, pages = {1511- 1515 vol.3 - 1511- 1515 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {To date, most solutions proposed for secure routing in mobile ad-hoc networks (MANETs), assume that secure associations between pairs of nodes can be established on-line; e.g., by a trusted third party, by distributed trust establishment. However, establishing such security associations, with or without trusted third parties, requires reliance on routing layer security. In this paper, we eliminate this apparent cyclic dependency between security services and secure routing in MANETs and show how to bootstrap security for the routing layer. We use the notion of statistically unique and cryptographically verifiable (SUCV) identifiers to implement a secure binding between IP addresses and keys that is independent of any trusted security service. We illustrate our solution with the dynamic source routing (DSR) protocol and compare it with other solutions for secure routing.}, keywords = {ad hoc networks, bootstrapping security association, Cryptographic protocols, dynamic source routing protocol, Fabrics, Intelligent networks, IP address, IP key, IP networks, Message authentication, mobile ad-hoc network, mobile radio, Protection, Public key, public key cryptography, routing layer security reliability, routing protocols, secure routing, Security, security service, statistically unique cryptographically verification, telecommunication security}, isbn = {0-7803-7974-8}, doi = {10.1109/GLOCOM.2003.1258490}, author = {Bobba,R. B and Eschenauer,L. and Gligor,V. and Arbaugh, William A.} } @article {16996, title = {Bringing Treasures to the Surface: Previews and Overviews in a Prototype for the Library of Congress National Digital Library}, journal = {The craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {388 - 388}, author = {Marchionini,A.S. and Nation,D. and Karasik,S. and Cronnell,T. and Shneiderman, Ben and Spotfire,V.D.M.U. and Bederson, Benjamin B. and Data,T.S. and Hochheiser,H. and Shneiderman, Ben and others} } @inbook {16128, title = {Broadening Access to Large Online Databases by Generalizing Query Previews}, booktitle = {The Craft of Information VisualizationThe Craft of Information Visualization}, year = {2003}, month = {2003///}, pages = {31 - 37}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, abstract = {Companies, government agencies, and other types of organizations are making their large databases available to the world over the Internet. Current database front-ends do not give users information about the distribution of data. This leads many users to waste time and network resources posing queries that have either zero-hit or mega-hit result sets. Query previews form a novel visual approach for browsing large databases. Query previews supply data distribution information about the database that is being searched and give continuous feedback about the size of the result set for the query as it is being formed. On the other hand, query previews use only a few pre-selected attributes of the database. The distribution information is displayed only on these attributes. Unfortunately, many databases are formed of numerous relations and attributes. This paper introduces a generalization of query previews. We allow users to browse all of the relations and attributes of a database using a hierarchical browser. Any of the attributes can be used to display the distribution information, making query previews applicable to many public online databases.}, isbn = {978-1-55860-915-0}, url = {http://www.sciencedirect.com/science/article/pii/B978155860915050007X}, author = {Tanin,Egemen and Plaisant, Catherine and Shneiderman, Ben}, editor = {Bederson, Benjamin B. and Shneiderman, Ben} } @article {13911, title = {A collaborative digital library for children}, journal = {Journal of Computer Assisted Learning}, volume = {19}, year = {2003}, month = {2003///}, pages = {239 - 248}, author = {Druin, Allison and Revelle,G. and Bederson, Benjamin B. and Hourcade,J. P and Farber,A. and Lee,J. and Campbell,D.} } @conference {12303, title = {Construction of an efficient overlay multicast infrastructure for real-time applications}, booktitle = {INFOCOM 2003. Twenty-Second Annual Joint Conference of the IEEE Computer and Communications. IEEE Societies}, volume = {2}, year = {2003}, month = {2003/04/03/march}, pages = {1521 - 1531 vol.2 - 1521 - 1531 vol.2}, abstract = {This paper presents an overlay architecture where service providers deploy a set of service nodes (called MSNs) in the network to efficiently implement media-streaming applications. These MSNs are organized into an overlay and act as application-layer multicast forwarding entities for a set of clients. We present a decentralized scheme that organizes the MSNs into an appropriate overlay structure that is particularly beneficial for real-time applications. We formulate our optimization criterion as a "degree-constrained minimum average-latency problem" which is known to be NP-hard. A key feature of this formulation is that it gives a dynamic priority to different MSNs based on the size of its service set. Our proposed approach iteratively modifies the overlay tree using localized transformations to adapt with changing distribution of MSNs, clients, as well as network conditions. We show that a centralized greedy approach to this problem does not perform quite as well, while our distributed iterative scheme efficiently converges to near-optimal solutions.}, keywords = {application-layer;, applications;, communication;, criterion;, decentralized, distributed, entities;, forwarding, infrastructure;, Internet;, iterative, media-streaming, methods;, MSN;, Multicast, nodes;, NP-hard;, OPTIMIZATION, overlay, real, real-time, scheme;, service, systems;, TIME}, doi = {10.1109/INFCOM.2003.1208987}, author = {Banerjee,S. and Kommareddy,C. and Kar,K. and Bhattacharjee, Bobby and Khuller, Samir} } @conference {12304, title = {Cooperative peer groups in NICE}, booktitle = {INFOCOM 2003. Twenty-Second Annual Joint Conference of the IEEE Computer and Communications. IEEE Societies}, volume = {2}, year = {2003}, month = {2003///}, pages = {1272 - 1282 vol.2 - 1272 - 1282 vol.2}, abstract = {A distributed scheme for trust inference in peer-to-peer networks is presented. Our work is in context of the NICE system, which is a platform for implementing cooperative applications over the Internet. We describe a technique for efficiently storing user reputation information in a completely decentralized manner, and show how this information can be used to efficiently identify noncooperative users in NICE. We present a simulation based study of our algorithms, in which we show our scheme scales to thousands of users using modest amounts of storage, processing, and bandwidth at any individual node. Lastly, we show that our scheme is robust and can form cooperative groups in systems where the vast majority of users are malicious.}, keywords = {algorithm;, cooperative, decentralized, distributed, identification;, individual, inference, inference;, information, Internet;, malicious, manner;, mechanisms;, networks;, NICE, node;, noncooperative, peer-to-peer, platform;, reputation, retrieval;, storage;, system;, trust, users, users;}, doi = {10.1109/INFCOM.2003.1208963}, author = {Lee,S. and Sherwood,R. and Bhattacharjee, Bobby} } @book {17406, title = {The craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, abstract = {Since the beginning of the computer age, researchers from many disciplines have sought to facilitate people{\textquoteright}s use of computers and to provide ways for scientists to make sense of the immense quantities of data coming out of them. One gainful result of these efforts has been the field of information visualization, whose technology is increasingly applied in scientific research, digital libraries, data mining, financial data analysis, market studies, manufacturing production control, and data discovery.This book collects 38 of the key papers on information visualization from a leading and prominent research lab, the University of Maryland{\textquoteright}s Human-Computer Interaction Lab (HCIL). Celebrating HCIL{\textquoteright}s 20th anniversary, this book presents a coherent body of work from a respected community that has had many success stories with its research and commercial spin-offs. Each chapter contains an introduction specifically written for this volume by two leading HCI researchers, to describe the connections among those papers and reveal HCIL{\textquoteright}s individual approach to developing innovations.*Presents key ideas, novel interfaces, and major applications of information visualization tools, embedded in inspirational prototypes.*Techniques can be widely applied in scientific research, digital libraries, data mining, financial data analysis, business market studies, manufacturing production control, drug discovery, and genomic studies.*Provides an "insider" view to the scientific process and evolution of innovation, as told by the researchers themselves.*This work comes from the prominent and high profile University of Maryland{\textquoteright}s Human Computer Interaction Lab}, keywords = {Computers / Computer Graphics, Computers / Computer Science, Computers / Digital Media / Desktop Publishing, Computers / General, Computers / Social Aspects / Human-Computer Interaction, Computers / User Interfaces, Human-computer interaction, Information Visualization, Science / General, User-centered system design}, isbn = {9781558609150}, author = {Bederson, Benjamin B. and Shneiderman, Ben} } @article {15380, title = {Critical fields and pulse durations for precessional switching of thin magnetic films}, journal = {Magnetics, IEEE Transactions on}, volume = {39}, year = {2003}, month = {2003/09//}, pages = {2504 - 2506}, abstract = {The precessional switching process of a uniformly magnetized thin film with in-plane anisotropy subject to pulsed magnetic fields applied in the film plane is analyzed. Critical fields required to achieve switching are studied for the case when the applied field is constant during the pulse duration and forms arbitrary angles with the hard axis. By using two integrals of magnetization motion, the explicit expressions for the critical field are derived. The formulas for durations of rectangular magnetic field pulses that guarantee the precessional switching of magnetization are presented as well.}, keywords = {anisotropy;, axis;, critical, durations;, field;, fields;, film;, films;, hard, in-plane, integrals;, magnetic, magnetisation, magnetization, magnetization;, magnetized, motion;, precessional, pulse, pulsed, rectangular, reversal;, switching;, thin, uniformly}, isbn = {0018-9464}, doi = {10.1109/TMAG.2003.816454}, author = {Bertotti,G. and Mayergoyz, Issak D and Serpico,C.} } @conference {15479, title = {DART: a framework for regression testing "nightly/daily builds" of GUI applications}, booktitle = {Software Maintenance, 2003. ICSM 2003. Proceedings. International Conference on}, year = {2003}, month = {2003/09//}, pages = {410 - 419}, abstract = {"Nightly/daily building and smoke testing" have become widespread since they often reveal bugs early in the software development process. During these builds, software is compiled, linked, and (re)tested with the goal of validating its basic functionality. Although successful for conventional software, smoke tests are difficult to develop and automatically rerun for software that has a graphical user interface (GUI). In this paper, we describe a framework called DART (daily automated regression tester) that addresses the needs of frequent and automated re-testing of GUI software. The key to our success is automation: DART automates everything from structural GUI analysis; test case generation; test oracle creation; to code instrumentation; test execution; coverage evaluation; regeneration of test cases; and their re-execution. Together with the operating system{\textquoteright}s task scheduler, DART can execute frequently with little input from the developer/tester to retest the GUI software. We provide results of experiments showing the time taken and memory required for GUI analysis, test case and test oracle generation, and test execution. We also empirically compare the relative costs of employing different levels of detail in the GUI test cases.}, keywords = {automated retesting, automatic test software, coverage evaluation, daily automated regression tester, DART, frequent retesting, graphical user interface, Graphical user interfaces, GUI software, instrumentation coding, program testing, regression testing, Software development management, Software development process, Software maintenance, Software quality, structural GUI analysis, Test Case Generation, test cases regeneration, Test execution, test oracle creation}, doi = {10.1109/ICSM.2003.1235451}, author = {Memon, Atif M. and Banerjee,I. and Hashmi,N. and Nagarajan,A.} } @article {12339, title = {Data partitioning for DSP software synthesis}, journal = {Lecture Notes in Computer Science}, year = {2003}, month = {2003///}, pages = {344 - 358}, author = {Ko,M. Y and Bhattacharyya, Shuvra S.} } @article {14056, title = {Data Structures, Optimal Choice of Parameters, and Complexity Results for Generalized Multilevel Fast Multipole Methods in $d$ Dimensions}, journal = {Technical Reports from UMIACS UMIACS-TR-2003-28}, year = {2003}, month = {2003/04/04/}, abstract = {We present an overview of the Fast Multipole Method, explain the use ofoptimal data structures and present complexity results for the algorithm. We explain how octree structures and bit interleaving can be simply used to create efficient versions of the multipole algorithm in $d$ dimensions. We then present simulations that demonstrate various aspects of the algorithm, including optimal selection of the clustering parameter, the influence of the error bound on the complexity, and others. The use of these optimal parameters results in a many-fold speed-up of the FMM, and prove very useful in practice. UMIACS-TR-2003-28 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1270}, author = {Gumerov, Nail A. and Duraiswami, Ramani and Borovikov,Eugene A.} } @article {17813, title = {A Deductive Database Approach to AI Planning}, journal = {Journal of Intelligent Information Systems}, volume = {20}, year = {2003}, month = {2003///}, pages = {215 - 253}, abstract = {In this paper, we show that the classical A.I. planning problem can be modelled using simple database constructs with logic-based semantics. The approach is similar to that used to model updates and nondeterminism in active database rules. We begin by showing that planning problems can be automatically converted to Datalog1S programs with nondeterministic choice constructs, for which we provide a formal semantics using the concept of stable models. The resulting programs are characterized by a syntactic structure (XY-stratification) that makes them amenable to efficient implementation using compilation and fixpoint computation techniques developed for deductive database systems. We first develop the approach for sequential plans, and then we illustrate its flexibility and expressiveness by formalizing a model for parallel plans, where several actions can be executed simultaneously. The characterization of parallel plans as partially ordered plans allows us to develop (parallel) versions of partially ordered plans that can often be executed faster than the original partially ordered plans.}, doi = {10.1023/A:1022808724136}, author = {Brogi,A. and V.S. Subrahmanian and Zaniolo,C.} } @article {18537, title = {Defeating Web censorship with untrusted messenger discovery}, journal = {Workshop on Privacy Enhancing Technologies}, year = {2003}, month = {2003///}, author = {Feamster, Nick and Balazinska,M. and Wang,W. and Balakrishnan,H. and Karger,D.} } @article {12301, title = {Deno: a decentralized, peer-to-peer object-replication system for weakly connected environments}, journal = {Computers, IEEE Transactions on}, volume = {52}, year = {2003}, month = {2003/07//}, pages = {943 - 959}, abstract = {This paper presents the design, implementation, and evaluation of the replication framework of Deno, a decentralized, peer-to-peer object-replication system targeted for weakly connected environments. Deno uses weighted voting for availability and pair-wise, epidemic information flow for flexibility. This combination allows the protocols to operate with less than full connectivity, to easily adapt to changes in group membership, and to make few assumptions about the underlying network topology. We present two versions of Deno{\textquoteright}s protocol that differ in the consistency levels they support. We also propose security extensions to handle a class of malicious actions that involve misrepresentation of protocol information. Deno has been implemented and runs on top of Linux and Win32 platforms. We use the Deno prototype to characterize the performance of the Deno protocols and extensions. Our study reveals several interesting results that provide fundamental insight into the benefits of decentralization and the mechanics of epidemic protocols.}, keywords = {actions;, connected, consistency, data, data;, databases;, decentralized, Deno;, distributed, environments;, epidemic, group, levels;, Linux;, malicious, management;, membership;, network, object, object-replication, of, operating, peer-to-peer, protocols;, replicated, replication;, Security, security;, synchronisation;, system;, systems;, topology;, Unix;, voting;, weakly, weighted, Win32;}, isbn = {0018-9340}, doi = {10.1109/TC.2003.1214342}, author = {Cetintemel,U. and Keleher,P. J and Bhattacharjee, Bobby and Franklin,M.J.} } @book {12377, title = {Design Considerations for Optically Connected Systems on Chip}, year = {2003}, month = {2003///}, publisher = {MARYLAND UNIV COLLEGE PARK DEPT OF ELECTRICAL AND COMPUTER ENGINEERING}, organization = {MARYLAND UNIV COLLEGE PARK DEPT OF ELECTRICAL AND COMPUTER ENGINEERING}, author = {Bhattacharyya, Shuvra S. and Bambha,N. K and Euliss,G.} } @article {12194, title = {Designing a digital library for young children: An intergenerational partnership}, journal = {The craft of information visualization: readings and reflections}, volume = {178}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Hourcade,J. P and Sherman,L. and Revelle,G. and Platner,M. and Weng,S.} } @article {13754, title = {Desparately seeking cebuano}, journal = {Third Conference on Human Language Technologies}, year = {2003}, month = {2003///}, abstract = {This paper describes an effort to rapidly de-velop language resources and component tech- nology to support searching Cebuano news sto- ries using English queries. Results from the first 60 hours of the exercise are presented. }, author = {Oard, Douglas and David Doermann and Dorr, Bonnie J and He,D. and Resnik, Philip and Weinberg, Amy and Byrne,W. and Khudanpur,S. and Yarowsky,D. and Leuski,A. and others} } @article {16902, title = {Digital government}, journal = {Communications of the ACM}, volume = {46}, year = {2003}, month = {2003///}, pages = {25 - 27}, abstract = {Information technologies are being applied vigorously by governmental units at national,regional, and local levels around the world. The application of IT to government service is often termed {\textquotedblleft}e-government{\textquotedblright} and the larger concept of government that depends upon IT to achieve basic missions is termed {\textquotedblleft}digital government.{\textquotedblright} This distinction is, of course, lexically arbitrary, but serves to distinguish R\&D specifically aimed at creating techniques for applying IT to government operations. Such R\&D efforts also consider the long-term impact of these applications on citizens and government itself. }, author = {Marchionini,G. and Samet, Hanan and Brandt,L.} } @article {16289, title = {The Dog Genome: Survey Sequencing and Comparative Analysis}, journal = {ScienceScience}, volume = {301}, year = {2003}, month = {2003/09/26/}, pages = {1898 - 1903}, abstract = {A survey of the dog genome sequence (6.22 million sequence reads; 1.5{\texttimes} coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25\%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1086432}, url = {http://www.sciencemag.org/content/301/5641/1898}, author = {Kirkness,Ewen F. and Bafna,Vineet and Halpern,Aaron L. and Levy,Samuel and Remington,Karin and Rusch,Douglas B and Delcher,Arthur L. and Pop, Mihai and Wang,Wei and Fraser,Claire M. and Venter,J. Craig} } @article {19078, title = {The dog genome: survey sequencing and comparative analysis}, journal = {Science}, volume = {301}, year = {2003}, month = {2003}, author = {Kirkness,E. F and Bafna,V. and Halpern,A. L and Levy,S. and Remington,K. and Rusch,D. B and Delcher,A. L and Pop, Mihai and Wang,W. and Fraser,C. M and others} } @article {17844, title = {Driving scientific applications by data in distributed environments}, journal = {Computational Science{\textemdash}ICCS 2003}, year = {2003}, month = {2003///}, pages = {713 - 713}, author = {Saltz, J. and Catalyurek,U. and Kurc, T. and Gray,M. and Hastings,S. and Langella,S. and Narayanan,S. and Martino,R. and Bryant,S. and Peszynska,M. and others} } @conference {17113, title = {Dynamic querying for pattern identification in microarray and genomic data}, booktitle = {2003 International Conference on Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings}, volume = {3}, year = {2003}, month = {2003/07/06/9}, pages = {III- 453-6 vol.3 - III- 453-6 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. Timesearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. Timesearcher can be used to search these data sets for candidate splicing signals.}, keywords = {Bioinformatics, data sets, Displays, dynamic querying, expression profiles, Frequency, Gene expression, genes, Genetics, genomic data, Genomics, linear ordered sequences, macromolecules, medical signal processing, Mice, Microarray, pattern identification, pattern recognition, premRNA splicing, Query processing, sequences, Signal processing, splicing, TimeSearcher}, isbn = {0-7803-7965-9}, doi = {10.1109/ICME.2003.1221346}, author = {Hochheiser,H. and Baehrecke,E. H and Mount, Stephen M. and Shneiderman, Ben} } @conference {14682, title = {Dynamic rebinding for marshalling and update, with destruct-time ?}, booktitle = {Proceedings of the eighth ACM SIGPLAN international conference on Functional programming}, series = {ICFP {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {99 - 110}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Most programming languages adopt static binding, but for distributed programming an exclusive reliance on static binding is too restrictive: dynamic binding is required in various guises, for example when a marshalled value is received from the network, containing identifiers that must be rebound to local resources. Typically it is provided only by ad-hoc mechanisms that lack clean semantics.In this paper we adopt a foundational approach, developing core dynamic rebinding mechanisms as extensions to simply-typed call-by-value ? -calculus. To do so we must first explore refinements of the call-by-value reduction strategy that delay instantiation, to ensure computations make use of the most recent versions of rebound definitions. We introduce redex-time and destruct-time strategies. The latter forms the basis for a ?marsh calculus that supports dynamic rebinding of marshalled values, while remaining as far as possible statically-typed. We sketch an extension of ? marsh with concurrency and communication, giving examples showing how wrappers for encapsulating untrusted code can be expressed. Finally, we show that a high-level semantics for dynamic updating can also be based on the destruct-time strategy, defining a ?marsh calculus with simple primitives to provide type-safe updating of running code. We thereby establish primitives and a common semantic foundation for a variety of real-world dynamic rebinding requirements.}, keywords = {distributed programming, dynamic binding, dynamic update, lambda calculus, marshalling, programming languages, serialisation}, isbn = {1-58113-756-7}, doi = {10.1145/944705.944715}, url = {http://doi.acm.org/10.1145/944705.944715}, author = {Bierman,Gavin and Hicks, Michael W. and Sewell,Peter and Stoyle,Gareth and Wansbrough,Keith} } @conference {19659, title = {Efficient particle filter-based tracking of multiple interacting targets using an MRF-based motion model}, booktitle = {2003 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2003. (IROS 2003). Proceedings}, volume = {1}, year = {2003}, month = {2003/10//}, pages = {254 - 259 vol.1}, abstract = {We describe a multiple hypothesis particle filter for tracking targets that are influenced by the proximity and/or behavior of other targets. Our contribution is to show how a Markov random field motion prior, built on the fly at each time step, can model these interactions to enable more accurate tracking. We present results for a social insect tracking application, where we model the domain knowledge that two targets cannot occupy the same space, and targets actively avoid collisions. We show that using this model improves track quality and efficiency. Unfortunately, the joint particle tracker we propose suffers from exponential complexity in the number of tracked targets. An approximation to the joint filter, however, consisting of multiple nearly independent particle filters can provide similar track quality at substantially lower computational cost.}, keywords = {collision avoidance, computational cost, Computational efficiency, Educational institutions, exponential complexity, Filtering, filtering theory, Insects, joint particle tracker, Markov processes, Markov random field motion, Markov random fields, multiple interacting targets, particle filter-based tracking, Particle filters, Particle tracking, Radar tracking, social insect tracking application, target tracking, Trajectory}, author = {Zia Khan and Balch, T. and Dellaert, F.} } @article {12305, title = {Efficient peer-to-peer searches using result-caching}, journal = {Peer-to-Peer Systems II}, year = {2003}, month = {2003///}, pages = {225 - 236}, abstract = {Existing peer-to-peer systems implement a single function well: data lookup. There is now a wealth of research describing how to reliably disseminate, and to later retrieve, data in a scalable and load-balanced manner.}, author = {Bhattacharjee, Bobby and Chawathe,S. and Gopalakrishnan,V. and Keleher,P. and Silaghi,B.} } @article {12129, title = {Eight lessons learned during COTS-based systems maintenance}, journal = {Software, IEEE}, volume = {20}, year = {2003}, month = {2003/10//sept}, pages = {94 - 96}, abstract = {To make better decisions relative to CBSs, we need empirical knowledge. To gain this knowledge, we must more fully understand the lifecycle processes people use when harnessing COTS packages. The initial findings reported here are but the first step in our attempts to capture this empirical knowledge. We plan to continue collecting data and investigating the phenomenology of COTS-based systems.}, keywords = {COTS, COTS-based, cycle, life, lifecycle, Maintenance, maintenance;, object-oriented, packages;, phase;, processes;, programming;, reusability;, software, systems}, isbn = {0740-7459}, doi = {10.1109/MS.2003.1231161}, author = {Reifer,D.J. and Basili, Victor R. and Boehm,B.W. and Clark,B.} } @conference {12200, title = {Electronic voting system usability issues}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2003}, month = {2003///}, pages = {145 - 152}, author = {Bederson, Benjamin B. and Lee,B. and Sherman,R.M. and Herrnson,P.S. and Niemi,R.G.} } @conference {12322, title = {Energy reduction techniques for multimedia applications with tolerance to deadline misses}, booktitle = {Proceedings of the 40th annual Design Automation Conference}, year = {2003}, month = {2003///}, pages = {131 - 136}, author = {Hua,S. and Qu,G. and Bhattacharyya, Shuvra S.} } @conference {11911, title = {Energy-efficient broadcast and multicast trees for reliable wireless communication}, booktitle = {Wireless Communications and Networking, 2003. WCNC 2003. 2003 IEEE}, volume = {1}, year = {2003}, month = {2003/03//}, pages = {660 -667 vol.1 - 660 -667 vol.1}, abstract = {We define energy-efficient broadband and multicast schemes for reliable communication in multi-hop wireless networks. Unlike previous techniques, the choice of neighbors in the broadband and multicast trees in these schemes, are based not only on the link distance, but also on the error rates associated with the link. Our schemes can be implemented using both positive and negative acknowledgement based reliable broadcast techniques in the link layer. Through simulations, we show that our scheme achieves up to 45\% improvement over previous schemes on realistic 100-node network topologies. A positive acknowledgment based implementation is preferred. Our simulations show that the additional benefits of a positive acknowledgement based implementation is marginal (1-2\%). Therefore a negative acknowledgement based implementation of our schemes is equally applicable in constructing energy-efficient reliable and multicast data delivery paths.}, keywords = {broadcast, channels;multicast, communication;broadcast, communication;network, data, delivery, energy-efficient, layer;multicast, network, networks;network, networks;telecommunication, paths;multicast, rates;link, reliability;, topologies;wireless, topology;radio, trees;error, trees;multihop, wireless}, doi = {10.1109/WCNC.2003.1200429}, author = {Banerjee,S. and Misra,A. and Yeo,Jihwang and Agrawala, Ashok K.} } @article {18393, title = {Experimental validation of new software technology}, journal = {SERIES ON SOFTWARE ENGINEERING AND KNOWLEDGE ENGINEERING}, volume = {12}, year = {2003}, month = {2003///}, pages = {229 - 263}, abstract = {When to apply a new technology in an organization is acritical decision for every software development organization. Earlier work defines a set of methods that the research community uses when a new technology is developed. This chapter presents a discussion of the set of methods that industrial organizations use before adopting a new technology. First there is a brief definition of the earlier research methods and then a definition of the set of industrial methods. A comparison of the two sets leads into the perspectives of these methods of experts in the research and industrial community via surveys made to those communities. }, author = {Zelkowitz, Marvin V and Wallace,D. R and Binkley,D. W} } @conference {12381, title = {Exploring the probabilistic design space of multimedia systems}, booktitle = {14th IEEE International Workshop on Rapid Systems Prototyping, 2003. Proceedings}, year = {2003}, month = {2003/06/09/11}, pages = {233 - 240}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we propose the novel concept of probabilistic design for multimedia systems and a methodology to quickly explore such design space at an early design stage. The probabilistic design is motivated by the challenge of how to design, but not over-design, multimedia embedded systems while systematically incorporating such application{\textquoteright}s performance requirements, uncertainties in execution time, and tolerance for reasonable execution failures. Our goal is to bridge the gap between real-time analysis and embedded software implementation for rapid and economic (multimedia) system prototyping. Our method takes advantage of multimedia system{\textquoteright}s unique features mentioned above to relax the rigid hardware requirements for software implementation and eventually avoid over-designing the system.}, keywords = {economic system prototyping, embedded software implementation, Embedded system, Energy consumption, execution time uncertainties, Hardware, multimedia embedded systems, multimedia system prototyping, multimedia systems, performance requirements, probabilistic design space, rapid system prototyping, Real time systems, real-time analysis, reasonable execution failure tolerance, Resource management, software prototyping, Space exploration, Streaming media, systems analysis, Timing, Uncertainty}, isbn = {0-7695-1943-1}, doi = {10.1109/IWRSP.2003.1207053}, author = {Shaoxiong Hua and Gang Qu and Bhattacharyya, Shuvra S.} } @article {16126, title = {Family Calendar Survey}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/01/21/}, abstract = {Beginning in late July 2002, we conducted a survey about people{\textquoteright}s personal andfamily calendaring habits. By the end of September, we had over 400 responses, which are summarized below. The survey was conducted to help inform our work in designing new technologies for families, motivated in part by our work on the interLiving project. InterLiving is a 3 year, European Union-funded project where we work with distributed, multi-generational families as design partners to create new technologies (see http://www.cs.umd.edu/hcil/interliving for details). The survey was administered from a web page (https://www.cs.umd.edu/users/hilary/survey/survey.htm), and participants were solicited via a "chain-mail" email approach. We began by sending a request to fill out a survey to our friends, families, and colleagues. We asked that they forward the request on to their friends, family and colleagues as well. While we realize that this was an imperfect approach, we believed that the respondents would be representative of the users we are initially targeting in our research on family calendaring and coordination - individuals who are already making relatively heavy use of computers at home and/or work. The results seem to validate this assumption. Many of our respondents likely come from the HCI community as the mailing went to our large lab mailing list. We may have some pollution in the data as a result of people in the same household (e.g. husband and wife) both filling out the survey. Despite these issues, the results we got were helpful in eliciting a number of important findings, namely that people rely on multiple calendars, many of which are still paper. (UMIACS-TR-2002-92) (HCIL-TR-2002-21) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1236}, author = {Hutchinson,Hilary and Bederson, Benjamin B. and Plaisant, Catherine and Druin, Allison} } @article {14697, title = {Formalizing dynamic software updating}, journal = {Proceedings of the Second International Workshop on Unanticipated Software Evolution (USE)}, year = {2003}, month = {2003///}, abstract = {Dynamic software updating (DSU) enables running programs to beupdated with new code and data without interrupting their execution. A number of DSU systems have been designed, but there is still little rig- orous understanding of how to use DSU technology so that updates are safe. As a first step in this direction, we introduce a small update calculus with a precise mathematical semantics. The calculus is formulated as an extension of a typed lambda calculus, and supports updating technology similar to that of the programming language Erlang [2]. Our goal is to provide a simple yet expressive foundation for reasoning about dynam- ically updateable software. In this paper, we present the details of the calculus, give some examples of its expressive power, and discuss how it might be used or extended to guarantee safety properties. }, author = {Bierman,G. and Hicks, Michael W. and Sewell,P. and Stoyle,G.} } @conference {16703, title = {A generative probabilistic OCR model for NLP applications}, booktitle = {Proceedings of the 2003 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology-Volume 1}, year = {2003}, month = {2003///}, pages = {55 - 62}, author = {Kolak,O. and Byrne,W. and Resnik, Philip} } @article {16290, title = {The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria}, journal = {Nature}, volume = {423}, year = {2003}, month = {2003/05/01/}, pages = {81 - 86}, abstract = {Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax1. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity{\textemdash}including haemolysins, phospholipases and iron acquisition functions{\textemdash}and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax4. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.}, isbn = {0028-0836}, doi = {10.1038/nature01586}, url = {http://www.nature.com/nature/journal/v423/n6935/full/nature01586.html}, author = {Read,Timothy D. and Peterson,Scott N. and Tourasse,Nicolas and Baillie,Les W. and Paulsen,Ian T. and Nelson,Karen E. and Tettelin,Herv|[eacute]| and Fouts,Derrick E. and Eisen,Jonathan A. and Gill,Steven R. and Holtzapple,Erik K. and |[Oslash]|kstad,Ole Andreas and Helgason,Erlendur and Rilstone,Jennifer and Wu,Martin and Kolonay,James F. and Beanan,Maureen J. and Dodson,Robert J. and Brinkac,Lauren M. and Gwinn,Michelle and DeBoy,Robert T. and Madpu,Ramana and Daugherty,Sean C. and Durkin,A. Scott and Haft,Daniel H. and Nelson,William C. and Peterson,Jeremy D. and Pop, Mihai and Khouri,Hoda M. and Radune,Diana and Benton,Jonathan L. and Mahamoud,Yasmin and Jiang,Lingxia and Hance,Ioana R. and Weidman,Janice F. and Berry,Kristi J. and Plaut,Roger D. and Wolf,Alex M. and Watkins,Kisha L. and Nierman,William C. and Hazen,Alyson and Cline,Robin and Redmond,Caroline and Thwaite,Joanne E. and White,Owen and Salzberg,Steven L. and Thomason,Brendan and Friedlander,Arthur M. and Koehler,Theresa M. and Hanna,Philip C. and Kolst|[oslash]|,Anne-Brit and Fraser,Claire M.} } @article {15387, title = {Geometrical analysis of precessional switching and relaxation in uniformly magnetized bodies}, journal = {Magnetics, IEEE Transactions on}, volume = {39}, year = {2003}, month = {2003/09//}, pages = {2501 - 2503}, abstract = {Precessional switching and relaxation in a single-domain particle or film is studied by using the Landau-Lifshitz-Gilbert equation. The analysis of the switching process is based on the explicit knowledge of two integrals of motion for the magnetization dynamics in the conservative case. The knowledge of these integrals of motions enables one to carry out the geometrical analysis of the system and give the complete phase portrait. The relaxation process which occurs after the magnetization is reversed is analyzed by using geometrical methods and it is showed that the dynamical system exhibits entanglement of separatrices and riddled basins of attraction.}, keywords = {analysis;, attraction;, basins, bodies;, dynamical, dynamics;, entanglement;, equation;, film;, films;, geometrical, integrals, Landau-Lifshitz-Gilbert, magnetic, magnetisation, magnetization, magnetized, motion;, of, particle;, particles;, phase, portrait;, precessional, relaxation;, reversal;, riddled, separatrices;, single-domain, spin, switching;, system;, thin, uniformly}, isbn = {0018-9464}, doi = {10.1109/TMAG.2003.816453}, author = {Bertotti,G. and Mayergoyz, Issak D and Serpico,C. and d{\textquoteright}Aquino,M.} } @article {12337, title = {Goal-Driven Reconfiguration of Polymorphous Architectures}, journal = {Domain-specific processors: systems, architectures, modeling, and simulation}, volume = {20}, year = {2003}, month = {2003///}, pages = {151 - 151}, author = {Lohani,S. and Bhattacharyya, Shuvra S.} } @article {15448, title = {GUI ripping: Reverse engineering of graphical user interfaces for testing}, journal = {Proceedings of the 10th working conference on reverse engineering (WCRE{\textquoteright}03)}, volume = {1095}, year = {2003}, month = {2003///}, pages = {17 - 00}, abstract = {Graphical user interfaces (GUIs) are important parts oftoday{\textquoteright}s software and their correct execution is required to ensure the correctness of the overall software. A popular technique to detect defects in GUIs is to test them by exe- cuting test cases and checking the execution results. Test cases may either be created manually or generated auto- matically from a model of the GUI. While manual testing is unacceptably slow for many applications, our experience with GUI testing has shown that creating a model that can be used for automated test case generation is difficult. We describe a new approach to reverse engineer a model represented as structures called a GUI forest, event-flow graphs and an integration tree directly from the executable GUI. We describe {\textquotedblleft}GUI Ripping{\textquotedblright}, a dynamic process in which the software{\textquoteright}s GUI is automatically {\textquotedblleft}traversed{\textquotedblright} by opening all its windows and extracting all their widgets (GUI objects), properties, and values. The extracted infor- mation is then verified by the test designer and used to auto- matically generate test cases. We present algorithms for the ripping process and describe their implementation in a tool suite that operates on Java and Microsoft Windows{\textquoteright} GUIs. We present results of case studies which show that our approach requires very little human intervention and is es- pecially useful for regression testing of software that is mod- ified frequently. We have successfully used the {\textquotedblleft}GUI Rip- per{\textquotedblright} in several large experiments and have made it avail- able as a downloadable tool. }, author = {Memon, Atif M. and Banerjee,I. and Nagarajan,A.} } @article {18572, title = {Guidelines for interdomain traffic engineering}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {33}, year = {2003}, month = {2003/10//}, pages = {19 - 30}, abstract = {Network operators must have control over the flow of traffic into, out of, and across their networks. However, the Border Gateway Protocol (BGP) does not facilitate common traffic engineering tasks, such as balancing load across multiple links to a neighboring AS or directing traffic to a different neighbor. Solving these problems is difficult because the number of possible changes to routing policies is too large to exhaustively test all possibilities, some changes in routing policy can have an unpredictable effect on the flow of traffic, and the BGP decision process implemented by router vendors limits an operator{\textquoteright}s control over path selection.We propose fundamental objectives for interdomain traffic engineering and specific guidelines for achieving these objectives within the context of BGP. Using routing and traffic data from the AT\&T backbone we show how certain BGP policy changes can move traffic in a predictable fashion, despite limited knowledge about the routing policies in neighboring AS{\textquoteright}s. Then, we show how operators can gain greater flexibility by relaxing some steps in the BGP decision process and ensuring that neighboring AS{\textquoteright}s send consistent advertisements at each peering location. Finally, we show that an operator can manipulate traffic efficiently by changing the routes for a small number of prefixes (or groups of related prefixes) that consistently receive a large amount of traffic.}, isbn = {0146-4833}, doi = {10.1145/963985.963988}, url = {http://doi.acm.org/10.1145/963985.963988}, author = {Feamster, Nick and Borkenhagen,Jay and Rexford,Jennifer} } @article {17188, title = {Help! I{\textquoteright}m lost: User frustration in web navigation}, journal = {IT \& Society}, volume = {1}, year = {2003}, month = {2003///}, pages = {18 - 26}, abstract = {Computers can be valuable tools, and networked resources via the Internet can be beneficial to many different populations and communities. Unfortunately, when people are unable to reach their task goals due to frustrating experiences, this can hinder the effectiveness of technology. This research summary provides information about the user frustration research that has been performed at the University of Maryland and Towson University. Causes of user frustration are discussed in this research summary, along with the surprising finding that nearly one-third to one-half of the time spent in front of the computer is wasted due to frustrating experiences. Furthermore, when interfaces are planned to be deceptive and confusing, this can lead to increased frustration. Implications for designers and users are discussed.}, author = {Lazar,J. and Bessiere,K. and Ceaparu,I. and Robinson,J. and Shneiderman, Ben} } @conference {17892, title = {A high performance multi-perspective vision studio}, booktitle = {Proceedings of the 17th annual international conference on Supercomputing}, series = {ICS {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {348 - 357}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe a multi-perspective vision studio as a flexible high performance framework for solving complex image processing and machine vision problems on multi-view image sequences. The studio abstracts multi-view image data from image sequence acquisition facilities, stores and catalogs sequences in a high performance distributed database, allows customization of back-end processing services, and can serve custom client applications, thus helping make multi-view video sequence processing efficient and generic. To illustrate our approach, we describe two multi-perspective studio applications, and discuss performance and scalability results.}, keywords = {database, distributed system, high-performance, IMAGE PROCESSING, multi-perspective, VISION, volumetric reconstruction}, isbn = {1-58113-733-8}, doi = {10.1145/782814.782862}, url = {http://doi.acm.org/10.1145/782814.782862}, author = {Borovikov,Eugene and Sussman, Alan} } @book {12138, title = {Identifying Relevant Information for Testing Technique Selection: An Instantiated Characterization Schema}, year = {2003}, month = {2003/04/01/}, publisher = {Springer}, organization = {Springer}, abstract = {The importance of properly selecting testing techniques is widely accepted in the software engineering community today. However, there are chiefly two reasons why the selections now made by software developers are difficult to evaluate as correct. First, there are several techniques with which the average developer is unfamiliar, often leaving testers with limited knowledge of all the techniques currently available. Second, the available information regarding the different testing techniques is primarily procedure (focused on how to use the technique), rather than pragmatic (focused on the effect and appropriateness of using the technique). The problem addressed in this book is aimed at improving software testing technique selection.Identifying Relevant Information for Testing Technique Selection: An Instantiated Characterization Schema will train its readers how to use the conceptual tool presented here in various ways. Developers will improve their testing technique selection process by systematically and objectively selecting the testing techniques for a software project. Developers will also build a repository containing their own experience with the application of various software testing techniques. Researchers will focus their research on the relevant aspects of testing technique when creating it, and when comparing different techniques.Identifying Relevant Information for Testing Technique Selection: An Instantiated Characterization Schema is designed to meet the needs of a professional audience in software engineering. This book is also suitable for graduate-level students in computer science and engineering.}, keywords = {Business \& Economics / Information Management, Computer software, Computer software - Testing, Computer software/ Testing, Computers / Information Technology, Computers / Internet / Application Development, Computers / Programming / General, Computers / Programming Languages / General, Computers / Software Development \& Engineering / General, Computers / Software Development \& Engineering / Quality Assurance \& Testing, Technology \& Engineering / Materials Science}, isbn = {9781402074356}, author = {Vegas,Sira and Juristo,Natalia and Basili, Victor R.} } @inbook {17237, title = {Innovating the Interaction}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {295 - 295}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, isbn = {978-1-55860-915-0}, author = {Bederson, Benjamin B. and Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben and Hochheiser,H. and Fekete,J. D and Czenvinski,M.} } @article {16418, title = {The interaction between zoning regulations and residential preferences as a driver of urban form}, journal = {Proceedings of the 2003 UTEP Distinguished Faculty and Student Symposium}, year = {2003}, month = {2003///}, author = {Zellner,M.L. and Riolo,R and Rand, William and Page,S.E. and Brown,D.G. and Fernandez,L.E.} } @conference {17248, title = {Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis}, booktitle = {Multimedia and Expo, 2003. ICME{\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {3}, year = {2003}, month = {2003///}, pages = {III{\textendash}461 - III{\textendash}461}, abstract = {Data analysis and visualization is strongly influenced by noise and noise filters. There are multiple sources of oisein microarray data analysis, but signal/noise ratios are rarely optimized, or even considered. Here, we report a noise analysis of a novel 13 million oligonucleotide dataset - 25 human U133A (~500,000 features) profiles of patient muscle biposies. We use our recently described interactive visualization tool, the Hierarchical Clustering Explorer (HCE) to systemically address the effect of different noise filters on resolution of arrays into orrectbiological groups (unsupervised clustering into three patient groups of known diagnosis). We varied probe set interpretation methods (MAS 5.0, RMA), resent callfilters, and clustering linkage methods, and investigated the results in HCE. HCE interactive features enabled us to quickly see the impact of these three variables. Dendrogram displays showed the clustering results systematically, and color mosaic displays provided a visual support for the results. We show that each of these three variables has a strong effect on unsupervised clustering. For this dataset, the strength of the biological variable was maximized, and noise minimized, using MAS 5.0, 10\% present call filter, and Average Group Linkage. We propose a general method of using interactive tools to identify the optimal signal/noise balance or the optimal combination of these three variables to maximize the effect of the desired biological variable on data interpretation.}, author = {Seo,J. and Bakay,M. and Zhao,P. and Chen,Y.W. and Clarkson,P. and Shneiderman, Ben and Hoffman,E.P.} } @conference {17939, title = {Interactive subsurface scattering for translucent meshes}, booktitle = {Proceedings of the 2003 symposium on Interactive 3D graphics}, series = {I3D {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {75 - 82}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose a simple lighting model to incorporate subsurface scattering effects within the local illumination framework. Subsurface scattering is relatively local due to its exponential falloff and has little effect on the appearance of neighboring objects. These observations have motivated us to approximate the BSSRDF model and to model subsurface scattering effects by using only local illumination. Our model is able to capture the most important features of subsurface scattering: reflection and transmission due to multiple scattering.In our approach we build the neighborhood information as a preprocess and modify the traditional local illumination model into a run-time two-stage process. In the first stage we compute the reflection and transmission of light on the surface. The second stage involves bleeding the scattering effects from a vertex{\textquoteright}s neighborhood to produce the final result. We then show how to merge the run-time two-stage process into a run-time single-stage process using precomputed integral. The complexity of our run-time algorithm is O(N), where N is the number of vertices. Using this approach, we achieve interactive frame rates with about one to two orders of magnitude speedup compared with the state-of-the-art methods.}, keywords = {BSSRDF, local illumination, reflection models, subsurface scattering}, isbn = {1-58113-645-5}, doi = {10.1145/641480.641497}, url = {http://doi.acm.org/10.1145/641480.641497}, author = {Hao,Xuejun and Baby,Thomas and Varshney, Amitabh} } @article {12190, title = {The International Children{\textquoteright}s Digital Library}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13928, title = {The International Children{\textquoteright}s Digital Library: Description and analysis of first use}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, pages = {315 - 315}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13904, title = {The International Children{\textquoteright}s Digital Library: viewing digital books online}, journal = {Interacting with Computers}, volume = {15}, year = {2003}, month = {2003///}, pages = {151 - 167}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison and Rose,A. and Farber,A. and Takayama,Y.} } @article {12300, title = {Intradomain Overlays: Architecture and Applications}, journal = {Technical Reports from UMIACS, UMIACS-TR-2003-70}, year = {2003}, month = {2003/08/01/}, abstract = {We introduce an architecture for {\textquoteleft}{\textquoteleft}Intradomain Overlays{\textquoteright}{\textquoteright}, where a subset of routers within a domain is augmented with a dedicated host. These strategically placed hosts form an overlay network, and we describe a number of applications for such overlays. These applications include efficient network monitoring, policy- and load-based packet re-routing, and network resource accounting. In this paper, we elaborate on the network monitoring application and describe a distributed protocol for monitoring routers within an AS which has been augmented with a few overlay nodes. The routers and other infrastructure are unaware of the overlay nodes, and the monitoring of individual elements is conducted using plain SNMP. We describe techniques for efficiently synthesizing and transporting the monitored SNMP data, and present results using trace data collected from an AS with 400+ routers. Our results show that the overlay-based monitoring reduces overheads by 2--4 orders of magnitude, and thus enables much finer grained monitoring and traffic engineering than is otherwise possible. (UMIACS-TR-2003-70) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1295}, author = {Kommareddy,Christopher and Guven,Tuna and Bhattacharjee, Bobby and La,Richard and Shayman,Mark} } @article {12140, title = {Iterative and incremental developments. a brief history}, journal = {Computer}, volume = {36}, year = {2003}, month = {2003/06//}, pages = {47 - 56}, abstract = {Although many view iterative and incremental development as a modern practice, its application dates as far back as the mid-1950s. Prominent software-engineering thought leaders from each succeeding decade supported IID practices, and many large projects used them successfully. These practices may have differed in their details, but all had a common theme-to avoid a single-pass sequential, document-driven, gated-step approach.}, keywords = {agile, and, developments;iterative, engineering;, engineering;software, enhancement;software, incremental, methods;iterative, system;history;software}, isbn = {0018-9162}, doi = {10.1109/MC.2003.1204375}, author = {Larman,C. and Basili, Victor R.} } @article {14886, title = {Lambertian reflectance and linear subspaces}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {25}, year = {2003}, month = {2003/02//}, pages = {218 - 233}, abstract = {We prove that the set of all Lambertian reflectance functions (the mapping from surface normals to intensities) obtained with arbitrary distant light sources lies close to a 9D linear subspace. This implies that, in general, the set of images of a convex Lambertian object obtained under a wide variety of lighting conditions can be approximated accurately by a low-dimensional linear subspace, explaining prior empirical results. We also provide a simple analytic characterization of this linear space. We obtain these results by representing lighting using spherical harmonics and describing the effects of Lambertian materials as the analog of a convolution. These results allow us to construct algorithms for object recognition based on linear methods as well as algorithms that use convex optimization to enforce nonnegative lighting functions. We also show a simple way to enforce nonnegative lighting when the images of an object lie near a 4D linear space. We apply these algorithms to perform face recognition by finding the 3D model that best matches a 2D query image.}, keywords = {2D, 4D, 9D, analog;, analytic, characterization;, convex, convolution, distant, functions;, harmonics;, image, image;, intensities;, Lambertian, light, lighting, linear, methods;, nonnegative, normals;, object, optimization;, programming;, query, recognition;, reflectance;, reflectivity;, set;, sources;, space;, spherical, subspace;, subspaces;, surface}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2003.1177153}, author = {Basri,R. and Jacobs, David W.} } @inbook {16129, title = {LifeLines: Using Visualization to Enhance Navigation and Analysis of Patient Records}, booktitle = {The Craft of Information VisualizationThe Craft of Information Visualization}, year = {2003}, month = {2003///}, pages = {308 - 312}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, isbn = {978-1-55860-915-0}, url = {http://www.sciencedirect.com/science/article/pii/B978155860915050038X}, author = {Plaisant, Catherine and Mushlin,Richard and Snyder,Aaron and Li,Jia and Heller,Dan and Shneiderman, Ben}, editor = {Bederson, Benjamin B. and Shneiderman, Ben} } @article {12392, title = {Logic foundry: rapid prototyping for FPGA-based DSP systems}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2003}, year = {2003}, month = {2003/01//}, pages = {565 - 579}, abstract = {We introduce the Logic Foundry, a system for the rapid creation and integration of FPGA-based digital signal processing systems. Recognizing that some of the greatest challenges in creating FPGA-based systems occur in the integration of the various components, we have proposed a system that targets the following four areas of integration: design flow integration, component integration, platform integration, and software integration. Using the Logic Foundry, a system can be easily specified, and then automatically constructed and integrated with system level software.}, keywords = {CAD tools, Design methodology, DSP, FPGA, integration, rapid prototyping}, isbn = {1110-8657}, doi = {10.1155/S1110865703301039}, url = {http://dx.doi.org/10.1155/S1110865703301039}, author = {Spivey,Gary and Bhattacharyya, Shuvra S. and Nakajima,Kazuo} } @conference {12145, title = {Matching Software Measurements to Business Goals}, booktitle = {Keynote Address at the 2003 Software Management Conference, San Jose, California}, year = {2003}, month = {2003///}, author = {Basili, Victor R.} } @article {18583, title = {Measuring the effects of internet path faults on reactive routing}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {31}, year = {2003}, month = {2003/06//}, pages = {126 - 137}, abstract = {Empirical evidence suggests that reactive routing systems improve resilience to Internet path failures. They detect and route around faulty paths based on measurements of path performance. This paper seeks to understand why and under what circumstances these techniques are effective.To do so, this paper correlates end-to-end active probing experiments, loss-triggered traceroutes of Internet paths, and BGP routing messages. These correlations shed light on three questions about Internet path failures: (1) Where do failures appear? (2) How long do they last? (3) How do they correlate with BGP routing instability?Data collected over 13 months from an Internet testbed of 31 topologically diverse hosts suggests that most path failures last less than fifteen minutes. Failures that appear in the network core correlate better with BGP instability than failures that appear close to end hosts. On average, most failures precede BGP messages by about four minutes, but there is often increased BGP traffic both before and after failures. Our findings suggest that reactive routing is most effective between hosts that have multiple connections to the Internet. The data set also suggests that passive observations of BGP routing messages could be used to predict about 20\% of impending failures, allowing re-routing systems to react more quickly to failures.}, isbn = {0163-5999}, doi = {10.1145/885651.781043}, url = {http://doi.acm.org/10.1145/885651.781043}, author = {Feamster, Nick and Andersen,David G. and Balakrishnan,Hari and Kaashoek,M. Frans} } @conference {13246, title = {Modelling pedestrian shapes for outlier detection: a neural net based approach}, booktitle = {Intelligent Vehicles Symposium, 2003. Proceedings. IEEE}, year = {2003}, month = {2003/06//}, pages = {428 - 433}, abstract = {In this paper we present an example-based approach to learn a given class of complex shapes, and recognize instances of that shape with outliers. The system consists of a two-layer custom-designed neural network. We apply this approach to the recognition of pedestrians carrying objects from a single camera. The system is able to capture and model an ample range of pedestrian shapes at varying poses and camera orientations, and achieves a 90\% correct recognition rate.}, keywords = {(artificial, complex, Computer, computing;, custom, design;, detection;, engineering, intelligence);, layer, learning, method;, modelling;, net;, nets;, neural, object, outlier, pedestrian, pedestrians, rate;, recognition, recognition;, SHAPE, shapes;, traffic, two, vision;}, doi = {10.1109/IVS.2003.1212949}, author = {Nanda,H. and Benabdelkedar,C. and Davis, Larry S.} } @inbook {16147, title = {Navigation Patterns and Usability of Zoomable User Interfaces With and Without an Overview}, booktitle = {The craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {120 - 120}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Bederson, Benjamin B. and Plaisant, Catherine} } @article {16127, title = {Navigation patterns \& usability of zoomable user interfaces: with and without an overview}, journal = {interactions}, volume = {10}, year = {2003}, month = {2003/01//}, pages = {11 - 12}, abstract = {The following abstracts are from recent issues and the forthcoming issue of ACM{\textquoteright}s Transactions of Computer Human Interaction (ToCHI). They are included here to alert interactions{\textquoteright} readers to what research is being done in the field of Computer Human Interaction. The complete papers, when published, can be found in ACM{\textquoteright}s Digital Library at www.acm.org/pubs/contents/journals/tochi/}, isbn = {1072-5520}, doi = {10.1145/604575.604582}, url = {http://doi.acm.org/10.1145/604575.604582}, author = {Hornbaek,Kasper and Bederson, Benjamin B. and Plaisant, Catherine} } @conference {14235, title = {New eyes for robotics}, booktitle = {2003 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2003. (IROS 2003). Proceedings}, volume = {1}, year = {2003}, month = {2003/10/27/31}, pages = {1018- 1023 vol.1 - 1018- 1023 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper describes an imaging system that has been designed to facilitate robotic tasks of motion. The system consists of a number of cameras in a network arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and consequently the estimation of shape models from the individual cameras. The reason is that inherent ambiguities of confusion between translation and rotation disappear. Pairs of cameras may also be arranged in multiple stereo configurations which provide additional advantages for segmentation. Algorithms for the calibration of the system and the 3D motion estimation are provided.}, keywords = {3D motion estimation, Argus eye, array signal processing, Birds, Calibration, CAMERAS, Control systems, Eyes, geometric configuration, imaging, imaging system, Layout, Motion estimation, multiple stereo configurations, Robot kinematics, robot vision, Robot vision systems, ROBOTICS, Robotics and automation, SHAPE, shape models}, isbn = {0-7803-7860-1}, doi = {10.1109/IROS.2003.1250761}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @inbook {16140, title = {Preserving Context with Zoomable User Interfaces}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {83 - 83}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Hombsek,K. and Bederson, Benjamin B. and Plaisant, Catherine} } @article {15019, title = {Recovery of a Digital Image Collection Through the SDSC/UMD/NARA Prototype Persistent Archive}, volume = {UMIACS-TR-2003-105}, year = {2003}, month = {2003/11/25/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The San Diego Supercomputer Center (SDSC), the University of Maryland, and theNational Archives and Records Administration (NARA) are collaborating on building a pilot persistent archive using and extending data grid and digital library technologies. The current prototype consists of node servers at SDSC, University of Maryland, and NARA, connected through the Storage Request Broker (SRB) data grid middleware, and currently holds several terabytes of NARA selected collections. In particular, a historically important image collection that was on the verge of becoming inaccessible was fully restored and ingested into our pilot system. In this report, we describe the methodology behind our approach to fully restore this image collection and the process used to ingest it into the prototype persistent archive. (UMIACS-TR-2003-105) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1321}, author = {Smorul,Mike and JaJa, Joseph F. and McCall,Fritz and Brown,Susan Fitch and Moore,Reagan and Marciano,Richard and Chen,Sheau-Yen and Lopez,Rick and Chadduck,Robert} } @article {12153, title = {Replicated studies: building a body of knowledge about software reading techniques}, journal = {SERIES ON SOFTWARE ENGINEERING AND KNOWLEDGE ENGINEERING}, volume = {12}, year = {2003}, month = {2003///}, pages = {39 - 84}, author = {Shull, F. and Carver, J. and Travassos,G.H. and Maldonado,J.C. and Conradi,R. and Basili, Victor R.} } @article {12302, title = {Resilient multicast using overlays}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {31}, year = {2003}, month = {2003/06//}, pages = {102 - 113}, abstract = {We introduce PRM (Probabilistic Resilient Multicast): a multicast data recovery scheme that improves data delivery ratios while maintaining low end-to-end latencies. PRM has both a proactive and a reactive component; in this paper we describe how PRM can be used to improve the performance of application-layer multicast protocols, especially when there are high packet losses and host failures. Further, using analytic techniques, we show that PRM can guarantee arbitrarily high data delivery ratios and low latency bounds. As a detailed case study, we show how PRM can be applied to the NICE application-layer multicast protocol. We present detailed simulations of the PRM-enhanced NICE protocol for 10,000 node Internet-like topologies. Simulations show that PRM achieves a high delivery ratio (> 97\%) with a low latency bound (600 ms) for environments with high end-to-end network losses (1-5\%) and high topology change rates (5 changes per second) while incurring very low overheads (< 5\%).}, keywords = {overlay multicast, randomized forwarding, Resilience}, isbn = {0163-5999}, doi = {10.1145/885651.781041}, url = {http://doi.acm.org/10.1145/885651.781041}, author = {Banerjee,Suman and Lee,Seungjoon and Bhattacharjee, Bobby and Srinivasan, Aravind} } @article {17814, title = {Secure agents}, journal = {Annals of Mathematics and Artificial Intelligence}, volume = {37}, year = {2003}, month = {2003///}, pages = {169 - 235}, abstract = {With the rapid proliferation of software agents, there comes an increased need for agents to ensure that they do not provide data and/or services to unauthorized users. We first develop an abstract definition of what it means for an agent to preserve data/action security. Most often, this requires an agent to have knowledge that is impossible to acquire {\textendash} hence, we then develop approximate security checks that take into account, the fact that an agent usually has incomplete/approximate beliefs about other agents. We develop two types of security checks {\textendash} static ones that can be checked prior to deploying the agent, and dynamic ones that are executed at run time. We prove that a number of these problems are undecidable, but under certain conditions, they are decidable and (our definition of) security can be guaranteed. Finally, we propose a language within which the developer of an agent can specify her security needs, and present provably correct algorithms for static/dynamic security verification.}, doi = {10.1023/A:1020233522878}, author = {Bonatti,P. A and Kraus,S. and V.S. Subrahmanian} } @inbook {16132, title = {Seeing the World Through Image Libraries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {47 - 47}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {North,C. and Shneiderman, Ben and Plaisant, Catherine and Kang,H. and Bederson, Benjamin B.} } @article {14104, title = {The sequence and analysis of Trypanosoma brucei chromosome II}, journal = {Nucleic acids research}, volume = {31}, year = {2003}, month = {2003///}, pages = {4856 - 4856}, author = {El-Sayed, Najib M. and Ghedin,E. and Song,J. and MacLeod,A. and Bringaud,F. and Larkin,C. and Wanless,D. and Peterson,J. and Hou,L. and Taylor,S. and others} } @book {14916, title = {Special section on perceptual organization in computer vision}, year = {2003}, month = {2003///}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, author = {Jacobs, David W. and Lindenbaum,M. and August,J. and Zucker,SW and Ben-Shahar,O. and Zucker,SW and Tuytelaars,T. and Turina,A. and Van Gool,L. and Mahamud,S.} } @conference {12208, title = {Starting an intergenerational technology design team: a case study}, booktitle = {Proceedings of the 2003 conference on Interaction design and children}, series = {IDC {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {51 - 58}, publisher = {ACM}, organization = {ACM}, address = {Preston, England}, abstract = {This paper presents a case study of the first three months of a new intergenerational design team with children ages 10--13. It discusses the research and design methods used for working with children of this age group, the challenges and opportunities of starting a new team, and the lessons learned.}, keywords = {children, cooperative inquiry, design methods, educational applications, intergenerational design teams, participatory design}, isbn = {1-58113-732-X}, doi = {10.1145/953536.953545}, author = {Knudtzon,Kendra and Druin, Allison and Kaplan,Nancy and Summers,Kathryn and Chisik,Yoram and Kulkarni,Rahul and Moulthrop,Stuart and Weeks,Holly and Bederson, Benjamin B.} } @article {12736, title = {Statistical physical model for foliage clutter in ultra-wideband synthetic aperture radar images}, journal = {Journal of the Optical Society of America AThe Journal of the Optical Society of America A}, volume = {20}, year = {2003}, month = {2003/01/01/}, pages = {32 - 39}, abstract = {Analyzing foliage-penetrating (FOPEN) ultra-wideband synthetic aperture radar (SAR) images is a challenging problem owing to the noisy and impulsive nature of foliage clutter. Indeed, many target-detection algorithms for FOPEN SAR data are characterized by high false-alarm rates. In this work, a statistical{\textendash}physical model for foliage clutter is proposed that explains the presence of outliers in the data and suggests the use of symmetric alpha-stable (SαS) distributions for accurate clutter modeling. Furthermore, with the use of general assumptions of the noise sources and propagation conditions, the proposed model relates the parameters of the SαS model to physical parameters such as the attenuation coefficient and foliage density.}, keywords = {IMAGE PROCESSING, Remote sensing and sensors}, doi = {10.1364/JOSAA.20.000032}, url = {http://josaa.osa.org/abstract.cfm?URI=josaa-20-1-32}, author = {Banerjee,Amit and Chellapa, Rama} } @article {16410, title = {Statistical validation of spatial patterns in agent-based models}, journal = {Proceedings of Agent Based Simulation}, volume = {4}, year = {2003}, month = {2003///}, abstract = {We present and evaluate an agent-based model(ABM) of land use change at the rural-urban fringe. This paper is part of a project that links the ABM to surveys of residential preferences and historical patterns of development. Validation is an important issue for such models and we discuss the use of distributional phenomena as a method of validation. We then highlight the ability of our ABM to gen- erate two phenomena evident in empirical analysis of urban development patterns: a power law rela- tionship between frequency and cluster size and a negative exponential relationship between density and distance from city center. We discuss these results in the light of validation of ABMs. }, author = {Rand, William and Brown,D.G. and Page,S.E. and Riolo,R and Fernandez,L.E. and Zellner,M} } @article {18505, title = {Techniques for interdomain traffic engineering}, journal = {Computer Communications Review}, volume = {33}, year = {2003}, month = {2003///}, abstract = {Network operators must have control over the flow of traffic into,out of, and across their networks. However, the Border Gateway Protocol (BGP) does not facilitate common traffic engineering tasks, such as balancing load across multiple links to a neighboring AS or directing traffic to a different neighbor. Solving these problems is difficult because the number of possible changes to routing policies is too large to exhaustively test all possibilities, some changes in routing policy can have an unpredictable effect on the flow of traf- fic, and the BGP decision process implemented by router vendors limits an operator{\textquoteright}s control over path selection. We analyze routing and traffic data from the AT\&T backbone to identify ways to use BGP policy for traffic engineering tasks. First, we show how cer- tain BGP policy changes can move traffic in a predictable fashion, despite limited knowledge about the routing policies in neighboring AS{\textquoteright}s. Then, we show how operators can gain greater flexibility by relaxing some steps in the BGP decision process and ensuring that neighboring AS{\textquoteright}s send consistent advertisements at each peering location. Finally, we show that an operator can manipulate traffic efficiently by changing the routes for a small number of prefixes (or groups of related prefixes) that consistently receive a large amount of traffic. These results can help operators accomplish common traffic engineering tasks using existing BGP features. }, author = {Feamster, Nick and Borkenhagen,J. and Rexford,J.} } @conference {16139, title = {Technology probes: inspiring design for and with families}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {17 - 24}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe a new method for use in the process of co-designing technologies with users called technology probes. Technology probes are simple, flexible, adaptable technologies with three interdisciplinary goals: the social science goal of understanding the needs and desires of users in a real-world setting, the engineering goal of field-testing the technology, and the design goal of inspiring users and researchers to think about new technologies. We present the results of designing and deploying two technology probes, the messageProbe and the videoProbe, with diverse families in France, Sweden, and the U.S. We conclude with our plans for creating new technologies for and with families based on our experiences.}, keywords = {computer mediated communication, ethnography, Home, participatory design and cooperative design}, isbn = {1-58113-630-7}, doi = {10.1145/642611.642616}, url = {http://doi.acm.org/10.1145/642611.642616}, author = {Hutchinson,Hilary and Mackay,Wendy and Westerlund,Bo and Bederson, Benjamin B. and Druin, Allison and Plaisant, Catherine and Beaudouin-Lafon,Michel and Conversy,St{\'e}phane and Evans,Helen and Hansen,Heiko and Roussel,Nicolas and Eiderb{\"a}ck,Bj{\"o}rn} } @article {17809, title = {Temporal probabilistic object bases}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {15}, year = {2003}, month = {2003/08//july}, pages = {921 - 939}, abstract = {There are numerous applications where we have to deal with temporal uncertainty associated with objects. The ability to automatically store and manipulate time, probabilities, and objects is important. We propose a data model and algebra for temporal probabilistic object bases (TPOBs), which allows us to specify the probability with which an event occurs at a given time point. In explicit TPOB-instances, the sets of time points along with their probability intervals are explicitly enumerated. In implicit TPOB-instances, sets of time points are expressed by constraints and their probability intervals by probability distribution functions. Thus, implicit object base instances are succinct representations of explicit ones; they allow for an efficient implementation of algebraic operations, while their explicit counterparts make defining algebraic operations easy. We extend the relational algebra to both explicit and implicit instances and prove that the operations on implicit instances correctly implement their counterpart on explicit instances.}, keywords = {algebra;, algebraic, bases;, constraints;, data, database, database;, databases;, distribution, explicit, functions;, handling;, implicit, instances;, integrity;, intervals;, management;, model;, models;, object, object-oriented, operations;, probabilistic, probability, probability;, relational, temporal, theory;, Uncertainty, uncertainty;}, isbn = {1041-4347}, doi = {10.1109/TKDE.2003.1209009}, author = {Biazzo,V. and Giugno,R. and Lukasiewicz,T. and V.S. Subrahmanian} } @inbook {18603, title = {Thwarting Web Censorship with Untrusted Messenger Discovery}, booktitle = {Privacy Enhancing TechnologiesPrivacy Enhancing Technologies}, series = {Lecture Notes in Computer Science}, volume = {2760}, year = {2003}, month = {2003///}, pages = {125 - 140}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {All existing anti-censorship systems for the Web rely on proxies to grant clients access to censored information. Therefore, they face the proxy discovery problem : how can clients discover the proxies without having the censor discover and block these proxies? To avoid widespread discovery and blocking, proxies must not be widely published and should be discovered in-band. In this paper, we present a proxy discovery mechanism called keyspace hopping that meets this goal. Similar in spirit to frequency hopping in wireless networks, keyspace hopping ensures that each client discovers only a small fraction of the total number of proxies. However, requiring clients to independently discover proxies from a large set makes it practically impossible to verify the trustworthiness of every proxy and creates the possibility of having untrusted proxies. To address this, we propose separating the proxy into two distinct components{\textemdash}the messenger , which the client discovers using keyspace hopping and which simply acts as a gateway to the Internet; and the portal , whose identity is widely-published and whose responsibility it is to interpret and serve the client{\textquoteright}s requests for censored content. We show how this separation, as well as in-band proxy discovery, can be applied to a variety of anti-censorship systems.}, keywords = {Computer science}, isbn = {978-3-540-20610-1}, url = {http://www.springerlink.com/content/1gg8p94deqek968t/abstract/}, author = {Feamster, Nick and Balazinska,Magdalena and Wang,Winston and Balakrishnan,Hari and Karger,David}, editor = {Dingledine,Roger} } @article {18606, title = {Towards a logic for wide-area Internet routing}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {33}, year = {2003}, month = {2003/08//}, pages = {289 - 300}, abstract = {Interdomain routing is a massive distributed computing task that propagates topological information for global reachability. Today{\textquoteright}s interdomain routing protocol, BGP4, is exceedingly complex because the wide variety of goals that it must meet---including fast convergence, failure resilience, scalability, policy expression, and global reachability---are accomplished by mechanisms that have complicated interactions and unintended side effects. The complexity of wide-area routing configuration and protocol dynamics requires mechanisms for expressing wide-area routing that adhere to a set of logical rules. We propose a set of rules, called the routing logic, which can be used to determine whether a routing protocol satisfies various properties. We demonstrate how this logic can aid in analyzing the behavior of BGP4 under various configurations. We also speculate on how the logic can be used to analyze existing configuration in real-world networks, synthesize network-wide router configuration from a high-level policy language, and assist protocol designers in reasoning about new routing protocols.}, isbn = {0146-4833}, doi = {10.1145/972426.944767}, url = {http://doi.acm.org/10.1145/972426.944767}, author = {Feamster, Nick and Balakrishnan,Hari} } @article {17449, title = {Understanding Computer User Frustration: Measuring and Modeling the Disruption from Poor Designs}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/01/21/}, abstract = {User frustration in the use of information and computing technology is apervasive and persistent problem. When computers crash, network congestion causes delays, and poor user interfaces trigger confusion there are dramatic consequences for individuals, organizations, and society. These frustrations not only cause personal dissatisfaction and loss of self-efficacy, but may disrupt workplaces, slow learning, and reduce participation in local and national communities. We propose a Computing Frustration Model with incident specific and individual variables to guide research. Our study of 108 computer users shows high levels of frustration and loss of 1/3 to 1/2 of time spent. The importance of the users{\textquoteright} goals and the severity of the disruption were correlated with frustration. Those who had strong self-efficacy, indicated by a willingness to stick to solving the problem, reported lower levels of frustration. Implications for users, software developers, managers, and policymakers are discussed. Keywords: user frustration, user interface design, training, helpdesk, computer experience, computer anxiety (UMIACS-TR-2002-89) (HCIL-TR-2002-18) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1233}, author = {Bessiere,Katie and Ceaparu,Irina and Lazar,Jonathan and Robinson,John and Shneiderman, Ben} } @conference {12299, title = {On the use of flow migration for handling short-term overloads}, booktitle = {Global Telecommunications Conference, 2003. GLOBECOM {\textquoteright}03. IEEE}, volume = {6}, year = {2003}, month = {2003/12//}, pages = {3108 - 3112 vol.6 - 3108 - 3112 vol.6}, abstract = {In this work, we investigate flow migration as a mechanism to sustain QoS to network users during short-term overloads in the context of an MPLS IP network. We experiment with three different control techniques: static long-term optimal mapping of flows to LSPs; on-line locally optimal mapping of flows to LSPs at flow set-up time; and dynamic flow migration in response to transient congestion. These techniques are applicable over different timescales, have different run-time overheads, and require different levels of monitoring and control software inside the network. We present results both from detailed simulations and a complete implementation using software IP routers. We use voice-over-IP as our test application, and show that if end-to-end quality is to be maintained during short unpredictable bursts of high load, then a fast-timescale control such as migration is required.}, keywords = {computing;, CONGESTION, congestion;, CONTROL, control;, dynamic, end-to-end, engineering, fast-timescale, flow, Internet, IP, label, long-term, mapping;, migration;, MPLS, multiprotocol, network, network;, networks;, of, optimal, overloads;, protocol;, QoS;, QUALITY, quality;, routers;, routing;, service;, set-up, short-term, software, software;, static, switching;, Telecommunication, telephony;, time;, transient, voice-over-IP;}, doi = {10.1109/GLOCOM.2003.1258807}, author = {Kuo,Kuo-Tung and Phuvoravan,S. and Bhattacharjee, Bobby and Jun La,R. and Shayman,M. and Chang,Hyeong Soo} } @article {16898, title = {Use of the SAND spatial browser for digital government applications}, journal = {Commun. ACM}, volume = {46}, year = {2003}, month = {2003/01//}, pages = {61 - 64}, abstract = {Numerous federal agencies produce official statistics made accessible to ordinary citizens for searching and data retrieval. This is frequently done via the Internet through a Web browser interface. If this data is presented in textual format, it can often be searched and retrieved by such attributes as topic, responsible agency, keywords, or press release. However, if the data is of spatial nature, for example, in the form of a map, then using text-based queries is often too cumbersome for the intended audience. We describe the use of the SAND Spatial Browser to provide more power to users of these databases by enabling them to define and explore the specific spatial region of interest graphically. The SAND Spatial Browser allows users to form either purely spatial or mixed spatial/nonspatial queries intuitively, which can present information to users that might have been missed if only a textual interface was available.}, keywords = {GIS}, isbn = {0001-0782}, doi = {10.1145/602421.602453}, url = {http://doi.acm.org/10.1145/602421.602453}, author = {Samet, Hanan and Alborzi,Houman and Brabec,Franti{\v s}ek and Esperan{\c c}a,Claudio and Hjaltason,G{\'\i}sli R. and Morgan,Frank and Tanin,Egemen} } @article {12165, title = {User interface evaluation and empirically-based evolution of a prototype experience management tool}, journal = {Software Engineering, IEEE Transactions on}, volume = {29}, year = {2003}, month = {2003/09//}, pages = {838 - 850}, abstract = {Experience management refers to the capture, structuring, analysis, synthesis, and reuse of an organization{\textquoteright}s experience in the form of documents, plans, templates, processes, data, etc. The problem of managing experience effectively is not unique to software development, but the field of software engineering has had a high-level approach to this problem for some time. The Experience Factory is an organizational infrastructure whose goal is to produce, store, and reuse experiences gained in a software development organization. This paper describes The Q-Labs Experience Management System (Q-Labs EMS), which is based on the Experience Factory concept and was developed for use in a multinational software engineering consultancy. A critical aspect of the Q-Labs EMS project is its emphasis on empirical evaluation as a major driver of its development and evolution. The initial prototype requirements were grounded in the organizational needs and vision of Q-Labs, as were the goals and evaluation criteria later used to evaluate the prototype. However, the Q-Labs EMS architecture, data model, and user interface were designed to evolve, based on evolving user needs. This paper describes this approach, including the evaluation that was conducted of the initial prototype and its implications for the further development of systems to support software experience management.}, keywords = {data, development;, empirical, EMS;, engineering;, evaluation;, experience, experience;, Factory;, interface, interfaces;, knowledge, management, management;, model;, models;, organization, performance, prototype, Q-Labs, re-engineering;, reusability;, reuse;, software, system;, systems, tool;, user}, isbn = {0098-5589}, doi = {10.1109/TSE.2003.1232288}, author = {Seaman,C.B and Mendonca,M.G. and Basili, Victor R. and Kim,Y. M} } @conference {16906, title = {VASCO: visualizing and animating spatial constructs and operations}, booktitle = {Proceedings of the nineteenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {374 - 375}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A video is used to demonstrate a set of spatial index JAVA applets that enable users on the worldwide web to experiment with a number of variants of the quadtree spatial data structure for different spatial data types, and, most importantly, enable them to see in an animated manner how a number of basic search operations are executed for them. The spatial data types are points, line segments, rectangles, and regions. The search operations are the window query (i.e., a spatial range query) and a nearest neighbor query that enables ranking spatial objects in the order of their distance from a given query object. The representations and algorithms are visualized and animated in a consistent manner using the same primitives and colors so that the differences between the effects of the representations can be easily understood. The video demonstrates the PR quadtree, PM1 quadtree, and R-tree. The applets can be found at: www.cs.umd.edu/~hjs/quadtree/.}, keywords = {k-d trees, Nearest neighbor algorithms, quadtrees, R-trees, Visualization}, isbn = {1-58113-663-3}, doi = {10.1145/777792.777849}, url = {http://doi.acm.org/10.1145/777792.777849}, author = {Brabec,Frantivsek and Samet, Hanan and Yilmaz,Cemal} } @article {17849, title = {The virtual microscope}, journal = {IEEE Transactions on Information Technology in Biomedicine}, volume = {7}, year = {2003}, month = {2003/12//}, pages = {230 - 248}, abstract = {We present the design and implementation of the virtual microscope, a software system employing a client/server architecture to provide a realistic emulation of a high power light microscope. The system provides a form of completely digital telepathology, allowing simultaneous access to archived digital slide images by multiple clients. The main problem the system targets is storing and processing the extremely large quantities of data required to represent a collection of slides. The virtual microscope client software runs on the end user{\textquoteright}s PC or workstation, while database software for storing, retrieving and processing the microscope image data runs on a parallel computer or on a set of workstations at one or more potentially remote sites. We have designed and implemented two versions of the data server software. One implementation is a customization of a database system framework that is optimized for a tightly coupled parallel machine with attached local disks. The second implementation is component-based, and has been designed to accommodate access to and processing of data in a distributed, heterogeneous environment. We also have developed caching client software, implemented in Java, to achieve good response time and portability across different computer platforms. The performance results presented show that the Virtual Microscope systems scales well, so that many clients can be adequately serviced by an appropriately configured data server.}, keywords = {biomedical optical imaging, client software, client/server architecture, Computer architecture, Computer Graphics, computer platforms, Computer simulation, Concurrent computing, configured data server, data server software, database management systems, database software, Database systems, digital slide images, digital telepathology, diseases, emulation, Environment, Equipment Design, Equipment Failure Analysis, high power light microscope, Image databases, Image Enhancement, Image Interpretation, Computer-Assisted, Image retrieval, Information retrieval, Information Storage and Retrieval, java, local disks, microscope image data, Microscopy, multiple clients, optical microscopy, PACS, software, Software design, software system, Software systems, Systems Integration, Telepathology, User-Computer Interface, virtual microscope design, Virtual reality, Workstations}, isbn = {1089-7771}, doi = {10.1109/TITB.2004.823952}, author = {Catalyurek,U. and Beynon,M. D and Chang,Chialin and Kurc, T. and Sussman, Alan and Saltz, J.} } @inbook {16135, title = {Visual Information Management for Network Configuration}, booktitle = {The Craft of Information VisualizationThe Craft of Information Visualization}, year = {2003}, month = {2003///}, pages = {239 - 256}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, abstract = {Current network management systems rely heavily on forms in their user interfaces. The interfaces reflect the intricacies of the network hardware components but provide little support for guiding users through tasks. There is a scarcity of useful graphical visualizations and decision-support tools.}, isbn = {978-1-55860-915-0}, url = {http://www.sciencedirect.com/science/article/pii/B9781558609150500329}, author = {Kumar,Harsha and Plaisant, Catherine and Teittinen,Marko and Shneiderman, Ben}, editor = {Bederson, Benjamin B. and Shneiderman, Ben} } @conference {15285, title = {What makes a good answer? The role of context in question answering}, booktitle = {Human-Computer Interaction, Interact {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {25 - 25}, author = {Jimmy Lin and Quan,D. and Sinha,V. and Bakshi,K. and Huynh,D. and Katz,B. and Karger,D. R} } @conference {15428, title = {What test oracle should I use for effective GUI testing?}, booktitle = {Automated Software Engineering, 2003. Proceedings. 18th IEEE International Conference on}, year = {2003}, month = {2003/10//}, pages = {164 - 173}, abstract = {Test designers widely believe that the overall effectiveness and cost of software testing depends largely on the type and number of test cases executed on the software. In this paper we show that the test oracle used during testing also contributes significantly to test effectiveness and cost. A test oracle is a mechanism that determines whether software executed correctly for a test case. We define a test oracle to contain two essential parts: oracle information that represents expected output; and an oracle procedure that compares the oracle information with the actual output. By varying the level of detail of oracle information and changing the oracle procedure, a test designer can create different types of test oracles. We design 11 types of test oracles and empirically compare them on four software systems. We seed faults in software to create 100 faulty versions, execute 600 test cases on each version, for all 11 types of oracles. In all, we report results of 660,000 test runs on software. We show (1) the time and space requirements of the oracles, (2) that faults are detected early in the testing process when using detailed oracle information and complex oracle procedures, although at a higher cost per test case, and (3) that employing expensive oracles results in detecting a large number of faults using relatively smaller number of test cases.}, keywords = {empirical studies, graphical user interface, Graphical user interfaces, GUI testing, oracle information, oracle procedure, oracle space requirement, oracle time requirements, program testing, software engineering, Software testing, test cost, test effectiveness, test oracle}, doi = {10.1109/ASE.2003.1240304}, author = {Memon, Atif M. and Banerjee,I. and Nagarajan,A.} } @inbook {16131, title = {The World{\textquoteright}s Information in Digital Libraries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {149 - 149}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Plaisant, Catherine and Marchimini,G. and Bruns,T. and Komlodi,A. and Campbell,L. and Rose,A. and Ding,G.M. and Beale Jr,J. and Nolet,V. and Shneiderman, Ben and others} } @inbook {14589, title = {1.375-Approximation Algorithm for Sorting by Reversals}, booktitle = {Algorithms {\textemdash} ESA 2002Algorithms {\textemdash} ESA 2002}, series = {Lecture Notes in Computer Science}, volume = {2461}, year = {2002}, month = {2002///}, pages = {401 - 408}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analysis of genomes evolving by inversions leads to a general combinatorial problem of Sorting by Reversals , MIN-SBR, the problem of sorting a permutation by a minimum number of reversals. Following a series of preliminary results, Hannenhalli and Pevzner developed the first exact polynomial time algorithm for the problem of sorting signed permutations by reversals, and a polynomial time algorithm for a special case of unsigned permutations. The best known approximation algorithm for MIN-SBR, due to Christie, gives a performance ratio of 1.5. In this paper, by exploiting the polynomial time algorithm for sorting signed permutations and by developing a new approximation algorithm for maximum cycle decomposition of breakpoint graphs, we design a new 1.375-algorithm for the MIN-SBR problem.}, isbn = {978-3-540-44180-9}, url = {http://dx.doi.org/10.1007/3-540-45749-6_21}, author = {Berman,Piotr and Hannenhalli, Sridhar and Karpinski,Marek}, editor = {M{\"o}hring,Rolf and Raman,Rajeev} } @article {13414, title = {AAAI 2002 Workshops}, journal = {AI Magazine}, volume = {23}, year = {2002}, month = {2002/12/15/}, pages = {113 - 113}, isbn = {0738-4602}, doi = {10.1609/aimag.v23i4.1678}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1678}, author = {Blake,Brian and Haigh,Karen and Hexmoor,Henry and Falcone,Rino and Soh,Leen-Kiat and Baral,Chitta and McIlraith,Sheila and Gmytrasiewicz,Piotr and Parsons,Simon and Malaka,Rainer and Krueger,Antonio and Bouquet,Paolo and Smart,Bill and Kurumantani,Koichi and Pease,Adam and Brenner,Michael and desJardins, Marie and Junker,Ulrich and Delgrande,Jim and Doyle,Jon and Rossi,Francesca and Schaub,Torsten and Gomes,Carla and Walsh,Toby and Guo,Haipeng and Horvitz,Eric J and Ide,Nancy and Welty,Chris and Anger,Frank D and Guegen,Hans W and Ligozat,Gerald} } @conference {16002, title = {ALLI: An Information Integration System Based on Active Logic Framework}, booktitle = {Proceedings of the Third International Conference on Management Information Systems, Greece}, year = {2002}, month = {2002///}, pages = {339 - 348}, author = {Barfourosh,A. A. and Nezhad,H. R.M and Anderson,M. and Perlis, Don} } @article {12308, title = {Analysis of the NICE Application Layer Multicast Protocol}, journal = {Technical Reports from UMIACS, UMIACS-TR-2002-60}, year = {2002}, month = {2002/08/01/}, abstract = {Application layer multicast protocols organize a set of hosts intoan overlay tree for data delivery. Each host on the overlay peers with a subset of other hosts. Since application layer multicast relies only on an underlying unicast architecture, multiple copies of the same packet can be carried by a single physical link or node on the overlay. The stress at a link or node is defined as the number of identical copies of a packet carried by that link or node. Stretch is another important metric in application layer multicast, which measures the relative increase in delay incurred by the overlay path between pairs of members with respect to the direct unicast path. In this paper we study the NICE application layer multicast protocol to quantify and study the tradeoff between these two important metrics --- stress and stretch in scalably building application layer multicast paths. Also UMIACS-TR-2002-60 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1212}, author = {Banerjee,Suman and Bhattacharjee, Bobby} } @article {12312, title = {Are virtualized overlay networks too much of a good thing?}, journal = {Peer-to-Peer Systems}, year = {2002}, month = {2002///}, pages = {225 - 231}, abstract = {The majority of recent high-profile work in peer-to-peer networks has approached the problem of location by abstracting over object lookup services. Namespace virtualization in the overlay layer provides load balance and provable bounds on latency at low costs.We contend that namespace virtualization comes at a significant cost for applications that naturally describe their data sets in a hierarchical manner. Opportunities for enhancing browsing, prefetching and efficient attribute-based searches are lost. A hierarchy exposes relationships between items near to each other in the topology; virtualization of the namespace discards this information even if present at client, higherlevel protocols. We advocate encoding application hierarchies directly into the structure of the overlay network, and revisit this argument through a newly proposed distributed directory service. }, author = {Keleher,P. and Bhattacharjee, Bobby and Silaghi,B.} } @conference {13729, title = {Automatic transcription of Czech language oral history in the MALACH project: resources and initial experiments}, booktitle = {Proceedings of the The 5th International Conference on Text, Speech and Dialogue}, year = {2002}, month = {2002///}, pages = {57 - 64}, author = {Oard, Douglas and Demner-Fushman,D. and Hajic,J. and Ramabhadran,B. and Gustman,S. and Byrne,WJ and Soergel,D. and Dorr, Bonnie J and Resnik, Philip and Picheny,M.} } @conference {17868, title = {On cache replacement policies for servicing mixed data intensive query workloads}, booktitle = {Proceedings of the 2nd Workshop on Caching, Coherence, and Consistency, held in conjunction with the 16th ACM International Conference on Supercomputing}, year = {2002}, month = {2002///}, abstract = {When data analysis applications are employed in a multi-client environment, a data server must service multiple si- multaneous queries, each of which may employ complex user-defined data structures and operations on the data. It is then necessary to harness inter- and intra-query com- monalities and system resources to improve the performance of the data server. We have developed a framework and customizable middleware to enable reuse of intermediate and final results among queries, through an in-memory ac- tive semantic cache and user-defined transformation func- tions. Since resources such as processing power and mem- ory space are limited on the machine hosting the server, ef- fective scheduling of incoming queries and efficient cache replacement policies are challenging issues that must be ad- dressed. We have worked on the scheduling problem in ear- lier work, and in this paper we describe and evaluate several cache replacement policies. We present experimental eval- uation of the policies on a shared-memory parallel system using two applications from different application domains. }, author = {Andrade,H. and Kurc, T. and Sussman, Alan and Borovikov,E. and Saltz, J.} } @inbook {14598, title = {Combinatorial Algorithms for Design of DNA Arrays}, booktitle = {Chip TechnologyChip Technology}, series = {Advances in Biochemical Engineering/Biotechnology}, volume = {77}, year = {2002}, month = {2002///}, pages = {1 - 19}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination ( border length minimization problem ) and reducing the complexity of masks ( mask decomposition problem ). We describe algorithms that reduce the number of rectangles in mask decomposition by 20{\textendash}30\% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.}, isbn = {978-3-540-43215-9}, url = {http://dx.doi.org/10.1007/3-540-45713-5_1}, author = {Hannenhalli, Sridhar and Hubbell,Earl and Lipshutz,Robert and Pevzner,Pavel}, editor = {Hoheisel,J{\"o}rg and Brazma,A. and B{\"u}ssow,K. and Cantor,C. and Christians,F. and Chui,G. and Diaz,R. and Drmanac,R. and Drmanac,S. and Eickhoff,H. and Fellenberg,K. and Hannenhalli, Sridhar and Hoheisel,J. and Hou,A. and Hubbell,E. and Jin,H. and Jin,P. and Jurinke,C. and Konthur,Z. and K{\"o}ster,H. and Kwon,S. and Lacy,S. and Lehrach,H. and Lipshutz,R. and Little,D. and Lueking,A. and McGall,G. and Moeur,B. and Nordhoff,E. and Nyarsik,L. and Pevzner,P. and Robinson,A. and Sarkans,U. and Shafto,J. and Sohail,M. and Southern,E. and Swanson,D. and Ukrainczyk,T. and van den Boom,D. and Vilo,J. and Vingron,M. and Walter,G. and Xu,C.} } @article {16250, title = {Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus Anthracis}, journal = {Science}, volume = {296}, year = {2002}, month = {2002/06/14/}, pages = {2028 - 2033}, abstract = {Comparison of the whole-genome sequence ofBacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced B. anthracischromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1071837}, url = {http://www.sciencemag.org/content/296/5575/2028}, author = {Read,Timothy D. and Salzberg,Steven L. and Pop, Mihai and Shumway,Martin and Umayam,Lowell and Jiang,Lingxia and Holtzapple,Erik and Busch,Joseph D and Smith,Kimothy L and Schupp,James M and Solomon,Daniel and Keim,Paul and Fraser,Claire M.} } @article {12313, title = {A comparative study of application layer multicast protocols}, journal = {Network}, volume = {4}, year = {2002}, month = {2002///}, pages = {3 - 3}, abstract = {Due to the sparse deployment of IP multicast inthe Internet today, some researchers have proposed applica- tion layer multicast as a new approach to implement wide- area multicast services. In this approach multicast func- tionality is implemented at the end-hosts instead of network routers. Unlike network-layer multicast, application layer multicast requires no infrastructure support and can be eas- ily deployed in the Internet. In this paper, we describe a set of application layer multicast protocols that have been pro- posed in recent literature, classify them based on some prop- erties and present a comparison of performance and appli- cability of these schemes. }, author = {Banerjee,S. and Bhattacharjee, Bobby} } @article {16411, title = {The complex interaction of agents and environments: An example in urban sprawl}, journal = {Proceedings of Agent Based Simulation}, year = {2002}, month = {2002///}, pages = {149 - 161}, abstract = {We present and evaluate a foundational agent-based model of land use change at therural-urban fringe within the context of a larger project that will link to surveys of the environmental and community preferences of residents with historical data on patterns of development. In this paper, we focus on the dynamics arising from a model of residential location resulting from preferences for services, density, and aesthetics focusing on the relationship between micro level preferences and policy relevant macro phenomena such as scattered development, largest city size, and the number of residential clusters. We consider two representations of agents{\textquoteright} utility functions {\textendash} one additively separable and one multiplicative {\textendash} to see if functional form has any impact on the dynamics of the system, and find that they produce similar results. Our analysis includes both representative agent runs, in which all agents have identical preferences, as well as runs in which the agents have diverse preferences. We find that diversity can increase sprawl through feedbacks associated with the spatial locations of services and agents. In addition, we examine cases in which the agents{\textquoteright} location decisions affect the aesthetic quality of neighboring sites and find that these feedbacks further exacerbate the sprawl effect. }, author = {Rand, William and Zellner,M and Page,S.E. and Riolo,R and Brown,D.G. and Fernandez,L.E.} } @conference {12372, title = {A component architecture for FPGA-based, DSP system design}, booktitle = {Application-Specific Systems, Architectures and Processors, 2002. Proceedings. The IEEE International Conference on}, year = {2002}, month = {2002///}, pages = {41 - 51}, author = {Spivey,G. and Bhattacharyya, Shuvra S. and Nakajima,K.} } @article {12125, title = {COTS-based software development: Processes and open issues}, journal = {Journal of Systems and Software}, volume = {61}, year = {2002}, month = {2002/04/01/}, pages = {189 - 199}, abstract = {The work described in this paper is an investigation of the COTS-based software development within a particular NASA environment, with an emphasis on the processes used. Fifteen projects using a COTS-based approach were studied and their actual process was documented. This process is evaluated to identify essential differences in comparison to traditional software development. The main differences, and the activities for which projects require more guidance, are requirements definition and COTS selection, high level design, integration and testing. Starting from these empirical observations, a new process and set of guidelines for COTS-based development are developed and briefly presented.}, keywords = {Commercial off-the-shelf, Component-based, COTS, empirical study, Software development process}, isbn = {0164-1212}, doi = {10.1016/S0164-1212(01)00147-9}, url = {http://www.sciencedirect.com/science/article/pii/S0164121201001479}, author = {Morisio,M and Seaman,C.B and Basili, Victor R. and Parra,A.T and Kraft,S.E and Condon,S.E} } @article {11912, title = {Efficient Data Processing using Cross Layer Hints}, journal = {Technical Reports from UMIACS, UMIACS-TR-2002-59}, year = {2002}, month = {2002/12/19/}, abstract = {Conventional network stacks define a layered architecture, whereeach layer implements a set of services and exports a well-defined interface to be used by its immediate upper layer. A key design choice of the layered architecture has been to provide isolation between the functional modules of distinct layers. While such an architecture provides an useful abstraction for system development, the strict isolation of this layered architecture limits the flexibility of tailoring the behavior of the lower layers of the stack to the needs of the application. In this paper we define a new architecture, called X-Tags, which allows flexible interaction between layers for cooperative data processing without impacting the isolation property. In this architecture, applications use special tags to provide semantic hints for data processing to lower layers. We motivate the usefulness of this architecture by describing ts applicability to some emerging applications. UMIACS-TR-2002-59 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1211}, author = {Banerjee,Suman and Agrawala, Ashok K. and Kramer,Michael J} } @conference {17838, title = {Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems}, booktitle = {Parallel and Distributed Processing Symposium, International}, volume = {2}, year = {2002}, month = {2002///}, pages = {0084 - 0084}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {In this paper we are concerned with the efficient use of a collection of disk-based storage systems and computing platforms in a heterogeneous setting for retrieving and processing large scientific datasets. We demonstrate, in the context of a data-intensive visualization application, how heterogeneity affects performance and show a set of optimization techniques that can be used to improve performance in a component-based framework. In particular, we examine the application of parallelism via transparent copies of application components in the pipelined processing of data.}, keywords = {component-based frameworks, data-intensive computing, load balancing}, isbn = {0-7695-1573-8}, doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2002.1015655}, author = {Beynon,Michael D. and Sussman, Alan and Kurc,Tahsin and Catalyurek,Umit and Saltz,Joel} } @conference {18384, title = {Empirical evaluation of techniques and methods used for achieving and assessing software high dependability}, booktitle = {Proc. DSN Workshop on Dependability Benchmarking}, year = {2002}, month = {2002///}, author = {Rus,I. and Basili, Victor R. and Zelkowitz, Marvin V and Boehm,B.} } @article {18385, title = {Empirical findings in agile methods}, journal = {Extreme Programming and Agile Methods{\textemdash}XP/Agile Universe 2002}, year = {2002}, month = {2002///}, pages = {81 - 92}, abstract = {In recent years, the use of, interest in, and controversy about Agile methodologies have realized dramatic growth. Anecdotal evidence is rising regarding the effectiveness of agile methodologies in certain environments and for specified projects. However, collection and analysis of empirical evidence of this effectiveness and classification of appropriate environments for Agile projects has not been conducted. Researchers from four institutions organized an eWorkshop to synchronously and virtually discuss and gather experiences and knowledge from eighteen Agile experts spread across the globe. These experts characterized Agile Methods and communicated experiences using these methods on small to very large teams. They discussed the importance of staffing Agile teams with highly skilled developers. They shared common success factors and identified warning signs of problems in Agile projects. These and other findings and heuristics gathered through this valuable exchange can be useful to researchers and to practitioners as they establish an experience base for better decision making.}, doi = {10.1007/3-540-45672-4_19}, author = {Lindvall,M. and Basili, Victor R. and Boehm,B. and Costa,P. and Dangle,K. and Shull, F. and Tesoriero,R. and Williams,L. and Zelkowitz, Marvin V} } @conference {17889, title = {Executing Multiple Pipelined Data Analysis Operations in the Grid}, booktitle = {SC Conference}, year = {2002}, month = {2002///}, pages = {54 - 54}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Processing of data in many data analysis applications can be represented as an acyclic, coarse grain data flow, from data sources to the client. This paper is concerned with scheduling of multiple data analysis operations, each of which is represented as a pipelined chain of processing on data. We define the scheduling problem for effectively placing components onto Grid resources, and propose two scheduling algorithms. Experimental results are presented using a visualization application.}, doi = {http://doi.ieeecomputersociety.org/10.1109/SC.2002.10015}, author = {Spencer,Matthew and Ferreira,Renato and Beynon,Michael and Kurc,Tahsin and Catalyurek,Umit and Sussman, Alan and Saltz,Joel} } @article {12159, title = {The Experience factory organization}, journal = {IEEE Software}, volume = {19}, year = {2002}, month = {2002///}, pages = {30 - 31}, author = {Basili, Victor R. and Seaman,C.} } @article {12133, title = {Experience in implementing a learning software organization}, journal = {Software, IEEE}, volume = {19}, year = {2002}, month = {2002/06//may}, pages = {46 - 49}, abstract = {In an effort to improve software development and acquisition processes and explicitly reuse knowledge from previous software projects, DaimlerChrysler created a software experience center (SEC). The authors report on challenges the company faced in creating the SEC}, keywords = {ACQUISITION, center;software, centres;project, DaimlerChrysler;explicit, development, experience, improvement;, improvement;automobile, industry;computer, knowledge, management;software, organization;previous, process, processes;software, projects;software, reuse;learning, software}, isbn = {0740-7459}, doi = {10.1109/MS.2002.1003453}, author = {Schneider,K. and von Hunnius,J.-P. and Basili, Victor R.} } @inbook {18671, title = {Experimental Evaluation of the Unavailability Induced by a Group Membership Protocol}, booktitle = {Dependable Computing EDCC-4}, series = {Lecture Notes in Computer Science}, volume = {2485}, year = {2002}, month = {2002///}, pages = {644 - 648}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Group communication is an important paradigm for building highly available distributed systems. However, group membership operations often require the system to block message traffic, causing system services to become unavailable. This makes it important to quantify the unavailability induced by membership operations. This paper experimentally evaluates the blocking behavior of the group membership protocol of the Ensemble group communication system using a novel global-state-based fault injection technique. In doing so, we demonstrate how a layered distributed protocol such as the Ensemble group membership protocol can be modeled in terms of a state machine abstraction, and show how the resulting global state space can be used to specify fault triggers and define important measures on the system. Using this approach, we evaluate the cost associated with important states of the protocol under varying workload and group size. We also evaluate the sensitivity of the protocol to the occurrence of a second correlated crash failure during its operation.}, keywords = {Computer science}, isbn = {978-3-540-00012-9}, url = {http://www.springerlink.com/content/mnkd4upqr14w2r7e/abstract/}, author = {Joshi,Kaustubh and Michel Cukier and Sanders,William}, editor = {Bondavalli,Andrea and Thevenod-Fosse,Pascale} } @article {18814, title = {An extraction-based verification methodology for MEMS}, journal = {Microelectromechanical Systems, Journal of}, volume = {11}, year = {2002}, month = {2002/02//}, pages = {2 - 11}, abstract = {Micromachining techniques are being increasingly used to develop miniaturized sensor and actuator systems. These system designs tend to be captured as layout, requiring extraction of the equivalent microelectromechanical circuit as a necessary step for design verification. This paper presents an extraction methodology to (re-)construct a circuit schematic representation from the layout, enabling the designer to use microelectromechanical circuit simulators to verify the functional behavior of the layout. This methodology uses a canonical representation of the given layout on which feature-based and graph-based recognition algorithms are applied to generate the equivalent extracted schematic. Extraction can be performed to either the atomic level or the functional level representation of the reconstructed circuit. The choice of level in hierarchy is governed by the trade off between simulation time and simulation accuracy of the extracted circuit. The combination of the MEMS layout extraction and lumped-parameter circuit simulation provides MEMS designers with VLSI-like tools enabling faster design cycles, and improved design productivity}, keywords = {atomic level, canonical representation, circuit schematic representation, circuit simulation, design cycles, design productivity, design verification, digital simulation, equivalent circuits, equivalent microelectromechanical circuit, extraction-based verification methodology, feature-based recognition algorithms, functional behavior, functional level, graph-based recognition algorithms, layout extraction, lumped parameter networks, lumped-parameter circuit simulation, MEMS, microelectromechanical circuit simulators, micromachining techniques, micromechanical devices, simulation accuracy, simulation time}, isbn = {1057-7157}, doi = {10.1109/84.982857}, author = {Baidya,B. and Gupta,S.K. and Mukherjee,T.} } @article {18837, title = {Generating 3D Models of MEMS Devices by Process Emulation}, volume = {ISR; TR 2002-57}, year = {2002}, month = {2002///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {MEMS designers often use numerical simulation for detecting errors in the mask layout. Numerical simulation involves generating 3D models of MEMS device from the mask layout and process description. The generated models can be meshed and simulated over different domains. This report describes an efficient algorithm that can generate 3D geometric models of MEMS devices. Specifically, the algorithm emulates the manufacturing of a single functional polysilicon layer MEMS devices using the MUMPSprocess.}, keywords = {Next-Generation Product Realization Systems}, url = {http://drum.lib.umd.edu//handle/1903/6285}, author = {Bellam,S. and Gupta, Satyandra K. and Priyadarshi,A. K.} } @article {16270, title = {Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii}, journal = {Nature}, volume = {419}, year = {2002}, month = {2002/10/03/}, pages = {512 - 519}, abstract = {Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.}, isbn = {0028-0836}, doi = {10.1038/nature01099}, url = {http://www.nature.com/nature/journal/v419/n6906/full/nature01099.html}, author = {Carlton,Jane M. and Angiuoli,Samuel V and Suh,Bernard B. and Kooij,Taco W. and Pertea,Mihaela and Silva,Joana C. and Ermolaeva,Maria D. and Allen,Jonathan E and Jeremy D Selengut and Koo,Hean L. and Peterson,Jeremy D. and Pop, Mihai and Kosack,Daniel S. and Shumway,Martin F. and Bidwell,Shelby L. and Shallom,Shamira J. and Aken,Susan E. van and Riedmuller,Steven B. and Feldblyum,Tamara V. and Cho,Jennifer K. and Quackenbush,John and Sedegah,Martha and Shoaibi,Azadeh and Cummings,Leda M. and Florens,Laurence and Yates,John R. and Raine,J. Dale and Sinden,Robert E. and Harris,Michael A. and Cunningham,Deirdre A. and Preiser,Peter R. and Bergman,Lawrence W. and Vaidya,Akhil B. and Lin,Leo H. van and Janse,Chris J. and Waters,Andrew P. and Smith,Hamilton O. and White,Owen R. and Salzberg,Steven L. and Venter,J. Craig and Fraser,Claire M. and Hoffman,Stephen L. and Gardner,Malcolm J. and Carucci,Daniel J.} } @conference {17178, title = {Getting real about speech: overdue or overhyped?}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {708 - 709}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Speech has recently made headway towards becoming a more mainstream interface modality. For example, there is an increasing number of call center applications, especially in the airline and banking industries. However, speech still has many properties that cause its use to be problematic, such as its inappropriateness in both very quiet and very noisy environments, and the tendency of speech to increase cognitive load. Concerns about such problems are valid; however, they do not explain why the use of speech is so controversial in the HCI community. This panel would like to address the issues underlying the controversy around speech, by discussing the current state of the art, the reasons it is so difficult to build a good speech interface, and how HCI research can contribute to the development of speech interfaces.}, keywords = {cognitive load, social responses, speech interfaces}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506557}, url = {http://doi.acm.org/10.1145/506443.506557}, author = {James,Frankie and Lai,Jennifer and Suhm,Bernhard and Balentine,Bruce and Makhoul,John and Nass,Clifford and Shneiderman, Ben} } @article {12386, title = {High-level synthesis of DSP applications using adaptive negative cycle detection}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2002}, year = {2002}, month = {2002/01//}, pages = {893 - 907}, abstract = {The problem of detecting negative weight cycles in a graph is examined in the context of the dynamic graph structures that arise in the process of high level synthesis (HLS). The concept of adaptive negative cycle detection is introduced, in which a graph changes over time and negative cycle detection needs to be done periodically, but not necessarily after every individual change. We present an algorithm for this problem, based on a novel extension of the well-known Bellman-Ford algorithm that allows us to adapt existing cycle information to the modified graph, and show by experiments that our algorithm significantly outperforms previous incremental approaches for dynamic graphs. In terms of applications, the adaptive technique leads to a very fast implementation of Lawlers algorithm for the computation of the maximum cycle mean (MCM) of a graph, especially for a certain form of sparse graph. Such sparseness often occurs in practical circuits and systems, as demonstrated, for example, by the ISCAS 89/93 benchmarks. The application of the adaptive technique to design-space exploration (synthesis) is also demonstrated by developing automated search techniques for scheduling iterative data-flow graphs.}, keywords = {adaptive performance estimation, dynamic graphs, maximum cycle mean, negative cycle detection}, isbn = {1110-8657}, url = {http://dl.acm.org/citation.cfm?id=1283100.1283192}, author = {Chandrachoodan,Nitin and Bhattacharyya, Shuvra S. and Liu,K. J.R} } @article {14091, title = {Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi}, journal = {Molecular and Biochemical Parasitology}, volume = {124}, year = {2002}, month = {2002/09/10/}, pages = {73 - 78}, abstract = {As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91\% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5{\textquoteright}-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.}, keywords = {Ingi, L1Tc, Non-LTR retrotransposon, RIME, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/S0166-6851(02)00167-6}, url = {http://www.sciencedirect.com/science/article/pii/S0166685102001676}, author = {Bringaud,Fr{\'e}d{\'e}ric and Garc{\'\i}a-P{\'e}rez,Jos{\'e} Luis and Heras,Sara R. and Ghedin,Elodie and El-Sayed, Najib M. and Andersson,Bj{\"o}rn and Baltz,Th{\'e}o and Lopez,Manuel C.} } @article {18395, title = {Impediments to software engineering technology transfer}, journal = {Journal of Systems and Software. Forthcoming}, year = {2002}, month = {2002///}, author = {Zelkowitz, Marvin V and Wallace,D. R and Binkley,D. W} } @article {15101, title = {Incremental unforgeable encryption}, journal = {Fast Software Encryption}, year = {2002}, month = {2002///}, pages = {317 - 325}, abstract = {The recent selection of the AES block cipher to replace DES has generated interest in developing new modes of operation to supplement the modes defined as part of the DES standard [1,16,23]. We initiate the study of modes of encryption which are both incremental and unforgeable, and point out a number of applications for modes meeting these requirements. We also propose three specific modes achieving these goals, and discuss the strengths and weaknesses of each.}, doi = {10.1007/3-540-45473-X_9}, author = {Buonanno,E. and Katz, Jonathan and Yung,M.} } @article {18489, title = {Infranet: Circumventing web censorship and surveillance}, journal = {Proceedings of the 11th USENIX Security Symposium}, year = {2002}, month = {2002///}, pages = {247 - 262}, abstract = {An increasing number of countries and companies routinely block or monitor access to parts of the Internet. To counteract these measures, we propose Infranet, a system that enables clients to surreptitiously retrieve sensitive content via cooperating Web servers distributed across the global Internet. These Infranet servers provide clients access to censored sites while continuing to host normal uncensored content. Infranet uses a tunnel protocol that provides a covert communication channel between its clients and servers, modulated over standard HTTP transactions that resemble innocuous Web browsing. In the upstream direction, Infranet clients send covert messages to Infranet servers by associating meaning to the sequence of HTTP requests being made. In the downstream direction, Infranet servers return content by hiding censored data in uncensored images using steganographic techniques. We describe the design, a prototype implementation, security properties, and performance of Infranet. Our security analysis shows that Infranet can successfully circumvent several sophisticated censoring techniques.}, author = {Feamster, Nick and Balazinska,M. and Harfst,G. and Balakrishnan,H. and Karger,D.} } @article {12320, title = {Intermediate representations for design automation of multiprocessor DSP systems}, journal = {Design Automation for Embedded Systems}, volume = {7}, year = {2002}, month = {2002///}, pages = {307 - 323}, author = {Bambha,N. and Kianzad,V. and Khandelia,M. and Bhattacharyya, Shuvra S.} } @conference {12143, title = {Lessons learned from 25 years of process improvement: the rise and fall of the NASA software engineering laboratory}, booktitle = {Proceedings of the 24th International Conference on Software Engineering}, series = {ICSE {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {69 - 79}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {For 25 years the NASA/GSFC Software Engineering Laboratory (SEL) has been a major resource in software process improvement activities. But due to a changing climate at NASA, agency reorganization, and budget cuts, the SEL has lost much of its impact. In this paper we describe the history of the SEL and give some lessons learned on what we did right, what we did wrong, and what others can learn from our experiences. We briefly describe the research that was conducted by the SEL, describe how we evolved our understanding of software process improvement, and provide a set of lessons learned and hypotheses that should enable future groups to learn from and improve on our quarter century of experiences.}, isbn = {1-58113-472-X}, doi = {10.1145/581339.581351}, url = {http://doi.acm.org/10.1145/581339.581351}, author = {Basili, Victor R. and McGarry,Frank E. and Pajerski,Rose and Zelkowitz, Marvin V} } @conference {12107, title = {A light-weight process for capturing and evolving defect reduction experience}, booktitle = {Engineering of Complex Computer Systems, 2002. Proceedings. Eighth IEEE International Conference on}, year = {2002}, month = {2002/12//}, pages = {129 - 132}, abstract = {Selecting technologies for developing software is a crucial activity in software projects. Defect reduction is an example of an area in which software developers have to decide what technologies to use. CeBASE is a NSF funded project that has the role of improving software development by providing decision support on the selection of techniques and tools. The decision support is based on empirical data organized in experience bases and refined into high-level models. Empirical data is collected through various activities, for example through eWorkshops in which experts discuss important issues, and formalized using the lightweight knowledge dust to knowledge pearl process.}, keywords = {bases;experience, CeBASE;NSF, defect, development;software, experience;software, funded, knowledge;software, management;lightweight, management;software, project;decision, projects;software, reduction, reusability;software, reuse;software, support;eWorkshops;experience, tools;, tools;knowledge}, doi = {10.1109/ICECCS.2002.1181505}, author = {Basili, Victor R. and Lindvall,M. and Shull, F.} } @article {16413, title = {Modeling the Effects of Greenbelts at the Urban-Rural Fringe}, journal = {Proceedings of IEMSS 2002}, year = {2002}, month = {2002///}, pages = {190 - 195}, abstract = {We present and evaluate an agent based model (ABM) of land use change at the rural-urban fringe,comparing its performance to a mathematical model of the same process. Our simplified model was developed in Swarm using agents with heterogeneous preferences and a landscape with heterogeneous properties. The context of this work is a larger project that includes surveys of the preferences of residents and data on historical patterns of development. Our broader goal is to use the model to evaluate the ecological effects of alternative policies and designs. We begin by evaluating the influence of a greenbelt, which is located next to a developing area and in which no development is permitted. We present results of a mathematical model that illustrates the necessary trade-off between greenbelt placement and greenbelt width on its effectiveness at delaying develop- ment beyond. Experiments run with the ABM are validated by the mathematical model and illustrate analyses that can be performed by extending to two-dimensions, variable agent preferences, and multiple, and ultimately realistic, patterns of landscape variability. }, author = {Brown,D.G. and Page,S.E. and Riolo,R and Rand, William} } @article {16152, title = {Navigation patterns and usability of zoomable user interfaces with and without an overview}, journal = {ACM Transactions on Computer-Human Interaction (TOCHI)}, volume = {9}, year = {2002}, month = {2002///}, pages = {362 - 389}, author = {Hornbaek,K. and Bederson, Benjamin B. and Plaisant, Catherine} } @article {14090, title = {A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei}, journal = {Eukaryotic cell}, volume = {1}, year = {2002}, month = {2002///}, pages = {137 - 137}, author = {Bringaud,F. and Biteau,N. and Melville,S. E. and Hez,S. and El-Sayed, Najib M. and Leech,V. and Berriman,M. and Hall,N. and Donelson,J. E and Baltz,T.} } @conference {11901, title = {A non-intrusive Kalman filter-based tracker for pursuit eye movement}, booktitle = {American Control Conference, 2002. Proceedings of the 2002}, volume = {2}, year = {2002}, month = {2002///}, pages = {1443- 1447 vol.2 - 1443- 1447 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we introduce a new non-intrusive approach to estimating the eye position during pursuit motion of the eye. We introduce a new characterization for the pursuit eye movement. Our characterization is based on the decomposition of the pursuit eye motion into a deterministic component and random component. We use a discrete Kalman filter to estimate the random component and calculate the deterministic component. We add the two components to obtain an estimate of the eye position. Simulation results are provided to illustrate the eye position estimation.}, keywords = {Application software, characterization, Computer vision, Current measurement, deterministic component, Electric variables measurement, eye position estimation, eye tracking, gaze tracking, Human computer interaction, Kalman filter, Kalman filters, Lenses, Motion estimation, Optical reflection, pursuit eye movement, pursuit motion, random component, Skin, tracking}, isbn = {0-7803-7298-0}, doi = {10.1109/ACC.2002.1023224}, url = {http://ieeexplore.ieee.org/ielx5/7965/22015/01023224.pdf?tp=\&arnumber=1023224\&isnumber=22015}, author = {Abd-Almageed, Wael and Fadali,M. S and Bebis,G.} } @article {12121, title = {An operational process for goal-driven definition of measures}, journal = {Software Engineering, IEEE Transactions on}, volume = {28}, year = {2002}, month = {2002/12//}, pages = {1106 - 1125}, abstract = {We propose an approach (GOM/MEDEA) for defining measures of product attributes in software engineering. The approach is driven by the experimental goals of measurement, expressed via the GQM paradigm, and a set of empirical hypotheses. To make the empirical hypotheses quantitatively verifiable, GQM/MEDEA supports the definition of theoretically valid measures for the attributes of interest based on their expected mathematical properties. The empirical hypotheses are subject to experimental verification. This approach integrates several research contributions from the literature into a consistent, practical, and rigorous approach.}, keywords = {attributes;, definition;, development, empirical, engineering;, expected, experimental, goal-driven, GQM, GQM/MEDEA;, hypotheses;, management;, mathematical, measure, measurement;, metrics;, operational, paradigm;, process;, Product, properties;, quality;, software, verification;}, isbn = {0098-5589}, doi = {10.1109/TSE.2002.1158285}, author = {Briand,L.C. and Morasca,S. and Basili, Victor R.} } @article {17836, title = {Optimizing execution of component-based applications using group instances}, journal = {Future Generation Computer Systems}, volume = {18}, year = {2002}, month = {2002/03//}, pages = {435 - 448}, abstract = {Recent research on programming models for developing applications on the Grid has proposed component-based models as a viable approach, in which an application is composed of multiple interacting computational objects. We have been developing a framework, called filter-stream programming, for building data-intensive applications that query, analyze and manipulate very large datasets in a distributed environment. In this model, the processing structure of an application is represented as a set of processing units, referred to as filters. In this paper, we develop the problem of scheduling instances of a filter group. A filter group is a set of filters collectively performing a computation for an application. In particular, we seek the answer to the following question: should a new instance be created, or an existing one reused? We experimentally investigate the effects on performance of instantiating multiple filter groups under varying application characteristics.}, keywords = {DataCutter, Grid, Wide-area network}, isbn = {0167-739X}, doi = {10.1016/S0167-739X(01)00070-X}, url = {http://www.sciencedirect.com/science/article/pii/S0167739X0100070X}, author = {Beynon,Michael D. and Kurc,Tahsin and Sussman, Alan and Saltz,Joel} } @article {17312, title = {Ordered and quantum treemaps: Making effective use of 2D space to display hierarchies}, journal = {ACM Transactions on Graphics (TOG)}, volume = {21}, year = {2002}, month = {2002/10//}, pages = {833 - 854}, abstract = {Treemaps, a space-filling method for visualizing large hierarchical data sets, are receiving increasing attention. Several algorithms have been previously proposed to create more useful displays by controlling the aspect ratios of the rectangles that make up a treemap. While these algorithms do improve visibility of small items in a single layout, they introduce instability over time in the display of dynamically changing data, fail to preserve order of the underlying data, and create layouts that are difficult to visually search. In addition, continuous treemap algorithms are not suitable for displaying fixed-sized objects within them, such as images.This paper introduces a new "strip" treemap algorithm which addresses these shortcomings, and analyzes other "pivot" algorithms we recently developed showing the trade-offs between them. These ordered treemap algorithms ensure that items near each other in the given order will be near each other in the treemap layout. Using experimental evidence from Monte Carlo trials and from actual stock market data, we show that, compared to other layout algorithms, ordered treemaps are more stable, while maintaining relatively favorable aspect ratios of the constituent rectangles. A user study with 20 participants clarifies the human performance benefits of the new algorithms. Finally, we present quantum treemap algorithms, which modify the layout of the continuous treemap algorithms to generate rectangles that are integral multiples of an input object size. The quantum treemap algorithm has been applied to PhotoMesa, an application that supports browsing of large numbers of images.}, keywords = {hierarchies, Human-computer interaction, image browsers, Information Visualization, jazz, ordered treemaps, treemaps, TREES, zoomable user interfaces (ZUIs).}, isbn = {0730-0301}, doi = {10.1145/571647.571649}, url = {http://doi.acm.org/10.1145/571647.571649}, author = {Bederson, Benjamin B. and Shneiderman, Ben and Wattenberg,Martin} } @conference {12206, title = {OZONE: A zoomable interface for navigating ontology information}, booktitle = {Proceedings of the Working Conference on Advanced Visual Interfaces}, year = {2002}, month = {2002///}, pages = {139 - 143}, author = {Suh,B. and Bederson, Benjamin B.} } @conference {17642, title = {P5 : a protocol for scalable anonymous communication}, booktitle = {2002 IEEE Symposium on Security and Privacy, 2002. Proceedings}, year = {2002}, month = {2002///}, pages = {58 - 70}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a protocol for anonymous communication over the Internet. Our protocol, called P5 (peer-to-peer personal privacy protocol) provides sender-, receiver-, and sender-receiver anonymity. P5 is designed to be implemented over current Internet protocols, and does not require any special infrastructure support. A novel feature of P5 is that it allows individual participants to trade-off degree of anonymity for communication efficiency, and hence can be used to scalably implement large anonymous groups. We present a description of P5, an analysis of its anonymity and communication efficiency, and evaluate its performance using detailed packet-level simulations.}, keywords = {Broadcasting, communication efficiency, Computer science, cryptography, data privacy, Educational institutions, Internet, large anonymous groups, P5 protocol, packet-level simulations, Particle measurements, Peer to peer computing, peer-to-peer personal privacy protocol, privacy, Protocols, receiver anonymity, scalable anonymous communication, security of data, sender anonymity, sender-receiver anonymity, Size measurement, telecommunication security}, isbn = {0-7695-1543-6}, doi = {10.1109/SECPRI.2002.1004362}, author = {Sherwood,R. and Bhattacharjee, Bobby and Srinivasan, Aravind} } @article {18486, title = {Packet loss recovery for streaming video}, journal = {12th International Packet Video Workshop}, year = {2002}, month = {2002///}, abstract = {While there is an increasing demand for streaming video applica-tions on the Internet, various network characteristics make the de- ployment of these applications more challenging than traditional TCP-based applications like email and the Web. Packet loss can be detrimental to compressed video with interdependent frames be- cause errors potentially propagate across many frames. While la- tency requirements do not permit retransmission of all lost data, we leverage the characteristics of MPEG-4 to selectively retrans- mit only the most important data in the bitstream. When latency constraints do not permit retransmission, we propose a mechanism for recovering this data using postprocessing techniques at the re- ceiver. We quantify the effects of packet loss on the quality of MPEG-4 video, develop an analytical model to explain these ef- fects, present a system to adaptively deliver MPEG-4 video in the face of packet loss and variable Internet conditions, and evaluate the effectiveness of the system under various network conditions. }, author = {Feamster, Nick and Balakrishnan,H.} } @article {15399, title = {Perturbation technique for LLG dynamics in uniformly magnetized bodies subject to RF fields}, journal = {Magnetics, IEEE Transactions on}, volume = {38}, year = {2002}, month = {2002/09//}, pages = {2403 - 2405}, abstract = {The problem of magnetization dynamics of a uniformly magnetized uniaxial particle or film, under elliptically polarized applied field, is considered. In the special case of circularly polarized applied field and particles (films) with a symmetry axis, pure time-harmonic magnetization modes exist that can be computed analytically. Deviations from these highly symmetric conditions are treated as perturbation of the symmetric case. The perturbation technique leads to the exactly solvable system of linear differential equations for the perturbations which enables one to compute higher order magnetization harmonic. The analytical solutions are obtained and then compared with numerical results.}, keywords = {analytical, anisotropy, anisotropy;, applied, bodies;, circularly, component;, constant-in-time, constant;, damping, demagnetisation;, demagnetizing, differential, dynamics;, effective, elliptically, equation;, equations;, exactly, factors;, field;, film;, films;, Frequency, gyromagnetic, harmonic;, higher, Landau-Lifshitz-Gilbert, large, linear, magnetic, magnetisation;, magnetization, magnetization;, magnetized, modes;, MOTION, order, partial, particle;, particles;, perturbation, polarized, radio, ratio;, RF, saturation, solution;, solvable, system;, technique;, techniques;, thin, time-harmonic, uniaxial, uniformly}, isbn = {0018-9464}, doi = {10.1109/TMAG.2002.803596}, author = {Bertotti,G. and Mayergoyz, Issak D and Serpico,C.} } @article {17865, title = {Processing large-scale multi-dimensional data in parallel and distributed environments}, journal = {Parallel Computing}, volume = {28}, year = {2002}, month = {2002/05//}, pages = {827 - 859}, abstract = {Analysis of data is an important step in understanding and solving a scientific problem. Analysis involves extracting the data of interest from all the available raw data in a dataset and processing it into a data product. However, in many areas of science and engineering, a scientist{\textquoteright}s ability to analyze information is increasingly becoming hindered by dataset sizes. The vast amount of data in scientific datasets makes it a difficult task to efficiently access the data of interest, and manage potentially heterogeneous system resources to process the data. Subsetting and aggregation are common operations executed in a wide range of data-intensive applications. We argue that common runtime and programming support can be developed for applications that query and manipulate large datasets. This paper presents a compendium of frameworks and methods we have developed to support efficient execution of subsetting and aggregation operations in applications that query and manipulate large, multi-dimensional datasets in parallel and distributed computing environments.}, keywords = {Data-intensive applications, Distributed computing, Multi-dimensional datasets, PARALLEL PROCESSING, Runtime systems}, isbn = {0167-8191}, doi = {10.1016/S0167-8191(02)00097-2}, url = {http://www.sciencedirect.com/science/article/pii/S0167819102000972}, author = {Beynon,Michael and Chang,Chialin and Catalyurek,Umit and Kurc,Tahsin and Sussman, Alan and Andrade,Henrique and Ferreira,Renato and Saltz,Joel} } @conference {12310, title = {Query routing in the TerraDir distributed directory}, booktitle = {Proceedings of the SPIE ITCOM}, volume = {4868}, year = {2002}, month = {2002///}, pages = {299 - 309}, abstract = {We present the design and evaluation of the query-routing protocol of the TerraDir distributed directory.TerraDir is a wide-area distributed directory designed for hierarchical namespaces, and provides a lookup service for mapping keys to objects. We introduce distributed lookup and caching algorithms that leverage the underlying data hierarchy. Our algorithms provide efficient lookups while avoiding the load imbalances often associated with hierarchical systems. The TerraDir load balancing scheme also incorporates a node replication algorithm that provides configurable failure resilience with provably low overheads. }, author = {Silaghi,B. and Bhattacharjee, Bobby and Keleher,P.} } @conference {16910, title = {Remote access to large spatial databases}, booktitle = {Proceedings of the 10th ACM international symposium on Advances in geographic information systems}, series = {GIS {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {5 - 10}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Enterprises in the public and private sectors have been making their large spatial data archives available over the Internet. However, interactive work with such large volumes of online spatial data is a challenging task. We propose two efficient approaches to remote access to large spatial data. First, we introduce a client-server architecture where the work is distributed between the server and the individual clients for spatial query evaluation, data visualization, and data management. We enable the minimization of the requirements for system resources on the client side while maximizing system responsiveness as well as the number of connections one server can handle concurrently. Second, for prolonged periods of access to large online data, we introduce APPOINT (an Approach for Peer-to-Peer Offloading the INTernet). This is a centralized peer-to-peer approach that helps Internet users transfer large volumes of online data efficiently. In APPOINT, active clients of the client-server architecture act on the server{\textquoteright}s behalf and communicate with each other to decrease network latency, improve service bandwidth, and resolve server congestions.}, keywords = {client/server, GIS, Internet, peer-to-peer}, isbn = {1-58113-591-2}, doi = {10.1145/585147.585150}, url = {http://doi.acm.org/10.1145/585147.585150}, author = {Tanin,Egemen and Brabec,Franti{\v s}ek and Samet, Hanan} } @conference {16912, title = {Remote thin-client access to spatial database systems}, booktitle = {Proceedings of the 2002 annual national conference on Digital government research}, series = {dg.o {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {1 - 8}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {Numerous federal agencies produce official statistics that are made accessible to ordinary citizens for searching and data retrieval. This is often done via the Internet through a web browser interface. If this data is presented in textual format, it can often be searched and retrieved by such attributes as topic, responsible agency, keywords, or press release. However, if the data is of spatial nature, e.g., in the form of a map, then using text-based queries is often too cumbersome for the intended audience. We propose to use the capabilities of the SAND Spatial Browser to provide more power to users of these databases. Using the SAND Spatial Browser allows users to define the spatial region of interest with greater specificity, instead of forcing them to retrieve data just for a particular location or a region with a predefined boundary. They can also make use of ranking which is the ability to retrieve data in the order of distance from other instances of the data or aggregates of data that are user-defined. Work is distributed between the SAND server and the individual clients for query evaluation, data visualization and data management. This enables the minimization of the necessary requirements for system resources on the client side while maximizing the number of connections one server can handle concurrently. Concrete experience with interfacing the SAND system with FedStats data is also discussed.}, url = {http://dl.acm.org/citation.cfm?id=1123098.1123170}, author = {Samet, Hanan and Brabec,Franti{\v s}ek} } @article {11913, title = {Rover: scalable location-aware computing}, journal = {Computer}, volume = {35}, year = {2002}, month = {2002/10//}, pages = {46 - 53}, abstract = {All the components necessary for realizing location-aware computing are available in the marketplace today. What has hindered the widespread deployment of location-based systems is the lack of an integration architecture that scales with user populations. The authors have completed the initial implementation of Rover, a system designed to achieve this sort of integration and to automatically tailor information and services to a mobile user{\textquoteright}s location. Their studies have validated Rover{\textquoteright}s underlying software architecture, which achieves system scalability through high-resolution, application-specific resource scheduling at the servers and network. The authors believe that this technology will greatly enhance the user experience in many places, including museums, amusement and theme parks, shopping malls, game fields, offices, and business centers. They designed the system specifically to scale to large user populations and expect its benefits to increase with them.}, keywords = {amusement, application-specific, architecture;, automation;, business, business;, computing;, data, entertainment;, handheld, humanities;, integration, LAN;, location-aware, malls;, mobile, museums;, office, parks;, processing;, resource, Rover;, scalability;, scalable, scheduling;, shopping, software, system, theme, units;, user;, wireless}, isbn = {0018-9162}, doi = {10.1109/MC.2002.1039517}, author = {Banerjee,S. and Agarwal,S. and Kamel,K. and Kochut, A. and Kommareddy,C. and Nadeem,T. and Thakkar,P. and Trinh,Bao and Youssef,A. and Youssef, M. and Larsen,R.L. and Udaya Shankar,A. and Agrawala, Ashok K.} } @article {12309, title = {Scalable application layer multicast}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {32}, year = {2002}, month = {2002/08//}, pages = {205 - 217}, abstract = {We describe a new scalable application-layer multicast protocol, specifically designed for low-bandwidth, data streaming applications with large receiver sets. Our scheme is based upon a hierarchical clustering of the application-layer multicast peers and can support a number of different data delivery trees with desirable properties.We present extensive simulations of both our protocol and the Narada application-layer multicast protocol over Internet-like topologies. Our results show that for groups of size 32 or more, our protocol has lower link stress (by about 25\%), improved or similar end-to-end latencies and similar failure recovery properties. More importantly, it is able to achieve these results by using orders of magnitude lower control traffic.Finally, we present results from our wide-area testbed in which we experimented with 32-100 member groups distributed over 8 different sites. In our experiments, average group members established and maintained low-latency paths and incurred a maximum packet loss rate of less than 1\% as members randomly joined and left the multicast group. The average control overhead during our experiments was less than 1 Kbps for groups of size 100.}, keywords = {application layer multicast, hierarchy, overlay networks, peer-to-peer systems, scalability}, isbn = {0146-4833}, doi = {10.1145/964725.633045}, url = {http://doi.acm.org/10.1145/964725.633045}, author = {Banerjee,Suman and Bhattacharjee, Bobby and Kommareddy,Christopher} } @conference {12306, title = {Scalable peer finding on the Internet}, booktitle = {Global Telecommunications Conference, 2002. GLOBECOM {\textquoteright}02. IEEE}, volume = {3}, year = {2002}, month = {2002/11//}, pages = {2205 - 2209 vol.3 - 2205 - 2209 vol.3}, abstract = {We consider the problem of finding nearby application peers over the Internet. We define a new peer-finding scheme (called Tiers) that scales to large application peer groups. Tiers creates a hierarchy of the peers, which allows an efficient and scalable solution to this problem. The scheme can be implemented entirely in the application-layer and does not require the deployment of either any additional measurement services, or well-known reference landmarks in the network. We present detailed evaluation of Tiers and compare it to one previously proposed scheme called Beaconing. Through analysis and detailed simulations on 10,000 node Internet-like topologies we show that Tiers achieves comparable or better performance with a significant reduction in control overheads for groups of size 32 or more.}, keywords = {application, application-layer;, Beaconing;, CONTROL, finding;, Internet-like, Internet;, measurement, network, overhead, peer, peer-finding, peers;, protocol;, protocols;, reduction;, scalable, scheme;, services;, simulations;, solution;, Tiers;, topologies;, topology;}, doi = {10.1109/GLOCOM.2002.1189023}, author = {Banerjee,S. and Kommareddy,C. and Bhattacharjee, Bobby} } @article {12307, title = {Scalable secure group communication over IP multicast}, journal = {Selected Areas in Communications, IEEE Journal on}, volume = {20}, year = {2002}, month = {2002/10//}, pages = {1511 - 1527}, abstract = {We introduce and analyze a scalable rekeying scheme for implementing secure group communications Internet protocol multicast. We show that our scheme incurs constant processing, message, and storage overhead for a rekey operation when a single member joins or leaves the group, and logarithmic overhead for bulk simultaneous changes to the group membership. These bounds hold even when group dynamics are not known a priori. Our rekeying algorithm requires a particular clustering of the members of the secure multicast group. We describe a protocol to achieve such clustering and show that it is feasible to efficiently cluster members over realistic Internet-like topologies. We evaluate the overhead of our own rekeying scheme and also of previously published schemes via simulation over an Internet topology map containing over 280 000 routers. Through analysis and detailed simulations, we show that this rekeying scheme performs better than previous schemes for a single change to group membership. Further, for bulk group changes, our algorithm outperforms all previously known schemes by several orders of magnitude in terms of actual bandwidth usage, processing costs, and storage requirements.}, keywords = {access, algorithm;, authentication;, Bandwidth, communication;, CONTROL, costs;, cryptography;, dynamics;, group, group;, Internet, Internet-like, Internet;, IP, logarithmic, map;, membership;, message, Multicast, multicast;, network, overhead;, PROCESSING, protocol, protocols;, rekeying, requirements;, routers;, routing;, scalable, secure, security;, server;, simulation;, storage, Telecommunication, topologies;, Topology, topology;, transport, usage;}, isbn = {0733-8716}, doi = {10.1109/JSAC.2002.803986}, author = {Banerjee,S. and Bhattacharjee, Bobby} } @conference {12209, title = {SpaceTree: Design evolution of a node link tree browser}, booktitle = {Proc. InfoVis}, year = {2002}, month = {2002///}, pages = {57 - 64}, author = {Plaisant, Catherine and Grosjean,J. and Bederson, Benjamin B.} } @conference {16150, title = {SpaceTree: supporting exploration in large node link tree, design evolution and empirical evaluation}, booktitle = {Information Visualization, 2002. INFOVIS 2002. IEEE Symposium on}, year = {2002}, month = {2002///}, pages = {57 - 64}, abstract = {We present a novel tree browser that builds on the conventional node link tree diagrams. It adds dynamic rescaling of branches of the tree to best fit the available screen space, optimized camera movement, and the use of preview icons summarizing the topology of the branches that cannot be expanded. In addition, it includes integrated search and filter functions. This paper reflects on the evolution of the design and highlights the principles that emerged from it. A controlled experiment showed benefits for navigation to already previously visited nodes and estimation of overall tree topology.}, keywords = {browser;, camera, data, design, diagrams;, dynamic, evolution;, experiment;, exploration;, filter, functions;, graphical, icons;, integrated, interfaces;, large, link, movement;, node, novel, optimized, rescaling;, search;, SpaceTree;, structures;, topology;, tree, user, visualisation;, visualization;}, doi = {10.1109/INFVIS.2002.1173148}, author = {Plaisant, Catherine and Grosjean,J. and Bederson, Benjamin B.} } @conference {15897, title = {Supporting access to large digital oral history archives}, booktitle = {Proceedings of the 2nd ACM/IEEE-CS joint conference on Digital libraries}, series = {JCDL {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {18 - 27}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes our experience with the creation, indexing, and provision of access to a very large archive of videotaped oral histories - 116,000 hours of digitized interviews in 32 languages from 52,000 survivors, liberators, rescuers, and witnesses of the Nazi Holocaust. It goes on to identify a set of critical research issues that must be addressed if we are to provide full and detailed access to collections of this size: issues in user requirement studies, automatic speech recognition, automatic classification, segmentation, summarization, retrieval, and user interfaces. The paper ends by inviting others to discuss use of these materials in their own research.}, keywords = {cataloging, oral history, research agenda}, isbn = {1-58113-513-0}, doi = {10.1145/544220.544224}, url = {http://doi.acm.org/10.1145/544220.544224}, author = {Gustman,Samuel and Soergel,Dagobert and Oard, Douglas and Byrne,William and Picheny,Michael and Ramabhadran,Bhuvana and Greenberg,Douglas} } @conference {18604, title = {Topology inference from BGP routing dynamics}, booktitle = {Proceedings of the 2nd ACM SIGCOMM Workshop on Internet measurment}, series = {IMW {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {243 - 248}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a method of inferring logical relationships between network prefixes within an Autonomous System (AS) using only passive monitoring of BGP messages. By clustering these prefixes based upon similarities between their update times, we create a hierarchy linking the prefixes within the larger AS. We can frequently identify groups of prefixes routed to the same ISP Point of Presence (POP), despite the lack of identifying information in the BGP messages. Similarly, we observe disparate prefixes under common organizational control, or with long shared network paths. In addition to discovering interesting network characteristics, our passive method facilitates topology discovery by potentially reducing the number of active probes required in traditional traceroute-based Internet mapping mechanisms.}, isbn = {1-58113-603-X}, doi = {10.1145/637201.637239}, url = {http://doi.acm.org/10.1145/637201.637239}, author = {Andersen,David G. and Feamster, Nick and Bauer,Steve and Balakrishnan,Hari} } @article {14101, title = {Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression}, journal = {Experimental Parasitology}, volume = {102}, year = {2002}, month = {2002/11//}, pages = {123 - 133}, abstract = {Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of [alpha]- and [beta]-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two [beta]-tubulin mRNAs of 1.9 and 2.3~kb were found to differ mainly by an additional 369 nucleotides at the end of the 3{\textquoteright} untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, [alpha]- and [beta]-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of [alpha]- and [beta]-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3{\textquoteright} UTR plus downstream intergenic region of the [alpha]-tubulin gene and that both positive and negative elements occur in the equivalent regions of the [beta]-tubulin gene.Index Descriptions and Abbreviations: Kinetoplastida; Trypanosoma cruzi; tubulin; gene regulation; PCR, polymerase chain reaction; UTR, untranslated region; IR, intergenic region; SL, spliced leader; BAC, bacterial artificial chromosome.}, isbn = {0014-4894}, doi = {16/S0014-4894(03)00034-1}, url = {http://www.sciencedirect.com/science/article/pii/S0014489403000341}, author = {Bartholomeu,Daniella C. and Silva,Rosiane A. and Galv{\~a}o,Lucia M. C. and El-Sayed, Najib M. and Donelson,John E. and Teixeira,Santuza M.R.} } @conference {16484, title = {Using latency-recency profiles for data delivery on the web}, booktitle = {Proceedings of the 28th international conference on Very Large Data Bases}, year = {2002}, month = {2002///}, pages = {550 - 561}, author = {Bright,L. and Raschid, Louiqa} } @article {13479, title = {Virtual Telescopes in Education}, journal = {Journal of Digital Information}, volume = {2}, year = {2002}, month = {2002///}, abstract = {Virtual Telescopes in Education is providing the services required to operate a virtual observatory comprising distributed telescopes, including an interactive, constraint-based scheduling service, data and resource archive, proposal preparation and review environment, and a VTIE Journal. A major goal of VTIE is to elicit from learners questions about the nature of celestial objects and the physical processes that give rise to the spectacular imagery that catches their imaginations. Generation of constrained science questions will assist learners in the science process. To achieve interoperability with other NSDL resources, our approach follows the Open Archives Initiative and the W3C Semantic Web activity.}, author = {Hoban,S. and desJardins, Marie and Farrell,N. and Rathod,P. and Sachs,J. and Sansare,S. and Yesha,Y. and Keating,J. and Busschots,B. and Means,J. and others} } @article {12175, title = {A visual search tool for early elementary science students}, journal = {Journal of Science Education and Technology}, volume = {11}, year = {2002}, month = {2002///}, pages = {49 - 57}, author = {Revelle,G. and Druin, Allison and Platner,M. and Bederson, Benjamin B. and Hourcade,J. P and Sherman,L.} } @article {12060, title = {Visual space-time geometry - A tool for perception and the imagination}, journal = {Proceedings of the IEEE}, volume = {90}, year = {2002}, month = {2002/07//}, pages = {1113 - 1135}, abstract = {Although the fundamental ideas underlying research efforts in the field of computer vision have not radically changed in the past two decades, there has been a transformation in the way work in this field is conducted. This is primarily due to the emergence of a number of tools, of both a practical and a theoretical nature. One such tool, celebrated throughout the nineties, is the geometry of visual space-time. It is known under a variety of headings, such as multiple view geometry, structure from motion, and model building. It is a mathematical theory relating multiple views (images) of a scene taken at different viewpoints to three-dimensional models of the (possibly dynamic) scene. This mathematical theory gave rise to algorithms that take as input images (or video) and provide as output a model of the scene. Such algorithms are one of the biggest successes of the field and they have many applications in other disciplines, such as graphics (image-based rendering, motion capture) and robotics (navigation). One of the difficulties, however is that the current tools cannot yet be fully automated, and they do not provide very accurate results. More research is required for automation and high precision. During the past few years we have investigated a number of basic questions underlying the structure from motion problem. Our investigations resulted in a small number of principles that characterize the problem. These principles, which give rise to automatic procedures and point to new avenues for studying the next level of the structure from motion problem, are the subject of this paper.}, keywords = {3-D motion estimation, Buildings, Computer vision, Geometry, Graphics, Image sequences, Layout, Mathematical model, mathematical theory, model building, Motion estimation, multiple view geometry, multiple views, Navigation, optical flow, optical illusions, patch correspondence, Rendering (computer graphics), Robotics and automation, Solid modeling, structure from motion, three-dimensional models, visual space-time}, isbn = {0018-9219}, doi = {10.1109/JPROC.2002.801440}, author = {Ferm{\"u}ller, Cornelia and Baker, P. and Aloimonos, J.} } @conference {15303, title = {Web question answering: is more always better?}, booktitle = {Proceedings of the 25th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {291 - 298}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a question answering system that is designed to capitalize on the tremendous amount of data that is now available online. Most question answering systems use a wide variety of linguistic resources. We focus instead on the redundancy available in large corpora as an important resource. We use this redundancy to simplify the query rewrites that we need to use, and to support answer mining from returned snippets. Our system performs quite well given the simplicity of the techniques being utilized. Experimental results show that question answering accuracy can be greatly improved by analyzing more and more matching passages. Simple passage ranking and n-gram extraction techniques work well in our system making it efficient to use with many backend retrieval engines.}, isbn = {1-58113-561-0}, doi = {10.1145/564376.564428}, url = {http://doi.acm.org/10.1145/564376.564428}, author = {Dumais,Susan and Banko,Michele and Brill,Eric and Jimmy Lin and Ng,Andrew} } @conference {18453, title = {What we have learned about fighting defects}, booktitle = {Software Metrics, 2002. Proceedings. Eighth IEEE Symposium on}, year = {2002}, month = {2002///}, pages = {249 - 258}, abstract = {The Center for Empirically Based Software Engineering helps improve software development by providing guidelines for selecting development techniques, recommending areas for further research, and supporting software engineering education. A central activity toward achieving this goal has been the running of "e- Workshops" that capture expert knowledge with a minimum of overhead effort to formulate heuristics on a particular topic. The resulting heuristics are a useful summary of the current state of knowledge in an area based on expert opinion. This paper discusses the results to date of a series of e-Workshops on software defect reduction. The original discussion items are presented along with an encapsulated summary of the expert discussion. The reformulated heuristics can be useful both to researchers (for pointing out gaps in the current state of the knowledge requiring further investigation) and to practitioners (for benchmarking or setting expectations about development practices).}, keywords = {based, Center, Computer, defect, development;, education;, electronic, Empiric, engineering, engineering;, eWorkshops;, for, heuristics;, reduction;, Science, software, workshops;}, doi = {10.1109/METRIC.2002.1011343}, author = {Shull, F. and Basili, Victor R. and Boehm,B. and Brown,A. W and Costa,P. and Lindvall,M. and Port,D. and Rus,I. and Tesoriero,R. and Zelkowitz, Marvin V} } @article {12204, title = {Zoomable user interfaces as a medium for slide show presentations}, journal = {Information Visualization}, volume = {1}, year = {2002}, month = {2002///}, pages = {35 - 35}, author = {Good,L. and Bederson, Benjamin B.} } @conference {12335, title = {Adaptive negative cycle detection in dynamic graphs}, booktitle = {Circuits and Systems, 2001. ISCAS 2001. The 2001 IEEE International Symposium on}, volume = {5}, year = {2001}, month = {2001///}, pages = {163 - 166}, author = {Chandrachoodan,N. and Bhattacharyya, Shuvra S. and Liu,K. J.R} } @conference {12823, title = {Automated Validation of Software Models}, booktitle = {Automated Software Engineering, International Conference on}, year = {2001}, month = {2001///}, pages = {91 - 91}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper describes the application of an automated verification tool to a software model developed at Ford. Ford already has in place an advanced model-based software development framework that employs the Matlab?, Simulink?, and Stateflow? modeling tools. During this project we applied the invariant checker Salsa to a Simulink?/ Stateflow? model of automotive software to check for nondeterminism, missing cases, dead code, and redundant code. During the analysis, a number of anomalies were detected that had not been found during manual review. We argue that the detection and correction of these problems demonstrates a cost-effective application of formal verification that elevates our level of confidence in the model.}, isbn = {0-7695-1426-X}, doi = {http://doi.ieeecomputersociety.org/10.1109/ASE.2001.989794}, author = {Sims,Steve and Cleaveland, Rance and Butts,Ken and Ranville,Scott} } @conference {19653, title = {Automatically Tracking and Analyzing the Behavior of Live Insect Colonies}, booktitle = {AGENTS {\textquoteright}01 Proceedings of the Fifth International Conference on Autonomous Agents }, series = {AGENTS {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {521 - 528}, publisher = {ACM}, organization = {ACM}, abstract = {We introduce the study of {\it live} social insect colonies as a relevant and exciting domain for the development and application of multi-agent systems modeling tools. Social insects provide a rich source of {\it traceable} social behavior for testing multi-agent tracking, prediction and modeling algorithms. An additional benefit of this research is the potential for contributions to experimental biology --- the principled techniques developed for analyzing artificial multi-agent systems can be applied to advance the state of knowledge of insect behavior. We contribute a novel machine vision system that addresses the challenge of tracking hundreds of small animals simultaneously. Fast color-based tracking is combined with movement-based tracking to locate ants in a real-time video stream. We also introduce new methods for analyzing the spatial activity of ant colonies. The system was validated in experiments with laboratory colonies of {\it Camponotus festinatus} and several example analyses of the colonies{\textquoteright} spatial behavior are provided.}, isbn = {1-58113-326-X}, url = {http://doi.acm.org/10.1145/375735.376434}, author = {Balch, Tucker and Zia Khan and Veloso, Manuela} } @article {12123, title = {Building an Experience Base for Software Engineering: A report on the first CeBASE eWorkshop}, journal = {Product Focused Software Process Improvement}, year = {2001}, month = {2001///}, pages = {110 - 125}, abstract = {New information is obtained by research and disseminated by papers in conferences and journals. The synthesis of knowledge depends upon social discourse among the experts in a given domain to discuss the impact of this new information. Meetings among such experts are, however, expensive and time consuming. In this paper we discuss the organization of CeBASE, a center whose goal is the collection and dissemination of empirically-based software engineering knowledge, and the concept of the online workshop or eWorkshop as a way to use the Internet to minimize the needs of face-to-face meetings. We discuss the design of our eWorkshop and give the results of one eWorkshop that discussed the impact of defect reduction strategies.We want to thank Barry Boehm, Scott Henninger, Rayford Vaughn, Winsor Brown, Dan Port and Michael Frey as well as all participants for their contribution to the success of the eWorkshop. We also want to thank students at USC and UMD for their contribution in testing the system and Jennifer Dix for proof reading this paper. }, doi = {10.1007/3-540-44813-6_13}, author = {Basili, Victor R. and Tesoriero,R. and Costa,P. and Lindvall,M. and Rus,I. and Shull, F. and Zelkowitz, Marvin V} } @article {12126, title = {COTS-based systems top 10 list}, journal = {Computer}, volume = {34}, year = {2001}, month = {2001/05//}, pages = {91 - 95}, abstract = {Presents a COTS-based system (CBS) software defect-reduction list as hypotheses, rather than results, that also serve as software challenges for enhancing our empirical understanding of CBSs. The hypotheses are: (1) more than 99\% of all executing computer instructions come from COTS products (each instruction passed a market test for value); (2) more than half the features in large COTS software products go unused; (3) the average COTS software product undergoes a new release every 8-9 months, with active vendor support for only its latest three releases; (4) CBS development and post-deployment efforts can scale as high as the square of the number of independently developed COTS products targeted for integration; (5) CBS post-deployment costs exceed CBS development costs; (6) although glue-code development usually accounts for less than half the total CBS software development effort, the effort per line of glue code averages about three times the effort per line of developed applications code; (7) non-development costs, such as licensing fees, are significant, and projects must plan for and optimize them; (8) CBS assessment and tailoring efforts vary significantly by COTS product class (operating system, database management system, user interface, device driver, etc.); (9) personnel capability and experience remain the dominant factors influencing CBS development productivity; and (10) CBS is currently a high-risk activity, with effort and schedule overruns exceeding non-CBS software overruns, yet many systems have used COTS successfully for cost reduction and early delivery}, keywords = {activity;hypotheses;independently, capability;personnel, challenges;software, code, COTS-based, defect, delivery;glue, developed, development, development;high-risk, effort;products, effort;software, efforts;unused, experience;post-deployment, features;software, instructions;costs;development, integration;schedule, management;software, off-the, overruns;software, packages;software, productivity;early, products;personnel, quality;, reduction;software, releases;system, shelf, support;commercial, systems;active, systems;computer, vendor}, isbn = {0018-9162}, doi = {10.1109/2.920618}, author = {Basili, Victor R. and Boehm,B.} } @article {12314, title = {The Design of TerraDir}, journal = {Technical Reports from UMIACS, UMIACS-TR-2001-4299}, year = {2001}, month = {2001/12/17/}, abstract = {We present the design and initial evaluation of TerraDir: an approach forimplementing customizable, distributed, peer-to-peer directories over which a broad range of wide-area resource discovery applications can be implemented. TerraDir{\textquoteright}s structure is two-tiered, consisting of a base protocol for providing arbitrary application-layer connectivity, and dynamic view materializations that efficiently realize different user-specified views of application-layer resources. TerraDir is specifically designed for data that can be arranged in a rooted hierarchy, and provides very efficient and robust lookups over such data while still being able to allow efficient searching. (Also referenced as UMIACS-TR-2001-4299) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1161}, author = {Bhattacharjee, Bobby and Keleher,Pete and Silaghi,Bujor} } @article {16154, title = {Designing an Interactive Message Board as a Technology Probe for Family Communication}, journal = {Technical Reports of the Computer Science Department}, year = {2001}, month = {2001/10/10/}, abstract = {In this paper, we describe the design issues and technical implementation of aninteractive Family Message Board. The Family Message Board enables members of a distributed family to communicate with one another both synchronously and asynchronously via simple, pen-based, digital notes. Each household running thi$ Java-based software can view, create, and manipulate notes in a zoomable space. The Family Message Board will be used as a technology probe to help us unders$ the communication needs of distributed families, and to help us design new devi$ to meet those needs. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/526}, author = {Browne,Hilary and Bederson, Benjamin B. and Plaisant, Catherine and Druin, Allison} } @article {17882, title = {Distributed processing of very large datasets with DataCutter}, journal = {Parallel Computing}, volume = {27}, year = {2001}, month = {2001/10//}, pages = {1457 - 1478}, abstract = {We describe a framework, called DataCutter, that is designed to provide support for subsetting and processing of datasets in a distributed and heterogeneous environment. We illustrate the use of DataCutter with several data-intensive applications from diverse fields, and present experimental results.}, keywords = {Component architectures, Data analysis, Distributed computing, Multi-dimensional datasets, Runtime systems}, isbn = {0167-8191}, doi = {10.1016/S0167-8191(01)00099-0}, url = {http://www.sciencedirect.com/science/article/pii/S0167819101000990}, author = {Beynon,Michael D. and Kurc,Tahsin and Catalyurek,Umit and Chang,Chialin and Sussman, Alan and Saltz,Joel} } @article {12128, title = {Editorial: Open source and empirical software engineering}, journal = {Empirical Software Engineering}, volume = {6}, year = {2001}, month = {2001///}, pages = {193 - 194}, author = {Basili, Victor R.} } @conference {12828, title = {Efficient Model Checking Via Buchi Tableau Automata*}, booktitle = {Computer aided verification: 13th International conference, CAV 2001, Paris, France, July 18-22, 2001: proceedings}, volume = {2102}, year = {2001}, month = {2001///}, pages = {38 - 38}, author = {Bhat,G. S and Cleaveland, Rance and Groce,A.} } @conference {16260, title = {Efficient perspective-accurate silhouette computation and applications}, booktitle = {Proceedings of the seventeenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {60 - 68}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Silhouettes are perceptually and geometrically salient features of geo metric models. Hence a number of graphics and visualization applications need to find them to aid further processing. The efficient computation of silhouettes, especially in the context of perspective projection, is known to be difficult. This paper presents a novel efficient and practical algorithm to compute silhouettes from a sequence of viewpoints under perspective projection. Parallel projection is a special case of this algorithm. Our approach is based on a point-plane duality in three dimensions, which allows an efficient computation of the \emph{changes} in the silhouette of a polygonal model between consecutive frames. In addition, we present several applications of our technique to problems from computer graphics and medical visualization. We also provide experimental data that show the efficiency of our approach. million vertices on an SGI Onyx workstation.}, keywords = {rendering, silhouette, simplification}, isbn = {1-58113-357-X}, doi = {10.1145/378583.378618}, url = {http://doi.acm.org/10.1145/378583.378618}, author = {Pop, Mihai and Duncan,Christian and Barequet,Gill and Goodrich,Michael and Huang,Wenjing and Kumar,Subodh} } @conference {17851, title = {An efficient system for multi-perspective imaging and volumetric shape analysis}, booktitle = {Proceedings of the 2001 Workshop on Parallel and Distributed Computing in Imaging Processing, Video Processing, and Multimedia}, year = {2001}, month = {2001///}, author = {Borovikov,E. and Sussman, Alan and Davis, Larry S.} } @conference {12120, title = {An experience management system for a software engineering research organization}, booktitle = {Software Engineering Workshop, 2001. Proceedings. 26th Annual NASA Goddard}, year = {2001}, month = {2001///}, pages = {29 - 35}, abstract = {Most businesses rely on the fact that their employees possess relevant knowledge and that they can apply it to the task at hand. The problem is that this knowledge is not owned by the organization. It is owned and controlled by its employees. Maintaining an appropriate level of knowledge in the organization is a very important issue. It is, however, not an easy task for most organizations, and it is particularly problematic for software organizations, which are human- and knowledge-intensive. Knowledge management is a relatively new area that has attempted to address these problems. This paper introduces an approach called the "knowledge dust-to-pearls" approach. This approach addresses some of the issues with knowledge management by providing low-barrier mechanisms to "jump start" the experience base. This approach allows the experience base to become more useful more quickly than traditional approaches. This paper describes the approach and gives an example of its use at the Fraunhofer Center for Experimental Software Engineering, Maryland, USA}, keywords = {and, approach;knowledge, base;experience, Center, control;knowledge, data, development, dust-to-pearls, engineering, Engineering;business, engineering;software, experimental, for, Fraunhofer, houses;, knowledge;employee, knowledge;experience, level, maintenance;knowledge, management, management;knowledge, management;software, mechanisms;software, organization;software, organizational, organizations;administrative, organizations;knowledge, organizations;low-barrier, ownership;knowledge-intensive, processing;personnel;research, research, software, system;human-intensive}, doi = {10.1109/SEW.2001.992652}, author = {Basili, Victor R. and Costa,P. and Lindvall,M. and Mendonca,M. and Seaman,C. and Tesoriero,R. and Zelkowitz, Marvin V} } @inbook {17594, title = {Experimental Analysis of Algorithms for Bilateral-Contract Clearing Mechanisms Arising in Deregulated Power Industry}, booktitle = {Algorithm EngineeringAlgorithm Engineering}, series = {Lecture Notes in Computer Science}, volume = {2141}, year = {2001}, month = {2001///}, pages = {172 - 184}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We consider the bilateral contract satisfaction problem arising from electrical power networks due to the proposed deregulation of the electric utility industry in the USA. Given a network and a (multi)set of pairs of vertices (contracts) with associated demands, the goal is to find the maximum number of simultaneously satisfiable contracts. We study how four different algorithms perform in fairly realistic settings; we use an approximate electrical power network from Colorado. Our experiments show that three heuristics outperform a theoretically better algorithm. We also test the algorithms on four types of scenarios that are likely to occur in a deregulated marketplace. Our results show that the networks that are adequate in a regulated marketplace might be inadequate for satisfying all the bilateral contracts in a deregulated industry.}, isbn = {978-3-540-42500-7}, url = {http://dx.doi.org/10.1007/3-540-44688-5_14}, author = {Barrett,Chris and Cook,Doug and Hicks,Gregory and Faber,Vance and Marathe,Achla and Marathe,Madhav and Srinivasan, Aravind and Sussmann,Yoram and Thornquist,Heidi}, editor = {Brodal,Gerth and Frigioni,Daniele and Marchetti-Spaccamela,Alberto} } @inbook {14217, title = {Eyes from Eyes}, booktitle = {3D Structure from Images {\textemdash} SMILE 20003D Structure from Images {\textemdash} SMILE 2000}, series = {Lecture Notes in Computer Science}, volume = {2018}, year = {2001}, month = {2001///}, pages = {204 - 217}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We describe a family of new imaging systems, called Argus eyes, that consist of common video cameras arranged in some network. The system we built consists of six cameras arranged so that they sample different parts of the visual sphere. This system has the capability of very accurately estimating its own 3D motion and consequently estimating shape models from the individual videos. The reason is that inherent ambiguities of confusion between translation and rotation disappear in this case. We provide an algorithm and several experiments using real outdoor or indoor images demonstrating the superiority of the new sensor with regard to 3D motion estimation.}, isbn = {978-3-540-41845-0}, url = {http://dx.doi.org/10.1007/3-540-45296-6_14}, author = {Baker,Patrick and Pless,Robert and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Pollefeys,Marc and Van Gool,Luc and Zisserman,Andrew and Fitzgibbon,Andrew} } @conference {12315, title = {Finding close friends on the Internet}, booktitle = {Network Protocols, 2001. Ninth International Conference on}, year = {2001}, month = {2001/11//}, pages = {301 - 309}, abstract = {We consider the problem of finding nearby application-peers (close friends) over the Internet. We focus on unicast-only solutions and introduce a new scheme -Beaconing-for finding peers that are near. Our scheme uses distance measurement points (called beacons) and can be implemented entirely in the application-layer without investing in large infrastructure changes. We present an extensive evaluation of Beaconing and compare it to existing schemes including Expanding Ring searches and Triangulation. Our experiments show that 3-8 beacons are sufficient to provide efficient peer-location service on 10 000 node Internet-like topologies. Further, our results are 2-5 times more accurate than existing techniques. We also present results from an implementation of Beaconing over a non-trivial wide-area testbed. In our experiments, Beaconing is able to efficiently (< 3 K Bytes and < 50 packets on average), quickly (< 1 second on average), and accurately (< 20 ms error on average) find nearby peers on the Internet.}, keywords = {application-layer;, application-peers;, Beaconing;, beacons;, close, distance, Expanding, friends;, Internet-like, Internet;, IP;, measurement, nearby, network, peer-location, points;, protocols;, Ring, searches;, service;, solutions;, testbed;, topologies;, topology;, transport, Triangulation;, unicast-only, wide-area}, doi = {10.1109/ICNP.2001.992910}, author = {Kommareddy,C. and Shankar,N. and Bhattacharjee, Bobby} } @conference {15949, title = {Handling uncertainty with active logic}, booktitle = {In Proceedings, AAAI Fall Symposium on Uncertainty in Computation}, year = {2001}, month = {2001///}, author = {Bhatia,M. and Chi,P. and Chong,W. and Josyula,D. P and Okamoto,Y. and Perlis, Don and Purang,K.} } @conference {12359, title = {Hybrid global/local search strategies for dynamic voltage scaling in embedded multiprocessors}, booktitle = {Hardware/Software Codesign, 2001. CODES 2001. Proceedings of the Ninth International Symposium on}, year = {2001}, month = {2001///}, pages = {243 - 248}, author = {Bambha,N. K and Bhattacharyya, Shuvra S. and Teich,J. and Zitzler,E.} } @conference {12139, title = {Implementing the Experience Factory concepts as a set of Experience Bases}, booktitle = {Proc. 13th Int{\textquoteright}l Conf. Software Eng. and Knowledge Eng}, year = {2001}, month = {2001///}, pages = {102 - 109}, abstract = {This talk takes the Experience Factory concept, which was originally developed as organizational support for softwaredevelopment and generalizes it to organizational support for any aspect of a business, e.g., business practices. The Experience Factory supports the evolution of processes and other forms of knowledge, based upon experiences within the organization, and related knowledge gathered from outside the organization. It then discusses how you might design an appropriate experience base for the particular set of organizational needs determined to be of importance. Specific examples are given in developing experience bases for specific organizations and it discusses the Experience Management System (EMS) currently being evolved and how it has been applied. }, author = {Basili, Victor R. and Lindvall,M. and Costa,P.} } @article {18852, title = {Integrated Microelectromechanical System (MEMS) Inertial Measurement Unit (IMIMU)}, year = {2001}, month = {2001/12//}, institution = {CARNEGIE-MELLON UNIVERSITY}, abstract = {Processes, designs and design tools are developed to enable the monolithic integration of arrays of inertial microsensors with electronics. Accelerometers and gyroscopes, fabricated in a single CMOS process, are functional and demonstrate a single chip IMU. Two integrated post CMOS micro-machining processes are demonstrated. Thin-film microstructures are defined from the metal-dielectric stack of a conventional process. In the second process, a back-side silicon etch, followed by front-side DRIE produces bulk silicon microstructures. Accelerometer and gyroscope designs are developed with accompanying low noise electronic circuitry. Noise performance was limited to 1/f circuit noise. The chip output sensibility is set by the interface circuit design. A thermally stabilized accelerometer and circuit design is demonstrated using embedded polysilicon resistors as temperature sensors and heaters in a closed loop. Nested gyroscope topologies are demonstrated with a lateral MEMS accelerometer used as a coriolis acceleration sensor. Modeling and simulation tools that simultaneously consider the electromechanical transducer and the electronic circuit to predict system performance are developed. Electrical, electromechanical and mechanical parasitics required to enable predictive lumped parameter simulation are identified and can be extracted, enabling a designer to confidently estimate design performance prior to fabrication. Generic physics-based fault models for surface-micromachined actuators and sensors are developed that enable effective testing, diagnosis and design for manufacturability.}, keywords = {*ELECTROMECHANICAL DEVICES, *GYROSCOPES, *INERTIAL MEASUREMENT UNITS, *INERTIAL NAVIGATION, *MICROELECTROMECHANICAL SYSTEMS, ACCELEROMETERS, BULK MATERIALS, CHIPS(ELECTRONICS), CIRCUITS, CLOSED LOOP SYSTEMS, CORIOLIS EFFECT, Detectors, DIELECTRICS, ELECTRICAL AND ELECTRONIC EQUIPMENT, EMBEDDING, METALS, MICROSENSORS., MICROSTRUCTURE, MONOLITHIC STRUCTURES(ELECTRONICS), NAVIGATION AND GUIDANCE, PARASITES, PE63739E, PERFORMANCE(ENGINEERING), POLYSILICONS, RESISTORS, SILICON, TEMPERATURE SENSITIVE ELEMENTS, THERMAL STABILITY, THIN FILMS, tools, Topology, WUAFRLE1170030}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA399565}, author = {Fedder,Gary K. and Blanton,Shawn and Carley,L. R. and Gupta, Satyandra K. and Koester,David} } @article {18488, title = {On the interactions between layered quality adaptation and congestion control for streaming video}, journal = {11th International Packet Video Workshop}, year = {2001}, month = {2001///}, abstract = {This paper uses analysis and experiments to study the impact of var-ious congestion control algorithms and receiver buffering strategies on the performance of streaming media delivery. While traditional congestion avoidance schemes such as TCP{\textquoteright}s additive-increase/- multiplicativedecrease (AIMD) achieve high utilization, they also cause large oscillations in transmission rates that degrade the smooth- ness and perceptual quality of the video stream. We focus on un- derstanding the interactions of a family of congestion control al- gorithms that generalize AIMD, with buffer-based quality adapta- tion algorithms for hierarchically-encoded and simulcast video. Our work builds on and extends the results of Rejaie et al. [19]; we find that the combination of a non-AIMD algorithm that has smaller os- cillations than AIMD and a suitable receiver buffer allocation and management strategy provides a good combination of low playout delay and TCP-friendly congestion control. The paper describes these mechanisms and the results of experiments conducted using a prototype video server for MPEG-4 video, showing that our ap- proach can improve the interactivity and adaptivity of Internet video. }, author = {Feamster, Nick and Bansal,D. and Balakrishnan,H.} } @inbook {13801, title = {Interpretation of Compound Nominals Using WordNet}, booktitle = {Computational Linguistics and Intelligent Text ProcessingComputational Linguistics and Intelligent Text Processing}, series = {Lecture Notes in Computer Science}, volume = {2004}, year = {2001}, month = {2001///}, pages = {169 - 181}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We describe an approach to interpreting noun-noun compounds within a question answering system. The system{\textquoteright}s lexicon, based on WordNet, provides the basis for heuristics that group noun-noun compounds with seman- tically similar words. The semantic relationship between the nouns in a com- pound is determined by the choice of heuristic for the compound. We discuss procedures for selecting one heuristic in cases where several can apply to a compound, the effects of lexical ambiguity, and some initial results of our methods.}, isbn = {978-3-540-41687-6}, url = {http://dx.doi.org/10.1007/3-540-44686-9_17}, author = {Barrett,Leslie and Davis,Anthony and Dorr, Bonnie J}, editor = {Gelbukh,Alexander} } @article {14912, title = {Judging whether multiple silhouettes can come from the same object}, journal = {Visual Form 2001}, year = {2001}, month = {2001///}, pages = {532 - 541}, abstract = {We consider the problem of recognizing an object from its silhouette. We focus on the case in which the camera translates, and rotates about a known axis parallel to the image, such as when a mobile robot explores an environment. In this case we present an algorithm for determining whether a new silhouette could come from the same object that produced two previously seen silhouettes. In a basic case, when cross-sections of each silhouette are single line segments, we can check for consistency between three silhouettes using linear programming. This provides the basis for methods that handle more complex cases. We show many experiments that demonstrate the performance of these methods when there is noise, some deviation from the assumptions of the algorithms, and partial occlusion. Previous work has addressed the problem of precisely reconstructing an object using many silhouettes taken under controlled conditions. Our work shows that recognition can be performed without complete reconstruction, so that a small number of images can be used, with viewpoints that are only partly constrained.}, doi = {10.1007/3-540-45129-3_49}, author = {Jacobs, David W. and Belhumeur,P. and Jermyn,I.} } @conference {14857, title = {Lambertian reflectance and linear subspaces}, booktitle = {Computer Vision, 2001. ICCV 2001. Proceedings. Eighth IEEE International Conference on}, volume = {2}, year = {2001}, month = {2001///}, pages = {383 -390 vol.2 - 383 -390 vol.2}, abstract = {We prove that the set of all reflectance functions (the mapping from surface normals to intensities) produced by Lambertian objects under distant, isotropic lighting lies close to a 9D linear subspace. This implies that the images of a convex Lambertian object obtained under a wide variety of lighting conditions can be approximated accurately with a low-dimensional linear subspace, explaining prior empirical results. We also provide a simple analytic characterization of this linear space. We obtain these results by representing lighting using spherical harmonics and describing the effects of Lambertian materials as the analog of a convolution. These results allow us to construct algorithms for object recognition based on linear methods as well as algorithms that use convex optimization to enforce non-negative lighting functions}, keywords = {functions;spherical, harmonics;convex, Lambertian, lighting;object, object;convex, objects;convex, optimization;isotropic, programming;object, recognition;, recognition;reflectance}, doi = {10.1109/ICCV.2001.937651}, author = {Basri,R. and Jacobs, David W.} } @conference {16597, title = {Learning word pronunciations using a recurrent neural network}, booktitle = {Neural Networks, 2001. Proceedings. IJCNN{\textquoteright}01. International Joint Conference on}, volume = {1}, year = {2001}, month = {2001///}, pages = {11 - 15}, author = {Radio,M. J and Reggia, James A. and Berndt,R. S} } @article {12327, title = {Multiprocessor clustering for embedded systems}, journal = {Euro-Par 2001 Parallel Processing}, year = {2001}, month = {2001///}, pages = {697 - 701}, author = {Kianzad,V. and Bhattacharyya, Shuvra S.} } @article {15237, title = {Optimal collective dichotomous choice under partial order constraints}, journal = {Mathematical Social Sciences}, volume = {41}, year = {2001}, month = {2001/05//}, pages = {349 - 364}, abstract = {This paper generalizes optimal collective dichotomous choices by including constraints which limit combinations of acceptance and rejection decisions for m projects under consideration. Two types of constraints are examined. The first type occurs when acceptance of some projects requires acceptance of others. This type reduces the choice problem to the tractable (solvable in polynomial time) problem of finding a maximum weight closed subset of a directed acyclic graph. The second type occurs when some projects must be accepted when certain others are rejected. We show that this type renders the choice problem to be NP-complete by reduction from the problem of Vertex Cover. Applicability of the generalization to information filtering is discussed.}, keywords = {constraints, Information filtering, Optimal collective dichotomous choice}, isbn = {0165-4896}, doi = {10.1016/S0165-4896(00)00069-X}, url = {http://www.sciencedirect.com/science/article/pii/S016548960000069X}, author = {Ben-Yashar,Ruth and Khuller, Samir and Kraus,Sarit} } @article {12319, title = {Parameterized dataflow modeling for DSP systems}, journal = {Signal Processing, IEEE Transactions on}, volume = {49}, year = {2001}, month = {2001///}, pages = {2408 - 2421}, author = {Bhattacharya,B. and Bhattacharyya, Shuvra S.} } @conference {17873, title = {Performance optimization for data intensive grid applications}, booktitle = {Active Middleware Services, 2001. Third Annual International Workshop on}, year = {2001}, month = {2001///}, pages = {97 - 105}, author = {Beynon,M. D and Sussman, Alan and Catalyurek,U. and Kurc, T. and Saltz, J.} } @article {14885, title = {Projective alignment with regions}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {23}, year = {2001}, month = {2001/05//}, pages = {519 - 527}, abstract = {We have previously proposed (Basri and Jacobs, 1999, and Jacobs and Basri, 1999) an approach to recognition that uses regions to determine the pose of objects while allowing for partial occlusion of the regions. Regions introduce an attractive alternative to existing global and local approaches, since, unlike global features, they can handle occlusion and segmentation errors, and unlike local features they are not as sensitive to sensor errors, and they are easier to match. The region-based approach also uses image information directly, without the construction of intermediate representations, such as algebraic descriptions, which may be difficult to reliably compute. We further analyze properties of the method for planar objects undergoing projective transformations. In particular, we prove that three visible regions are sufficient to determine the transformation uniquely and that for a large class of objects, two regions are insufficient for this purpose. However, we show that when several regions are available, the pose of the object can generally be recovered even when some or all regions are significantly occluded. Our analysis is based on investigating the flow patterns of points under projective transformations in the presence of fixed points}, keywords = {algebra;object, alignment;projective, approach;segmentation, errors;image, fixed, objects;pose, occlusion;planar, patterns;partial, points;flow, recognition;, recovery;projective, segmentation;matrix, transformations;region-based}, isbn = {0162-8828}, doi = {10.1109/34.922709}, author = {Basri,R. and Jacobs, David W.} } @conference {12110, title = {A prototype experience management system for a software consulting organization}, booktitle = {Thirteenth International Conference on Software Engineering and Knowledge Engineering}, year = {2001}, month = {2001///}, pages = {29 - 36}, abstract = {The Experience Management System (EMS) is aimed atsupporting the capture and reuse of software-related experience, based on the Experience Factory concept. It is being developed for use in a multinational software engineering consultancy, Q-Labs. Currently, a prototype EMS exists and has been evaluated. This paper focuses on the EMS architecture, underlying data model, implementation, and user interface. }, author = {Mendon{\c c}a Neto,M. G. and Seaman,C. and Basili, Victor R. and Kim,Y. M} } @article {18271, title = {Rotation, scale, and translation resilient public watermarking for images using a log-polar fourier transform}, year = {2001}, month = {2001/08/28/}, abstract = {A method for detecting a watermark signal in digital image data. The detecting method includes the steps of: computing a log-polar Fourier transform of the image data to obtain a log-polar Fourier spectrum; projecting the log-polar Fourier spectrum down to a lower dimensional space to obtain an extracted signal; comparing the extracted signal to a target watermark signal; and declaring the presence or absence of the target watermark signal in the image data based on the comparison. Also provided is a method for inserting a watermark signal in digital image data to obtain a watermarked image. The inserting method includes the steps of: computing a log-polar Fourier transform of the image data to obtain a log-polar Fourier spectrum; projecting the log-polar Fourier spectrum down to a lower dimensional space to obtain an extracted signal; modifying the extracted signal such that it is similar to a target watermark; performing a one-to-many mapping of the modified signal back to...}, url = {http://www.google.com/patents?id=v4AIAAAAEBAJ}, author = {Bloom,Jeffrey A. and Cox,Ingemar J. and Miller,Matthew L. and M. Wu and Lin,Ching-Yung and Lui,Yui Man}, editor = {Signafy, Inc.} } @article {18272, title = {Rotation, scale, and translation resilient watermarking for images}, journal = {Image Processing, IEEE Transactions on}, volume = {10}, year = {2001}, month = {2001/05//}, pages = {767 - 782}, abstract = {Many electronic watermarks for still images and video content are sensitive to geometric distortions. For example, simple rotation, scaling, and/or translation (RST) of an image can prevent blind detection of a public watermark. In this paper, we propose a watermarking algorithm that is robust to RST distortions. The watermark is embedded into a one-dimensional (1-D) signal obtained by taking the Fourier transform of the image, resampling the Fourier magnitudes into log-polar coordinates, and then summing a function of those magnitudes along the log-radius axis. Rotation of the image results in a cyclical shift of the extracted signal. Scaling of the image results in amplification of the extracted signal, and translation of the image has no effect on the extracted signal. We can therefore compensate for rotation with a simple search, and compensate for scaling by using the correlation coefficient as the detection measure. False positive results on a database of 10 000 images are reported. Robustness results on a database of 2000 images are described. It is shown that the watermark is robust to rotation, scale, and translation. In addition, we describe tests examining the watermarks resistance to cropping and JPEG compression}, keywords = {axis;one-dimensional, coding;security, coefficient;cropping;cyclical, compression;RST, coordinates;log-radius, data;, detection;correlation, distortions;blind, distortions;images;log-polar, encapsulation;image, Fourier, images;translation, magnitudes;Fourier, measure;geometric, of, protection;data, resilient, shift;detection, signal;public, transform;JPEG, transforms;copy, watermark;resampling;rotation;scale;search;still, watermarking;video;Fourier}, isbn = {1057-7149}, doi = {10.1109/83.918569}, author = {Lin,C.-Y. and Wu,M. and Bloom,J.A. and Cox,I.J. and Miller,M.L. and Lui,Y.M.} } @article {12156, title = {Software Defect Reduction Top 10 List}, journal = {Computer}, volume = {34}, year = {2001}, month = {2001/01//}, pages = {135 - 137}, abstract = {Software{\textquoteright}s complexity and accelerated development schedules make avoiding defects difficult. These 10 techniques can help reduce the flaws in your code.}, isbn = {0018-9162}, doi = {10.1109/2.962984}, url = {http://dx.doi.org/10.1109/2.962984}, author = {Boehm,Barry and Basili, Victor R.} } @conference {14188, title = {A spherical eye from multiple cameras (makes better models of the world)}, booktitle = {Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2001. CVPR 2001}, volume = {1}, year = {2001}, month = {2001///}, pages = {I-576- I-583 vol.1 - I-576- I-583 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {The paper describes an imaging system that has been designed specifically for the purpose of recovering egomotion and structure from video. The system consists of six cameras in a network arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and consequently the estimation of shape models from the individual cameras. The reason is that inherent ambiguities of confusion between translation and rotation disappear. We provide algorithms for the calibration of the system and 3D motion estimation. The calibration is based on a new geometric constraint that relates the images of lines parallel in space to the rotation between the cameras. The 3D motion estimation uses a constraint relating structure directly to image gradients.}, keywords = {3D motion estimation, Calibration, camera network, CAMERAS, Computer vision, egomotion recovery, geometric configuration, geometric constraint, image gradients, image sampling, imaging system, Laboratories, Layout, Motion estimation, multiple cameras, Pixel, Robot vision systems, SHAPE, shape models, Space technology, spherical eye, system calibration, video, video cameras, video signal processing, visual sphere sampling}, isbn = {0-7695-1272-0}, doi = {10.1109/CVPR.2001.990525}, author = {Baker, P. and Ferm{\"u}ller, Cornelia and Aloimonos, J. and Pless, R.} } @conference {16434, title = {Statistical Analysis in Music Information Retrieval}, booktitle = {Proceedings of the Second Annual International Symposium on Music Information Retrieval ISMIR 2001}, volume = {25--26}, year = {2001}, month = {2001///}, pages = {25 - 26}, abstract = {We introduce a statistical model of music that allows for the retrieval of music based upon an audio input. This model uses frequency counts of state transitions to index pieces of music. Several methods of comparing these index values to choose an appropriate match are examined. We describe how this model can serve as the basis for a query-by-humming system. The model is also shown to be robust to several kinds of errors.}, author = {Rand, William and Birmingham,William P.} } @conference {12021, title = {Towards the ultimate motion capture technology}, booktitle = {Deformable avatars: IFIP TC5/WG5. 10 DEFORM{\textquoteright}2000 Workshop, November 29-30, 2000, Geneva, Switzerland and AVATARS{\textquoteright}2000 Workshop, November 30-December 1, 2000, Lausanne, Switzerland}, volume = {68}, year = {2001}, month = {2001///}, pages = {143 - 143}, author = {Stuart, B. and Baker, P. and Aloimonos, J.} } @conference {12098, title = {A trend analysis of exploitations}, booktitle = {2001 IEEE Symposium on Security and Privacy, 2001. S\&P 2001. Proceedings}, year = {2001}, month = {2001///}, pages = {214 - 229}, publisher = {IEEE}, organization = {IEEE}, abstract = {We have conducted an empirical study of a number of computer security exploits and determined that the rates at which incidents involving the exploit are reported to CERT can be modeled using a common mathematical framework. Data associated with three significant exploits involving vulnerabilities in phf, imap, and bind can all be modeled using the formula C=I+S{\texttimes}√M where C is the cumulative count of reported incidents, M is the time since the start of the exploit cycle, and I and S are the regression coefficients determined by analysis of the incident report data. Further analysis of two additional exploits involving vulnerabilities in mountd and statd confirm the model. We believe that the models will aid in predicting the severity of subsequent vulnerability exploitations, based on the rate of early incident reports}, keywords = {Computer science, computer security exploits, Data analysis, data mining, Educational institutions, exploitations, Performance analysis, Predictive models, Regression analysis, Risk management, security of data, software engineering, system intrusions, System software, trend analysis, vulnerabilities, vulnerability exploitation}, isbn = {0-7695-1046-9}, doi = {10.1109/SECPRI.2001.924300}, author = {Browne,H. K and Arbaugh, William A. and McHugh,J. and Fithen,W. L} } @conference {16488, title = {Validating an access cost model for wide area applications}, booktitle = {Cooperative Information Systems}, year = {2001}, month = {2001///}, pages = {371 - 385}, author = {Zadorozhny,V. and Raschid, Louiqa and Zhan,T. and Bright,L.} } @conference {16155, title = {VEHICLE SPEED INFORMATION DISPLAYS FOR PUBLIC WEBSITES: A STUDY OF USER PREFERENCES}, booktitle = {ITS 2001: Conference Proceedings}, year = {2001}, month = {2001///}, author = {Plaisant, Catherine and Bhamidipati,P. and Tarnoff,P.} } @article {18475, title = {Active source location and beamforming}, journal = {The Journal of the Acoustical Society of America}, volume = {107}, year = {2000}, month = {2000///}, pages = {2790 - 2790}, isbn = {00014966}, doi = {10.1121/1.428978}, url = {http://asadl.org/jasa/resource/1/jasman/v107/i5/p2790_s4}, author = {Duraiswami, Ramani and Zotkin,Dmitry N and Borovikov,Eugene A. and Davis, Larry S.} } @article {14802, title = {An API for Runtime Code Patching}, journal = {International Journal of High Performance Computing Applications}, volume = {14}, year = {2000}, month = {2000///}, pages = {317 - 329}, abstract = {The authors present a postcompiler program manipulation tool called Dyninst, which provides a C++ class library for program instrumentation. Using this library, it is possible to instrument and modify application programs during execution. A unique feature of this library is that it permits machine-independent binary instrumentation programs to be written. The authors describe the interface that a tool sees when using this library. They also discuss three simple tools built using this interface: a utility to count the number of times a function is called, a program to capture the output of an already running program to a file, and an implementation of conditional breakpoints. For the conditional breakpoint example, the authors show that by using their interface compared with gdb, they are able to execute a program with conditional breakpoints up to 900 times faster.}, doi = {10.1177/109434200001400404}, url = {http://hpc.sagepub.com/content/14/4/317.abstract}, author = {Buck, Bryan and Hollingsworth, Jeffrey K} } @article {17555, title = {Approximating low-congestion routing and column-restricted packing problems}, journal = {Information Processing Letters}, volume = {74}, year = {2000}, month = {2000/04//}, pages = {19 - 25}, abstract = {We contribute to a body of research asserting that the fractional and integral optima of column-sparse integer programs are {\textquotedblleft}nearby{\textquotedblright}. This yields improved approximation algorithms for some generalizations of the knapsack problem, with applications to low-congestion routing in networks, file replication in distributed databases, and other packing problems.}, keywords = {algorithms, Approximation algorithms, integer programming, Packing, Routing}, isbn = {0020-0190}, doi = {10.1016/S0020-0190(00)00033-8}, url = {http://www.sciencedirect.com/science/article/pii/S0020019000000338}, author = {Baveja,Alok and Srinivasan, Aravind} } @article {17560, title = {Approximation Algorithms for Disjoint Paths and Related Routing and Packing Problems}, journal = {Mathematics of Operations ResearchMathematics of Operations Research}, volume = {25}, year = {2000}, month = {2000/05/01/}, pages = {255 - 280}, abstract = {Given a network and a set of connection requests on it, we consider the maximum edge-disjoint paths and related generalizations and routing problems that arise in assigning paths for these requests. We present improved approximation algorithms and/or integrality gaps for all problems considered; the central theme of this work is the underlying multicommodity flow relaxation. Applications of these techniques to approximating families of packing integer programs are also presented.}, keywords = {Approximation algorithms, Disjoint paths, integer programming, Linear programming, multicommodity flow, Packing, randomized algorithms, rounding, Routing, unsplittable flow}, isbn = {0364-765X, 1526-5471}, doi = {10.1287/moor.25.2.255.12228}, url = {http://mor.journal.informs.org/content/25/2/255}, author = {Baveja,Alok and Srinivasan, Aravind} } @conference {15287, title = {Comparative Evaluation of a Natural Language Dialog Based System and a Menu-Driven System for Information Access: A Case Study}, booktitle = {In Proceedings of the International Conference on Multimedia Information Retrieval (RIAO 2000)}, year = {2000}, month = {2000///}, abstract = {This paper describes the evaluation of a natural language dialog based navigation system (HappyAssistant) thathelps users access e-commerce sites to find relevant information about products and services. The prototype system leverages technologies in natural language processing and human computer interaction to create a faster and more intuitive way of interacting with websites, especially for the less experienced users. The result of a comparative study shows that users prefer the natural language enabled navigation two to one over the menu driven navigation. In addition, the study confirmed the efficiency of using natural language dialog in terms of the number of clicks and the amount of time required to obtain the relevant information. In the case study, comparing to the menu driven system, the average number of clicks used in the natural language system was reduced by 63.2\% and the average time was reduced by 33.3\%. }, author = {Chai,J. and Jimmy Lin and Zadrozny,W. and Ye,Y. and Budzikowska,M. and Horvath,V. and Kambhatla,N. and Wolf,C.} } @article {14879, title = {Convexity in Perceptual Completion}, journal = {KLUWER INTERNATIONAL SERIES IN ENGINEERING AND COMPUTER SCIENCE}, year = {2000}, month = {2000///}, pages = {73 - 90}, author = {Liu,Z. and Jacobs, David W. and Basri,R.} } @conference {17847, title = {DataCutter: Middleware for filtering very large scientific datasets on archival storage systems}, booktitle = {NASA conference publication}, year = {2000}, month = {2000///}, pages = {119 - 134}, author = {Beynon, M. and Ferreira,R. and Kurc, T. and Sussman, Alan and Saltz, J.} } @article {18296, title = {Design and use of linear models for image motion analysis}, journal = {International Journal of Computer Vision}, volume = {36}, year = {2000}, month = {2000///}, pages = {171 - 193}, author = {Fleet,D. J and Black,M. J and Yacoob,Yaser and Jepson,A. D} } @conference {17831, title = {Design of a Framework for Data-Intensive Wide-Area Applications}, booktitle = {Heterogeneous Computing Workshop}, year = {2000}, month = {2000///}, pages = {116 - 116}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Applications that use collections of very large, distributed datasets have become an increasingly important part of science and engineering. With high performance wide-area networks become more pervasive, there is interest in making collective use of distributed computational and data resources. Recent work has converged to the notion of the Grid, which attempts to uniformly present a heterogeneous collection of distributed resources. Current Grid research covers many areas from low-level infrastructure issues to high-level application concerns. However, providing support for efficient exploration and processing of very large scientific datasets stored in distributed archival storage systems remains a challenging research issue.We have initiated an effort that focuses on developing efficient data-intensive applications in a Grid environment. In this paper, we present a framework, called filter-stream programming that represents the processing units of a data-intensive application as a set of filters, which are designed to be efficient in their use of memory and scratch space. We describe a prototype infrastructure that supports execution of applications using the proposed framework. We present the implementation of two applications using the filter-stream programming framework, and discuss experimental results demonstrating the effects of heterogeneous resources on application performance.}, keywords = {application decomposition, data analysis and exploration, Data-intensive applications}, doi = {http://doi.ieeecomputersociety.org/10.1109/HCW.2000.843737}, author = {Beynon,Michael D. and Kurc,Tahsin and Sussman, Alan and Saltz,Joel} } @conference {13893, title = {Designing StoryRooms: interactive storytelling spaces for children}, booktitle = {Proceedings of the 3rd conference on Designing interactive systems: processes, practices, methods, and techniques}, year = {2000}, month = {2000///}, pages = {95 - 104}, author = {Alborzi,H. and Druin, Allison and Montemayor,J. and Platner,M. and Porteous,J. and Sherman,L. and Boltman,A. and Tax{\'e}n,G. and Best,J. and Hammer,J. and others} } @conference {13912, title = {Designing storytelling technologies to encouraging collaboration between young children}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2000}, month = {2000///}, pages = {556 - 563}, author = {Benford,S. and Bederson, Benjamin B. and \AAkesson,K. P and Bayon,V. and Druin, Allison and Hansson,P. and Hourcade,J. P and Ingram,R. and Neale,H. and O{\textquoteright}Malley,C. and others} } @article {12027, title = {Detecting independent motion: The statistics of temporal continuity}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {22}, year = {2000}, month = {2000///}, pages = {768 - 773}, author = {Pless, R. and Brodsky, T. and Aloimonos, J.} } @conference {12197, title = {Domain name based visualization of Web histories in a zoomable user interface}, booktitle = {11th International Workshop on Database and Expert Systems Applications, 2000. Proceedings}, year = {2000}, month = {2000///}, pages = {591 - 598}, publisher = {IEEE}, organization = {IEEE}, abstract = {Users of hypertext systems like the World Wide Web (WWW) often find themselves following hypertext links deeper and deeper, only to find themselves {\textquotedblleft}lost{\textquotedblright} and unable to find their way back to the previously visited pages. We have implemented a Web browser companion called Domain Tree Browser (DTB) that builds a tree structured visual navigation history while browsing the Web. The Domain Tree Browser organizes the URLs visited based on the domain name of each URL and shows thumbnails of each page in a zoomable window}, keywords = {Computer science, data visualisation, domain name, domain name based visualization, Domain Tree Browser, Educational institutions, History, hypermedia, hypertext links, hypertext systems, information resources, Navigation, online front-ends, thumbnails, Tree graphs, tree structured visual navigation history, Uniform resource locators, URLs, User interfaces, Visualization, Web browser companion, Web histories, Web pages, World Wide Web, zoomable user interface, zoomable window}, isbn = {0-7695-0680-1}, doi = {10.1109/DEXA.2000.875085}, author = {Gandhi,R. and Kumar,G. and Bederson, Benjamin B. and Shneiderman, Ben} } @conference {16444, title = {Efficient remote data access in a mobile computing environment}, booktitle = {ICPP}, year = {2000}, month = {2000///}, pages = {57 - 57}, author = {Bright,L. and Raschid, Louiqa} } @book {12383, title = {Embedded multiprocessors: Scheduling and synchronization}, volume = {3}, year = {2000}, month = {2000///}, publisher = {CRC}, organization = {CRC}, author = {Sriram,S. and Bhattacharyya, Shuvra S.} } @article {18440, title = {The experimental validation and packaging of software technologies}, journal = {ACM SIGSOFT Software Engineering Notes}, volume = {25}, year = {2000}, month = {2000/01//}, pages = {82 - 83}, isbn = {0163-5948}, doi = {10.1145/340855.341021}, url = {http://doi.acm.org/10.1145/340855.341021}, author = {Shull, Forrest and Basili, Victor R. and Zelkowitz, Marvin V} } @conference {14287, title = {A first step towards automated detection of buffer overrun vulnerabilities}, booktitle = {The 2000 Network and Distributed Systems Security Conference. San Diego, CA}, volume = {14}, year = {2000}, month = {2000///}, author = {Wagner,D. and Foster, Jeffrey S. and Brewer,E.A. and Aiken,A.} } @article {14971, title = {High performance computing algorithms for land cover dynamics using remote sensing data}, journal = {International Journal of Remote Sensing}, volume = {21}, year = {2000}, month = {2000///}, pages = {1513 - 1536}, abstract = {Global and regional land cover studies need to apply complex models on selected subsets of large volumes of multi-sensor and multi-temporal data sets that have been derived from raw instrument measurements using widely accepted pre-processing algorithms. The computational and storage requirements of most of these studies far exceed what is possible on a single workstation environment. We have been pursuing a new approach that couples scalable and open distributed heterogeneous hardware with the development of high performance software for processing, indexing and organizing remotely sensed data. Hierarchical data management tools are used to ingest raw data, create metadata and organize the archived data so as to automatically achieve computational load balancing among the available nodes and minimize input/output overheads. We illustrate our approach with four specific examples. The first is the development of the first fast operational scheme for the atmospheric correction of Landsat Thematic Mapper scenes, while the second example focuses on image segmentation using a novel hierarchical connected components algorithm. Retrieval of the global Bidirectional Reflectance Distribution Function in the red and near-infrared wavelengths using four years (1983 to 1986) of Pathfinder Advanced Very High Resolution Radiometer (AVHRR) Land data is the focus of our third example. The fourth example is the development of a hierarchical data organization scheme that allows on-demand processing and retrieval of regional and global AVHRR data sets. Our results show that substantial reductions in computational times can be achieved by the high performance computing technology.}, isbn = {0143-1161}, doi = {10.1080/014311600210290}, url = {http://www.tandfonline.com/doi/abs/10.1080/014311600210290}, author = {Kalluri, SNV and JaJa, Joseph F. and Bader, D.A. and Zhang,Z. and Townshend,J.R.G. and Fallah-Adl,H.} } @conference {14844, title = {In search of illumination invariants}, booktitle = {Computer Vision and Pattern Recognition, 2000. Proceedings. IEEE Conference on}, volume = {1}, year = {2000}, month = {2000///}, pages = {254 -261 vol.1 - 254 -261 vol.1}, abstract = {We consider the problem of determining functions of an image of an object that are insensitive to illumination changes. We first show that for an object with Lambertian reflectance there are no discriminative functions that are invariant to illumination. This result leads as to adopt a probabilistic approach in which we analytically determine a probability distribution for the image gradient as a function of the surface{\textquoteright}s geometry and reflectance. Our distribution reveals that the direction of the image gradient is insensitive to changes in illumination direction. We verify this empirically by constructing a distribution for the image gradient from more than 20 million samples of gradients in a database of 1,280 images of 20 inanimate objects taken under varying lighting condition. Using this distribution we develop an illumination insensitive measure of image comparison and test it on the problem of face recognition}, keywords = {comparison;image, gradient;face, invariants;image, Lambertian, recognition;, recognition;illumination, recognition;object, reflectance;face}, doi = {10.1109/CVPR.2000.855827}, author = {Chen,H. F and Belhumeur,P. N. and Jacobs, David W.} } @conference {12168, title = {Jazz: an extensible zoomable user interface graphics toolkit in Java}, booktitle = {Proceedings of the 13th annual ACM symposium on User interface software and technology}, year = {2000}, month = {2000///}, pages = {171 - 180}, author = {Bederson, Benjamin B. and Meyer,J. and Good,L.} } @article {14980, title = {Kronos: A software system for the processing and retrieval of large-scale AVHRR data sets}, journal = {PE \& RS- Photogrammetric Engineering and Remote Sensing}, volume = {66}, year = {2000}, month = {2000///}, pages = {1073 - 1082}, abstract = {Raw remotely sensed satellite data have to be processed andmapped into a standard projection in order to produce a multi- temporal data set which can then be used for regional or global Earth science studies. However, traditional methods of processing remotely sensed satellite data have inherent limitations because they are based on a fixed processing chain. Different users may need the data in different forms with possibly different processing steps; hence, additional transformations may have to be applied to the processed data, resulting in potentially significant errors. In this paper, we describe a software system, Kronos, for the generation of custom-tailored products from the Advanced Very High Resolution Radiometer (AVHRR) sensor. It allows the generation of a rich set of products that can be easily specified through a simple interface by scientists wishing to carry out Earth system modeling or analysis. Kronos is based on a flexible methodology and consists of four major components: ingest and preprocessing, indexing and storage, a search and processing engine, and a Java interface. After geo-location and calibration, every pixel is indexed and stored using a combination of data structures. Following the users{\textquoteright} queries, data are selectively retrieved and secondary processing such as atmospheric correction, compositing, and projection are performed as specified. The processing is divided into two stages, the first of which involves the geo-location and calibration of the remotely sensed data and, hence, results in no loss of information. The second stage involves the retrieval of the appropriate data subsets and the application of the secondary processing specified by the user. This scheme allows the indexing and the storage of data from different sensors without any loss of information and, therefore, allows assimilation of data from multiple sensors. User specified processing can be applied later as needed. }, author = {Zhang,Z. and JaJa, Joseph F. and Bader, D.A. and Kalluri, SNV and Song,H. and El Saleous,N. and Vermote,E. and Townshend,J.R.G.} } @article {14626, title = {Ligand-Receptor Pairing Via Tree Comparison}, journal = {Journal of Computational Biology}, volume = {7}, year = {2000}, month = {2000/02//}, pages = {59 - 70}, abstract = {This paper introduces a novel class of tree comparison problems strongly motivated by an important and cost intensive step in drug discovery pipeline viz., mapping cell bound receptors to the ligands they bind to and vice versa. Tree comparison studies motivated by problems such as virus-host tree comparison, gene-species tree comparison and consensus tree problem have been reported. None of these studies are applicable in our context because in all these problems, there is a well-defined mapping of the nodes the trees are built on across the set of trees being compared. A new class of tree comparison problems arises in cases where finding the correspondence among the nodes of the trees being compared is itself the problem. The problem arises while trying to find the interclass correspondence between the members of a pair of coevolving classes, e.g., cell bound receptors and their ligands. Given the evolution of the two classes, the combinatorial problem is to find a mapping among the leaves of the two trees that optimizes a given cost function. In this work we formulate various combinatorial optimization problems motivated by the aforementioned biological problem for the first time. We present hardness results, give an efficient algorithm for a restriction of the problem and demonstrate its applicability.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/10665270050081388}, url = {http://www.liebertonline.com/doi/abs/10.1089/10665270050081388}, author = {Bafna,Vineet and Hannenhalli, Sridhar and Rice,Ken and Vawter,Lisa} } @article {15233, title = {The Loading Time Scheduling Problem}, journal = {Journal of Algorithms}, volume = {36}, year = {2000}, month = {2000/07//}, pages = {1 - 33}, abstract = {In this paper we study precedence constrained scheduling problems, where the tasks can only be executed on a specified subset of the set of machines. Each machine has a loading time that is incurred only for the first task that is scheduled on the machine in a particular run. This basic scheduling problem arises in the context of machining on numerically controlled machines and query optimization in databases and in other artificial intelligence applications. We give the first nontrivial approximation algorithm for this problem. We also prove nontrivial lower bounds on best possible approximation ratios for these problems. These improve on the nonapproximability results that are implied by the nonapproximability results for the shortest common supersequence problem. We use the same algorithm technique to obtain approximation algorithms for a problem arising in the context of code generation for parallel machines and for the weighted shortest common supersequence problem.}, isbn = {0196-6774}, doi = {10.1006/jagm.2000.1076}, url = {http://www.sciencedirect.com/science/article/pii/S0196677400910769}, author = {Bhatia,Randeep and Khuller, Samir and Naor,Joseph (Seffi)} } @conference {15232, title = {On local search and placement of meters in networks}, booktitle = {Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {319 - 328}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, isbn = {0-89871-453-2}, url = {http://dl.acm.org/citation.cfm?id=338219.338268}, author = {Khuller, Samir and Bhatia,Randeep and Pless,Robert} } @conference {14232, title = {Multi-camera networks: eyes from eyes}, booktitle = {IEEE Workshop on Omnidirectional Vision, 2000. Proceedings}, year = {2000}, month = {2000///}, pages = {11 - 18}, publisher = {IEEE}, organization = {IEEE}, abstract = {Autonomous or semi-autonomous intelligent systems, in order to function appropriately, need to create models of their environment, i.e., models of space time. These are descriptions of objects and scenes and descriptions of changes of space over time, that is, events and actions. Despite the large amount of research on this problem, as a community we are still far from developing robust descriptions of a system{\textquoteright}s spatiotemporal environment using video input (image sequences). Undoubtedly, some progress has been made regarding the understanding of estimating the structure of visual space, but it has not led to solutions to specific applications. There is, however, an alternative approach which is in line with today{\textquoteright}s {\textquotedblleft}zeitgeist.{\textquotedblright} The vision of artificial systems can be enhanced by providing them with new eyes. If conventional video cameras are put together in various configurations, new sensors can be constructed that have much more power and the way they {\textquotedblleft}see{\textquotedblright} the world makes it much easier to solve problems of vision. This research is motivated by examining the wide variety of eye design in the biological world and obtaining inspiration for an ensemble of computational studies that relate how a system sees to what that system does (i.e. relating perception to action). This, coupled with the geometry of multiple views that has flourished in terms of theoretical results in the past few years, points to new ways of constructing powerful imaging devices which suit particular tasks in robotics, visualization, video processing, virtual reality and various computer vision applications, better than conventional cameras. This paper presents a number of new sensors that we built using common video cameras and shows their superiority with regard to developing models of space and motion}, keywords = {Biosensors, CAMERAS, Computer vision, Eyes, Image sequences, intelligent systems, Layout, Machine vision, Robot vision systems, Robustness, Spatiotemporal phenomena, video cameras, Virtual reality}, isbn = {0-7695-0704-2}, doi = {10.1109/OMNVIS.2000.853797}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J. and Baker, P. and Pless, R. and Neumann, J. and Stuart, B.} } @article {12371, title = {Multidimensional exploration of software implementations for DSP algorithms}, journal = {The Journal of VLSI Signal Processing}, volume = {24}, year = {2000}, month = {2000///}, pages = {83 - 98}, author = {Zitzler,E. and Teich,J. and Bhattacharyya, Shuvra S.} } @article {14234, title = {New eyes for building models from video}, journal = {Computational Geometry}, volume = {15}, year = {2000}, month = {2000/02//}, pages = {3 - 23}, abstract = {Models of real-world objects and actions for use in graphics, virtual and augmented reality and related fields can only be obtained through the use of visual data and particularly video. This paper examines the question of recovering shape models from video information. Given video of an object or a scene captured by a moving camera, a prerequisite for model building is to recover the three-dimensional (3D) motion of the camera which consists of a rotation and a translation at each instant. It is shown here that a spherical eye (an eye or system of eyes providing panoramic vision) is superior to a camera-type eye (an eye with restricted field of view such as a common video camera) as regards the competence of 3D motion estimation. This result is derived from a geometric/statistical analysis of all the possible computational models that can be used for estimating 3D motion from an image sequence. Regardless of the estimation procedure for a camera-type eye, the parameters of the 3D rigid motion (translation and rotation) contain errors satisfying specific geometric constraints. Thus, translation is always confused with rotation, resulting in inaccurate results. This confusion does not happen for the case of panoramic vision. Insights obtained from this study point to new ways of constructing powerful imaging devices that suit particular tasks in visualization and virtual reality better than conventional cameras, thus leading to a new camera technology. Such new eyes are constructed by putting together multiple existing video cameras in specific ways, thus obtaining eyes from eyes. For a new eye of this kind we describe an implementation for deriving models of scenes from video data, while avoiding the correspondence problem in the video sequence.}, keywords = {model building, shape reconstruction, structure from motion, video analysis}, isbn = {0925-7721}, doi = {10.1016/S0925-7721(99)00044-9}, url = {http://www.sciencedirect.com/science/article/pii/S0925772199000449}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J. and Brodsk{\'y},Tom{\'a}{\v s}} } @inbook {14236, title = {New Eyes for Shape and Motion Estimation}, booktitle = {Biologically Motivated Computer VisionBiologically Motivated Computer Vision}, series = {Lecture Notes in Computer Science}, volume = {1811}, year = {2000}, month = {2000///}, pages = {23 - 47}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Motivated by the full field of view of insect eyes and their fast and accurate estimation of egomotion, we constructed a system of cameras to take advantage of the full field of view (FOV) constraints that insects use. In this paper, we develop a new ego-motion algorithm for a rigidly mounted set of cameras undergoing arbitrary rigid motion. This egomotion algorithm combines the unambiguous components of the motion computed by each separate camera. We prove that the cyclotorsion is resistant to errors and show this empirically. We show how to calibrate the system with two novel algorithms, one using secondary cameras and one using self calibration. Given this system calibration, the new 3D motion algorithm first computes the rotation and then the 3D translation. We apply this algorithm to a camera system constructed with four rigidly mounted synchronized cameras pointing in various directions and present motion estimation results at www.cfar.umd.edu/ pbaker/argus.html.}, isbn = {978-3-540-67560-0}, url = {http://dx.doi.org/10.1007/3-540-45482-9_12}, author = {Baker,Patrick and Pless,Robert and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Lee,Seong-Whan and B{\"u}lthoff,Heinrich and Poggio,Tomaso} } @article {14900, title = {Perceptual Completion Behind Occluders: The Role of Convexity}, journal = {Perceptual Organization for Artificial Vision Systems}, year = {2000}, month = {2000///}, pages = {73 - 90}, abstract = {An important problem in perceptual organization is to determine whether two image regions belong to the same object. In this chapter, we consider the situation when two image regions potentially group into a single object behind a common occluder. We study the extent to which two image regions are grouped more strongly than two other image regions. Existing theories in both human and computer vision have mainly emphasized the role of good continuation. Namely, the shorter and smoother the completing contours are between two image regions, the stronger the grouping will be. In contrast, Jacobs [3] has proposed a theory that considers relative positions and orientations of two image regions. For instance, the theory predicts that two image regions that can be linked by convex completing contours are grouped more strongly than those that can only be linked by concave completing contours, even though the completing contours are identical in shape. We present, in addition to our previous work (Liu, Jacobs, and Basri, 1999), human psychophysical evidence that concurs with the predictions of this theory and suggests an important role of convexity in perceptual grouping.}, doi = {10.1007/978-1-4615-4413-5_6}, author = {Liu,Z. and Jacobs, David W. and Basri,R.} } @conference {17532, title = {Receiver based management of low bandwidth access links}, booktitle = {IEEE INFOCOM 2000. Nineteenth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {1}, year = {2000}, month = {2000///}, pages = {245-254 vol.1 - 245-254 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we describe a receiver-based congestion control policy that leverages TCP flow control mechanisms to prioritize mixed traffic loads across access links. We manage queueing at the access link to: (1) improve the response time of interactive network applications; (2) reduce congestion-related packet losses; while (3) maintaining high throughput for bulk-transfer applications. Our policy controls queue length by manipulating receive socket buffer sizes. We have implemented this solution in a dynamically loadable Linux kernel module, and tested it over low-bandwidth links. Our approach yields a 7-fold improvement in packet latency over an unmodified system while maintaining 94\% link utilization. In the common case, congestion-related packet losses at the access link can be eliminated. Finally, by prioritizing short flows, we show that our system reduces the time to download a complex Web page during a large background transfer by a factor of two}, keywords = {Bandwidth, buffer storage, bulk-transfer applications, complex Web page, congestion control policy, Delay, dynamically loadable Linux kernel module, information resources, interactive network, Internet, Kernel, link utilization, Linux, low-bandwidth access links, mixed traffic load, packet latency, queue length, queueing theory, receive socket buffer sizes, receiver-based management, response time, short flow prioritizing, Size control, Sockets, subscriber loops, TCP flow control, telecommunication congestion control, telecommunication network management, Telecommunication traffic, Testing, Throughput, Transport protocols, Unix, Web pages}, isbn = {0-7803-5880-5}, doi = {10.1109/INFCOM.2000.832194}, author = {Spring, Neil and Chesire,M. and Berryman,M. and Sahasranaman,V. and Anderson,T. and Bershad,B.} } @article {12363, title = {Resynchronization for multiprocessor DSP systems}, journal = {Circuits and Systems I: Fundamental Theory and Applications, IEEE Transactions on}, volume = {47}, year = {2000}, month = {2000///}, pages = {1597 - 1609}, author = {Bhattacharyya, Shuvra S. and Sriram,S. and Lee,E. A} } @article {17651, title = {Retrieval scheduling for collaborative multimedia presentations}, journal = {Multimedia Systems}, volume = {8}, year = {2000}, month = {2000///}, pages = {146 - 155}, abstract = {The single-system approach is no longer sufficient to handle the load on popular Internet servers, especially for those offering extensive multimedia content. Such services have to be replicated to enhance their availability, performance, and reliability. In a highly replicated and available environment, server selection is an important issue. In this paper, we propose an application-layer broker (ALB) for this purpose. ALB employs a content-based, client-centric approach to negotiate with the servers and to identify the best server for the requested objects. ALB aims to maximize client buffer utilization in order to efficiently handle dynamic user interactions such as skip, reverse presentation, go back in time. We also present details of a collaborative multimedia presentation platform that we have developed based on ALB.}, isbn = {0942-4962}, url = {http://dx.doi.org/10.1007/s005300050157}, author = {Bai,Ping and Prabhakaran,B. and Srinivasan, Aravind} } @article {16437, title = {Reverse Engineering and UML: A Case Study of AuctionBot}, volume = {EECS 581}, year = {2000}, month = {2000///}, institution = {University of Michigan}, author = {Bangera,R. and Rand, William} } @article {18314, title = {Robustly estimating changes in image appearance}, journal = {Computer Vision and Image Understanding}, volume = {78}, year = {2000}, month = {2000///}, pages = {8 - 31}, author = {Black,M. J and Fleet,D. J and Yacoob,Yaser} } @article {18270, title = {Rotation, scale, and translation resilient public watermarking for images}, journal = {PROC SPIE INT SOC OPT ENG}, volume = {3971}, year = {2000}, month = {2000///}, pages = {90 - 98}, abstract = {Many electronic watermarks for still images and video content are sensitive to geometric distortions. For example,simple rotation, scaling, and/or translation (RST) of an image can prevent detection of a public watermark. In this paper, we propose a watermarking algorithm that is robust to RST distortions. The watermark is embedded into a 1-dimensional signal obtained by first taking the Fourier transform of the image, resampling the Fourier magnitudes into log-polar coordinates, and then summing a function of those magnitudes along the log-radius axis. If the image is rotated, the resulting signal is cyclically shifted. If it is scaled, the signal is multiplied by some value. And if the image is translated, the signal is unaffected. We can therefore compensate for rotation with a simple search, and for scaling by using the correlation coefficient for the detection metric. False positive results on a database of 10,000 images are reported. Robustness results on a database of 2,000 images are described. It is shown that the watermark is robust to rotation, scale and translation. In addition, the algorithm shows resistance to cropping. }, author = {Lin,C.Y. and Wu,M. and Bloom,J.A. and Cox,I.J. and Miller,M.L. and Lui,Y.M.} } @article {11968, title = {Structure from motion: Beyond the epipolar constraint}, journal = {International Journal of Computer Vision}, volume = {37}, year = {2000}, month = {2000///}, pages = {231 - 258}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {12323, title = {Systematic consolidation of input and output buffers in synchronous dataflow specifications}, booktitle = {Signal Processing Systems, 2000. SiPS 2000. 2000 IEEE Workshop on}, year = {2000}, month = {2000///}, pages = {673 - 682}, author = {Murthy,P. K and Bhattacharyya, Shuvra S.} } @conference {14765, title = {Using hardware performance monitors to isolate memory bottlenecks}, booktitle = {Proceedings of the 2000 ACM/IEEE conference on Supercomputing (CDROM)}, year = {2000}, month = {2000///}, pages = {40 - 40}, author = {Buck, B. R and Hollingsworth, Jeffrey K} } @article {16159, title = {Vehicle Speed Information Displays for Public Websites A Survey of User Preferences}, journal = {Technical Reports from UMIACS}, year = {2000}, month = {2000/10/09/}, abstract = {The paper reports on a study comparing alternative presentations offreeway speed data on maps. The goal of the study was to inform the design of displays of real time speed data over the Internet to the general public. Subjects were presented with a series of displays and asked to rate their preferences. We looked at different choices of color (3 colors, 6 colors or a continuous range), and proposed line, sensor, and segment representations of the speed data. We also collected feedback on more complex displays such as comparison between current and "normal" speeds, and a chart of speed variation over a period of time at given locations. (Also cross-referenced as HCIL-TR-2000-23) (Also cross-referenced as UMIACS-TR-2000-73) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1109}, author = {Plaisant, Catherine and Bhamidipati,Phanikumar} } @conference {16455, title = {Web Query Optimizer}, booktitle = {Data Engineering, International Conference on}, year = {2000}, month = {2000///}, pages = {661 - 661}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {We demonstrate a Web Query Optimizer (WQO) within an architecture of mediators and wrappers, for WebSources of limited capability in a wide area environment. The WQO has several innovative features including a CBR (capability based rewriting) Tool, an enhanced randomized relational optimizer extended to a Web environment, and a WebWrapper cost model that can provide relevant metrics for accessing WebSources. The prototype has been tested against a number of WebSources.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDE.2000.839484}, author = {Zadorozhny,Vladimir and Bright,Laura and Raschid, Louiqa and Urhan,Tolga and Vidal,Maria Esther} } @article {14874, title = {3-d to 2-d pose determination with regions}, journal = {International Journal of Computer Vision}, volume = {34}, year = {1999}, month = {1999///}, pages = {123 - 145}, abstract = {This paper presents a novel approach to parts-based object recognition in the presence of occlusion. We focus on the problem of determining the pose of a 3-D object from a single 2-D image when convex parts of the object have been matched to corresponding regions in the image. We consider three types of occlusions: self-occlusion, occlusions whose locus is identified in the image, and completely arbitrary occlusions. We show that in the first two cases this is a convex optimization problem, derive efficient algorithms, and characterize their performance. For the last case, we prove that the problem of finding valid poses is computationally hard, but provide an efficient, approximate algorithm. This work generalizes our previous work on region-based object recognition, which focused on the case of planar models.}, doi = {10.1023/A:1008135819955}, author = {Jacobs, David W. and Basri,R.} } @conference {15376, title = {Advances in spherical harmonic device modeling: calibration and nanoscale electron dynamics}, booktitle = {Simulation of Semiconductor Processes and Devices, 1999. SISPAD {\textquoteright}99. 1999 International Conference on}, year = {1999}, month = {1999///}, pages = {167 - 170}, abstract = {Improvements in the Spherical Harmonic (SH) method for solving Boltzmann Transport Equation (BTE) are presented. The simulation results provide the same physical detail as analytical band Monte Carlo (MC) calculations, and are obtained approximately a thousand times faster. A new physical model for surface scattering has also been developed. As a result, the SHBTE model achieves calibration for a complete process of I-V characteristics and substrate current consistently for the first time}, keywords = {Boltzmann, characteristics;SHBTE, current;surface, device, dynamics;spherical, electron, equation;calibration;semiconductor, equation;I-V, harmonic, model;substrate, models;surface, scattering;, scattering;Boltzmann, simulation;calibration;nanoscale, transport}, doi = {10.1109/SISPAD.1999.799287}, author = {Lin,Chung-Kai and Goldsman,N. and Mayergoyz, Issak D and Aronowitz,S. and Belova,N.} } @conference {17553, title = {Application-layer broker for scalable Internet services with resource reservation}, booktitle = {Proceedings of the seventh ACM international conference on Multimedia (Part 2)}, series = {MULTIMEDIA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {103 - 106}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-239-5}, doi = {10.1145/319878.319906}, url = {http://doi.acm.org/10.1145/319878.319906}, author = {Bai,Ping and Prabhakaran,B. and Srinivasan, Aravind} } @conference {18666, title = {Building dependable distributed applications using AQUA}, year = {1999}, month = {1999///}, pages = {189 - 196}, abstract = {Building dependable distributed systems using ad hoc methods is a challenging task. Without proper support, an application programmer must face the daunting requirement of having to provide fault tolerance at the application level, in addition to dealing with the complexities of the distributed application itself. This approach requires a deep knowledge of fault tolerance on the part of the application designer, and has a high implementation cost. What is needed is a systematic approach to providing dependability to distributed applications. Proteus, part of the AQuA architecture, fills this need and provides facilities to make a standard distributed CORBA application dependable, with minimal changes to an application. Furthermore, it permits applications to specify, either directly or via the Quality Objects (QuO) infrastructure, the level of dependability they expect of a remote object, and will attempt to configure the system to achieve the requested dependability level. Our previous papers have focused on the architecture and implementation of Proteus. This paper describes how to construct dependable applications using the AQuA architecture, by describing the interface that a programmer is presented with and the graphical monitoring facilities that it provides}, keywords = {ad hoc methods, application programmer, AQuA, complexities, computational complexity, dependable distributed applications, distributed CORBA application, distributed object management, Fault tolerance, fault tolerant computing, proteus}, doi = {10.1109/HASE.1999.809494}, author = {Ren,J. and Michel Cukier and Rubel,P. and Sanders,W. H. and Bakken,D. E. and Karr,D. A.} } @conference {18639, title = {Building dependable distributed objects with the AQuA architecture}, year = {1999}, month = {1999///}, pages = {17 - 18}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.16.2819\&rep=rep1\&type=pdf}, author = {Michel Cukier and Ren,J. and Rubel,P. and Bakken,D. E. and Karr,D. A.} } @conference {13938, title = {Designing PETS: a personal electronic teller of stories}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: the CHI is the limit}, series = {CHI {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {326 - 329}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We have begun the development of a new robotic pet that cansupport children in the storytelling process. Children can build their own pet by snapping together the modular animal parts of the PETS robot. After their pet is built, children can tell stories using the My Pets software. These stories can then be acted out by their robotic pet. This video paper describes the motivation for this research and the design process of our intergenerational design team in building the first PETS prototypes. We will discuss our progress to date and our focus for the future. }, keywords = {children, cooperative inquiry, design techniques, educational applications, intergenerational design team, PETS, ROBOTICS}, isbn = {0-201-48559-1}, doi = {10.1145/302979.303103}, url = {http://doi.acm.org/10.1145/302979.303103}, author = {Druin, Allison and Montemayor,Jamie and Hendler,Jim and McAlister,Britt and Boltman,Angela and Fiterman,Eric and Plaisant,Aurelie and Kruskal,Alex and Olsen,Hanne and Revett,Isabella and Schwenn,Thomas Plaisant and Sumida,Lauren and Wagner,Rebecca} } @conference {12199, title = {Does animation help users build mental maps of spatial information?}, booktitle = {Information Visualization, 1999.(Info Vis{\textquoteright} 99) Proceedings. 1999 IEEE Symposium on}, year = {1999}, month = {1999///}, pages = {28 - 35}, author = {Bederson, Benjamin B. and Boltman,A.} } @conference {12184, title = {Does zooming improve image browsing}, booktitle = {Proceedings of the fourth ACM conference on Digital libraries}, year = {1999}, month = {1999///}, pages = {130 - 137}, author = {Tammara,T.A.C. and Bederson, Benjamin B.} } @conference {16259, title = {Efficient perspective-accurate silhouette computation}, booktitle = {Proceedings of the fifteenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {417 - 418}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-068-6}, doi = {10.1145/304893.304999}, url = {http://doi.acm.org/10.1145/304893.304999}, author = {Barequet,G. and Duncan,C. A and Goodrich,M. T and Kumar,S. and Pop, Mihai} } @conference {14927, title = {A hierarchical data archiving and processing system to generate custom tailored products from AVHRR data}, booktitle = {Geoscience and Remote Sensing Symposium, 1999. IGARSS {\textquoteright}99 Proceedings. IEEE 1999 International}, volume = {5}, year = {1999}, month = {1999///}, pages = {2374 -2376 vol.5 - 2374 -2376 vol.5}, abstract = {A novel indexing scheme is described to catalogue satellite data on a pixel basis. The objective of this research is to develop an efficient methodology to archive, retrieve and process satellite data, so that data products can be generated to meet the specific needs of individual scientists. When requesting data, users can specify the spatial and temporal resolution, geographic projection, choice of atmospheric correction, and the data selection methodology. The data processing is done in two stages. Satellite data is calibrated, navigated and quality flags are appended in the initial processing. This processed data is then indexed and stored. Secondary processing such as atmospheric correction and projection are done after a user requests the data to create custom made products. By dividing the processing in to two stages saves time, since the basic processing tasks such as navigation and calibration which are common to all requests are not repeated when different users request satellite data. The indexing scheme described can be extended to allow fusion of data sets from different sensors}, keywords = {archiving;image, AVHRR;GIS;PACS;custom, data, image;land, image;remote, mapping;, mapping;PACS;geophysical, measurement, PROCESSING, processing;geophysical, product;data, remote, scheme;infrared, sensing;optical, sensing;terrain, signal, surface;multispectral, system;indexing, tailored, technique;hierarchical, techniques;remote}, doi = {10.1109/IGARSS.1999.771514}, author = {Kalluri, SNV and Zhang,Z. and JaJa, Joseph F. and Bader, D.A. and Song,H. and El Saleous,N. and Vermote,E. and Townshend,J.R.G.} } @article {17209, title = {Human-centered computing, online communities, and virtual environments}, journal = {IEEE Computer Graphics and Applications}, volume = {19}, year = {1999}, month = {1999/12//Nov}, pages = {70 - 74}, abstract = {This report summarizes results of the first EC/NSF joint Advanced Research Workshop, which identified key research challenges and opportunities in information technology. The group agreed that the first joint research workshop should concentrate on the themes of human-centered computing and VEs. Human-centered computing is perceived as an area of strategic importance because of the move towards greater decentralization and decomposition in the location and provision of computation. The area of VEs is one where increased collaboration should speed progress in solving some of the more intractable problems in building effective applications}, keywords = {Books, Collaboration, Collaborative work, Conferences, EC/NSF joint Advanced Research Workshop, Feeds, Human computer interaction, human-centered computing, Internet, Joining materials, Laboratories, Online communities, Research initiatives, USA Councils, User interfaces, Virtual environment, virtual environments, Virtual reality}, isbn = {0272-1716}, doi = {10.1109/38.799742}, author = {Brown,J. R and van Dam,A. and Earnshaw,R. and Encarnacao,J. and Guedj,R. and Preece,J. and Shneiderman, Ben and Vince,J.} } @conference {11986, title = {Independent motion: the importance of history}, booktitle = {Computer Vision and Pattern Recognition, 1999. IEEE Computer Society Conference on.}, volume = {2}, year = {1999}, month = {1999///}, pages = {97 Vol. 2 - 97 Vol. 2}, publisher = {IEEE}, organization = {IEEE}, abstract = {We consider a problem central in aerial visual surveillance applications-detection and tracking of small, independently moving objects in long and noisy video sequences. We directly use spatiotemporal image intensity gradient measurements to compute an exact model of background motion. This allows the creation of accurate mosaics over many frames and the definition of a constraint violation function which acts as an indication of independent motion. A novel temporal integration method maintains confidence measures over long subsequences without computing the optic flow, requiring object models, or using a Kalman filler. The mosaic acts as a stable feature frame, allowing precise localization of the independently moving objects. We present a statistical analysis of the effects of image noise on the constraint violation measure and find a good match between the predicted probability distribution function and the measured sample frequencies in a test sequence}, keywords = {aerial visual surveillance, background image, Fluid flow measurement, Frequency measurement, History, Motion detection, Motion estimation, Motion measurement, Noise measurement, Optical computing, Optical noise, spatiotemporal image intensity gradient measurements, Spatiotemporal phenomena, Surveillance, Video sequences}, isbn = {0-7695-0149-4}, doi = {10.1109/CVPR.1999.784614}, author = {Pless, R. and Brodsky, T. and Aloimonos, J.} } @article {16165, title = {Interface and data architecture for query preview in networked information systems}, journal = {ACM Trans. Inf. Syst.}, volume = {17}, year = {1999}, month = {1999/07//}, pages = {320 - 341}, abstract = {There are numerous problems associated with formulating queries onnetworked information systems. These include increased data volume and complexity, accompanied by slow network access. This article proposes a new approach to a network query user interfaces that consists of two phases: query preview and query refinement. This new approach is based on the concepts of dynamic queries and query previews, which guides users in rapidly and dynamically eliminating undesired records, reducing the data volume to a manageable size, and refining queries locally before submission over a network. Examples of two applications are given: a Restaurant Finder and a prototype for NASA{\textquoteright}s Earth Observing Systems Data Information Systems (EOSDIS). Data architecture is discussed, and user feedback is presented. }, keywords = {direct manipulation, dynamic query, EOSDIS, graphical user interface, query preview, query refinement, science data}, isbn = {1046-8188}, doi = {10.1145/314516.314522}, url = {http://doi.acm.org/10.1145/314516.314522}, author = {Plaisant, Catherine and Shneiderman, Ben and Doan,Khoa and Bruns,Tom} } @article {13820, title = {Machine Translation}, journal = {Multilingual Information Management: Current Levels and Future Abilities}, year = {1999}, month = {1999///}, pages = {18 - 18}, author = {Bel,N. and Dorr, Bonnie J and Hovy,E. and Knight,K. and Iida,H. and Boitet,C. and Maegaard,B. and Wilks,Y.} } @article {16354, title = {Model-checking concurrent systems with unbounded integer variables: symbolic representations, approximations, and experimental results}, journal = {ACM Transactions on Programming Languages and SystemsACM Trans. Program. Lang. Syst.}, volume = {21}, year = {1999}, month = {1999/07//}, pages = {747 - 789}, isbn = {01640925}, doi = {10.1145/325478.325480}, url = {http://dl.acm.org/citation.cfm?id=325480}, author = {Bultan,Tevfik and Gerber,Richard and Pugh, William} } @conference {12041, title = {Motion Segmentation: A Synergistic Approach}, booktitle = {Computer Vision and Pattern Recognition, IEEE Computer Society Conference on}, volume = {2}, year = {1999}, month = {1999///}, pages = {2226 - 2226}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Since estimation of camera motion requires knowledge of independent motion, and moving object detection and localization requires knowledge about the camera motion, the two problems of motion estimation and segmentation need to be solved together in a synergistic manner. This paper provides an approach to treating both these problems simultaneously. The technique introduced here is based on a novel concept, {\textquoteleft}{\textquoteleft}scene ruggedness,{\textquoteright}{\textquoteright} which parameterizes the variation in estimated scene depth with the error in the underlying three-dimensional (3D) motion. The idea is that incorrect 3D motion estimates cause distortions in the estimated depth map, and as a result smooth scene patches are computed as rugged surfaces. The correct 3D motion can be distinguished, as it does not cause any distortion and thus gives rise to the background patches with the least depth variation between depth discontinuities, with the locations corresponding to independent motion being rugged. The algorithm presented employs a binocular observer whose nature is exploited in the extraction of depth discontinuities, a step that facilitates the overall procedure, but the technique can be extended to a monocular observer in a variety of ways.}, keywords = {epipolar minimization, independent motion detection, Motion analysis}, doi = {http://doi.ieeecomputersociety.org/10.1109/CVPR.1999.784633}, author = {Ferm{\"u}ller, Cornelia and Brodsky, Tomas and Aloimonos, J.} } @inbook {14712, title = {Network Programming Using PLAN}, booktitle = {Internet Programming LanguagesInternet Programming Languages}, series = {Lecture Notes in Computer Science}, volume = {1686}, year = {1999}, month = {1999///}, pages = {127 - 143}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present here a methodology for programming active networks in the environment defined by our new language PLAN (Packet Language for Active Networks). This environment presumes a two-level architecture consisting of: 1. active packets carrying PLAN code; and 2. downloadable, node-resident services written in more general-purpose languages. We present several examples which illustrate how these two features can be combined to implement various network functions.}, isbn = {978-3-540-66673-8}, url = {http://dx.doi.org/10.1007/3-540-47959-7_7}, author = {Hicks, Michael W. and Kakkar,Pankaj and Moore,Jonathan and Gunter,Carl and Nettles,Scott}, editor = {Bal,Henri and Belkhouche,Boumediene and Cardelli,Luca} } @article {17855, title = {Object-relational queries into multidimensional databases with the active data repository}, journal = {Parallel Processing Letters}, volume = {9}, year = {1999}, month = {1999///}, pages = {173 - 195}, author = {Ferreira,R. and Kurc, T. and Beynon, M. and Chang,C. and Sussman, Alan and Saltz,J. H} } @article {18409, title = {OSMA Software Program: Domain Analysis Guidebook}, journal = {Technical Reports from UMIACS, UMIACS-TR-99-16}, year = {1999}, month = {1999/03/31/}, abstract = {Domain analysis is the process of identifying and organizing knowledge abouta class of problems. This guidebook presents a method of performing experience domain analysis in software development organizations. The purpose of the guidebook is to facilitate the reader in characterizing two given development environments, applying domain analysis to model each, and then applying an evaluation process, based upon the Goal/Metric/Paradigm, to transfer a given development technology from one of the environments to the other. This guidebook describes this process and gives an example of its use within NASA. Also cross-referenced as UMIACS-TR-99-16 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1000}, author = {Basili, Victor R. and Seaman,Carolyn and Tesoriero,Roseanne and Zelkowitz, Marvin V} } @book {14913, title = {Perceptual Organization in Computer Vision}, year = {1999}, month = {1999///}, publisher = {Academic Press}, organization = {Academic Press}, author = {Boyer,K.L. and Sarkar,S. and Feldman,J. and Granlund,G. and Horaud,R. and Hutchinson,S. and Jacobs, David W. and Kak,A. and Lowe,D. and Malik,J.} } @conference {17863, title = {Performance impact of proxies in data intensive client-server applications}, booktitle = {Proceedings of the 13th international conference on Supercomputing}, year = {1999}, month = {1999///}, pages = {383 - 390}, author = {Beynon,M. D and Sussman, Alan and Saltz, J.} } @article {17322, title = {Perspective-based Usability Inspection: An Empirical Validation of Efficacy}, journal = {Empirical Software Engineering}, volume = {4}, year = {1999}, month = {1999///}, pages = {43 - 69}, abstract = {Inspection is a fundamental means of achieving software usability. Past research showed that the current usability inspection techniques were rather ineffective. We developed perspective-based usability inspection, which divides the large variety of usability issues along different perspectives and focuses each inspection session on one perspective. We conducted a controlled experiment to study its effectiveness, using a post-test only control group experimental design, with 24 professionals as subjects. The control group used heuristic evaluation, which is the most popular technique for usability inspection. The experimental design and the results are presented, which show that inspectors applying perspective-based inspection not only found more usability problems related to their assigned perspectives, but also found more overall problems. Perspective-based inspection was shown to be more effective for the aggregated results of multiple inspectors, finding about 30\% more usability problems for 3 inspectors. A management implication of this study is that assigning inspectors more specific responsibilities leads to higher performance. Internal and external threats to validity are discussed to help better interpret the results and to guide future empirical studies.}, isbn = {1382-3256}, url = {http://dx.doi.org/10.1023/A:1009803214692}, author = {Zhang,Zhijun and Basili, Victor R. and Shneiderman, Ben} } @article {12790, title = {A practical approach to implementing real-time semantics}, journal = {Annals of Software Engineering}, volume = {7}, year = {1999}, month = {1999///}, pages = {127 - 155}, author = {Bhat,G. and Cleaveland, Rance and L\{\"u}ttgen,G.} } @conference {18689, title = {Proteus: a flexible infrastructure to implement adaptive fault tolerance in AQuA}, year = {1999}, month = {1999/11//}, pages = {149 - 168}, abstract = {Building dependable distributed systems from commercial off-the-shelf components is of growing practical importance. For both cost and production reasons, there is interest in approaches and architectures that facilitate building such systems. The AQuA architecture is one such approach; its goal is to provide adaptive fault tolerance to CORBA applications by replicating objects, providing a high-level method for applications to specify their desired dependability, and providing a dependability manager that attempts to reconfigure a system at runtime so that dependability requests are satisfied. This paper describes how dependability is provided in AQuA. In particular it describes Proteus, the part of AQuA that dynamically manages replicated distributed objects to make them dependable. Given a dependability request, Proteus chooses a fault tolerance approach and reconfigures the system to try to meet the request. The infrastructure of Proteus is described in this paper, along with its use in implementing active replication and a simple dependability policy}, keywords = {adaptive fault tolerance, AQuA, commercial off-the-shelf components, CORBA applications, cost, dependable distributed systems, distributed object management, object replication, proteus, reconfigurable architectures, Runtime, Software architecture, software fault tolerance}, doi = {10.1109/DCFTS.1999.814294}, author = {Sabnis,C. and Michel Cukier and Ren,J. and Rubel,P. and Sanders,W. H. and Bakken,D. E. and Karr,D.} } @conference {16167, title = {Refining query previews techniques for data with multivalued attributes: the case of NASA EOSDIS}, booktitle = {Research and Technology Advances in Digital Libraries, 1999. ADL {\textquoteright}99. Proceedings. IEEE Forum on}, year = {1999}, month = {1999///}, pages = {50 - 59}, abstract = {Query Previews allow users to rapidly gain an understanding of the content and scope of a digital data collection. These previews present overviews of abstracted metadata, enabling users to rapidly and dynamically avoid undesired data. We present our recent work on developing query previews for a variety of NASA EOSDIS situations. We focus on approaches that successfully address the challenge of multi-valued attribute data. Memory requirements and processing time associated with running these new solutions remain independent of the number of records in the dataset. We describe two techniques and their respective prototypes used to preview NASA Earth science data}, keywords = {attribute, attributes;processing, collection;memory, computing;meta, data, data;abstracted, data;digital, data;multivalued, data;query, Earth, EOSDIS;NASA, libraries;geophysics, metadata;dataset;digital, NASA, previews, processing;, requirements;multi-valued, Science, techniques;undesired, time;query}, doi = {10.1109/ADL.1999.777690}, author = {Plaisant, Catherine and Venkatraman,M. and Ngamkajorwiwat,K. and Barth,R. and Harberts,B. and Feng,Wenlan} } @article {14911, title = {The role of convexity in perceptual completion: beyond good continuation}, journal = {Vision Research}, volume = {39}, year = {1999}, month = {1999/12//}, pages = {4244 - 4257}, abstract = {Since the seminal work of the Gestalt psychologists, there has been great interest in understanding what factors determine the perceptual organization of images. While the Gestaltists demonstrated the significance of grouping cues such as similarity, proximity and good continuation, it has not been well understood whether their catalog of grouping cues is complete {\textemdash} in part due to the paucity of effective methodologies for examining the significance of various grouping cues. We describe a novel, objective method to study perceptual grouping of planar regions separated by an occluder. We demonstrate that the stronger the grouping between two such regions, the harder it will be to resolve their relative stereoscopic depth. We use this new method to call into question many existing theories of perceptual completion (Ullman, S. (1976). Biological Cybernetics, 25, 1{\textendash}6; Shashua, A., \& Ullman, S. (1988). 2nd International Conference on Computer Vision (pp. 321{\textendash}327); Parent, P., \& Zucker, S. (1989). IEEE Transactions on Pattern Analysis and Machine Intelligence, 11, 823{\textendash}839; Kellman, P. J., \& Shipley, T. F. (1991). Cognitive psychology, Liveright, New York; Heitger, R., \& von der Heydt, R. (1993). A computational model of neural contour processing, figure-ground segregation and illusory contours. In Internal Conference Computer Vision (pp. 32{\textendash}40); Mumford, D. (1994). Algebraic geometry and its applications, Springer, New York; Williams, L. R., \& Jacobs, D .W. (1997). Neural Computation, 9, 837{\textendash}858) that are based on Gestalt grouping cues by demonstrating that convexity plays a strong role in perceptual completion. In some cases convexity dominates the effects of the well known Gestalt cue of good continuation. While convexity has been known to play a role in figure/ground segmentation (Rubin, 1927; Kanizsa \& Gerbino, 1976), this is the first demonstration of its importance in perceptual completion.}, keywords = {Amodal completion, Convexity, Good continuation, Grouping, Stereoscopic depth}, isbn = {0042-6989}, doi = {10.1016/S0042-6989(99)00141-8}, url = {http://www.sciencedirect.com/science/article/pii/S0042698999001418}, author = {Liu,Zili and Jacobs, David W. and Basri,Ronen} } @conference {18158, title = {A rotation, scale and translation resilient public watermark}, booktitle = {Acoustics, Speech, and Signal Processing, 1999. Proceedings., 1999 IEEE International Conference on}, volume = {4}, year = {1999}, month = {1999/03//}, pages = {2065 vol.4 - 2065 vol.4}, abstract = {Summary form only given. Watermarking algorithms that are robust to the common geometric transformations of rotation, scale and translation (RST) have been reported for cases in which the original unwatermarked content is available at the detector so as to allow the transformations to be inverted. However, for public watermarks the problem is significantly more difficult since there is no original content to register with. Two classes of solution have been proposed. The first embeds a registration pattern into the content while the second seeks to apply detection methods that are invariant to these geometric transformations. This paper describes a public watermarking method which is invariant (or bares a simple relation) to the common geometric transforms of rotation, scale, and translation. It is based on the Fourier-Mellin transform which has previously been suggested. We extend this work, using a variation based on the Radon transform. The watermark is inserted into a projection of the image. The properties of this projection are such that RST transforms produce simple or no effects on the projection waveform. When a watermark is inserted into a projection, the signal must eventually be back projected to the original image dimensions. This is a one to many mapping that allows for considerable flexibility in the watermark insertion process. We highlight some theoretical and practical issues that affect the implementation of an RST invariant watermark. Finally, we describe preliminary experimental results}, keywords = {algorithms;Fourier, coding;, coding;image, data;transform, dimensions;projection, Fourier-Mellin, image, invariant, methods;detector;experimental, of, pattern;rotation, projection;mapping;original, public, registration;security, resilient, results;geometric, transform;detection, transform;RST, transformations;image, transforms;image, transforms;Radon, watermark;RST, watermark;scale, watermark;translation, watermark;watermarking, waveform;registration}, doi = {10.1109/ICASSP.1999.758337}, author = {Wu,M. and Miller,M.L. and Bloom,J.A. and Cox,I.J.} } @conference {17529, title = {Running EveryWare on the computational grid}, booktitle = {Proceedings of the 1999 ACM/IEEE conference on Supercomputing (CDROM)}, year = {1999}, month = {1999///}, pages = {6{\textendash}es - 6{\textendash}es}, author = {Wolski,R. and Brevik,J. and Krintz,C. and Obertelli,G. and Spring, Neil and Su,A.} } @conference {12054, title = {Shape from Video}, booktitle = {Computer Vision and Pattern Recognition, IEEE Computer Society Conference on}, volume = {2}, year = {1999}, month = {1999///}, pages = {2146 - 2146}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper presents a novel technique for recovering the shape of a static scene from a video sequence due to a rigidly moving camera. The solution procedure consists of two stages. In the first stage, the rigid motion of the camera at each instant in time is recovered. This provides the transformation between successive viewing positions. The solution is achieved through new constraints which relate 3D motion and shape directly to the image derivatives. These constraints allow the combination of the processes of 3D motion estimation and segmentation by exploiting the geometry and statistics inherent in the data. In the second stage the scene surfaces are reconstructed through an optimization procedure which utilizes data from all the frames of a short video sequence. A number of experimental results demonstrate the potential of the approach.}, keywords = {epipolar minimization, model extraction, Motion analysis, vision and graphics}, doi = {http://doi.ieeecomputersociety.org/10.1109/CVPR.1999.784622}, author = {Brodsky, Tomas and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {18738, title = {Sheet metal bending: generating shared setups}, journal = {TRANSACTIONS-AMERICAN SOCIETY OF MECHANICAL ENGINEERS JOURNAL OF MANUFACTURING SCIENCE AND ENGINEERING}, volume = {121}, year = {1999}, month = {1999///}, pages = {689 - 694}, abstract = {Contemporary process planners for sheet metal bending solve the process planning problemfor individual parts. Quite often, many different parts can be produced on shared setups. However, plans generated by current process planning systems fail to exploit this commonality between setups and try to generate optimal setups for individual parts. In this paper, we present an algorithm for multi-part setup planning for sheet metal bending. This algorithm takes a set of parts and operation sequences for these parts, and tries to find a shared setup plan that can work for every part in the set. Setup changes constitute a major portion of the production time in batch production environments. Therefore, multi-part setup planning techniques can be used to significantly cut down the total number of setups and increase the overall through-put. }, url = {http://terpconnect.umd.edu/~skgupta/Publication/JMSE99_Gupta_draft.pdf}, author = {Gupta,S.K. and Bourne,D. A.} } @article {15024, title = {Simple: A Methodology for Programming High Performance Algorithms on Clusters of Symmetric Multiprocessors (SMPs)}, journal = {Journal of Parallel and Distributed Computing}, volume = {58}, year = {1999}, month = {1999/07//}, pages = {92 - 108}, abstract = {We describe a methodology for developing high performance programs running on clusters of SMP nodes. The SMP cluster programming methodology is based on a small prototype kernel (Simple) of collective communication primitives that make efficient use of the hybrid shared and message-passing environment. We illustrate the power of our methodology by presenting experimental results for sorting integers, two-dimensional fast Fourier transforms (FFT), and constraint-satisfied searching. Our testbed is a cluster of DEC AlphaServer 2100 4/275 nodes interconnected by an ATM switch.}, keywords = {cluster computing, communication primitives, experimental parallel algorithms, message passing (MPI), Parallel algorithms, parallel performance, shared memory, symmetric multiprocessors (SMP)}, isbn = {0743-7315}, doi = {10.1006/jpdc.1999.1541}, url = {http://www.sciencedirect.com/science/article/pii/S0743731599915411}, author = {Bader,David A. and JaJa, Joseph F.} } @conference {13930, title = {Single display groupware: a model for co-present collaboration}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: the CHI is the limit}, year = {1999}, month = {1999///}, pages = {286 - 293}, author = {Stewart,J. and Bederson, Benjamin B. and Druin, Allison} } @inbook {13716, title = {A Survey of Current Paradigms in Machine Translation}, booktitle = {Advances in Computers}, volume = {Volume 49}, year = {1999}, month = {1999///}, pages = {1 - 68}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {This paper is a survey of the current machine translation research in the US, Europe and Japan. A short history of machine translation is presented first, followed by an overview of the current research work. Representative examples of a wide range of different approaches adopted by machine translation researchers are presented. These are described in detail along with a discussion of the practicalities of scaling up these approaches for operational environments. In support of this discussion, issues in, and techniques for, evaluating machine translation systems are addressed.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S006524580860282X}, author = {Dorr, Bonnie J and Jordan,Pamela W. and Benoit,John W.}, editor = {Zelkowitz, Marvin V} } @article {12321, title = {Synthesis of embedded software from synchronous dataflow specifications}, journal = {The Journal of VLSI Signal Processing}, volume = {21}, year = {1999}, month = {1999///}, pages = {151 - 166}, author = {Bhattacharyya, Shuvra S. and Murthy,P. K and Lee,E. A} } @article {17398, title = {TennisViewer: A Browser for Competition Trees}, journal = {Readings in information visualization: using vision to think}, year = {1999}, month = {1999///}, pages = {149 - 149}, author = {Johnson,B. and Shneiderman, Ben and Baker,MJ and Eick,SG} } @article {12845, title = {A Theory of Efficiency for Markovian Processes}, journal = {University of Bologna}, year = {1999}, month = {1999///}, author = {Bernardo,M. and Cleaveland, Rance} } @article {18149, title = {XMT-M: A Scalable Decentralized Processor}, volume = {UMIACS-TR-99-55}, year = {1999}, month = {1999/10/09/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {A defining challenge for research in computer science and engineering hasbeen the ongoing quest for reducing the completion time of a single computation task. Even outside the parallel processing communities, there is little doubt that the key to further progress in this quest is to do parallel processing of some kind. A recently proposed parallel processing framework that spans the entire spectrum from (parallel) algorithms to architecture to implementation is the explicit multi-threading (XMT) framework. This framework provides: (i) simple and natural parallel algorithms for essentially every general-purpose application, including notoriously difficult irregular integer applications, and (ii) a multi-threaded programming model for these algorithms which allows an {\textquoteleft}{\textquoteleft}independence-of-order{\textquoteright}{\textquoteright} semantics: every thread can proceed at its own speed, independent of other concurrent threads. To the extent possible, the XMT framework uses established ideas in parallel processing. This paper presents XMT-M, a microarchitecture implementation of the XMT model that is possible with current technology. XMT-M offers an engineering design point that addresses four concerns: buildability, programmability, performance, and scalability. The XMT-M hardware is geared to execute multiple threads in parallel on a single chip: relying on very few new gadgets, it can execute parallel threads without busy-waits! Existing code can be run on XMT-M as a single thread without any modifications, thereby providing backward compatibility for commercial acceptance. Simulation-based studies of XMT-M demonstrate considerable improvements in performance relative to the best serial processor even for small, and therefore practical, input sizes. (Also cross-referenced as UMIACS-TR-99-55) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1030}, author = {Berkovich,Efraim and Nuzman,Joseph and Franklin,Manoj and Jacob,Bruce and Vishkin, Uzi} } @conference {18662, title = {AQuA: an adaptive architecture that provides dependable distributed objects}, booktitle = {Seventeenth IEEE Symposium on Reliable Distributed Systems}, year = {1998}, month = {1998/10//}, pages = {245 - 253}, abstract = {Dependable distributed systems are difficult to build. This is particularly true if they have dependability requirements that change during the execution of an application, and are built with commercial off-the-shelf hardware. In that case, fault tolerance must be achieved using middleware software, and mechanisms must be provided to communicate the dependability requirements of a distributed application to the system and to adapt the system{\textquoteright}s configuration to try to achieve the desired dependability. The AQuA architecture allows distributed applications to request a desired level of availability using the Quality Objects (QuO) framework and includes a dependability manager that attempts to meet requested availability levels by configuring the system in response to outside requests and changes in system resources due to faults. The AQuA architecture uses the QuO runtime to process and invoke availability requests, the Proteus dependability manager to configure the system in response to faults and availability requests, and the Ensemble protocol stack to provide group communication services. Furthermore, a CORBA interface is provided to application objects using the AQuA gateway. The gateway provides a mechanism to translate between process-level communication, as supported by Ensemble, and IIOP messages, understood by Object Request Brokers. Both active and passive replication are supported, and the replication type to use is chosen based on the performance and dependability requirements of particular distributed applications}, keywords = {adaptive architecture, AQuA, availability requests, client-server systems, commercial off-the-shelf hardware, CORBA, dependability manager, dependability requirements, dependable distributed objects, distributed object management, Ensemble protocol stack, Fault tolerance, group communication services, middleware software, Object Request Brokers, process-level communication, proteus, Quality Objects, replication, software fault tolerance, Software quality}, doi = {10.1109/RELDIS.1998.740506}, author = {Cukier, Michel and Ren,J. and Sabnis,C. and Henke,D. and Pistole,J. and Sanders,W. H. and Bakken,D. E. and Berman,M.E. and Karr,D. A. and Schantz,R.E.} } @inbook {14202, title = {Beyond the Epipolar Constraint: Integrating 3D Motion and Structure Estimation}, booktitle = {3D Structure from Multiple Images of Large-Scale Environments3D Structure from Multiple Images of Large-Scale Environments}, series = {Lecture Notes in Computer Science}, volume = {1506}, year = {1998}, month = {1998///}, pages = {109 - 123}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper develops a novel solution to the problem of recovering the structure of a scene given an uncalibrated video sequence depicting the scene. The essence of the technique lies in a method for recovering the rigid transformation between the different views in the image sequence. Knowledge of this 3D motion allows for self-calibration and for subsequent recovery of 3D structure. The introduced method breaks away from applying only the traditionally used epipolar constraint and introduces a new constraint based on the interaction between 3D motion and shape. Up to now, structure from motion algorithms proceeded in two well defined steps, where the first and most important step is recovering the rigid transformation between two views, and the subsequent step is using this transformation to compute the structure of the scene in view. Here both aforementioned steps are accomplished in a synergistic manner. Existing approaches to 3D motion estimation are mostly based on the use of optic flow which however poses a problem at the locations of depth discontinuities. If we knew where depth discontinuities were, we could (using a multitude of approaches based on smoothness constraints) estimate accurately flow values for image patches corresponding to smooth scene patches; but to know the discontinuities requires solving the structure from motion problem first. In the past this dilemma has been addressed by improving the estimation of flow through sophisticated optimization techniques, whose performance often depends on the scene in view. In this paper the main idea is based on the interaction between 3D motion and shape which allows us to estimate the 3D motion while at the same time segmenting the scene. If we use a wrong 3D motion estimate to compute depth, then we obtain a distorted version of the depth function. The distortion, however, is such that the worse the motion estimate, the more likely we are to obtain depth estimates that are locally unsmooth, i.e., they vary more than the correct ones. Since local variability of depth is due either to the existence of a discontinuity or to a wrong 3D motion estimate, being able to differentiate between these two cases provides the correct motion, which yields the {\textquotedblleft}smoothest{\textquotedblright} estimated depth as well as the image locations of scene discontinuities. Although no optic flow values are computed, we show that our algorithm is very much related to minimizing the epipolar constraint when the scene in view is smooth. When however the imaged scene is not smooth, the introduced constraint has in general different properties from the epipolar constraint and we present experimental results with real sequences where it performs better.}, isbn = {978-3-540-65310-3}, url = {http://dx.doi.org/10.1007/3-540-49437-5_8}, author = {Brodsk{\'y},Tom{\'a}{\v s} and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Koch,Reinhard and Van Gool,Luc} } @conference {14842, title = {Clustering appearances of 3D objects}, booktitle = {Computer Vision and Pattern Recognition, 1998. Proceedings. 1998 IEEE Computer Society Conference on}, year = {1998}, month = {1998/06//}, pages = {414 - 420}, abstract = {We introduce a method for unsupervised clustering of images of 3D objects. Our method examines the space of all images and partitions the images into sets that form smooth and parallel surfaces in this space. It further uses sequences of images to obtain more reliable clustering. Finally, since our method relies on a non-Euclidean similarity measure we introduce algebraic techniques for estimating local properties of these surfaces without first embedding the images in a Euclidean space. We demonstrate our method by applying it to a large database of images}, keywords = {3D, clustering;image, clustering;sequences, images;unsupervised, objects;local, of, properties;reliable, recognition;, sequences;object}, doi = {10.1109/CVPR.1998.698639}, author = {Basri,R. and Roth,D. and Jacobs, David W.} } @conference {14843, title = {Comparing images under variable illumination}, booktitle = {Computer Vision and Pattern Recognition, 1998. Proceedings. 1998 IEEE Computer Society Conference on}, year = {1998}, month = {1998/06//}, pages = {610 - 617}, abstract = {We consider the problem of determining whether two images come from different objects or the same object in the same pose, but under different illumination conditions. We show that this problem cannot be solved using hard constraints: even using a Lambertian reflectance model, there is always an object and a pair of lighting conditions consistent with any two images. Nevertheless, we show that for point sources and objects with Lambertian reflectance, the ratio of two images from the same object is simpler than the ratio of images from different objects. We also show that the ratio of the two images provides two of the three distinct values in the Hessian matrix of the object{\textquoteright}s surface. Using these observations, we develop a simple measure for matching images under variable illumination, comparing its performance to other existing methods on a database of 450 images of 10 individuals}, keywords = {conditions;matching, illumination;visual, images;point, Lambertian, matching;object, model;database;lighting, object, recognition;, recognition;image, reflectance, sources;pose;variable}, doi = {10.1109/CVPR.1998.698668}, author = {Jacobs, David W. and Belhumeur,P. N. and Basri,R.} } @conference {18379, title = {Culture conflicts in software engineering technology transfer}, booktitle = {NASA Goddard Software Engineering Workshop}, year = {1998}, month = {1998///}, pages = {52 - 52}, abstract = {Although the need to transition new technology to improve the process of developing quality software products is well understood, the computer software industry has done a poor job of carrying out that need. All too often new software technology is touted as the next "silver bullet" to be adopted, only to fail and disappear within a very short period. New technologies are often adopted without any convincing evidence that they will be effective, yet other technologies are ignored despite the published data that they will be useful. It is cClearly there is a clash between those developing new technologies and those responsible for developing quality products. In this paper we discuss a study conducted among a large group of computer software professionals in order to understand what techniques can be used to support the introduction of new technologies, and to understand the biases and opinions of those charged with researching, developing or implementing those new technologies. This study indicates which evaluation techniques are viewed as most successful under various conditions. We show that the research and industrial communities do indeed have different perspectives, which leads to a clash between the goals of the technology developers researchers and the needs of the technology users.}, author = {Zelkowitz, Marvin V and Wallace,D. R and Binkley,D.} } @article {17076, title = {Designing to facilitate browsing: A look back at the Hyperties workstation browser}, year = {1998}, month = {1998/10/15/}, abstract = {Since browsing hypertext can present a formidable cognitivechallenge, user interface design plays a major role in determining acceptability. In the Unix workstation version of Hyperties, a research-oriented prototype, we focussed on design features that facilitate browsing. We first give a general overview of Hyperties and its markup language. Customizable documents can be generated by the conditional text feature that enables dynamic and selective display of text and graphics. In addition we present: - an innovative solution to link identification: pop-out graphical buttons of arbitrary shape. - application of pie menus to permit low cognitive load actions that reduce the distraction of common actions, such as page turning or window selection. - multiple window selection strategies that reduce clutter and housekeeping effort. We preferred piles-of-tiles, in which standard-sized windows were arranged in a consistent pattern on the display and actions could be done rapidly, allowing users to concentrate on the contents. (Also cross-referenced as CAR-TR-494) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/362}, author = {Shneiderman, Ben and Plaisant, Catherine and Botafogo,Rodrigo and Hopkins,Don and Weiland,William} } @article {14910, title = {Determining the similarity of deformable shapes}, journal = {Vision Research}, volume = {38}, year = {1998}, month = {1998/08//}, pages = {2365 - 2385}, abstract = {Determining the similarity of two shapes is a significant task in both machine and human vision systems that must recognize or classify objects. The exact properties of human shape similarity judgements are not well understood yet, and this task is particularly difficult in domains where the shapes are not related by rigid transformations. In this paper we identify a number of possibly desirable properties of a shape similarity method, and determine the extent to which these properties can be captured by approaches that compare local properties of the contours of the shapes, through elastic matching. Special attention is devoted to objects that possess articulations, i.e. articulated parts. Elastic matching evaluates the similarity of two shapes as the sum of local deformations needed to change one shape into another. We show that similarities of part structure can be captured by such an approach, without the explicit computation of part structure. This may be of importance, since although parts appear to play a significant role in visual recognition, it is difficult to stably determine part structure. We also show novel results about how one can evaluate smooth and polyhedral shapes with the same method. Finally, we describe shape similarity effects that cannot be handled by current approaches.}, isbn = {0042-6989}, doi = {10.1016/S0042-6989(98)00043-1}, url = {http://www.sciencedirect.com/science/article/pii/S0042698998000431}, author = {Basri,Ronen and Costa,Luiz and Geiger,Davi and Jacobs, David W.} } @conference {17832, title = {Digital dynamic telepathology{\textendash}the Virtual Microscope.}, booktitle = {Proceedings of the AMIA Symposium}, year = {1998}, month = {1998///}, pages = {912 - 912}, author = {Afework,A. and Beynon,M. D and Bustamante,F. and Cho,S. and Demarzo,A. and Ferreira,R. and Miller,R. and Silberman,M. and Saltz, J. and Sussman, Alan and others} } @article {17695, title = {Direction of Arrival and the Rank-Revealing URV Decomposition}, volume = {UMIACS-TR-91-166}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In many practical direction-of-arrival (DOA) problems the numberof sources and their directions from an antenna array do not remain stationary. Hence a practical DOA algorithm must be able to track changes with a minimal number of snapshots. In this paper we describe DOA algorithms, based on a new decomposition, that are not expensive to compute or difficult to update. The algorithms are compared with algorithms based on the singular value decomposition (SVD). (Also cross-referenced as UMIACS-TR-91-166) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/561}, author = {Boman,E. C and Griffen,M. F and Stewart, G.W.} } @article {14214, title = {Directions of Motion Fields are Hardly Ever Ambiguous}, journal = {International Journal of Computer Vision}, volume = {26}, year = {1998}, month = {1998///}, pages = {5 - 24}, abstract = {If instead of the full motion field, we consider only the direction of the motion field due to a rigid motion, what can we say about the three-dimensional motion information contained in it? This paper provides a geometric analysis of this question based solely on the constraint that the depth of the surfaces in view is positive. The motivation behind this analysis is to provide a theoretical foundation for image constraints employing only the sign of flow in various directions and justify their utilization for addressing 3D dynamic vision problems.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/A:1007928406666}, author = {Brodsky, Tomas and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14895, title = {EFFICIENT DETERMINATION OF SHAPE FROM MULTIPLE IMAGES CONTAINING PARTIAL INFORMATION}, journal = {Pattern Recognition}, volume = {31}, year = {1998}, month = {1998/11//}, pages = {1691 - 1703}, abstract = {We consider the problem of reconstructing the shape of a 2-D object from multiple partial images related by scaled translations, in the presence of occlusion. Lindenbaum and Bruckstein have considered this problem in the specific case of a translating object seen by small sensors, for application to the understanding of insect vision. Their solution is limited by the fact that its run time is exponential in the number of images and sensors. We generalize the problem to allow for arbitrary types of occlusion of objects that translate and change scale. We show that this more general version of the problem can be solved in time that is polynomial in the number of sensors, but that even the original problem posed by Lindenbaum and Bruckstein is, in fact, NP-hard when the number of images is unbounded. Finally, we consider the case where the object is known to be convex. We show that Lindenbaum and Bruckstein{\textquoteright}s version of the problem is then efficiently solvable even when many images are used, as is the general problem in certain more restricted cases.}, keywords = {2-D shape recovery from multiple images, NP-complete, Shape recovery with occlusion}, isbn = {0031-3203}, doi = {10.1016/S0031-3203(98)00050-8}, url = {http://www.sciencedirect.com/science/article/pii/S0031320398000508}, author = {Basri,Ronen and GROVE,ADAM J. and Jacobs, David W.} } @article {17130, title = {Emergent patterns of teaching/learning in electronic classrooms}, journal = {Educational Technology Research and Development}, volume = {46}, year = {1998}, month = {1998///}, pages = {23 - 42}, abstract = {Novel patterns of teaching/learning have emerged from faculty and students who use our three teaching/learning theaters at the University of Maryland, College Park. These fully-equipped electronic classrooms have been used by 74 faculty in 264 semester-long courses since the fall of 1991 with largely enthusiastic reception by both faculty and students. The designers of the teaching/learning theaters sought to provide a technologically rich environment and a support staff so that faculty could concentrate on changing the traditional lecture from its unidirectional information flow to a more collaborative activity. As faculty have evolved their personal styles in using the electronic classrooms, novel patterns of teaching/learning have emerged. In addition to enhanced lectures, we identified three common patterns: (a) active individual learning, (b) small-group collaborative learning, and (c) entire-class collaborative learning.}, isbn = {1042-1629}, url = {http://dx.doi.org/10.1007/BF02299671}, author = {Shneiderman, Ben and Borkowski,Ellen and Alavi,Maryam and Norman,Kent} } @article {16964, title = {An Empirical Study of Perspective-Based Usability Inspection}, journal = {Proceedings of the Human Factors and Ergonomics Society Annual MeetingProceedings of the Human Factors and Ergonomics Society Annual Meeting}, volume = {42}, year = {1998}, month = {1998/10/01/}, pages = {1346 - 1350}, abstract = {Inspection is a fundamental means of achieving software usability. Past research showed that during usability inspection the success rate (percentage of problems detected) of each individual inspector was rather low. We developed perspective-based usability inspection, which divides the large variety of usability issues along different perspectives and focuses each inspection session on one perspective. We conducted a controlled experiment to study its effectiveness, using a post-test only control group experimental design, with 24 professionals as subjects. The control group used heuristic evaluation, which is the most popular technique for usability inspection. The experimental results are that 1) for usability problems covered by each perspective, the inspectors using that perspective had higher success rate than others; 2) for all usability problems, perspective inspectors had higher average success rate than heuristic inspectors; 3) for all usability problems, the union of three perspective inspectors (with one from each perspective) had higher average success rate than the union of three heuristic inspectors.}, isbn = {1071-1813,}, doi = {10.1177/154193129804201904}, url = {http://pro.sagepub.com/content/42/19/1346}, author = {Zhang,Zhijun and Basili, Victor R. and Shneiderman, Ben} } @conference {18036, title = {Explicit Multi-Threading (XMT) bridging models for instruction parallelism (extended abstract)}, booktitle = {Proceedings of the tenth annual ACM symposium on Parallel algorithms and architectures}, year = {1998}, month = {1998///}, pages = {140 - 151}, author = {Vishkin, Uzi and Dascal,S. and Berkovich,E. and Nuzman,J.} } @article {15367, title = {Extension of Spherical Harmonic Method to RF Transient Regime}, journal = {Simulation of semiconductor processes and devices 1998: SISPAD 98}, year = {1998}, month = {1998///}, pages = {42 - 42}, abstract = {The space and time dependent electron Boltzmann transport equation (BTE)is solved sclf-consistently with the Poisson and transient hole current-continuity equation. A transient Spherical Harmonic expansion method is used to solve the BTE. By this method we can efficiently solve the BTE in the RF regime to observe how the complete distribution function responds to a rapid transient. Calculations on a BJT, which give the time dependent distribution function over a large energy range 0-3eV, throughout the device, as well as average quantities, require only 40 minutes CPU time on an Alpha workstation. }, author = {Lin,C. K. and Goldsman,N. and Chang,C. H. and Mayergoyz, Issak D and Aronowitz,S. and Dong,J. and Belova,N.} } @article {15226, title = {Facility Location with Dynamic Distance Functions}, journal = {Journal of Combinatorial Optimization}, volume = {2}, year = {1998}, month = {1998///}, pages = {199 - 217}, abstract = {Facility location problems have always been studied with theassumption that the edge lengths in the network are static anddo not change over time. The underlying network could be used to model a city street networkfor emergency facility location/hospitals, or an electronic network for locating information centers. In any case, it is clear that due to trafficcongestion the traversal time on links changes with time. Very often, we have estimates as to how the edge lengths change over time, and our objective is to choose a set of locations (vertices) ascenters, such that at every time instant each vertex has a center close to it (clearly, the center close to a vertex may change over time). We also provide approximation algorithms as well as hardness results forthe K-center problem under this model. This is the first comprehensive study regarding approximation algorithmsfor facility location for good time-invariant solutions.}, doi = {10.1023/A:1009796525600}, author = {Khuller, Samir and Sussmann,Y. J and Bhatia,Randeep and Guha,Sudipto} } @conference {18736, title = {Feature-recognition for MEMS extraction}, year = {1998}, month = {1998///}, pages = {13 - 16}, url = {http://www.ece.cmu.edu/~mems/pubs/pdfs/asme/detc/0029_baidya-1998.pdf}, author = {Baidya,B. and Gupta,S.K. and Mukherjee,T.} } @conference {18324, title = {A framework for modeling appearance change in image sequences}, booktitle = {Computer Vision, 1998. Sixth International Conference on}, year = {1998}, month = {1998/01//}, pages = {660 - 667}, abstract = {Image ldquo;appearance rdquo; may change over time due to a variety of causes such as: 1) object or camera motion; 2) generic photometric events including variations in illumination (e.g. shadows) and specular reflections; and 3) ldquo;iconic changes rdquo; which are specific to the objects being viewed and include complex occlusion events and changes in the material properties of the objects. We propose a general framework for representing and recovering these ldquo;appearance changes rdquo; in an image sequence as a ldquo;mixture rdquo; of different causes. The approach generalizes previous work on optical flow to provide a richer description of image events and more reliable estimates of image motion}, keywords = {appearance change, camera motion, complex occlusion events, generic photometric events, iconic changes, illumination, image motion, Image sequences, Motion estimation, optical flow}, doi = {10.1109/ICCV.1998.710788}, author = {Black,M. J and Fleet,D. J and Yacoob,Yaser} } @article {14102, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Molecular and biochemical parasitology}, volume = {97}, year = {1998}, month = {1998///}, pages = {221 - 221}, author = {Clayton,C. and Adams,M. and Almeida,R. and Baltz,T. and Barrett,M. and Bastien,P. and Belli,S. and Beverley,S. and Biteau,N. and Blackwell,J. and others} } @article {20053, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Mol Biochem Parasitol}, volume = {97}, year = {1998}, month = {1998 Nov 30}, pages = {221-4}, keywords = {Animals, Leishmania, Terminology as Topic, Trypanosoma}, issn = {0166-6851}, author = {Clayton, C and Adams, M and Almeida, R and Baltz, T and Barrett, M and Bastien, P and Belli, S and Beverley, S and Biteau, N and Blackwell, J and Blaineau, C and Boshart, M and Bringaud, F and Cross, G and Cruz, A and Degrave, W and Donelson, J and El-Sayed, N and Fu, G and Ersfeld, K and Gibson, W and Gull, K and Ivens, A and Kelly, J and Vanhamme, L} } @article {12174, title = {Implementing a zooming User Interface: experience building Pad++}, journal = {Software: Practice and Experience}, volume = {28}, year = {1998}, month = {1998/08/01/}, pages = {1101 - 1135}, abstract = {We are investigating a novel user interface paradigm based on zooming, in which users are presented with a zooming view of a huge planar information surface. We have developed a system called Pad++ to explore this approach. The implementation of Pad++ is related to real-time 3D graphics systems and to 2D windowing systems. However, the zooming nature of Pad++ requires new approaches to rendering, screen management, and spatial indexing. In this paper, we describe the design and implementation of the Pad++ engine, focusing in particular on rendering and data structure issues. Our goal is to present useful techniques that can be adopted in other real-time graphical systems, and also to discuss how 2D zooming systems differ from other graphical systems. {\textcopyright} 1998 John Wiley \& Sons, Ltd.}, keywords = {3D graphics, animation, Pad++, real-time computer graphics, User Interface Management Systems (UIMS), windowing systems, zooming User Interfaces (ZUIs)}, isbn = {1097-024X}, doi = {10.1002/(SICI)1097-024X(199808)28:10<1101::AID-SPE190>3.0.CO;2-V}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-024X(199808)28:10<1101::AID-SPE190>3.0.CO;2-V/abstract}, author = {Bederson, Benjamin B. and Meyer,Jon} } @conference {18739, title = {An intelligent environment for simulating mechanical assembly operations}, year = {1998}, month = {1998///}, pages = {13 - 16}, abstract = {Rapid technical advances in many different areas of scientificcomputing provide the enabling technologies for creating a com- prehensive simulation and visualization environment for assembly design and planning. We have built an intelligent environment in which simple simulations can be composed together to create com- plex simulations for detecting potential assembly problems. Our goal in this project is to develop high fidelity assembly simulation and visualization tools that can detect assembly related problems without going through physical mock-ups. In addition, these tools can be used to create easy-to-visualize instructions for performing assembly and service operations. }, url = {http://www.cs.cmu.edu/afs/cs.cmu.edu/Web/People/paredis/pubs/DFM98.pdf}, author = {Gupta,S.K. and Paredis,C. J. J. and Sinha,R. and Wang,C. H. and Brown,P. F.} } @article {18147, title = {Looking to Parallel Algorithms for ILP and Decentralization}, volume = {CS-TR-3921}, year = {1998}, month = {1998/10/15/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {We introduce explicit multi-threading (XMT), a decentralized architecturethat exploits fine-grained SPMD-style programming; a SPMD program can translate directly to MIPS assembly language using three additional instruction primitives. The motivation for XMT is: (i) to define an inherently decentralizable architecture, taking into account that the performance of future integrated circuits will be dominated by wire costs, (ii) to increase available instruction-level parallelism (ILP) by leveraging expertise in the world of parallel algorithms, and (iii) to reduce hardware complexity by alleviating the need to detect ILP at run-time: if parallel algorithms can give us an overabundance of work to do in the form of thread-level parallelism, one can extract instruction-level parallelism with greatly simplified dependence-checking. We show that implementations of such an architecture tend towards decentralization and that, when global communication is necessary, overall performance is relatively insensitive to large on-chip delays. We compare the performance of the design to more traditional parallel architectures and to a high-performance superscalar implementation, but the intent is merely to illustrate the performance behavior of the organization and to stimulate debate on the viability of introducing SPMD to the single-chip processor domain. We cannot offer at this stage hard comparisons with well-researched models of execution. When programming for the SPMD model, the total number of operations that the processor has to perform is often slightly higher. To counter this, we have observed that the length of the critical path through the dynamic execution graph is smaller than in the serial domain, and the amount of ILP is correspondingly larger. Fine-grained SPMD programming connects with a broad knowledge base in parallel algorithms and scales down to provide good performance relative to high-performance superscalar designs even with small input sizes and small numbers of functional units. Keywords: Fine-grained SPMD, parallel algorithms. spawn-join, prefix-sum, instruction-level parallelism, decentralized architecture. (Also cross-referenced as UMIACS-TR- 98-40) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/496}, author = {Berkovich,Efraim and Jacob,Bruce and Nuzman,Joseph and Vishkin, Uzi} } @article {14931, title = {A new deterministic parallel sorting algorithm with an experimental evaluation}, journal = {Journal of Experimental Algorithmics (JEA)}, volume = {3}, year = {1998}, month = {1998/09//}, abstract = {We introduce a new deterministic parallel sorting algorithm for distributed memory machines based on the regular sampling approach. The algorithm uses only two rounds of regular all-to-all personalized communication in a scheme that yields very good load balancing with virtually no overhead. Moreover, unlike previous variations, our algorithm efficiently handles the presence of duplicate values without the overhead of tagging each element with a unique identifier. This algorithm was implemented in SPLIT-C and run on a variety of platforms, including the Thinking Machines CM-5, the IBM SP-2-WN, and the Cray Research T3D. We ran our code using widely different benchmarks to examine the dependence of our algorithm on the input distribution. Our experimental results illustrate the efficiency and scalability of our algorithm across different platforms. In fact, the performance compares closely to that of our random sample sort algorithm, which seems to outperform all similar algorithms known to the authors on these platforms. Together, their performance is nearly invariant over the set of input distributions, unlike previous efficient algorithms. However, unlike our randomized sorting algorithm, the performance and memory requirements of our regular sorting algorithm can be deterministically guaranteed.}, keywords = {generalized sorting, integer sorting, Parallel algorithms, parallel performance, sorting by regular sampling}, isbn = {1084-6654}, doi = {10.1145/297096.297128}, url = {http://doi.acm.org/10.1145/297096.297128}, author = {Helman,David R. and JaJa, Joseph F. and Bader,David A.} } @conference {16450, title = {Optimization of wrappers and mediators for web accessible data sources (websources)}, booktitle = {Workshop Web Inf. Data Management (WIDM), Washington DC}, year = {1998}, month = {1998///}, author = {Bright,L. and Raschid, Louiqa and Vidal,M. E} } @article {15008, title = {Parallel Algorithms for Image Histogramming and Connected Components with an Experimental Study}, volume = {UMIACS-TR-94-133}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper presents efficient and portable implementations of two useful primitives in image processing algorithms, histogramming and connected components. Our general framework is a single-address space, distributed memory programming model. We use efficient techniques for distributing and coalescing data as well as efficient combinations of task and data parallelism. Our connected components algorithm uses a novel approach for parallel merging which performs drastically limited updating during iterative steps, and concludes with a total consistency update at the final step. The algorithms have been coded in Split-C and run on a variety of platforms. Our experimental results are consistent with the theoretical analysis and provide the best known execution times for these two primitives, even when compared with machine specific implementations. More efficient implementations of Split-C will likely result in even faster execution times. (Also cross-referenced as UMIACS-TR-94-133.) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/681}, author = {Bader,David A. and JaJa, Joseph F.} } @article {14934, title = {A Parallel Sorting Algorithm With an Experimental Study}, volume = {UMIACS-TR-95-102}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Previous schemes for sorting on general-purpose parallel machineshave had to choose between poor load balancing and irregular communication or multiple rounds of all-to-all personalized communication. In this paper, we introduce a novel variation on sample sort which uses only two rounds of regular all-to-all personalized communication in a scheme that yields very good load balancing with virtually no overhead. This algorithm was implemented in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, the IBM SP-2, and the Cray Research T3D. We ran our code using widely different benchmarks to examine the dependence of our algorithm on the input distribution. Our experimental results are consistent with the theoretical analysis and illustrate the efficiency and scalability of our algorithm across different platforms. In fact, it seems to outperform all similar algorithms known to the authors on these platforms, and its performance is invariant over the set of input distributions unlike previous efficient algorithms. Our results also compare favorably with those reported for the simpler ranking problem posed by the NAS Integer Sorting (IS) Benchmark. (Also cross-referenced as UMIACS-TR-95-102) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/768}, author = {Helman,David R. and Bader,David A. and JaJa, Joseph F.} } @conference {18325, title = {Parameterized modeling and recognition of activities}, booktitle = {Computer Vision, 1998. Sixth International Conference on}, year = {1998}, month = {1998/01//}, pages = {120 - 127}, abstract = {A framework for modeling and recognition of temporal activities is proposed. The modeling of sets of exemplar activities is achieved by parameterizing their representation in the form of principal components. Recognition of spatio-temporal variants of modeled activities is achieved by parameterizing the search in the space of admissible transformations that the activities can undergo. Experiments on recognition of articulated and deformable object motion from image motion parameters are presented}, keywords = {activities recognition, admissible transformations, articulated object motion, deformable object motion, exemplar activities, image motion parameters, Image sequences, Motion estimation, parameterized modeling, recognition, spatio-temporal variants}, doi = {10.1109/ICCV.1998.710709}, author = {Yacoob,Yaser and Black,M. J} } @article {14936, title = {A Randomized Parallel Sorting Algorithm with an Experimental Study}, journal = {Journal of Parallel and Distributed Computing}, volume = {52}, year = {1998}, month = {1998/07/10/}, pages = {1 - 23}, abstract = {Previous schemes for sorting on general-purpose parallel machines have had to choose between poor load balancing and irregular communication or multiple rounds of all-to-all personalized communication. In this paper, we introduce a novel variation on sample sort which uses only two rounds of regular all-to-all personalized communication in a scheme that yields very good load balancing with virtually no overhead. Moreover, unlike previous variations, our algorithm efficiently handles the presence of duplicate values without the overhead of tagging each element with a unique identifier. This algorithm was implemented in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, the IBM SP-2, and the Cray Research T3D. We ran our code using widely different benchmarks to examine the dependence of our algorithm on the input distribution. Our experimental results illustrate the efficiency and scalability of our algorithm across different platforms. In fact, it seems to outperform all similar algorithms known to the authors on these platforms, and its performance is invariant over the set of input distributions unlike previous efficient algorithms. Our results also compare favorably with those reported for the simpler ranking problem posed by the NAS Integer Sorting (IS) Benchmark.}, keywords = {generalized sorting, integer sorting, sample sort, parallel performance, Parallel algorithms}, isbn = {0743-7315}, doi = {10.1006/jpdc.1998.1462}, url = {http://www.sciencedirect.com/science/article/pii/S0743731598914629}, author = {Helman,David R. and Bader,David A. and JaJa, Joseph F.} } @article {15021, title = {Scalable Data Parallel Algorithms for Texture Synthesis and Compression using Gibbs Random Fields}, volume = {UMIACS-TR-93-80}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper introduces scalable data parallel algorithms for image processing. Focusing on Gibbs and Markov Random Field model representation for textures, we present parallel algorithms for texture synthesis, compression, and maximum likelihood parameter estimation, currently implemented on Thinking Machines CM-2 and CM-5. Use of fine-grained, data parallel processing techniques yields real-time algorithms for texture synthesis and compression that are substantially faster than the previously known sequential implementations. Although current implementations are on Connection Machines, the methodology presented here enables machine independent scalable algorithms for a number of problems in image processing and analysis. (Also cross-referenced as UMIACS-TR-93-80.) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/596}, author = {Bader,David A. and JaJa, Joseph F. and Chellapa, Rama} } @conference {11993, title = {Self-calibration from image derivatives}, booktitle = {Sixth International Conference on Computer Vision, 1998}, year = {1998}, month = {1998/01/04/7}, pages = {83 - 89}, publisher = {IEEE}, organization = {IEEE}, abstract = {This study investigates the problem of estimating the calibration parameters from image motion fields induced by a rigidly moving camera with unknown calibration parameters, where the image formation is modeled with a linear pinhole-camera model. The equations obtained show the flow to be clearly separated into a component due to the translation and the calibration parameters and a component due to the rotation and the calibration parameters. A set of parameters encoding the latter component are linearly related to the flow, and from these parameters the calibration can be determined. However, as for discrete motion, in the general case it is not possible, to decouple image measurements from two frames only into their translational and rotational component. Geometrically, the ambiguity takes the form of a part of the rotational component being parallel to the translational component, and thus the scene can be reconstructed only up to a projective transformation. In general, for a full calibration at least four successive image frames are necessary with the 3D-rotation changing between the measurements. The geometric analysis gives rise to a direct self-calibration method that avoids computation of optical flow or point correspondences and uses only normal flow measurements. In this technique the direction of translation is estimated employing in a novel way smoothness constraints. Then the calibration parameters are estimated from the rotational components of several flow fields using Levenberg-Marquardt parameter estimation, iterative in the calibration parameters only. The technique proposed does not require calibration objects in the scene or special camera motions and it also avoids the computation of exact correspondence. This makes it suitable for the calibration of active vision systems which have to acquire knowledge about their intrinsic parameters while they perform other tasks, or as a tool for analyzing image sequences in large video databases}, keywords = {3D-rotation, active vision, Calibration, CAMERAS, discrete motion, Encoding, Equations, image derivatives, image formation, image measurements, Image motion analysis, image motion fields, Image reconstruction, Image sequences, large video databases, Layout, Levenberg-Marquardt parameter estimation, linear pinhole-camera model, Motion estimation, Motion measurement, Optical computing, parameter estimation, projective transformation, rigidly moving camera, self-calibration, smoothness constraints, unknown calibration parameters}, isbn = {81-7319-221-9}, doi = {10.1109/ICCV.1998.710704}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14257, title = {Shape from video: Beyond the epipolar constraint}, journal = {Proceedings of the DARPA Image Understanding Workshop}, year = {1998}, month = {1998///}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @inbook {14258, title = {Simultaneous estimation of viewing geometry and structure}, booktitle = {Computer Vision {\textemdash} ECCV{\textquoteright}98Computer Vision {\textemdash} ECCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1406}, year = {1998}, month = {1998///}, pages = {342 - 358}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Up to now, structure from motion algorithms proceeded in two well defined steps, where the first and most important step is recovering the rigid transformation between two views, and the subsequent step is using this transformation to compute the structure of the scene in view. This paper introduces a novel approach to structure from motion in which both aforementioned steps are accomplished in a synergistic manner. Existing approaches to 3D motion estimation are mostly based on the use of optic flow which however poses a problem at the locations of depth discontinuities. If we knew where depth discontinuities were, we could (using a multitude of approaches based on smoothness constraints) estimate accurately flow values for image patches corresponding to smooth scene patches; but to know the discontinuities requires solving the structure from motion problem first. In the past this dilemma has been addressed by improving the estimation of flow through sophisticated optimization techniques, whose performance often depends on the scene in view. In this paper we follow a different approach. The main idea is based on the interaction between 3D motion and shape which allows us to estimate the 3D motion while at the same time segmenting the scene. If we use a wrong 3D motion estimate to compute depth, then we obtain a distorted version of the depth function. The distortion, however, is such that the worse the motion estimate, the more likely we are to obtain depth estimates that are locally unsmooth, i.e., they vary more than the correct ones. Since local variability of depth is due either to the existence of a discontinuity or to a wrong 3D motion estimate, being able to differentiate between these two cases provides the correct motion, which yields the {\textquotedblleft}smoothest{\textquotedblright} estimated depth as well as the image location of scene discontinuities. Although no optic flow values are computed, we show that our algorithm is very much related to minimizing the epipolar constraint and we present a number of experimental results with real image sequences indicating the robustness of the method.}, isbn = {978-3-540-64569-6}, url = {http://dx.doi.org/10.1007/BFb0055677}, author = {Brodsk{\'y},Tom{\'a}{\v s} and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Burkhardt,Hans and Neumann,Bernd} } @article {17375, title = {Sorting out searching: a user-interface framework for text searches}, journal = {Communications of the ACM}, volume = {41}, year = {1998}, month = {1998/04//}, pages = {95 - 98}, isbn = {0001-0782}, doi = {10.1145/273035.273069}, url = {http://doi.acm.org/10.1145/273035.273069}, author = {Shneiderman, Ben and Byrd,Donald and Croft,W. Bruce} } @article {17734, title = {SRRIT--A FORTRAN Subroutine to Calculate the Dominant Invariant Subspace of a Nonsymmetric Matrix}, volume = {UMIACS-TR-92-61}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {SRRIT is a FORTRAN program to calculate an approximateorthonormal basis for a dominant invariant subspace of a real matrix $A$ by the method of simultaneous iteration \cite{stewart76a}. Specifically, given an integer $m$, {\sl SRRIT} attempts to compute a matrix $Q$ with $m$ orthonormal columns and real quasi-triangular matrix $T$ of order $m$ such that the equation \[ AQ = QT \] is satisfied up to a tolerance specified by the user. The eigenvalues of $T$ are approximations to the $m$ largest eigenvalues of $A$, and the columns of $Q$ span the invariant subspace corresponding to those eigenvalues. {\sl SRRIT} references $A$ only through a user provided subroutine to form the product $AQ$; hence it is suitable for large sparse problems. (Also cross-referenced as UMIACS-TR-92-61) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/572}, author = {Bai,Z. and Stewart, G.W.} } @article {13715, title = {A Survey of Current Paradigms in Machine Translation}, year = {1998}, month = {1998///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This is paper is a survey of the current machine translation research in the US, Eu-rope, and Japan. A short history of machine translation is presented first, followed by an overview of the current research work. Representative examples of a wide range of different approaches adopted by machine translation researchers are presented. These are described in detail along with a discussion of the practicalities of scaling up these approaches for operational environments. In support of this discussion, issues in, and techniques for, evaluating machine translation systems are discussed. }, author = {Dorr, Bonnie J and Jordan,P.W. and Benoit,J.W.} } @book {13028, title = {Trends in the Early Careers of Life Scientists}, year = {1998}, month = {1998///}, publisher = {National Academy Press}, organization = {National Academy Press}, address = {Washington, DC}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @article {13029, title = {Trends in the early careers of life scientists - Preface and executive summary}, journal = {Mol Biol Cell}, volume = {9}, year = {1998}, month = {1998/11//}, pages = {3007 - 3015}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @inbook {14268, title = {The Video Yardstick}, booktitle = {Modelling and Motion Capture Techniques for Virtual EnvironmentsModelling and Motion Capture Techniques for Virtual Environments}, series = {Lecture Notes in Computer Science}, volume = {1537}, year = {1998}, month = {1998///}, pages = {144 - 158}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Given uncalibrated video sequences, how can we recover rich descriptions of the scene content, beyond two-dimensional (2D) measurements such as color/texture or motion fields {\textemdash} descriptions of shape and three-dimensional (3D) motion? This is the well known structure from motion (SFM) problem. Up to now, SFM algorithms proceeded in two well defined steps, where the first and most important step is recovering the rigid transformation between two views, and the subsequent step is using this transformation to compute the structure of the scene in view. This paper introduces a novel approach to structure from motion in which both steps are accomplished in a synergistic manner. It deals with the classical structure from motion problem considering a calibrated camera as well as the extension to an uncalibrated optical device. Existing approaches to estimation of the viewing geometry are mostly based on the use of optic flow, which, however, poses a problem at the locations of depth discontinuities. If we knew where depth discontinuities were, we could (using a multitude of approaches based on smoothness constraints) accurately estimate flow values for image patches corresponding to smooth scene patches; but to know the discontinuities requires solving the structure from motion problem first. In the past this dilemma has been addressed by improving the estimation of flow through sophisticated optimization techniques, whose performance often depends on the scene in view. In this paper we follow a different approach. We directly utilize the image derivatives and employ constraints which involve the 3D motion and shape of the scene, leading to a geometric and statistical estimation problem. The main idea is based on the interaction between 3D motion and shape which allows us to estimate the 3D motion while at the same time segmenting the scene. If we use a wrong 3D motion estimate to compute depth, we obtain a distorted version of the depth function. The distortion, however, is such that the worse the motion estimate, the more likely we are to obtain depth estimates that are locally unsmooth, i.e., they vary more than the correct ones. Since local variability of depth is due either to the existence of a discontinuity or to a wrong 3D motion estimate, being able to differentiate between these two cases provides the correct motion, which yields the {\textquotedblleft}smoothest{\textquotedblright} estimated depth as well as the image locations of scene discontinuities. We analyze the new constraints introduced by our approach and show their relationship to the minimization of the epipolar constraint, which becomes a special case of our theory. Finally, we present a number of experimental results with real image sequences indicating the robustness of our method and the improvement over traditional methods. The resulting system is a video yardstick that can be applied to any video sequence to recover first the calibration parameters of the camera that captured the video and, subsequently, the structure of the scene.}, isbn = {978-3-540-65353-0}, url = {http://dx.doi.org/10.1007/3-540-49384-0_12}, author = {Brodsk{\'y},Tom{\'a}{\v s} and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Magnenat-Thalmann,Nadia and Thalmann,Daniel} } @conference {17269, title = {Is the Web really different from everything else?}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {92 - 93}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {design, user experience, World Wide Web}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286545}, url = {http://doi.acm.org/10.1145/286498.286545}, author = {Shneiderman, Ben and Nielsen,Jakob and Butler,Scott and Levi,Michael and Conrad,Frederick} } @inbook {14277, title = {What is computed by structure from motion algorithms?}, booktitle = {Computer Vision {\textemdash} ECCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1406}, year = {1998}, month = {1998///}, pages = {359 - 375}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In the literature we find two classes of algorithms which, on the basis of two views of a scene, recover the rigid transformation between the views and subsequently the structure of the scene. The first class contains techniques which require knowledge of the correspondence or the motion field between the images and are based on the epipolar constraint. The second class contains so-called direct algorithms which require knowledge about the value of the flow in one direction only and are based on the positive depth constraint. Algorithms in the first class achieve the solution by minimizing a function representing deviation from the epipolar constraint while direct algorithms find the 3D motion that, when used to estimate depth, produces a minimum number of negative depth values. This paper presents a stability analysis of both classes of algorithms. The formulation is such that it allows comparison of the robustness of algorithms in the two classes as well as within each class. Specifically, a general statistical model is employed to express the functions which measure the deviation from the epipolar constraint and the number of negative depth values, and these functions are studied with regard to their topographic structure, specifically as regards the errors in the 3D motion parameters at the places representing the minima of the functions. The analysis shows that for algorithms in both classes which estimate all motion parameters simultaneously, the obtained solution has an error such that the projections of the translational and rotational errors on the image plane are perpendicular to each other. Furthermore, the estimated projection of the translation on the image lies on a line through the origin and the projection of the real translation.}, isbn = {978-3-540-64569-6}, url = {http://dx.doi.org/10.1007/BFb0055678}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Burkhardt,Hans and Neumann,Bernd} } @conference {13921, title = {When Two Hands Are Better Than One: Enhancing Collaboration Using Single Display Groupware. CHI{\textquoteright}98}, booktitle = {Extended Abstracts}, year = {1998}, month = {1998///}, pages = {287 - 288}, author = {Stewart,J. and Raybourn,E. and Bederson, Benjamin B. and Druin, Allison} } @conference {16499, title = {Wrapper generation for Web accessible data sources}, booktitle = {3rd IFCIS International Conference on Cooperative Information Systems, 1998. Proceedings}, year = {1998}, month = {1998/08/22/22}, pages = {14 - 23}, publisher = {IEEE}, organization = {IEEE}, abstract = {There is an increase in the number of data sources that can be queried across the WWW. Such sources typically support HTML forms-based interfaces and search engines query collections of suitably indexed data. The data is displayed via a browser: One drawback to these sources is that there is no standard programming interface suitable for applications to submit queries. Second, the output (answer to a query) is not well structured. Structured objects have to be extracted from the HTML documents which contain irrelevant data and which may be volatile. Third, domain knowledge about the data source is also embedded in HTML documents and must be extracted. To solve these problems, we present technology to define and (automatically) generate wrappers for Web accessible sources. Our contributions are as follows: (1) Defining a wrapper interface to specify the capability of Web accessible data sources. (2) Developing a wrapper generation toolkit of graphical interfaces and specification languages to specify the capability of sources and the functionality of the wrapper (3) Developing the technology to automatically generate a wrapper appropriate to the Web accessible source, from the specifications.}, keywords = {application program interfaces, data mining, Databases, Educational institutions, Electrical capacitance tomography, HTML, HTML documents, Internet, Query processing, Read only memory, Search engines, Specification languages, Uniform resource locators, World Wide Web, wrapper generation toolkit, WWW}, isbn = {0-8186-8380-5}, doi = {10.1109/COOPIS.1998.706180}, author = {Gruser,J. and Raschid, Louiqa and Vidal,M. E and Bright,L.} } @conference {14841, title = {3-D to 2-D recognition with regions}, booktitle = {Computer Vision and Pattern Recognition, 1997. Proceedings., 1997 IEEE Computer Society Conference on}, year = {1997}, month = {1997/06//}, pages = {547 - 553}, abstract = {This paper presents a novel approach to parts-based object recognition in the presence of occlusion. We focus on the problem of determining the pose of a 3-D object from a single 2-D image when convex parts of the object have been matched to corresponding regions in the image. We consider three types of occlusions: self-occlusion, occlusions whose locus is identified in the image, and completely arbitrary occlusions. We derive efficient algorithms for the first two cases, and characterize their performance. For the last case, we prove that the problem of finding valid poses is computationally hard, but provide an efficient, approximate algorithm. This work generalizes our previous work on region-based object recognition, which focused on the case of planar models}, keywords = {2-D, algorithms;object, complexity;image, hard;efficient, image;3-D, object;computationally, poses;computational, recognition;, recognition;occlusion;occlusions;performance;regions;valid, segmentation;object}, doi = {10.1109/CVPR.1997.609379}, author = {Jacobs, David W. and Basri,R.} } @article {17682, title = {Algorithm 776: SRRIT: a Fortran subroutine to calculate the dominant invariant subspace of a nonsymmetric matrix}, journal = {ACM Trans. Math. Softw.}, volume = {23}, year = {1997}, month = {1997/12//}, pages = {494 - 513}, abstract = {SRRT is a Fortran program to calculate an approximate orthonomral basis fr a dominant invariant subspace of a real matrix A by the method of simultaneous iteration. Specifically, given an integer m, SRRIT computes a matrix Q with m orthonormal columns and real quasi-triangular matrix T or order m such that the equation AQ = QT is satisfied up to a tolerance specified by the user. The eigenvalues of T are approximations to the m eigenvalues of largest absolute magnitude of A and the columns of Q span the invariant subspace corresponding to those eigenvalues. SRRIT references A only through a user-provided subroutine to form the product AQ; hence it is suitable for large sparse problems.}, keywords = {invariant subspace, nonsymmetric eigenvalue problem, project method}, isbn = {0098-3500}, doi = {10.1145/279232.279234}, url = {http://doi.acm.org/10.1145/279232.279234}, author = {Bai,Z. and Stewart, G.W.} } @article {12336, title = {APGAN and RPMC: Complementary heuristics for translating DSP block diagrams into efficient software implementations}, journal = {Design Automation for Embedded Systems}, volume = {2}, year = {1997}, month = {1997///}, pages = {33 - 60}, author = {Bhattacharyya, Shuvra S. and Murthy,P. K and Lee,E. A} } @conference {16195, title = {Bringing treasures to the surface: iterative design for the Library of Congress National Digital Library Program}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {518 - 525}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {browse, design process, digital libraries, dynamic query, java, preview, search, web design}, isbn = {0-89791-802-9}, doi = {10.1145/258549.259009}, url = {http://doi.acm.org/10.1145/258549.259009}, author = {Plaisant, Catherine and Marchionini,Gary and Bruns,Tom and Komlodi,Anita and Campbell,Laura} } @article {17012, title = {Clarifying search: A user-interface framework for text searches}, journal = {D-lib magazine}, volume = {3}, year = {1997}, month = {1997///}, pages = {18 - 20}, abstract = {Current user interfaces for textual database searching leave much to be desired: individually, they are often confusing, and as a group, they are seriously inconsistent. We propose a four- phase framework for user-interface design: the framework provides common structure and terminology for searching while preserving the distinct features of individual collections and search mechanisms. Users will benefit from faster learning, increased comprehension, and better control, leading to more effective searches and higher satisfaction.}, author = {Shneiderman, Ben and Byrd,D. and Croft, W.B.} } @article {18377, title = {Comments on "Towards a framework for software measurement validation"}, journal = {Software Engineering, IEEE Transactions on}, volume = {23}, year = {1997}, month = {1997/03//}, pages = {187 - 189}, abstract = {A view of software measurement that disagrees with the model presented by Kitchenham, Pfleeger, and Fenton (1995), is given. Whereas Kitchenham et al. argue that properties used to define measures should not constrain the scale type of measures, the authors contend that that is an inappropriate restriction. In addition, a misinterpretation of Weyuker{\textquoteright}s (1988) properties is noted.}, keywords = {measurement, metrics;, software, testing;program, validation;program, verification;software}, isbn = {0098-5589}, doi = {10.1109/32.585506}, author = {Morasca,S. and Briand,L.C. and Basili, Victor R. and Weyuker,E.J. and Zelkowitz, Marvin V and Kitchenham,B. and Lawrence Pfleeger,S. and Fenton,N.} } @article {16538, title = {Computer models: A new approach to the investigation of disease}, journal = {MD Computing}, volume = {14}, year = {1997}, month = {1997///}, pages = {160 - 168}, author = {Reggia, James A. and Ruppin,E. and Berndt,R. S} } @article {14826, title = {Constancy and similarity}, journal = {Computer Vision and Image Understanding}, volume = {65}, year = {1997}, month = {1997///}, pages = {447 - 449}, author = {Basri,R. and Jacobs, David W.} } @conference {17056, title = {Design and evaluation of incremental data structures and algorithms for dynamic query interfaces}, booktitle = {IEEE Symposium on Information Visualization, 1997. Proceedings}, year = {1997}, month = {1997/10/21/21}, pages = {81 - 86}, publisher = {IEEE}, organization = {IEEE}, abstract = {A dynamic query interface (DQI) is a database access mechanism that provides continuous real-time feedback to the user during query formulation. Previous work shows that DQIs are elegant and powerful interfaces to small databases. Unfortunately, when applied to large databases, previous DQI algorithms slow to a crawl. We present a new incremental approach to DQI algorithms and display updates that work well with large databases, both in theory and in practice.}, keywords = {Algorithm design and analysis, Bars, Computer science, continuous real-time feedback, Data structures, data visualisation, Data visualization, database access mechanism, Displays, DQI algorithms, dynamic query interfaces, Feedback, Graphical user interfaces, Heuristic algorithms, incremental data structures, Information Visualization, large databases, Manipulator dynamics, NASA, query formulation, query languages, Query processing, real-time systems, small databases, User interfaces, very large databases, visual databases, visual languages}, isbn = {0-8186-8189-6}, doi = {10.1109/INFVIS.1997.636790}, author = {Tanin,E. and Beigel,R. and Shneiderman, Ben} } @conference {16461, title = {The distributed information search component (disco) and the world wide web}, booktitle = {Proc. of ACM SIGMOD Conf. on Management of Data}, year = {1997}, month = {1997///}, author = {Naacke,H. and Kapitskaia,O. and Tomasic,A. and Bonnet,P. and Raschid, Louiqa and Amouroux,R.} } @article {12791, title = {Dynamic priorities for modeling real-time}, journal = {Proc. of the Formal Description Techniques and Protocol Specification, Testing and Verification (FORTE X/PSTV XVII{\textquoteright}97)}, year = {1997}, month = {1997///}, pages = {321 - 336}, author = {Bhat,G. and Cleaveland, Rance and L\{\"u}ttgen,G.} } @article {18382, title = {Editorial: Evaluation and assessment in software engineering}, journal = {Information and Software Technology}, volume = {39}, year = {1997}, month = {1997///}, author = {Kitchenham,B. and Brereton,P. and Budgen,D. and Linkman,S. and Almstrum,V. L and Pfleeger,S. L and Zelkowitz, Marvin V and Wallace,D.} } @conference {16328, title = {If your version control system could talk}, booktitle = {ICSE Workshop on Process Modelling and Empirical Studies of Software Engineering}, year = {1997}, month = {1997///}, author = {Ball,T. and Kim,J. M and Porter, Adam and Siy,H. P} } @article {12385, title = {Joint minimization of code and data for synchronous dataflow programs}, journal = {Formal Methods in System Design}, volume = {11}, year = {1997}, month = {1997///}, pages = {41 - 70}, author = {Murthy,P. K and Bhattacharyya, Shuvra S. and Lee,E. A} } @conference {12217, title = {KidPad: a design collaboration between children, technologists, and educators}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {1997}, month = {1997///}, pages = {463 - 470}, author = {Druin, Allison and Stewart,J. and Proft,D. and Bederson, Benjamin B. and Hollan,J.} } @conference {18321, title = {Learning parameterized models of image motion}, booktitle = {Computer Vision and Pattern Recognition, 1997. Proceedings., 1997 IEEE Computer Society Conference on}, year = {1997}, month = {1997/06//}, pages = {561 - 567}, abstract = {A framework for learning parameterized models of optical flow from image sequences is presented. A class of motions is represented by a set of orthogonal basis flow fields that are computed from a training set using principal component analysis. Many complex image motions can be represented by a linear combination of a small number of these basis flows. The learned motion models may be used for optical flow estimation and for model-based recognition. For optical flow estimation we describe a robust, multi-resolution scheme for directly computing the parameters of the learned flow models from image derivatives. As examples we consider learning motion discontinuities, non-rigid motion of human mouths, and articulated human motion}, keywords = {image motion, Image sequences, learning, learning (artificial intelligence), model-based recognition, Motion estimation, multi-resolution scheme, non-rigid motion, optical flow, optical flow estimation, parameterized models, Principal component analysis, training set}, doi = {10.1109/CVPR.1997.609381}, author = {Black,M. J and Yacoob,Yaser and Jepson,A. D and Fleet,D. J} } @article {14627, title = {Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model}, journal = {Journal of Computational Biology}, volume = {4}, year = {1997}, month = {1997/01//}, pages = {275 - 296}, abstract = {We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill (1985), which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail (1996a) gave approximation algorithms for folding proteins on the cubic lattice under the HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that the triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.1997.4.275}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.1997.4.275}, author = {Agarwala,Richa and Batzoglou,Serafim and Dan{\v c}{\'\i}K,Vlado and Decatur,Scott E. and Hannenhalli, Sridhar and Farach,Martin and Muthukrishnan,S. and Skiena,Steven} } @article {14106, title = {A note on conjugate gradient convergence}, journal = {Numerische Mathematik}, volume = {76}, year = {1997}, month = {1997///}, pages = {209 - 230}, author = {Naiman, A. E and Babu{\v s}ka, I. M and Elman, Howard} } @article {12324, title = {Optimized software synthesis for synchronous dataflow}, journal = {Proceedings of the ASAP97}, year = {1997}, month = {1997///}, author = {Bhattacharyya, Shuvra S. and America,H.} } @article {12366, title = {Optimizing synchronization in multiprocessor DSP systems}, journal = {Signal Processing, IEEE Transactions on}, volume = {45}, year = {1997}, month = {1997///}, pages = {1605 - 1618}, author = {Bhattacharyya, Shuvra S. and Sriram,S. and Lee,E. A} } @article {16199, title = {Query previews for networked information systems: a case study with NASA environmental data}, journal = {SIGMOD Record}, volume = {26}, year = {1997}, month = {1997///}, pages = {75 - 81}, abstract = {Formulating queries on networked information systemsis laden with problems: data diversity, data complexity, network growth, varied user base, and slow network access. This paper proposes a new approach to a network query user interface which consists of two phases: query preview and query refinement. This new approach is based on dynamic queries and tight coupling, guiding users to rapidly and dynamically eliminate undesired items, reduce the data volume to a manageable size, and refine queries locally before submission over a network. A two-phase dynamic query system for NASA{\textquoteright}s Earth Observing Systems--Data Information Systems (EOSDIS) is presented. The prototype was well received by the team of scientists who evaluated the interface. }, author = {Doan,K. and Plaisant, Catherine and Shneiderman, Ben and Bruns,T.} } @conference {16196, title = {Query previews in networked information systems: the case of EOSDIS}, booktitle = {CHI {\textquoteright}97 extended abstracts on Human factors in computing systems: looking to the future}, series = {CHI EA {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {202 - 203}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Dynamic queries have been shown to be an effective technique to browse information, and to find patterns and exceptions. Dynamic queries involve the interactive control by a user of visual query parameters that generate rapid (100 ms update), animated, and visual displays of database search results. The data of early implementations was stored in local memory to guarantee optimal speed. Problems arise when the data is very large and distributed over a network. To overcome the problems of slow networks and data volume we propose a two-phase approach to query formulation using query previews and query refinements [1]. Preview mechanisms have been used in the past [2] and we believe that their use will be a major component of successful networked information systems interfaces (e.g. [3]).}, keywords = {direct manipulation, dynamic query, earth science, network information system, query preview, Visualization}, isbn = {0-89791-926-2}, doi = {10.1145/1120212.1120343}, url = {http://doi.acm.org/10.1145/1120212.1120343}, author = {Plaisant, Catherine and Bruns,Tom and Shneiderman, Ben and Doan,Khoa} } @article {14872, title = {Recognition using region correspondences}, journal = {International Journal of Computer Vision}, volume = {25}, year = {1997}, month = {1997///}, pages = {145 - 166}, abstract = {Recognition systems attempt to recover information about the identity of observed objects and their location in the environment. A fundamental problem in recognition is pose estimation. This is the problem of using a correspondence between some portions of an object model and some portions of an image to determine whether the image contains an instance of the object, and, in case it does, to determine the transformation that relates the model to the image. The current approaches to this problem are divided into methods that use ldquoglobalrdquo properties of the object (e.g., centroid and moments of inertia) and methods that use ldquolocalrdquo properties of the object (e.g., corners and line segments). Global properties are sensitive to occlusion and, specifically, to self occlusion. Local properties are difficult to locate reliably, and their matching involves intensive computation.We present a novel method for recognition that uses region information. In our approach the model and the image are divided into regions. Given a match between subsets of regions (without any explicit correspondence between different pieces of the regions) the alignment transformation is computed. The method applies to planar objects under similarity, affine, and projective transformations and to projections of 3-D objects undergoing affine and projective transformations. The new approach combines many of the advantages of the previous two approaches, while avoiding some of their pitfalls. Like the global methods, our approach makes use of region information that reflects the true shape of the object. But like local methods, our approach can handle occlusion. }, doi = {10.1023/A:1007919917506}, author = {Basri,R. and Jacobs, David W.} } @conference {16359, title = {Symbolic model checking of infinite state systems using Presburger arithmetic}, booktitle = {Computer Aided Verification}, year = {1997}, month = {1997///}, pages = {400 - 411}, author = {Bultan,T. and Gerber,R. and Pugh, William} } @article {15562, title = {Testing simple polygons}, journal = {Computational Geometry}, volume = {8}, year = {1997}, month = {1997/07//}, pages = {97 - 114}, abstract = {We consider the problem of verifying a simple polygon in the plane using {\textquotedblleft}test points{\textquotedblright}. A test point is a geometric probe that takes as input a point in Euclidean space, and returns {\textquotedblleft}+{\textquotedblright} if the point is inside the object being probed or {\textquotedblleft}-{\textquotedblright} if it is outside. A verification procedure takes as input a description of a target object, including its location and orientation, and it produces a set of test points that are used to verify whether a test object matches the description. We give a procedure for verifying an n-sided, non-degenerate, simple target polygon using 5n test points. This testing strategy works even if the test polygon has n + 1 vertices, and we show a lower bound of 3n + 1 test points for this case. We also give algorithms using O(n) test points for simple polygons that may be degenerate and for test polygons that may have up to n + 2 vertices. All of these algorithms work for polygons with holes. We also discuss extensions of our results to higher dimensions.}, keywords = {probing, Testing, Verifying}, isbn = {0925-7721}, doi = {10.1016/S0925-7721(96)00015-6}, url = {http://www.sciencedirect.com/science/article/pii/S0925772196000156}, author = {Arkin,Esther M. and Belleville,Patrice and Mitchell,Joseph S.B. and Mount, Dave and Romanik,Kathleen and Salzberg,Steven and Souvaine,Diane} } @conference {17856, title = {Titan: a High-Performance Remote-sensing Database}, booktitle = {In Proceedings of the 1997 International Conference on Data Engineering}, year = {1997}, month = {1997///}, author = {Bongki,C. C and Chang,C. and Moon,B. and Acharya, A. and Shock,C. and Sussman, Alan and Saltz, J.} } @inbook {14269, title = {Toward motion picture grammars}, booktitle = {Computer Vision {\textemdash} ACCV{\textquoteright}98Computer Vision {\textemdash} ACCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1352}, year = {1997}, month = {1997///}, pages = {283 - 290}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We are interested in processing video data for the purpose of solving a variety of problems in video search, analysis, indexing, browsing and compression. Instead of concentrating on a particular problem, in this paper we present a framework for developing video applications. Our basic thesis is that video data can be represented at a higher level of abstraction as a string generated by a grammar, termed motion picture grammar. The rules of that grammar relate different spatiotemporal representations of the video content and, in particular, representations of action.}, isbn = {978-3-540-63931-2}, url = {http://dx.doi.org/10.1007/3-540-63931-4_228}, author = {Bolle,Ruud and Aloimonos, J. and Ferm{\"u}ller, Cornelia}, editor = {Chin,Roland and Pong,Ting-Chuen} } @conference {15040, title = {The vegetation canopy lidar mission}, booktitle = {Proceedings of Land Satellite Information in the Next Decade, II: Sources and Applications. Bethesda (MD): American Society of Photogrammetry and Remote Sensing}, year = {1997}, month = {1997///}, pages = {100 - 112}, abstract = {The Vegetation Canopy Lidar (VCL) is the first selected mission of NASA{\textquoteright}s new EarthSystem Science Pathfinder program. The principal goal of VCL is the characterization of the three-dimensional structure of the earth; in particular, canopy vertical and horizontal structure and land surface topography. Its primary science objectives are: landcover characterization for terrestrial ecosystem modeling, monitoring and prediction; landcover characterization for climate modeling and prediction; and, production of a global reference data set of topographic spot heights and transects. VCL will provide unique data sets for understanding important environ- mental issues including climatic change and variability, biotic erosion and sustainable landuse, and will dramatically improve our estimation of global biomass and carbon stocks, fractional forest cover, forest extent and condition. It will also provide canopy data critical for biodiversity, natural hazard, and climate studies. Scheduled for launch in early 2000, VCL is an active lidar remote sensing system consisting of a five-beam instrument with 25 m contiguous along track resolution. The five beams are in a circular configuration 8 km across and each beam traces a separate ground track spaced 2 km apart, eventually producing 2 km coverage between 65{\textdegree} N and S. VCL{\textquoteright}s core measurement objectives are: (1) canopy top heights; (2) vertical distribution of intercepted surfaces (e.g. leaves and branches); and, (3) ground surface topographic elevations. These measurements are used to derive a variety of science data products including canopy heights, canopy vertical distribution, and ground elevations gridded monthly at 1{\textdegree} resolution and every 6 months at 2 km resolution, as well as a 2 km fractional forest cover product. }, author = {Dubayah, R. and Blair,J. B. and Bufton,J. L. and Clark,D. B. and JaJa, Joseph F. and Knox,R. and Luthcke,S. B. and Prince,S. and Weishampel,J.} } @article {18305, title = {Visual surveillance of human activity}, journal = {Computer Vision{\textemdash}ACCV{\textquoteright}98}, year = {1997}, month = {1997///}, pages = {267 - 274}, author = {Davis, Larry S. and Fejes,S. and Harwood,D. and Yacoob,Yaser and Hariatoglu,I. and Black,M.} } @article {12177, title = {A zooming web browser}, journal = {Human Factors in Web Development}, year = {1997}, month = {1997///}, author = {Bederson, Benjamin B. and Hollan,J.D. and Stewart,J. and Rogers,D. and Druin, Allison and Vick,D. and Ring,L. and Grose,E. and Forsythe,C.} } @inbook {14213, title = {Directions of motion fields are hardly ever ambiguous}, booktitle = {Computer Vision {\textemdash} ECCV {\textquoteright}96Computer Vision {\textemdash} ECCV {\textquoteright}96}, series = {Lecture Notes in Computer Science}, volume = {1065}, year = {1996}, month = {1996///}, pages = {119 - 128}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Recent literature [7, 10, 11, 9, 13, 17] provides a number of results regarding uniqueness aspects of motion fields and exact image displacements due to 3-D rigid motion. Here instead of the full motion field we consider only the direction of the motion field due to a rigid motion and ask what can we say about the three-dimensional motion information contained in it. This paper provides a geometric analysis of this question based solely on the fact that the depth of the surfaces in view is positive (i.e. that the surface in view is in front of the camera). With this analysis we thus offer a theoretical foundation for image constraints employing only the sign of flow in various directions and provide a solid basis for their utilization in addressing 3D dynamic vision problems.}, isbn = {978-3-540-61123-3}, url = {http://dx.doi.org/10.1007/3-540-61123-1_132}, author = {Brodsky, Tomas and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Buxton,Bernard and Cipolla,Roberto} } @article {12831, title = {Efficient local model-checking for fragments of the modal $\mu$-calculus}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {1996}, month = {1996///}, pages = {107 - 126}, author = {Bhat,G. and Cleaveland, Rance} } @conference {12799, title = {Efficient model checking via the equational μ-calculus}, booktitle = {, Eleventh Annual IEEE Symposium on Logic in Computer Science, 1996. LICS {\textquoteright}96. Proceedings}, year = {1996}, month = {1996/07/27/30}, pages = {304 - 312}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper studies the use of an equational variant of the modal μ-calculus as a unified framework for efficient temporal logic model checking. In particular we show how an expressive temporal logic, CTL*, may be efficiently translated into the μ-calculus. Using this translation, one may then employ μ-calculus model-checking techniques, including on-the-fly procedures, BDD-based algorithms and compositional model-checking approaches, to determine if systems satisfy formulas in CTL*}, keywords = {Automata, BDD-based algorithms, Boolean functions, Calculus, compositional model-checking approaches, computational complexity, Computer science, CTL*, Data structures, Encoding, equational variant, equational μ-calculus, Equations, expressive temporal logic, Logic, Maintenance, modal μ-calculus, Model checking, on-the-fly procedures, Surges, temporal logic, temporal logic model checking, unified framework}, isbn = {0-8186-7463-6}, doi = {10.1109/LICS.1996.561358}, author = {Bhat,G. and Cleaveland, Rance} } @article {18438, title = {The empirical investigation of Perspective-Based Reading}, journal = {Empirical Software Engineering}, volume = {1}, year = {1996}, month = {1996///}, pages = {133 - 164}, abstract = {We consider reading techniques a fundamental means of achieving high quality software. Due to the lack of research in this area, we are experimenting with the application and comparison of various reading techniques. This paper deals with our experiences with a family of reading techniques known as Perspective-Based Reading (PBR), and its application to requirements documents. The goal of PBR is to provide operational scenarios where members of a review team read a document from a particular perspective, e.g., tester, developer, user. Our assumption is that the combination of different perspectives provides better coverage of the document, i.e., uncovers a wider range of defects, than the same number of readers using their usual technique.}, keywords = {Computer, Science}, isbn = {1382-3256}, url = {http://dx.doi.org/10.1007/BF00368702}, author = {Basili, Victor R. and Green,Scott and Laitenberger,Oliver and Lanubile,Filippo and Shull, Forrest and S{\o}rumg{\r a}rd,Sivert and Zelkowitz, Marvin V} } @article {12994, title = {Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics}, journal = {Parasitol Today}, volume = {12}, year = {1996}, month = {1996/02//}, pages = {66 - 71}, abstract = {As our appreciation of the diversity within the flatworms has grown, so too has our curiosity about the ways in which these varied creatures are related to one another. In particular, the parasitic groups (trematodes, cestodes and monogeneans have been the focus of enquiry. Until recently, morphology, anatomy and life histories have provided the raw data for building hypotheses on relationships. Now, ultrastructural evidence, and most recently, molecular data from nucleic acid sequences, have been brought to bear on the topic. Here, David Blair, Andr{\'e}s Campos, Michael Cummings and Juan Pedro Laclette discuss the ways in which molecular data, in particular, are helping us recognize the various lineages of flatworms.}, author = {Blair,D and Campos,A. and Cummings, Michael P. and Laclette,J. P} } @article {18042, title = {A fast parallel algorithm for finding the convex hull of a sorted point set}, journal = {International Journal of Computational Geometry and Applications}, volume = {6}, year = {1996}, month = {1996///}, pages = {231 - 242}, author = {Berkman,O. and Schieber,B. and Vishkin, Uzi} } @inbook {14610, title = {Fast sorting by reversal}, booktitle = {Combinatorial Pattern MatchingCombinatorial Pattern Matching}, series = {Lecture Notes in Computer Science}, volume = {1075}, year = {1996}, month = {1996///}, pages = {168 - 185}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. Following a series of work recently, Hannenhalli and Pevzner developed the first polynomial algorithm for the problem of sorting signed permutations by reversals and proposed an O(n 4 ) implementation of the algorithm. In this paper we exploit a few combinatorial properties of the cycle graph of a permutation and propose an O(n 2 (n)) implementation of the algorithm where is the inverse Ackerman function. Besides making this algorithm practical, our technique improves implementations of the other rearrangement distance problems.}, isbn = {978-3-540-61258-2}, url = {http://dx.doi.org/10.1007/3-540-61258-0_14}, author = {Berman,Piotr and Hannenhalli, Sridhar}, editor = {Hirschberg,Dan and Myers,Gene} } @article {16656, title = {Feature discovery and classification of Doppler umbilical artery blood flow velocity waveforms}, journal = {Computers in Biology and Medicine}, volume = {26}, year = {1996}, month = {1996/11//}, pages = {451 - 462}, abstract = {Doppler umbilical artery blood flow velocity waveform measurements are used in perinatal surveillance for the evaluation of fetal condition. There is an ongoing debate on the predictive value of Doppler measurements concerning the critical effect of the selection of parameters for the interpretation of Doppler waveforms. In this paper, we describe how neural network methods can be used both to discover relevant classification features and subsequently to classify Doppler umbilical artery blood flow velocity waveforms. Results obtained from 199 normal and high risk patients{\textquoteright} umbilical artery waveforms highlighted a classification concordance varying from 90 to 98\% accuracy.}, keywords = {Doppler umbilical artery blood flow velocity waveforms, Feature extraction, IMAGE PROCESSING, Pattern classification}, isbn = {0010-4825}, doi = {10.1016/S0010-4825(96)00018-2}, url = {http://www.sciencedirect.com/science/article/pii/S0010482596000182}, author = {Baykal,Nazife and Reogia,James A. and Yalabik,Nese and Erkmen,Aydan and Beksac,M.Sinan} } @article {16206, title = {Hybrid network management (communication systems)}, journal = {16th AIAA International Communications Satellite Systems Conference}, year = {1996}, month = {1996///}, abstract = {We describe our collaborative efforts towards the design and implementation of a next-generation integrated network management system for hybrid networks (INMS/HN). We describe the overall software architecture of the system at its current stage of development. This NMS is specifically designed to address issues relevant to complex heterogeneous networks consisting of seamlessly interoperable terrestrial and satellite networks. NMSs are a key element for interoperability in such networks. We describe the integration of configuration management and performance management. The next step in this integration is fault management. In particular, we describe the object model, issues concerning the graphical user interface, browsing tools, performance data graphical widget displays, and management information database organization issues.}, author = {Baras,J. S and Ball,M. and Karne,R. K and Kelley,S. and Jang,K.D. and Plaisant, Catherine and Roussopoulos, Nick and Stathatos,K. and Vakhutinsky,A. and Valluri,J.} } @article {17231, title = {Incremental data structures and algorithms for dynamic query interfaces}, journal = {ACM SIGMOD Record}, volume = {25}, year = {1996}, month = {1996/12//}, pages = {21 - 24}, abstract = {Dynamic query interfaces (DQIs) form a recently developed method of database access that provides continuous realtime feedback to the user during the query formulation process. Previous work shows that DQIs are elegant and powerful interfaces to small databases. Unfortunately, when applied to large databases, previous DQI algorithms slow to a crawl. We present a new approach to DQI algorithms that works well with large databases.}, keywords = {algorithm, data structure, database, direct manipulation, dynamic query, Information Visualization, user interface}, isbn = {0163-5808}, doi = {10.1145/245882.245891}, url = {http://doi.acm.org/10.1145/245882.245891}, author = {Tanin,Egemen and Beigel,Richard and Shneiderman, Ben} } @article {16202, title = {Integrated network management of hybrid networks}, journal = {AIP Conference Proceedings}, volume = {361}, year = {1996}, month = {1996/03/01/}, pages = {345 - 350}, abstract = {We describe our collaborative efforts towards the design and implementation of a next generation integrated network management system for hybrid networks (INMS/HN). We describe the overall software architecture of the system at its current stage of development. This network management system is specifically designed to address issues relevant for complex heterogeneous networks consisting of seamlessly interoperable terrestrial and satellite networks. Network management systems are a key element for interoperability in such networks. We describe the integration of configuration management and performance management. The next step in this integration is fault management. In particular we describe the object model, issues of the Graphical User Interface (GUI), browsing tools and performance data graphical widget displays, management information database (MIB) organization issues. Several components of the system are being commercialized by Hughes Network Systems. {\textcopyright} 1996 American Institute of Physics.}, isbn = {0094243X}, doi = {doi:10.1063/1.50028}, url = {http://proceedings.aip.org/resource/2/apcpcs/361/1/345_1?isAuthorized=no}, author = {Baras,John S and Ball,Mike and Karne,Ramesh K and Kelley,Steve and Jang,Kap D and Plaisant, Catherine and Roussopoulos, Nick and Stathatos,Kostas and Vakhutinsky,Andrew and Jaibharat,Valluri and Whitefield,David} } @conference {16551, title = {Learning activation rules for associative networks}, booktitle = {Neural Networks, 1996., IEEE International Conference on}, volume = {1}, year = {1996}, month = {1996///}, pages = {365 - 370}, author = {Reggia, James A. and Grundstrom,E. and Berndt,R. S} } @conference {13924, title = {Local tools: an alternative to tool palettes}, booktitle = {Proceedings of the 9th annual ACM symposium on User interface software and technology}, year = {1996}, month = {1996///}, pages = {169 - 170}, author = {Bederson, Benjamin B. and Hollan,J.D. and Druin, Allison and Stewart,J. and Rogers,D. and Proft,D.} } @article {14825, title = {Matching convex polygons and polyhedra, allowing for occlusion}, journal = {Applied Computational Geometry Towards Geometric Engineering}, year = {1996}, month = {1996///}, pages = {133 - 147}, abstract = {We review our recent results on visual object recognition and reconstruction allowing for occlusion. Our scheme uses matches between convex parts of objects in the model and image to determine structure and pose, without relying on specific correspondences between local or global geometric features of the objects. We provide results determining the minimal number of regions required to uniquely determine the pose under a variety of situations, and also showing that, depending on the situation, the problem of determining pose may be a convex optimization problem that is efficiently solved, or it may be a non-convex optimization problem which has no known, efficient solution. We also relate the problem of determining pose using region matching to the problem of finding the transformation that places one polygon inside another and the problem of finding a line that intersects each of a set of 3-D volumes.}, doi = {10.1007/BFb0014491}, author = {Basri,R. and Jacobs, David W.} } @article {15007, title = {Parallel algorithms for image enhancement and segmentation by region growing, with an experimental study}, journal = {The Journal of Supercomputing}, volume = {10}, year = {1996}, month = {1996///}, pages = {141 - 168}, abstract = {This paper presents efficient and portable implementations of a powerful image enhancement process, the Symmetric Neighborhood Filter (SNF), and an image segmentation technique that makes use of the SNF and a variant of the conventional connected components algorithm which we call delta-Connected Components. We use efficient techniques for distributing and coalescing data as well as efficient combinations of task and data parallelism. The image segmentation algorithm makes use of an efficient connected components algorithm based on a novel approach for parallel merging. The algorithms have been coded in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-1 and SP-2, Cray Research T3D, Meiko Scientific CS-2, Intel Paragon, and workstation clusters. Our experimental results are consistent with the theoretical analysis (and provide the best known execution times for segmentation, even when compared with machine-specific implementations). Our test data include difficult images from the Landsat Thematic Mapper (TM) satellite data.}, doi = {10.1007/BF00130707}, author = {Bader, D.A. and JaJa, Joseph F. and Harwood,D. and Davis, Larry S.} } @conference {15010, title = {Parallel algorithms for personalized communication and sorting with an experimental study (extended abstract)}, booktitle = {Proceedings of the eighth annual ACM symposium on Parallel algorithms and architectures}, series = {SPAA {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {211 - 222}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-809-6}, doi = {10.1145/237502.237558}, url = {http://doi.acm.org/10.1145/237502.237558}, author = {Helman,David R. and Bader,David A. and JaJa, Joseph F.} } @conference {15016, title = {Practical parallel algorithms for dynamic data redistribution, median finding, and selection}, booktitle = {Parallel Processing Symposium, 1996., Proceedings of IPPS {\textquoteright}96, The 10th International}, year = {1996}, month = {1996/04//}, pages = {292 - 301}, abstract = {A common statistical problem is that of finding the median element in a set of data. This paper presents a fast and portable parallel algorithm for finding the median given a set of elements distributed across a parallel machine. In fact, our algorithm solves the general selection problem that requires the determination of the element of rank i, for an arbitrarily given integer i. Practical algorithms needed by our selection algorithm for the dynamic redistribution of data are also discussed. Our general framework is a distributed memory programming model enhanced by a set of communication primitives. We use efficient techniques for distributing, coalescing, and load balancing data as well as efficient combinations of task and data parallelism. The algorithms have been coded in SPLIT-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-1 and SP-2, Gray Research T3D, Meiko Scientific CS-2, Intel Paragon, and workstation clusters. Our experimental results illustrate the scalability and efficiency of our algorithms across different platforms and improve upon all the related experimental results known to the authors}, keywords = {algorithms;performance, algorithms;scalability;statistical, allocation;, balancing, clusters;distributed, CM-5;communication, CS-2;SPLIT-C;Thinking, data, data;median, evaluation;resource, finding;parallel, Gray, Machines, memory, model;dynamic, Paragon;Meiko, primitives;distributed, problem;workstation, Programming, redistribution;load, research, scientific, SP-1;Intel, systems;parallel, T3D;IBM}, doi = {10.1109/IPPS.1996.508072}, author = {Bader, D.A. and JaJa, Joseph F.} } @article {15017, title = {Practical parallel algorithms for personalized communication and integer sorting}, journal = {Journal of Experimental Algorithmics (JEA)}, volume = {1}, year = {1996}, month = {1996/01//}, abstract = {A fundamental challenge for parallel computing is to obtain high-level, architecture independent, algorithms which efficiently execute on general-purpose parallel machines. With the emergence of message passing standards such as MPI, it has become easier to design efficient and portable parallel algorithms by making use of these communication primitives. While existing primitives allow an assortment of collective communication routines, they do not handle an important communication event when most or all processors have non-uniformly sized personalized messages to exchange with each other. We focus in this paper on the h-relation personalized communication whose efficient implementation will allow high performance implementations of a large class of algorithms. While most previous h-relation algorithms use randomization, this paper presents a new deterministic approach for h-relation personalized communication with asymptotically optimal complexity for h>p2. As an application, we present an efficient algorithm for stable integer sorting. The algorithms presented in this paper have been coded in Split-C and run on a variety of platforms, including the Thinking Machines CM-5, IBM SP-1 and SP-2, Cray Research T3D, Meiko Scientific CS-2, and the Intel Paragon. Our experimental results are consistent with the theoretical analysis and illustrate the scalability and efficiency of our algorithms across different platforms. In fact, they seem to outperform all similar algorithms known to the authors on these platforms.}, isbn = {1084-6654}, doi = {10.1145/235141.235148}, url = {http://doi.acm.org/10.1145/235141.235148}, author = {Bader,David A. and Helman,David R. and JaJa, Joseph F.} } @conference {17940, title = {Simplification envelopes}, booktitle = {Proceedings of the 23rd annual conference on Computer graphics and interactive techniques}, series = {SIGGRAPH {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {119 - 128}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {geometric modeling, hierarchical approximation, levels-of-detail generation, model simplification, offsets, shape approximation}, isbn = {0-89791-746-4}, doi = {10.1145/237170.237220}, url = {http://doi.acm.org/10.1145/237170.237220}, author = {Cohen,Jonathan and Varshney, Amitabh and Manocha,Dinesh and Turk,Greg and Weber,Hans and Agarwal,Pankaj and Brooks,Frederick and Wright,William} } @book {12332, title = {Software synthesis from dataflow graphs}, year = {1996}, month = {1996///}, publisher = {Springer}, organization = {Springer}, author = {Bhattacharyya, Shuvra S. and Murthy,P. K and Lee,E. A} } @inbook {14259, title = {Spatiotemporal representations for visual navigation}, booktitle = {Computer Vision {\textemdash} ECCV {\textquoteright}96Computer Vision {\textemdash} ECCV {\textquoteright}96}, series = {Lecture Notes in Computer Science}, volume = {1064}, year = {1996}, month = {1996///}, pages = {671 - 684}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The study of visual navigation problems requires the integration of visual processes with motor control. Most essential in approaching this integration is the study of appropriate spatio-temporal representations which the system computes from the imagery and which serve as interfaces to all motor activities. Since representations resulting from exact quantitative reconstruction have turned out to be very hard to obtain, we argue here for the necessity of representations which can be computed easily, reliably and in real time and which recover only the information about the 3D world which is really needed in order to solve the navigational problems at hand. In this paper we introduce a number of such representations capturing aspects of 3D motion and scene structure which are used for the solution of navigational problems implemented in visual servo systems. In particular, the following three problems are addressed: (a) to change the robot{\textquoteright}s direction of motion towards a fixed direction, (b) to pursue a moving target while keeping a certain distance from the target, and (c) to follow a wall-like perimeter. The importance of the introduced representations lies in the following: \&$\#$x96; They can be extracted using minimal visual information, in particular the sign of flow measurements or the the first order spatiotemporal derivatives of the image intensity function. In that sense they are direct representations needing no intermediate level of computation such as correspondence. \&$\#$x96; They are global in the sense that they represent how three-dimensional information is globally encoded in them. Thus, they are robust representations since local errors do not affect them. \&$\#$x96; Usually, from sequences of images, three-dimensional quantities such as motion and shape are computed and used as input to control processes. The representations discussed here are given directly as input to the control procedures, thus resulting in a real time solution.}, isbn = {978-3-540-61122-6}, url = {http://dx.doi.org/10.1007/BFb0015577}, author = {LoongFah Cheong and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Buxton,Bernard and Cipolla,Roberto} } @conference {14796, title = {Tuning the performance of I/O-intensive parallel applications}, booktitle = {Proceedings of the fourth workshop on I/O in parallel and distributed systems: part of the federated computing research conference}, year = {1996}, month = {1996///}, pages = {15 - 27}, author = {Acharya, A. and Uysal, M. and Bennett, R. and Mendelson, A. and Beynon, M. and Hollingsworth, Jeffrey K and Saltz, J. and Sussman, Alan} } @article {12841, title = {Verification of an active control system using temporal process algebra}, journal = {Engineering with computers}, volume = {12}, year = {1996}, month = {1996///}, pages = {46 - 61}, author = {Elseaidy,W. M and Baugh,J. W. and Cleaveland, Rance} } @inbook {14272, title = {Video representations}, booktitle = {Recent Developments in Computer Vision}, series = {Lecture Notes in Computer Science}, volume = {1035}, year = {1996}, month = {1996///}, pages = {33 - 41}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, isbn = {978-3-540-60793-9}, url = {http://dx.doi.org/10.1007/3-540-60793-5_60}, author = {Bolle,Ruud and Aloimonos, J. and Ferm{\"u}ller, Cornelia}, editor = {Li,Stan and Mital,Dinesh and Teoh,Eam and Wang,Han} } @article {18048, title = {Almost fully-parallel parentheses matching}, journal = {Discrete applied mathematics}, volume = {57}, year = {1995}, month = {1995///}, pages = {11 - 28}, author = {Berkman,O. and Vishkin, Uzi} } @article {17918, title = {Automatic generation of multiresolution for polygonal models}, journal = {First Workshop on Simulation and Interaction in Virtual Environments}, year = {1995}, month = {1995///}, author = {Varshney, Amitabh and Agarwal,P. and Brooks,F. and Wright,W. and Weber,H.} } @article {14073, title = {cDNA expressed sequence tags of Trypanosoma brucei rhodesiense provide new insights into the biology of the parasite}, journal = {Molecular and Biochemical Parasitology}, volume = {73}, year = {1995}, month = {1995/07//}, pages = {75 - 90}, abstract = {A total of 518 expressed sequence tags (ESTs) have been generated from clones randomly selected from a cDNA library and a spliced leader sub-library of a Trypanosoma brucei rhodesiense bloodstream clone. 205 (39\%) of the clones were identified based on matches to 113 unique genes in the public databases. Of these, 71 cDNAs display significant similarities to genes in unrelated organisms encoding metabolic enzymes, signal transduction proteins, transcription factors, ribosomal proteins, histones, a proliferation-associated protein and thimet oligopeptidase, among others. 313 of the cDNAs are not related to any other sequences in the databases. These cDNA ESTs provide new avenues of research for exploring both the novel trypanosome-specific genes and the genome organization of this parasite, as well as a resource for identifying trypanosome homologs to genes expressed in other organisms.}, keywords = {cDNA, Expressed sequence tag, Trypanosoma brucei rhodesiense}, isbn = {0166-6851}, doi = {16/0166-6851(95)00098-L}, url = {http://www.sciencedirect.com/science/article/pii/016668519500098L}, author = {El-Sayed, Najib M. and Alarcon,Clara M. and Beck,John C. and Sheffield,Val C. and Donelson,John E.} } @article {16314, title = {Comparing detection methods for software requirements inspections: a replicated experiment}, journal = {IEEE Transactions on Software Engineering}, volume = {21}, year = {1995}, month = {1995/06//}, pages = {563 - 575}, abstract = {Software requirements specifications (SRS) are often validated manually. One such process is inspection, in which several reviewers independently analyze all or part of the specification and search for faults. These faults are then collected at a meeting of the reviewers and author(s). Usually, reviewers use Ad Hoc or Checklist methods to uncover faults. These methods force all reviewers to rely on nonsystematic techniques to search for a wide variety of faults. We hypothesize that a Scenario-based method, in which each reviewer uses different, systematic techniques to search for different, specific classes of faults, will have a significantly higher success rate. We evaluated this hypothesis using a 3{\texttimes}24 partial factorial, randomized experimental design. Forty eight graduate students in computer science participated in the experiment. They were assembled into sixteen, three-person teams. Each team inspected two SRS using some combination of Ad Hoc, Checklist or Scenario methods. For each inspection we performed four measurements: (1) individual fault detection rate, (2) team fault detection rate, (3) percentage of faults first identified at the collection meeting (meeting gain rate), and (4) percentage of faults first identified by an individual, but never reported at the collection meeting (meeting loss rate). The experimental results are that (1) the Scenario method had a higher fault detection rate than either Ad Hoc or Checklist methods, (2) Scenario reviewers were more effective at detecting the faults their scenarios are designed to uncover, and were no less effective at detecting other faults than both Ad Hoc or Checklist reviewers, (3) Checklist reviewers were no more effective than Ad Hoc reviewers, and (4) Collection meetings produced no net improvement in the fault detection rate-meeting gains were offset by meeting losses}, keywords = {Assembly, Computer science, Design for experiments, detection methods, Fault detection, fault detection rate, Fault diagnosis, formal specification, formal verification, Gain measurement, individual fault detection rate, Inspection, Loss measurement, nonsystematic techniques, performance evaluation, Performance gain, replicated experiment, scenario-based method, Software development management, software requirements inspections, software requirements specifications, team fault detection rate}, isbn = {0098-5589}, doi = {10.1109/32.391380}, author = {Porter, Adam and Votta,L. G. and Basili, Victor R.} } @conference {17944, title = {Defining, Computing, and Visualizing Molecular Interfaces}, booktitle = {Proceedings of the 6th conference on Visualization {\textquoteright}95}, series = {VIS {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {36{\textendash} - 36{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {A parallel, analytic approach for defining and computing the inter- and intra-molecular interfaces in three dimensions is described. The "molecular interface surfaces" are derived from approximations to the power-diagrams over the participating molecular units. For a given molecular interface our approach can generate a family of interface surfaces parametrized by alpha and beta, where alpha is the radius of the solvent molecule (also known as the probe-radius) and beta is the interface radius that defines the size of the molecular interface. Molecular interface surfaces provide biochemists with a powerful tool to study surface complementarity and to efficiently characterize the interactions during a protein-substrate docking. The complexity of our algorithm for molecular environments is O(n k \log^2{k}), where n is the number of atoms in the participating molecular units and k is the average number of neighboring atoms -- a constant, given alpha and beta.}, keywords = {Computational Biochemistry Algorithms Molecular Graphics, Connolly Surfaces, Molecular Interfaces, Molecular Surfaces, Protein-Protein Recognition}, isbn = {0-8186-7187-4}, url = {http://dl.acm.org/citation.cfm?id=832271.833834}, author = {Varshney, Amitabh and Brooks Jr,Frederick P. and Manocha,Dinesh and Wright,William V. and Richardson,David C.} } @conference {12787, title = {Efficient on-the-fly model checking for CTL}, booktitle = {, Tenth Annual IEEE Symposium on Logic in Computer Science, 1995. LICS {\textquoteright}95. Proceedings}, year = {1995}, month = {1995/06/26/29}, pages = {388 - 397}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper gives an on-the-fly algorithm for determining whether a finite-state system satisfies a formula in the temporal logic CTL. The time complexity of our algorithm matches that of the best existing {\textquotedblleft}global algorithm{\textquotedblright} for model checking in this logic, and it performs as well as the best known global algorithms for the sublogics CTL and LTL. In contrast with these approaches, however, our routine constructs the state space of the system under consideration in a need-driven fashion and will therefore perform better in practice}, keywords = {Algorithm design and analysis, Automata, computational complexity, Computer science, CTL, Encoding, finite automata, finite-state system, global algorithm, Logic, LTL, on-the-fly model checking, Performance analysis, Safety, State-space methods, sublogic, temporal logic, time complexity}, isbn = {0-8186-7050-9}, doi = {10.1109/LICS.1995.523273}, author = {Bhat,G. and Cleaveland, Rance and Grumberg,O.} } @article {12384, title = {Generating compact code from dataflow specifications of multirate signal processing algorithms}, journal = {Circuits and Systems I: Fundamental Theory and Applications, IEEE Transactions on}, volume = {42}, year = {1995}, month = {1995///}, pages = {138 - 150}, author = {Bhattacharyya, Shuvra S. and Buck,J. T and Ha,S. and Lee,E. A} } @article {17977, title = {Generating levels of detail for large-scale polygonal models}, volume = {CS-1995-20}, year = {1995}, month = {1995///}, institution = {Department of Computer Science, Duke University, North Carolina}, abstract = {We present an e cient algorithm for generating various levels-of-detail approximations for agiven polygonal model. Our algorithm guarantees that all points of an approximation are within a user-speci able distance from the original model and all points of the original model are within a distance from the approximation. Each approximation attempts to minimize the total number of polygons required to satisfy the previous constraint. We show how the problem of generating levels- of-detail approximations reduces to the classic set partition problem. The various approximations are guaranteed to be topologically consistent with the input polygonal model. The approximations can be constrained by the user to preserve any desired edges of the input model. We also propose a method to compute an estimate of the quality of the approximation generated by our algorithm with respect to the optimal approximation satisfying the same constraints. We have implemented our algorithm and have obtained experimental results of multiresolution hierarchy generation on over a thousand polygonal objects from a CAD model of a notional submarine. }, author = {Varshney, Amitabh and Agarwal,P. K and Brooks Jr,F. P and Wright,W. V and Weber,H.} } @book {13298, title = {Image Analysis and Processing: 8th International Conference, Iciap {\textquoteright}95, San Remo, Italy, September 13-15, 1995 : Proceedings}, year = {1995}, month = {1995/09/28/}, publisher = {Springer}, organization = {Springer}, abstract = {This book presents the proceedings of the 8th International Conference on Image Analysis and Processing, ICIAP {\textquoteright}95, held in Sanremo, Italy in September 1995 under the sponsorship of the International Association of Pattern Recognition IAPR.The volume presents 108 papers selected from more than 180 submissions together with six invited contributions. The papers are written by a total of 265 contributing authors and give a comprehensive state-of-the-art report on all current issues of image analysis and processing. Theoretical aspects are addressed as well as systems design and advanced applications, particularly in medical imaging.}, keywords = {Artificial intelligence, COMPUTER AIDED DESIGN, Computer Graphics, Computer science, Computer vision, Computers / CAD-CAM, Computers / Computer Graphics, Computers / Computer Science, Computers / Computer Vision \& Pattern Recognition, Computers / Image Processing, Computers / Intelligence (AI) \& Semantics, Computers / Optical Data Processing, Computers / Software Development \& Engineering / General, Electronic books, IMAGE PROCESSING, Image processing/ Congresses, Imaging systems, Optical data processing, Optical pattern recognition, software engineering}, isbn = {9783540602989}, author = {Braccini,Carlo and De Floriani, Leila and Vernazza,Gianni} } @conference {14171, title = {The information in the direction of image flow}, booktitle = {, International Symposium on Computer Vision, 1995. Proceedings}, year = {1995}, month = {1995/11/21/23}, pages = {461 - 466}, publisher = {IEEE}, organization = {IEEE}, abstract = {If instead of the full motion field, we consider only the direction of the motion field due to a rigid motion, what can we say about the information regarding the three-dimensional motion? In this paper it is shown that considering as the imaging surface the whole sphere, independently of the scene in view, two different rigid motions cannot give rise to the same directional motion field. If we restrict the image to half of a sphere (or an infinitely large image plane) two different rigid motions with instantaneous translational and rotational velocities (t1, ω1) and (t2, ω2) cannot give rise to the same directional motion field unless the plane through t1 and t2 is perpendicular to the plane through ω1 and ω2 (i.e., (t1{\texttimes}t2){\textperiodcentered}(ω1 {\texttimes}ω2)=0). In addition, in order to give a practical significance to these uniqueness results for the case of a limited field of view we also characterize the locations on the image where the motion vectors due to the different motions must have different directions. If (ω1{\texttimes}ω2){\textperiodcentered}(t1 {\texttimes}t2)=0 and certain additional constraints are met, then the two rigid motions could produce motion fields with the same direction. For this to happen the depth of each corresponding surface has to be within a certain range, defined by a second and a third order surface}, keywords = {Automation, CAMERAS, Computer vision, Educational institutions, image flow, Image motion analysis, Image sequences, imaging surface, Laboratories, Layout, Motion analysis, Motion estimation, motion field, motion vectors, Optical imaging, rigid motion, rigid motions, three-dimensional motion}, isbn = {0-8186-7190-4}, doi = {10.1109/ISCV.1995.477071}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {12213, title = {A miniaturized space-variant active vision system: Cortex-I}, journal = {Machine Vision and applications}, volume = {8}, year = {1995}, month = {1995///}, pages = {101 - 109}, author = {Bederson, Benjamin B. and Wallace,R.S. and Schwartz,E.} } @article {16210, title = {Next generation network management technology}, journal = {AIP Conference Proceedings}, volume = {325}, year = {1995}, month = {1995/01/25/}, pages = {75 - 82}, abstract = {Today{\textquoteright}s telecommunications networks are becoming increasingly large, complex, mission critical and heterogeneous in several dimensions. For example, the underlying physical transmission facilities of a given network may be {\textquoteleft}{\textquoteleft}mixed media{\textquoteright}{\textquoteright} (copper, fiber-optic, radio, and satellite); the subnetworks may be acquired from different vendors due to economic, performance, or general availability reasons; the information being transmitted over the network may be {\textquoteleft}{\textquoteleft}multimedia{\textquoteright}{\textquoteright} (video, data, voice, and images) and, finally, varying performance criteria may be imposed e.g., data transfer may require high throughput while the others, whose concern is voice communications, may require low call blocking probability. For these reasons, future telecommunications networks are expected to be highly complex in their services and operations. Due to this growing complexity and the disparity among management systems for individual sub-networks, efficient network management systems have become critical to the current and future success of telecommunications companies. This paper addresses a research and development effort which focuses on prototyping configuration management, since that is the central process of network management and all other network management functions must be built upon it. Our prototype incorporates ergonomically designed graphical user interfaces tailored to the network configuration management subsystem and to the proposed advanced object-oriented database structure. The resulting design concept follows open standards such as Open Systems Interconnection (OSI) and incorporates object oriented programming methodology to associate data with functions, permit customization, and provide an open architecture environment. {\textcopyright} 1995 American Institute of Physics}, isbn = {0094243X}, doi = {doi:10.1063/1.47255}, url = {http://proceedings.aip.org/resource/2/apcpcs/325/1/75_1?isAuthorized=no}, author = {Baras,John S and Atallah,George C and Ball,Mike and Goli,Shravan and Karne,Ramesh K and Kelley,Steve and Kumar,Harsha and Plaisant, Catherine and Roussopoulos, Nick and Schneiderman,Ben and Srinivasarao,Mulugu and Stathatos,Kosta and Teittinen,Marko and Whitefield,David} } @article {15009, title = {Parallel algorithms for image histogramming and connected components with an experimental study (extended abstract)}, journal = {ACM SIGPLAN Notices}, volume = {30}, year = {1995}, month = {1995/08//}, pages = {123 - 133}, abstract = {This paper presents efficient and portable implementations of two useful primitives in image processing algorithms, histogramming and connected components. Our general framework is a single-address space, distributed memory programming model. We use efficient techniques for distributing and coalescing data as well as efficient combinations of task and data parallelism. Our connected components algorithm uses a novel approach for parallel merging which performs drastically limited updating during iterative steps, and concludes with a total consistency update at the final step. The algorithms have been coded in Split-C and run on a variety of platforms. Our experimental results are consistent with the theoretical analysis and provide the best known execution times for these two primitives, even when compared with machine-specific implementations. More efficient implementations of Split-C will likely result in even faster execution times.}, keywords = {connected components, histogramming, IMAGE PROCESSING, image understanding, Parallel algorithms, scalable parallel processing}, isbn = {0362-1340}, doi = {10.1145/209937.209950}, url = {http://doi.acm.org/10.1145/209937.209950}, author = {Bader,David A. and JaJa, Joseph F.} } @article {13679, title = {The representation of document structure: A generic object-process approach}, volume = {CAR-TR-785}, year = {1995}, month = {1995///}, institution = {University of Maryland, College Park}, author = {Dori,D. and David Doermann and Shin,C. and Haralick,R. and Phillips,I. and Buchman,M. and Ross,D.} } @article {15022, title = {Scalable data parallel algorithms for texture synthesis using Gibbs random fields}, journal = {Image Processing, IEEE Transactions on}, volume = {4}, year = {1995}, month = {1995/10//}, pages = {1456 - 1460}, abstract = {This article introduces scalable data parallel algorithms for image processing. Focusing on Gibbs and Markov random field model representation for textures, we present parallel algorithms for texture synthesis, compression, and maximum likelihood parameter estimation, currently implemented on Thinking Machines CM-2 and CM-5. The use of fine-grained, data parallel processing techniques yields real-time algorithms for texture synthesis and compression that are substantially faster than the previously known sequential implementations. Although current implementations are on Connection Machines, the methodology presented enables machine-independent scalable algorithms for a number of problems in image processing and analysis}, keywords = {algorithms;maximum, algorithms;parallel, algorithms;scalable, algorithms;texture, analysis;image, CM-2;Thinking, CM-5;fine-grained, compression;image, compression;texture, Connection, data, estimation;model, estimation;parallel, field;Thinking, fields;Markov, likelihood, machine, Machines;Gibbs, machines;random, Parallel, parameter, processes;, processes;data, processing;image, processing;machine-independent, random, representation;real-time, scalable, synthesis;Markov, texture;maximum}, isbn = {1057-7149}, doi = {10.1109/83.465111}, author = {Bader, D.A. and JaJa, Joseph F. and Chellapa, Rama} } @article {18426, title = {SEL{\textquoteright}s software process improvement program}, journal = {Software, IEEE}, volume = {12}, year = {1995}, month = {1995/11//}, pages = {83 - 87}, abstract = {We select candidates for process change on the basis of quantified Software Engineering Laboratory (SEL) experiences and clearly defined goals for the software. After we select the changes, we provide training and formulate experiment plans. We then apply the new process to one or more production projects and take detailed measurements. We assess process success by comparing these measures with the continually evolving baseline. Based upon the results of the analysis, we adopt, discard, or revise the process}, keywords = {baseline;detailed, engineering, engineering;, evolving, improvement, Laboratory;continually, measurements;experiment, plans;production, process, program;software, projects;training;software, SEL, software}, isbn = {0740-7459}, doi = {10.1109/52.469763}, author = {Basili, Victor R. and Zelkowitz, Marvin V and McGarry,F. and Page,J. and Waligora,S. and Pajerski,R.} } @conference {12176, title = {Space-scale diagrams: understanding multiscale interfaces}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {1995}, month = {1995///}, pages = {234 - 241}, author = {Furnas,G.W. and Bederson, Benjamin B.} } @conference {18316, title = {Tracking and recognizing rigid and non-rigid facial motions using local parametric models of image motion}, booktitle = {Computer Vision, 1995. Proceedings., Fifth International Conference on}, year = {1995}, month = {1995///}, pages = {374 - 381}, author = {Black,M. J and Yacoob,Yaser} } @article {17483, title = {Vision, Graphic Design, and Visual Display}, journal = {Readings in human-computer interaction: toward the year 2000}, year = {1995}, month = {1995///}, pages = {411 - 411}, author = {Marcus,A. and Murch,G.M. and Baecker,R. and Small,I. and Mander,R. and Ahlberg,C. and Shneiderman, Ben} } @article {17512, title = {Windows of opportunity in electronic classrooms}, journal = {Communications of the ACM}, volume = {38}, year = {1995}, month = {1995/11//}, pages = {19 - 24}, abstract = {Paradigm-shifting landmark buildings are cherished by their occupants and remembered because they reshape our expectations of schools, homes, or offices. Classic examples include Thomas Jefferson{\textquoteright}s communal design of the {\textquotedblleft}academical village{\textquotedblright} at the University of Virginia where faculty and students lived close to classrooms, Frank Lloyd Wright{\textquoteright}s organic harmony with nature in Fallingwater (in western Pennsylvania) where the waterfall sounds and leafy surroundings offered a stress-reducing getaway for an urban executive, or Kevin Roche{\textquoteright}s open glass-walled Ford Foundation (in New York City) that promoted new team-oriented management strategies.}, isbn = {0001-0782}, doi = {10.1145/219717.219725}, url = {http://doi.acm.org/10.1145/219717.219725}, author = {Shneiderman, Ben and Alavi,Maryann and Norman,Kent and Borkowski,Ellen Yu} } @article {13413, title = {AAAI 1994 Spring Symposium Series Reports}, journal = {AI Magazine}, volume = {15}, year = {1994}, month = {1994/09/15/}, pages = {22 - 22}, isbn = {0738-4602}, doi = {10.1609/aimag.v15i3.1101}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1101}, author = {Woods,William and Uckun,Sendar and Kohane,Isaac and Bates,Joseph and Hulthage,Ingemar and Gasser,Les and Hanks,Steve and Gini,Maria and Ram,Ashwin and desJardins, Marie and Johnson,Peter and Etzioni,Oren and Coombs,David and Whitehead,Steven} } @article {16982, title = {AVI {\textquoteright}94: An International Workshop}, journal = {ACM SIGCHI Bulletin}, volume = {26}, year = {1994}, month = {1994/10//}, pages = {54 - 55}, abstract = {The fresh Mediterranean breezes of innovation enlivened the workshop conversations at Advanced Visual Interfaces {\textquoteright}94 (Bari, Italy June 1--4, 1994). More than 100 participants met on the flower-gardened grounds of the Grande Albergo di Villa Romanazzi Carducci, whose modern hotel plus conference center complemented the beautifully restored old villa and the marble-lined swimming pool. Being together with active professionals from Europe and America for 4 days gave us an in-depth chance to learn about each other{\textquoteright}s professional and personal outlooks. The ancient Roman architecture and the traditional Italian surroundings reminded us that the impact of our work could also last for two thousand years and shape many people{\textquoteright}s daily lives.}, isbn = {0736-6906}, doi = {10.1145/191642.1047934}, url = {http://doi.acm.org/10.1145/191642.1047934}, author = {Shneiderman, Ben and Badre,AI and Santos,Paulo} } @article {15379, title = {Calculation of head sensitivity function from 3-D magnetic fields}, journal = {Magnetics, IEEE Transactions on}, volume = {30}, year = {1994}, month = {1994/11//}, pages = {4278 - 4280}, abstract = {A head sensitivity function is calculated using 3-D magnetic fields. The 3-D magnetic fields are calculated for recorded tracks with finite widths. The magnetization in the medium is expressed in 2-D Fourier series in the plane of the film and is assumed uniform through the thickness of the film. The reproduce head is idealized. These techniques are applied to data found in the literature for very narrow tracks ( 0.5 mu;m). A surprising amount of the experimental data can be explained by the finite width of the tracks. The fine structure of the measurements can then be isolated and attributed to the particular features of the individual heads}, keywords = {3-D, fields;finite, fields;magnetic, function;magnetization;recorded, head;very, heads;magnetisation;sensitivity;, magnetic, narrow, Sensitivity, series;magnetic, tracks;Fourier, tracks;reproduce, widths;head}, isbn = {0018-9464}, doi = {10.1109/20.334060}, author = {Burke,E.R. and Gomez,R.D. and Madabhushi,R. and Mayergoyz, Issak D} } @article {17910, title = {Computing smooth molecular surfaces}, journal = {Computer Graphics and Applications, IEEE}, volume = {14}, year = {1994}, month = {1994/09//}, pages = {19 - 25}, abstract = {We consider how we set out to formulate a parallel analytical molecular surface algorithm that has expected linear complexity with respect to the total number of atoms in a molecule. To achieve this goal, we avoided computing the complete 3D regular triangulation over the entire set of atoms, a process that takes time O(n log n), where n is the number of atoms in the molecule. We aim to compute and display these surfaces at interactive rates, by taking advantage of advances in computational geometry, making further algorithmic improvements and parallelizing the computations.<>}, keywords = {3D, algorithm;smooth, algorithms;physics, analytical, atoms;three, complexity;computational, complexity;parallel, computing;, computing;surface, dimensional, geometry;interactive, geometry;parallel, improvements;computation, molecular, rates;linear, regular, surface, time;computational, triangulation;algorithmic, triangulation;computational}, isbn = {0272-1716}, doi = {10.1109/38.310720}, author = {Varshney, Amitabh and Brooks, F.P.,Jr. and Wright,W. V} } @conference {18746, title = {Design for manufacture in multi-enterprise partnerships: current status and future directions}, year = {1994}, month = {1994///}, pages = {117 - 125}, abstract = {To pursue market and technology opportunities effectively, US commercial and defense industries will be relying increasingly on multi-enterprise partnerships. Horizontal partnering combines the strengths of multiple firms in product design, manufacture, after sales support and customer service, in order to launch superior products in the global market. To support effective partnering, new approaches will be needed for integrating the activities of design, planning, and production. It is important to address both the fundamental modeling of design, process planning, and production planning in ways that account for the capabilities of potential manufacturing partners, and the development of optimization procedures to address the underlying decision problems. This paper elaborates on these issues and discusses approaches for addressing them.}, url = {http://www.csa.com/partners/viewrecord.php?requester=gs\&collection=TRD\&recid=0160471CI}, author = {Nau, Dana S. and Ball,M. O and Gupta,S.K. and Minis,I. E. and Zhang, G.} } @article {18061, title = {Finding level-ancestors in trees}, journal = {Journal of Computer and System Sciences}, volume = {48}, year = {1994}, month = {1994///}, pages = {214 - 230}, author = {Berkman,O. and Vishkin, Uzi} } @conference {17948, title = {Interactive visualization of weighted three-dimensional alpha hulls}, booktitle = {Proceedings of the tenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}94}, year = {1994}, month = {1994///}, pages = {395 - 396}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {An interactive visualization of weighted three-dimensional \&agr;-hulls is presented for static and dynamic spheres. The \&agr;-hull is analytically computed and represented by a triangulated mesh. The entire surface is computed and displayed in real-time at interactive rates. The weighted three-dimensional \&agr;-hulls are equivalent to smooth molecular surfaces of biochemistry. Biochemistry applications of interactive computation and display of \&agr;-hulls or smooth molecular surfaces are outlined.}, isbn = {0-89791-648-4}, doi = {10.1145/177424.178120}, url = {http://doi.acm.org/10.1145/177424.178120}, author = {Varshney, Amitabh and Brooks,Frederick P. and Wright,William V.} } @conference {16629, title = {Interpretation of Doppler blood flow velocity waveforms using neural networks.}, booktitle = {Proceedings of the Annual Symposium on Computer Application in Medical Care}, year = {1994}, month = {1994///}, pages = {865 - 865}, author = {Baykal,N. and Reggia, James A. and Yalabik,N. and Erkmen,A. and Beksac,M. S.} } @conference {17857, title = {Jovian: A framework for optimizing parallel I/O}, booktitle = {Scalable Parallel Libraries Conference, 1994., Proceedings of the 1994}, year = {1994}, month = {1994///}, pages = {10 - 20}, author = {Bennett, R. and Bryant,K. and Sussman, Alan and Das,R. and Saltz, J.} } @article {12380, title = {Looped schedules for dataflow descriptions of multirate signal processing algorithms}, journal = {Formal Methods in System Design}, volume = {5}, year = {1994}, month = {1994///}, pages = {183 - 205}, author = {Bhattacharyya, Shuvra S. and Lee,E. A} } @article {12216, title = {A miniature pan-tilt actuator: the spherical pointing motor}, journal = {IEEE Transactions on Robotics and Automation}, volume = {10}, year = {1994}, month = {1994/06//}, pages = {298 - 308}, abstract = {A pan-tilt mechanism is a computer-controlled actuator designed to point an object such as a camera sensor. For applications in active vision, a pan-tilt mechanism should be accurate, fast, small, inexpensive and have low power requirements. The authors have designed and constructed a new type of actuator meeting these requirements, which incorporates both pan and tilt into a single, two-degree-of-freedom device. The spherical pointing motor (SPM) consists of three orthogonal motor windings in a permanent magnetic field, configured to move a small camera mounted on a gimbal. It is an absolute positioning device and is run open-loop. The SPM is capable of panning and tilting a load of 15 grams, for example a CCD image sensor, at rotational velocities of several hundred degrees per second with a repeatability of .15{\textdegree}. The authors have also built a miniature camera consisting of a single CCD sensor chip and miniature lens assembly that fits on the rotor of this motor. In this paper, the authors discuss the theory of the SPM, which includes its basic electromagnetic principles, and derive the relationship between applied currents and resultant motor position. The authors present an automatic calibration procedure and discuss open- and closed-loop control strategies. Finally, the authors present the physical characteristics and results of their prototype}, keywords = {absolute positioning device, active vision, Actuators, Application software, Assembly, automatic calibration, camera sensor, CAMERAS, CCD image sensors, CCD sensor chip, Charge coupled devices, Charge-coupled image sensors, closed-loop control strategies, computerised control, Lenses, Magnetic fields, miniature lens assembly, miniature pan-tilt actuator, open-loop control strategies, orthogonal motor windings, pan-tilt mechanism, Permanent magnet motors, position control, Scanning probe microscopy, spherical pointing motor, two-degree-of-freedom device}, isbn = {1042-296X}, doi = {10.1109/70.294205}, author = {Bederson, Benjamin B. and Wallace,R.S. and Schwartz,E.L.} } @article {17305, title = {Navigating in hyperspace: designing a structure-based toolbox}, journal = {Communications of the ACM}, volume = {37}, year = {1994}, month = {1994/02//}, pages = {87 - 96}, isbn = {0001-0782}, doi = {10.1145/175235.175242}, url = {http://doi.acm.org/10.1145/175235.175242}, author = {Rivlin,Ehud and Botafogo,Rodrigo and Shneiderman, Ben} } @article {16217, title = {Next Generation Network Management Technology}, year = {1994}, month = {1994///}, abstract = {Today{\textquoteright}s telecommunications networks are becoming increasingly large, complex, mission critical and heterogeneous in several dimensions. For example, the underlying physical transmission facilities of a given network may be ﲭixed media (copper, fiber- optic, radio, and satellite); the sub networks may be acquired from different vendors due to economic, performance, or general availability reasons; the information being transmitted over the network may be ﲭultimedia (video, data, voice, and images) and, finally, varying performance criteria may be imposed e.g. data transfer may require high throughput while the others, whose concern is voice communications, may require low call blocking probability. For these reasons, future telecommunications networks are expected to be highly complex in their services and operations. Due to this growing complexity and the disparity among management systems for individual sub networks, efficient network management systems have become critical to the current and future success of telecommunications companies. This paper addresses a research and development effort which focuses on prototyping configuration management, since that is the central process of network management and all other network management functions must be built upon it. Our prototype incorporates ergonomically designed graphical user interfaces tailored to the network configuration management subsystem and to the proposed advanced object-oriented database structure. The resulting design concept follows open standards such as Open Systems Interconnection (OSI) and incorporates object oriented programming methodology to associate data with functions, permit customization, and provide an open architecture environment. }, keywords = {Constraints for Network Management., Network Configuration Management, network management, Object Oriented Data Base Model for Network Management, Rules, Systems Integration, Visual Information Management for Network Configuration Management}, url = {http://drum.lib.umd.edu/handle/1903/5519}, author = {Atallah,George C and Ball,Michael O and Baras,John S and Goli,Shravan K and Karne,Ramesh K and Kelley,Stephen and Kumar,Harsha P. and Plaisant, Catherine and Roussopoulos, Nick and Shneiderman, Ben and Srinivasarao,Mulugu and Stathatos,Kostas and Teittinen,Marko and Whitefield,David} } @inbook {18049, title = {On a parallel-algorithms method for string matching problems (overview)}, booktitle = {Algorithms and ComplexityAlgorithms and Complexity}, series = {Lecture Notes in Computer Science}, volume = {778}, year = {1994}, month = {1994///}, pages = {22 - 32}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, keywords = {Computer, Science}, isbn = {978-3-540-57811-6}, url = {http://dx.doi.org/10.1007/3-540-57811-0_3}, author = {Sahinalp,Suleyman and Vishkin, Uzi}, editor = {Bonuccelli,M. and Crescenzi,P. and Petreschi,R.} } @article {13460, title = {Planning-based integrated decision support systems}, journal = {Artificial Intelligence Planning Systems: Proceedings of the Second International Conference (AIPS-94)}, year = {1994}, month = {1994///}, pages = {196 - 201}, author = {Bienkowski,M.A. and desJardins, Marie} } @conference {16688, title = {A rule-based approach to prepositional phrase attachment disambiguation}, booktitle = {Proceedings of the 15th conference on Computational linguistics-Volume 2}, year = {1994}, month = {1994///}, pages = {1198 - 1204}, author = {Brill,E. and Resnik, Philip} } @conference {14579, title = {A SIMD solution to the sequence comparison problem on the MGAP}, booktitle = {International Conference on Application Specific Array Processors, 1994. Proceedings}, year = {1994}, month = {1994/08/22/24}, pages = {336 - 345}, publisher = {IEEE}, organization = {IEEE}, abstract = {Molecular biologists frequently compare an unknown biosequence with a set of other known biosequences to find the sequence which is maximally similar, with the hope that what is true of one sequence, either physically or functionally, could be true of its analogue. Even though efficient dynamic programming algorithms exist for the problem, when the size of the database is large, the time required is quite long, even for moderate length sequences. In this paper, we present an efficient pipelined SIMD solution to the sequence alignment problem on the Micro-Grain Array Processor (MGAP), a fine-grained massively parallel array of processors with nearest-neighbor connections. The algorithm compares K sequences of length O(M) with the actual sequence of length N, in O(M+N+K) time with O(MN) processors, which is AT-optimal. The implementation on the MGAP computes at the rate of about 0.1 million comparisons per second for sequences of length 128}, keywords = {AT-optimal algorithm, Biological information theory, biology computing, biosequence comparison problem, computational complexity, Computer science, Costs, database size, Databases, DNA computing, dynamic programming, dynamic programming algorithms, fine-grained massively parallel processor array, Genetics, Heuristic algorithms, maximally similar sequence, MGAP parallel computer, Micro-Grain Array Processor, Military computing, molecular biology, molecular biophysics, Nearest neighbor searches, nearest-neighbor connections, Parallel algorithms, pipeline processing, pipelined SIMD solution, sequence alignment problem, sequences}, isbn = {0-8186-6517-3}, doi = {10.1109/ASAP.1994.331791}, author = {Borah,M. and Bajwa,R. S and Hannenhalli, Sridhar and Irwin,M. J} } @article {18432, title = {Software Process Improvement in the NASA Software Engineering Laboratory.}, year = {1994}, month = {1994/12//}, institution = {CARNEGIE-MELLON UNIV PITTSBURGH PA SOFTWARE ENGINEERING INSTITUTE}, abstract = {The Software Engineering Laboratory (SEL) was established in 1976 for the purpose of studying and measuring software processes with the intent of identifying improvements that could be applied to the production of ground support software within the Flight Dynamics Division (FDD) at the National Aeronautics and Space Administration (NASA)/Goddard Space Flight Center (GSFC). The SEL has three member organizations: NASA/GSFC, the University of Maryland, and Computer Sciences Corporation (CSC). The concept of process improvement within the SEL focuses on the continual understanding of both process and product as well as goal-driven experimentation and analysis of process change within a production environment.}, keywords = {*AWARDS, *SOFTWARE ENGINEERING, *SYSTEMS ANALYSIS, *WORK MEASUREMENT, ADMINISTRATION AND MANAGEMENT, COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER PROGRAMS, COMPUTERS, data acquisition, ENVIRONMENTS, EXPERIMENTAL DATA, GROUND SUPPORT., measurement, Organizations, PE63756E, Production, SOFTWARE PROCESS IMPROVEMENT, SPI(SOFTWARE PROCESS IMPROVEMENT), SPN-19950120014}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA289912}, author = {McGarry,Frank and Pajerski,Rose and Page,Gerald and Waligora,Sharon and Basili, Victor R.} } @article {12183, title = {Space variant image processing}, journal = {International Journal of Computer Vision}, volume = {13}, year = {1994}, month = {1994///}, pages = {71 - 90}, author = {Wallace,R.S. and Ong,P.W. and Bederson, Benjamin B. and Schwartz,E.L.} } @article {15042, title = {Top-Bottom Routing around a Rectangle is as Easy as Computing Prefix Minima}, journal = {SIAM Journal on Computing}, volume = {23}, year = {1994}, month = {1994///}, pages = {449 - 465}, abstract = {A new parallel algorithm for the prefix minima problem is presented for inputs drawn from the range of integers $[1..s]$. For an input of size $n$, it runs in $O(\log \log \log s)$ time and $O(n)$ work (which is optimal). A faster algorithm is presented for the special case $s = n$; it runs in $O(\log ^ * n)$ time with optimal work. Both algorithms are for the Priority concurrent-read concurrent-write parallel random access machine (CROW PRAM). A possibly surprising outcome of this work is that, whenever the range of the input is restricted, the prefix minima problem can be solved significantly faster than the $\Omega (\log \log n)$ time lower bound in a decision model of parallel computation, as described by Valiant [SIAM J. Comput., 4 (1975), pp. 348{\textendash}355].The top-bottom routing problem, which is an important subproblem of routing wires around a rectangle in two layers, is also considered. It is established that, for parallel (and hence for serial) computation, the problem of top-bottom routing is no harder than the prefix minima problem with $s = n$, thus giving an $O(\log ^ * n)$ time optimal parallel algorithm for the top-bottom routing problem. This is one of the first nontrivial problems to be given an optimal parallel algorithm that runs in sublogarithmic time. }, keywords = {Parallel algorithms, pram algorithms, prefix minima, VLSI routing}, doi = {10.1137/S0097539791218275}, url = {http://link.aip.org/link/?SMJ/23/449/1}, author = {Berkman,Omer and JaJa, Joseph F. and Krishnamurthy,Sridhar and Thurimella,Ramakrishna and Vishkin, Uzi} } @conference {12783, title = {Verifying an intelligent structural control system: a case study}, booktitle = {Real-Time Systems Symposium, 1994., Proceedings.}, year = {1994}, month = {1994/12/07/9}, pages = {271 - 275}, publisher = {IEEE}, organization = {IEEE}, abstract = {Describes the formal verification of the timing properties of the design of an intelligent structural control system using the Concurrency Workbench, an automatic verification tool for finite-state processes. The high-level design of the system is first given in Modechart, a graphical specification language for real-time systems, and then translated into a temporal process algebra supported by the Workbench. The facilities provided by this tool are then used to analyze the system and ultimately show it to be correct}, keywords = {automatic verification tool, case study, Concurrency Workbench, Distributed computing, Distributed control, distributed processing, finite automata, finite-state processes, formal verification, graphical specification language, high-level design, intelligent control, intelligent structural control system verification, Logic, Modechart, Process algebra, Real time systems, real-time systems, Specification languages, structural engineering computing, temporal logic, temporal process algebra, time-varying systems, Timing, timing properties, visual languages}, isbn = {0-8186-6600-5}, doi = {10.1109/REAL.1994.342708}, author = {Elseaidy,W. M and Cleaveland, Rance and Baugh,J. W.} } @article {17978, title = {Bounding the number of neighbors in protein molecules}, volume = {UNC-CS-TR-93-039}, year = {1993}, month = {1993///}, institution = {Department of Computer Science, University of North Carolina at Chapel Hill}, author = {Varshney, Amitabh and Wright,W. V and Brooks Jr,F. P} } @conference {12201, title = {Control and design of the spherical pointing motor}, booktitle = {, 1993 IEEE International Conference on Robotics and Automation, 1993. Proceedings}, year = {1993}, month = {1993/05/02/6}, pages = {630-636 vol.2 - 630-636 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {A miniature pan-tilt actuator, the spherical pointing motor (SPM) has been built. The SPM is an absolute positioning device, designed to orient a small camera sensor in two degrees-of-rotational-freedom. It is 4 cm{\texttimes}5 cm{\texttimes}6 cm and weighs 160 g. The operating principle of the SPM is to orient a permanent magnet to the magnetic field induced by three orthogonal coils by applying the appropriate ratio of currents to the coils. The open-loop control and design of the SPM are described. Physical characteristics and velocity measurements of the prototype are reported. The SPM is modeled with a simple second order system. Without control, it oscillates substantially when a single impulse is applied. By applying a second impulse without feedback, the oscillation can be reduced by as much as a factor of ten}, keywords = {absolute positioning device, Actuators, camera sensor, CAMERAS, Coils, electric actuators, electric motors, Magnetic field measurement, Magnetic sensors, Open loop systems, open-loop control, orthogonal coils, pan-tilt actuator, permanent magnet, Permanent magnet motors, Permanent magnets, position control, Scanning probe microscopy, second order system, spherical pointing motor, velocity control, Velocity measurement, velocity measurements}, isbn = {0-8186-3450-2}, doi = {10.1109/ROBOT.1993.291888}, author = {Bederson, Benjamin B. and Wallace,R.S. and Schwartz,E.L.} } @inbook {16218, title = {Evaluating three museum installations of a hypertext system}, booktitle = {Sparks of innovation in human-computer interaction}, volume = {40}, year = {1993}, month = {1993///}, pages = {404 - 404}, publisher = {Intellect Books}, organization = {Intellect Books}, isbn = {9781567500783}, author = {Shneiderman, Ben and Brethauer,D. and Plaisant, Catherine and Potter,R.} } @conference {17942, title = {Fast analytical computation of Richards{\textquoteright}s smooth molecular surface}, booktitle = {Proceedings of the 4th conference on Visualization {\textquoteright}93}, series = {VIS {\textquoteright}93}, year = {1993}, month = {1993///}, pages = {300 - 307}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {An algorithm for rapid computation of Richards{\textquoteright}s smooth molecular surface is described. The entire surface is computed analytically, triangulated, and displayed at interactive rates. The faster speeds for our program have been achieved by algorithmic improvements, parallelizing the computations, and by taking advantage of the special geometrical properties of such surfaces. Our algorithm is easily parallelizable and it has a time complexity of O(k log k) over n processors, where n is the number of atoms of the molecule and k is the average number of neighbors per atom.}, isbn = {0-8186-3940-7}, url = {http://dl.acm.org/citation.cfm?id=949845.949900}, author = {Varshney, Amitabh and Brooks,Frederick P.} } @article {13703, title = {A first-pass approach for evaluating machine translation systems}, journal = {Machine Translation}, volume = {8}, year = {1993}, month = {1993///}, pages = {49 - 58}, abstract = {This paper describes a short-term survey and evaluation project that covered a large number of machine translation products and research. We discuss our evaluation approach and address certain issues and implications relevant to our findings. We represented a variety of potential users of MT systems and were faced with the task of identifying which systems would best help them solve their translation problems.}, author = {Jordan,P.W. and Dorr, Bonnie J and Benoit,J.W.} } @article {16735, title = {MANDATE: managing networks using database technology}, journal = {IEEE Journal on Selected Areas in Communications}, volume = {11}, year = {1993}, month = {1993/12//}, pages = {1360 - 1372}, abstract = {There has been a growing demand for the development of tools to manage enterprise communication networks. A management information database is the heart of a network management system-it provides the interface between all functions of the network management system and, therefore, has to provide sophisticated functionality allied with high performance. The authors introduce the design of MANDATE (MAnaging Networks using DAtabase TEchnology), a proposed database system for effectively supporting the management of large enterprise networks. The MANDATE design makes a conscious attempt to take advantage of the special characteristics of network data and transactions, and of advances in database technology, to efficiently derive some of the required management functionality}, keywords = {Communication networks, database management systems, enterprise communication networks, Heart, Information management, interface, internetworking, Local area networks, management functionality, management information database, managing networks using database technology, MANDATE, Manufacturing, network operating systems, open systems, Optical fiber cables, Research and development management, Technology management, telecommunication network management, Transaction databases, wide area networks}, isbn = {0733-8716}, doi = {10.1109/49.257929}, author = {Haritsa,J. R and Ball,M. O and Roussopoulos, Nick and Datta,A. and Baras,J. S} } @article {18068, title = {Optimal doubly logarithmic parallel algorithms based on finding all nearest smaller values}, journal = {Journal of Algorithms}, volume = {14}, year = {1993}, month = {1993///}, pages = {344 - 370}, author = {Berkman,O. and Schieber,B. and Vishkin, Uzi} } @article {18067, title = {On parallel integer merging}, journal = {Information and Computation}, volume = {106}, year = {1993}, month = {1993///}, pages = {266 - 285}, author = {Berkman,O. and Vishkin, Uzi} } @inbook {16221, title = {Scheduling home control devices: a case study of the transition from the research project to a product}, booktitle = {Sparks of innovation in human-computer interactionSparks of innovation in human-computer interaction}, year = {1993}, month = {1993///}, pages = {205 - 205}, publisher = {Intellect Books}, organization = {Intellect Books}, isbn = {9781567500783}, author = {Plaisant, Catherine and Shneiderman, Ben and Battagtia,J.} } @article {12365, title = {Scheduling synchronous dataflow graphs for efficient looping}, journal = {The Journal of VLSI Signal Processing}, volume = {6}, year = {1993}, month = {1993///}, pages = {271 - 288}, author = {Bhattacharyya, Shuvra S. and Lee,E. A} } @conference {13469, title = {SOCAP: lessons learned in automating military operations planning}, booktitle = {Proceedings of the 6th international conference on Industrial and engineering applications of artificial intelligence and expert systems}, series = {IEA/AIE{\textquoteright}93}, year = {1993}, month = {1993///}, pages = {384 - 393}, publisher = {Gordon \& Breach Science Publishers}, organization = {Gordon \& Breach Science Publishers}, isbn = {2-88124-604-4}, url = {http://dl.acm.org/citation.cfm?id=1114022.1114082}, author = {Desimone,R. and Wilkins,D. E. and Bienkowski,M. and desJardins, Marie} } @book {13885, title = {Use of lexical conceptual structure for intelligent tutoring}, year = {1993}, month = {1993///}, publisher = {University of Maryland}, organization = {University of Maryland}, abstract = {We describe the use of an LCS-based semantics for question-answeringexercises in foreign language training. We start by reviewing the LCS model and show how this representation can be used to support a question answering lesson as well as a limited domain discourse. An authoring tool for entering the relevant semantic knowledge is also described. }, author = {Dorr, Bonnie J and Hendler,J. and Blanksteen,S. and Migdalof,B.} } @conference {16976, title = {Anthropomorphism: from Eliza to Terminator 2}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}92}, year = {1992}, month = {1992///}, pages = {67 - 70}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-513-5}, doi = {10.1145/142750.142760}, url = {http://doi.acm.org/10.1145/142750.142760}, author = {Don,Abbe and Brennan,Susan and Laurel,Brenda and Shneiderman, Ben} } @article {15737, title = {Constrained Matrix Sylvester Equations}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {13}, year = {1992}, month = {1992///}, pages = {1 - 9}, abstract = {The problem of finding matrices $L$ and $T$ satisfying $TA - FT = LC$ and $TB = 0$ is considered. Existence conditions for the solution are established and an algorithm for computing the solution is derived. Conditions under which the matrix $[C^T ,T^T ]$ is full rank are also discussed. The problem arises in control theory in the design of reduced-order observers that achieve loop transfer recovery.}, keywords = {loop transfer recovery, matrix Liapunov equation, Sylvester operator}, doi = {10.1137/0613002}, url = {http://link.aip.org/link/?SML/13/1/1}, author = {Barlow,Jewel B. and Monahemi,Moghen M. and O{\textquoteright}Leary, Dianne P.} } @article {15818, title = {The Design of Reduced Order Observers with Precise Loop Transfer Recovery}, journal = {AIAA Journal of Guidance, Control, and Dynamics}, volume = {15}, year = {1992}, month = {1992///}, pages = {1320 - 1326}, author = {Monahemi,Moghen M. and Barlow,Jewel B. and O{\textquoteright}Leary, Dianne P.} } @conference {15207, title = {Efficient minimum cost matching using quadrangle inequality}, booktitle = {Foundations of Computer Science, 1992. Proceedings., 33rd Annual Symposium on}, year = {1992}, month = {1992/10//}, pages = {583 - 592}, abstract = {The authors present efficient algorithms for finding a minimum cost perfect matching, and for solving the transportation problem in bipartite graphs, G = (Red cup; Blue, Red times; Blue), where |Red| = n, |Blue| = m, n les; m, and the cost function obeys the quadrangle inequality. The first results assume that all the red points and all the blue points lie on a curve that is homeomorphic to either a line or a circle and the cost function is given by the Euclidean distance along the curve. They present a linear time algorithm for the matching problem. They generalize the method to solve the corresponding transportation problem in O((m+n)log(m+n)) time. The next result is an O(n log m) algorithm for minimum cost matching when the cost array is a bitonic Monge array. An example of this is when the red points lie on one straight line and the blue points lie on another straight line (that is not necessarily parallel to the first one). Finally, they provide a weakly polynomial algorithm for the transportation problem in which the associated cost array is a bitonic Monge array}, keywords = {algorithm;, array;, bipartite, bitonic, blue, complexity;, computational, cost, distance;, Euclidean, function;, geometry;, graph, graphs;, inequality;, linear, MATCHING, matching;, minimisation;, minimum, Monge, perfect, points;, polynomial, problem;, quadrangle, red, theory;, TIME, transportation, transportation;, weakly}, doi = {10.1109/SFCS.1992.267793}, author = {Aggarwal,A. and Bar-Noy,A. and Khuller, Samir and Kravets,D. and Schieber,B.} } @inbook {15779, title = {On the Precise Loop Transfer Recovery and Transmission Zeroes}, booktitle = {First IEEE Conference on Control ApplicationsFirst IEEE Conference on Control Applications}, year = {1992}, month = {1992/09//}, address = {Dayton, Ohio}, author = {Monahemi,M. and Barlow,J. and O{\textquoteright}Leary, Dianne P.} } @article {18074, title = {Randomized range-maxima in nearly-constant parallel time}, journal = {Computational Complexity}, volume = {2}, year = {1992}, month = {1992///}, pages = {350 - 373}, author = {Berkman,O. and Matias,Y. and Vishkin, Uzi} } @conference {17935, title = {Real-time procedural textures}, booktitle = {Proceedings of the 1992 symposium on Interactive 3D graphics}, series = {I3D {\textquoteright}92}, year = {1992}, month = {1992///}, pages = {95 - 100}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-467-8}, doi = {10.1145/147156.147171}, url = {http://doi.acm.org/10.1145/147156.147171}, author = {Rhoades,John and Turk,Greg and Bell,Andrew and State,Andrei and Neumann,Ulrich and Varshney, Amitabh} } @article {17971, title = {Six Generations of Building Walkthrough: Final Technical Report to the National Science Foundation}, year = {1992}, month = {1992///}, institution = {University of North Carolina at Chapel Hill}, address = {Chapel Hill, NC, USA}, author = {Brooks,Frederick P. and Airey,John and Alspaugh,John and Bell,Andrew and Brown,Randolph and Hill,Curtis and Nimscheck,Uwe and Rheingans,Penny and Rohlf,John and Smith,Dana and Turner,Douglass and Varshney, Amitabh and Wang,Yulan and Weber,Hans and Yuan,Xialin} } @article {16545, title = {Software approaches to segmentation analysis}, journal = {Computer Science Technical Report Series; Vol. CS-TR-2991}, year = {1992}, month = {1992///}, pages = {24 - 24}, author = {D{\textquoteright}Autrechy,C. L and Reggia, James A. and Berndt,R. S} } @article {19000, title = {Splicing signals in Drosophila: intron size, information content, and consensus sequences}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {20}, year = {1992}, month = {1992/08/25/}, pages = {4255 - 4262}, abstract = {A database of 209 Drosophila Introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger RNA splicing. A tight distribution of sizes was observed: while the smallest introns in the database are 51 nucleotides, more than half are less than 80 nucleotides in length, and most of these have lengths in the range of 59 {\textendash} 67 nucleotides. Drosophila splice sites found in large and small introns differ in only minor ways from each other and from those found in vertebrate Introns. However, larger introns have greater pyrimidlne-richness in the region between 11 and 21 nucleotides upstream of 3' splice sites. The Drosophila branchpoint consensus matrix resembles C T A A T (in which branch formation occurs at the underlined A), and differs from the corresponding mammalian signal in the absence of G at the position immediately preceding the branchpoint. The distribution of occurrences of this sequence suggests a minimum distance between 5' splice shies and branchpoints of about 38 nucleotides, and a minimum distance between 3' splice sites and branchpoints of 15 nucleotides. The methods we have used detect no information in exon sequences other than in the few nucleotides immediately adjacent to the splice sites. However, Drosophila resembles many other species in that there is a discontinuity in A + T content between exons and introns, which are A + T rich.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/20.16.4255}, url = {http://nar.oxfordjournals.org/content/20/16/4255}, author = {Mount, Stephen M. and Burks,Christian and Herts,Gerald and Stormo,Gary D. and White,Owen and Fields,Chris} } @article {18434, title = {Standards-are software engineering process standards really necessary?}, journal = {Computer}, volume = {25}, year = {1992}, month = {1992/11//}, pages = {82 - 84}, abstract = {The need for software engineering process standards-as opposed to product standards-is discussed from two different viewpoints. M.V. Zelkowitz states that process standards are generally written as policy statements on how to conduct certain processes. As such, they give the framework of the underlying model, but not enough guidance to specify details. They are fuzzy and hard to implement, and they make conformance testing extremely difficult. F.J. Buckley responds to several significant issues raised in Zelkowitz{\textquoteright}s arguments}, keywords = {conformance, engineering, engineering;standards;, process, standards;software, statements;product, testing;policy}, isbn = {0018-9162}, doi = {10.1109/2.166422}, author = {Zelkowitz, Marvin V and Buckley,F.J.} } @article {17382, title = {Structural analysis of hypertexts: identifying hierarchies and useful metrics}, journal = {ACM Transactions on Information Systems}, volume = {10}, year = {1992}, month = {1992/04//}, pages = {142 - 180}, abstract = {Hypertext users often suffer from the {\textquotedblleft}lost in hyperspace{\textquotedblright} problem: disorientation from too many jumps while traversing a complex network. One solution to this problem is improved authoring to create more comprehensible structures. This paper proposes several authoring tools, based on hypertext structure analysis.In many hypertext systems authors are encouraged to create hierarchical structures, but when writing, the hierarchy is lost because of the inclusion of cross-reference links. The first part of this paper looks at ways of recovering lost hierarchies and finding new ones, offering authors different views of the same hypertext. The second part helps authors by identifying properties of the hypertext document. Multiple metrics are developed including compactness and stratum. Compactness indicates the intrinsic connectedness of the hypertext, and stratum reveals to what degree the hypertext is organized so that some nodes must be read before others. Several existing hypertexts are used to illustrate the benefits of each technique. The collection of techniques provides a multifaceted view of the hypertext, which should allow authors to reduce undesired structural complexity and create documents that readers can traverse more easily. }, keywords = {graph theory, hierarchies, hypertext, metrics, structural analysis}, isbn = {1046-8188}, doi = {10.1145/146802.146826}, url = {http://doi.acm.org/10.1145/146802.146826}, author = {Botafogo,Rodrigo A. and Rivlin,Ehud and Shneiderman, Ben} } @conference {12172, title = {Two miniature pan-tilt devices}, booktitle = {Robotics and Automation, 1992. Proceedings., 1992 IEEE International Conference on}, year = {1992}, month = {1992///}, pages = {658 - 663}, author = {Bederson, Benjamin B. and Wallace,R.S. and Schwartz,E.L.} } @inbook {13719, title = {A two-level knowledge representation for machine translation: Lexical semantics and tense/aspect}, booktitle = {Lexical Semantics and Knowledge RepresentationLexical Semantics and Knowledge Representation}, series = {Lecture Notes in Computer Science}, volume = {627}, year = {1992}, month = {1992///}, pages = {269 - 287}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper proposes a two-level model that integrates contemporary theories of tense and aspect with lexical semantics. The model is intended to be extensible to realms outside of the temporal domain (e.g., the spatial domain). The integration of tense and aspect with lexical-semantics is especially critical in machine translation because of the lexical selection process during generation: there is often a number of lexical connective and tense/aspect possibilities that may be produced from a lexical semantic representation, which, as defined in the model presented here, is largely underspecified. Temporal/aspectual information from the source-language sentence constrains the choice of target-language terms. In turn, the target-language terms limit the possibilities for generation of tense and aspect. Thus, there is a two-way communication channel between the two processes.}, isbn = {978-3-540-55801-9}, url = {http://dx.doi.org/10.1007/3-540-55801-2_41}, author = {Dorr, Bonnie J}, editor = {Pustejovsky,James and Bergler,Sabine} } @conference {12193, title = {Voice-bandwidth visual communication through logmaps: the Telecortex}, booktitle = {Applications of Computer Vision, Proceedings, 1992., IEEE Workshop on}, year = {1992}, month = {1992///}, pages = {4 - 10}, author = {Wallace,R.S. and Bederson, Benjamin B. and Schwartz,E.L.} } @article {11929, title = {Computer based systems engineering workshop}, journal = {Software Engineering Education}, year = {1991}, month = {1991///}, pages = {149 - 163}, abstract = {Modern computer based systems are complex multi-systems consisting of many connected individual subsystems; each one of them is typically also a multicomputer system. The subsystems in a multi-system can be either geographically distributed or locally connected systems. Typical examples of computer based systems are medical systems, process control systems, communications systems, weapon systems and large information systems.The development of these complex systems requires the establishment of a new engineering discipline in its own right, Computer Based Systems Engineering {\textemdash} CBSE. The definition of the discipline, its current and future practice and the ways to establish and promote it were discussed in an international IEEE workshop held in Neve-Ilan, Israel in May 1990. The major conclusion of the workshop was that CBSE should be established as a new field in its own right. To achieve this goal, the workshop participants recommended that the IEEE Computer Society shall set up a task force for the promotion of the field, the establishment of CBSE Institutes and the development of the educational framework of CBSE. The paper describes the major findings of the workshop that led to these conclusions and recommendations. }, author = {Lavi,J. and Agrawala, Ashok K. and Buhr,R. and Jackson,K. and Jackson,M. and Lang,B.} } @inbook {15736, title = {Considerations on Loop Transfer Recovery for Non-minimum Phase Plants}, booktitle = {Proceedings of the AIAA Aircraft Design Systems and Operations MeetingProceedings of the AIAA Aircraft Design Systems and Operations Meeting}, volume = {AIAA-91-3086}, year = {1991}, month = {1991/09//}, address = {Baltimore}, author = {Monahemi,M. and Barlow,J. and O{\textquoteright}Leary, Dianne P.} } @inbook {15817, title = {The Design of Reduced Order Luenberger Observers with Precise LTR}, booktitle = {Proceedings of the AIAA Meeting on Guidance, Navigation and ControlProceedings of the AIAA Meeting on Guidance, Navigation and Control}, volume = {AIAA-91-2731}, year = {1991}, month = {1991/08//}, address = {New Orleans}, abstract = {This work concerns the design of reduced-order observers for controllable, observable, and regular systems in which the number of measurements is more than the number of controls. It uses eigenstructure assignment whereas other approaches use Kalman filter (LQG/LTR) methods. The advantages of this approach are: (1) precise LTR rather than approximate LTR, (2) no restriction to minimum phase systems, (3) finite observer gain rather than asymptotic observer gain, and (4) simpler and more efficient numerical calculation. Case studies are presented illustrating these features in aircraft control applications.}, author = {Monahemi,M. and Barlow,J. and O{\textquoteright}Leary, Dianne P.} } @inbook {17118, title = {Editing to structure a reader{\textquoteright}s experience}, booktitle = {Hypertext/hypermedia handbookHypertext/hypermedia handbook}, year = {1991}, month = {1991///}, pages = {143 - 164}, author = {Shneiderman, Ben and Kreitzberg,C. and Berk,E.} } @conference {17218, title = {Identifying aggregates in hypertext structures}, booktitle = {Proceedings of the third annual ACM conference on Hypertext}, series = {HYPERTEXT {\textquoteright}91}, year = {1991}, month = {1991///}, pages = {63 - 74}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-461-9}, doi = {10.1145/122974.122981}, url = {http://doi.acm.org/10.1145/122974.122981}, author = {Botafogo,Rodrigo A. and Shneiderman, Ben} } @conference {16332, title = {Metric-driven analysis and feedback systems for enabling empirically guided software development}, booktitle = {Proceedings of the 13th international conference on Software engineering}, year = {1991}, month = {1991///}, pages = {288 - 298}, author = {Selby,R. W and Porter, Adam and Schmidt,D. C and Berney,J.} } @article {15575, title = {Pyramid computation of neighbor distance statistics in dot patterns}, journal = {CVGIP: Graphical Models and Image Processing}, volume = {53}, year = {1991}, month = {1991/07//}, pages = {373 - 381}, abstract = {This paper describes an algorithm for computing statistics of Voronoi neighbor distances in a dot pattern, using a cellular pyramid computer, in a logarithmic number of computational steps. Given a set of dots in a square region of the digital plane, the algorithm determines with high probability the Voronoi neighbors of the dots in the interior of the region and then computes statistics of the neighbor distances. An algorithm of this type may account for the ability of humans to perceive at a glance whether the dots in a pattern are randomly or regularly spaced, i.e., their neighbor distances have high or low variance.}, isbn = {1049-9652}, doi = {10.1016/1049-9652(91)90040-Q}, url = {http://www.sciencedirect.com/science/article/pii/104996529190040Q}, author = {Banerjee,Saibal and Mount, Dave and Rosenfeld,Azriel} } @article {16514, title = {Recent applications of competitive activation mechanisms}, journal = {Neural Networks: Advances and Applications}, year = {1991}, month = {1991///}, pages = {33 - 62}, author = {Reggia, James A. and Peng,Y. and Bourret,P.} } @article {11988, title = {Image motion estimation by clustering}, journal = {International Journal of Imaging Systems and Technology}, volume = {2}, year = {1990}, month = {1990/12/01/}, pages = {345 - 355}, abstract = {Image motion is estimated by matching feature {\textquotedblleft}interest{\textquotedblright} points in different frames of video image sequences. The matching is based on local similarity of the displacement vectors. Clustering in the displacement vector space is used to determine the set of plausible match vectors. Subsequently, a similarity-based algorithm performs the actual matching. The feature points are computed using a multiple-filter image decomposition operator. The algorithm has been tested on synthetic as well as real video images. The novelty of the approach is that it handles multiple motions and performs motion segmentation.}, isbn = {1098-1098}, doi = {10.1002/ima.1850020409}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ima.1850020409/abstract}, author = {Bandopadhay, Amit and Aloimonos, J.} } @conference {16680, title = {Multiple underlying systems: Translating user requests into programs to produce answers}, booktitle = {Proceedings of the 28th annual meeting on Association for Computational Linguistics}, year = {1990}, month = {1990///}, pages = {227 - 234}, author = {Bobrow,R.J. and Resnik, Philip and Weischedel,R.M.} } @article {16969, title = {An experimental evaluation of three touch screen strategies within a hypertext database}, journal = {International Journal of Human-Computer Interaction}, volume = {1}, year = {1989}, month = {1989///}, pages = {41 - 52}, abstract = {High resolution touch screens and novel usage strategies have overcome earlier problems with parallax and inaccurate pointing. A study testing the utility of three touch screen strategies within the Hyperties hypertext environment was performed. This provided a replication and extension of an earlier touch screen strategy comparison that focused on small closely?spaced targets. The experiment compared three touch screen strategies in three experimental tasks that reflect hypertext usage. The results showed that a strategy that only uses the initial impact with the touch screen causes the user to miss the target more than other touch strategies. A statistically significant difference in errors was found. Our results should encourage system implementers and touch screen hardware designers to support ?touch mouse? strategies that enable cursor dragging on the touch screen surface.High resolution touch screens and novel usage strategies have overcome earlier problems with parallax and inaccurate pointing. A study testing the utility of three touch screen strategies within the Hyperties hypertext environment was performed. This provided a replication and extension of an earlier touch screen strategy comparison that focused on small closely?spaced targets. The experiment compared three touch screen strategies in three experimental tasks that reflect hypertext usage. The results showed that a strategy that only uses the initial impact with the touch screen causes the user to miss the target more than other touch strategies. A statistically significant difference in errors was found. Our results should encourage system implementers and touch screen hardware designers to support ?touch mouse? strategies that enable cursor dragging on the touch screen surface. }, isbn = {1044-7318}, doi = {10.1080/10447318909525956}, url = {http://www.tandfonline.com/doi/abs/10.1080/10447318909525956}, author = {Potter,Richard and Berman,Mitchell and Shneiderman, Ben} } @article {12344, title = {Gabriel: A design environment for DSP}, journal = {Acoustics, Speech and Signal Processing, IEEE Transactions on}, volume = {37}, year = {1989}, month = {1989///}, pages = {1751 - 1762}, author = {Lee,E. A and Ho,W. H and Goei,E. E and Bier,J. C and Bhattacharyya, Shuvra S.} } @conference {17215, title = {Hypertext and software engineering}, booktitle = {Proceedings of the second annual ACM conference on Hypertext}, series = {HYPERTEXT {\textquoteright}89}, year = {1989}, month = {1989///}, pages = {395 - 396}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The purpose of this panel is to bring together researchers in software engineering and hypertext and help identify the major issues in the application of hypertext technology and concepts to software engineering and vice versa.}, isbn = {0-89791-339-6}, doi = {10.1145/74224.74259}, url = {http://doi.acm.org/10.1145/74224.74259}, author = {Balzer,R. and Begeman,M. and Garg,P. K. and Schwartz,M. and Shneiderman, Ben} } @article {12023, title = {On the kinetic depth effect}, journal = {Biological cybernetics}, volume = {60}, year = {1989}, month = {1989///}, pages = {445 - 455}, author = {Aloimonos, J. and Brown, C. M.} } @conference {16602, title = {A method for interactive satellite failure diagnosis: Towards a connectionist solution}, booktitle = {NASA. Goddard Space Flight Center, The 1989 Goddard Conference on Space Applications of Artificial Intelligence p 143-152(SEE N 89-26578 20-63)}, year = {1989}, month = {1989///}, author = {Bourret,P. and Reggia, James A.} } @article {14144, title = {Some aspects of parallel implementation of the finite-element method on message passing architectures}, journal = {Journal of Computational and Applied Mathematics}, volume = {27}, year = {1989}, month = {1989/09//}, pages = {157 - 187}, abstract = {We discuss some aspects of implementing the finite-element method on parallel computers with local memory and message passing. In particular, we compare the costs of using high-order and low-order elements and of direct and iterative solvers for solving the linear systems that occur. Our model of parallel computation is a two-dimensional grid of processors chosen to be similar in shape to the underlying grid. Our main conclusions are that use of high-order methods is an effective way to achieve high accuracy for some problems, on both serial and parallel computers, and that such methods provide a natural way to achieve efficiency in parallel implementations. In addition, we show that sparse direct solvers generalize naturally to methods based on high-order elements, and that direct solvers are adequate for two-dimensional problems, especially for multiple load vectors.}, keywords = {Finite-element methods, hp-version, nested dissection, parallel computations, preconditioned conjugate gradient}, isbn = {0377-0427}, doi = {16/0377-0427(89)90365-8}, url = {http://www.sciencedirect.com/science/article/pii/0377042789903658}, author = {Babuska, I. and Elman, Howard} } @article {12005, title = {Active vision}, journal = {International Journal of Computer Vision}, volume = {1}, year = {1988}, month = {1988///}, pages = {333 - 356}, author = {Aloimonos, J. and Weiss, I. and Bandyopadhyay, A.} } @article {16517, title = {Competitive dynamics in a dual-route connectionist model of print-to-sound transformation}, journal = {Complex Systems}, volume = {2}, year = {1988}, month = {1988///}, pages = {509 - 547}, author = {Reggia, James A. and Marsland,P. M and Berndt,R. S} } @article {18415, title = {Program complexity using Hierarchical Abstract Computers}, journal = {Computer Languages}, volume = {13}, year = {1988}, month = {1988///}, pages = {109 - 123}, abstract = {A model of program complexity is introduced which combines structural control flow measures with data flow measures. This complexity measure is based upon the prime program decomposition of a program written for a Hierarchical Abstract Computer. It is shown that this measure is consistent with the ideas of information hiding and data abstraction. Because this measure is sensitive to the linear form of a program, it can be used to measure different concrete representations of the same algorithm, as in a structured and an unstructured version of the same program. Application of the measure as a model of system complexity is given for {\textquotedblleft}upstream{\textquotedblright} processes (e.g. specification and design phases) where there is no source program to measure by other techniques.}, keywords = {CASE tools, complexity, ENVIRONMENTS, measurement, Prime programs}, isbn = {0096-0551}, doi = {10.1016/0096-0551(88)90019-7}, url = {http://www.sciencedirect.com/science/article/pii/0096055188900197}, author = {Bail,William G and Zelkowitz, Marvin V} } @article {12011, title = {Robust computation of intrinsic images from multiple cues}, journal = {Advances in Computer Vision}, volume = {1}, year = {1988}, month = {1988///}, pages = {115 - 163}, author = {Aloimonos, J. and Brown, C. M.} } @inbook {17084, title = {Direct manipulation user interfaces for expert systems}, booktitle = {Expert systems: the user interfaceExpert systems: the user interface}, year = {1987}, month = {1987///}, pages = {99 - 125}, author = {Baroff,J. and Simon,R. and Gilman,F. and Shneiderman, Ben} } @book {11944, title = {A robust algorithm for determining the translation of a rigidly moving surface without correspondence, for robotics applications}, year = {1987}, month = {1987///}, publisher = {University of Maryland}, organization = {University of Maryland}, author = {Basu, A. and Aloimonos, J.} } @article {11984, title = {Determining the Translation of a Rigidly Moving Surface, without Correspondence,}, year = {1986}, month = {1986/01//}, abstract = {A method is presented for the recovery of the three-dimensional translation of a rigidly moving textured object from its images. The novelty of the method consists of the fact that four cameras are used in order to avoid the solution of the correspondence problem. The method seems to be immune to small noise percentages and to have good behavior when the noise increases. Keywords: Computer vision.}, keywords = {*IMAGE PROCESSING, *OPTICAL DETECTION, *Translation(Image processing), CAMERAS, Computer vision, COMPUTERS, IMMUNITY., MOTION, MOVING TARGETS, NOISE, OPTICAL DETECTION AND DETECTORS, SURFACES, THREE DIMENSIONAL, VISION}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA179409}, author = {Aloimonos, J. and Basu, Anup} } @article {16638, title = {Modelling reading aloud and its relevance to acquired dyslexia}, journal = {Computer methods and programs in biomedicine}, volume = {22}, year = {1986}, month = {1986///}, pages = {13 - 19}, author = {Reggia, James A. and Berndt,R. S} } @conference {11966, title = {Shape and 3-d motion from contour without point to point correspondences: General principles}, booktitle = {CVPR86}, year = {1986}, month = {1986///}, pages = {518 - 527}, author = {Aloimonos, J. and Basu, A.} } @conference {12058, title = {Contour, orientation and motion}, booktitle = {Proceedings: Image Understanding Workshop (Miami Beach, FL, December 9{\textendash}10, 1985)}, year = {1985}, month = {1985///}, pages = {129 - 136}, author = {Aloimonos, J. and Basu, A. and Brown, C. M.} } @conference {18927, title = {Deterministic parsing: A modern view}, volume = {15}, year = {1985}, month = {1985///}, pages = {15 - 33}, author = {Berwick,R. and Weinberg, Amy} } @article {16804, title = {Dynamic access control for relational views.}, journal = {INFO. SYST.}, volume = {10}, year = {1985}, month = {1985///}, pages = {361 - 369}, author = {Roussopoulos, Nick and Bader,C.} } @article {18123, title = {Optimal parallel generation of a computation tree form}, journal = {ACM Transactions on Programming Languages and Systems (TOPLAS)}, volume = {7}, year = {1985}, month = {1985///}, pages = {348 - 357}, author = {Bar-On,I. and Vishkin, Uzi} } @article {17420, title = {The Psychology of Program Documentation}, journal = {Conference on Software Maintenance, 1985, Sheraton Inn Washington-Northwest, November 11-13, 1985}, year = {1985}, month = {1985///}, pages = {191 - 191}, author = {Brooks,R. and Sheppard,S. and Shneiderman, Ben} } @article {18420, title = {Research in Programming Languages and Software Engineering.}, year = {1985}, month = {1985/12/24/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {During the past year three research papers were written and two published conference presentations were given. Titles of the published research articles are: A Stochastic Analysis of a Modified Gain Extended Kalman Filter with Applications to Estimation with Bearings only Measurements; The Modified Gain Extended Kalman Kilter and Parameter Identification in Linear Systems and Maximum Information Guidance for Homing Missiles.}, keywords = {*BEARINGS, *COMPUTER PROGRAMS, *ESTIMATES, *GUIDANCE, *KALMAN FILTERING, *LINEAR SYSTEMS, *STOCHASTIC PROCESSES, COMPUTER PROGRAMMING AND SOFTWARE, GAIN, identification, measurement, programming languages, STATISTICS AND PROBABILITY, SYSTEMS ENGINEERING., TARGET DIRECTION, RANGE AND POSITION FINDING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA186269}, author = {Gannon,John and Basili, Victor R. and Zelkowitz, Marvin V and Yeh,Raymond} } @article {16610, title = {Computer-aided assessment of transient ischemic attacks. A clinical evaluation.}, journal = {Archives of neurology}, volume = {41}, year = {1984}, month = {1984///}, pages = {1248 - 1248}, author = {Reggia, James A. and Tabb,D. R. and Price,T. R. and Banko,M. and Hebel,R.} } @conference {12012, title = {Direct processing of curvilinear sensor motion from a sequence of perspective images}, booktitle = {Proc. Workshop on Computer Vision: Representation and Control}, volume = {72}, year = {1984}, month = {1984///}, pages = {77 - 77}, author = {Aloimonos, J. and Brown, C. M.} } @article {18405, title = {Monitoring an Ada software development}, journal = {ACM SIG Ada Letters}, volume = {IV}, year = {1984}, month = {1984/07//}, pages = {32 - 39}, isbn = {1094-3641}, doi = {10.1145/998401.998402}, url = {http://doi.acm.org/10.1145/998401.998402}, author = {Basili, Victor R. and Chang,Shih and Gannon,John and Katz,Elizabeth and Panlilio-Yap,N. Monina and Ramsey,Connie Loggia and Zelkowitz, Marvin V and Bailey,John and Kruesi,Elizabeth and Sheppard,Sylvia} } @article {12001, title = {The relationship between optical flow and surface orientation}, journal = {Proc. of the 7-th ICPR, Montreal-Canada}, year = {1984}, month = {1984///}, author = {Aloimonos, J. and Brown, C. M.} } @article {18429, title = {Software Engineering Practices in the US and Japan}, journal = {Computer}, volume = {17}, year = {1984}, month = {1984/06//}, pages = {57 - 66}, isbn = {0018-9162}, doi = {10.1109/MC.1984.1659162}, author = {Zelkowitz, Marvin V and Yeh,R. T and Hamlet,R.G. and Gannon,J. D and Basili, Victor R.} } @inbook {17199, title = {Human factors of interactive software}, booktitle = {Enduser Systems and Their Human FactorsEnduser Systems and Their Human Factors}, series = {Lecture Notes in Computer Science}, volume = {150}, year = {1983}, month = {1983///}, pages = {9 - 29}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {There is intense interest about human factors issues in interactive computer systems for life-critical applications, industrial/commercial uses, and personal computing in the office or home. Primary design goals include proper functionality, adequate reliability, suitable cost, and adherence to schedule. Measurable human factors issues include time to learn, speed of performance, rate of errors, subjective satisfaction, and retention over time. Specific human factors acceptance tests are described as a natural complement to hardware and software acceptance tests. Project management ideas, information resources, and potential research directions are presented.}, isbn = {978-3-540-12273-9}, url = {http://dx.doi.org/10.1007/3-540-12273-7_16}, author = {Shneiderman, Ben}, editor = {Blaser,Albrecht and Zoeppritz,Magdalena} } @article {18988, title = {Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites}, journal = {CellCell}, volume = {32}, year = {1983}, month = {1983/02//}, pages = {461 - 472}, abstract = {We find that both human and rat U3 snRNA can function as self-priming templates for AMV reverse transcriptase in vitro. The 74 base cDNA is primed by the 3{\textquoteright} end of intact U3 snRNA, and spans the characteristically truncated 69 or 70 base U3 sequence found in four different human U3 pseudogenes. The ability of human and rat U3 snRNA to self-prime is consistent with a U3 secondary structure model derived by a comparison between rat U3 snRNA and the homologous D2 snRNA from Dictyostelium discoideum. We propose that U3 pseudogenes are generated in vivo by integration of a self-primed cDNA copy of U3 snRNA at new chromosomal sites. We also consider the possibility that the same cDNA mediates gene conversion at the 5{\textquoteright} end of bona fide U3 genes where, over the entire region spanned by the U3 cDNA, the two rat U3 sequence variants U3A and U3B are identical.}, keywords = {Animals, Base Sequence, DNA, genes, HUMANS, Nucleic Acid Conformation, Rats, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, RNA, RNA, Small Nuclear, RNA-Directed DNA Polymerase, Templates, Genetic, Transcription, Genetic}, isbn = {0092-8674}, url = {http://www.ncbi.nlm.nih.gov/pubmed/6186397}, author = {Bernstein,L B and Mount, Stephen M. and Weiner,A M} } @article {18444, title = {The Software Industry: A State of the Art Survey}, journal = {Foundations of Empirical Software Engineering: The Legacy of Victor R. Basili}, volume = {1}, year = {1983}, month = {1983///}, pages = {383 - 383}, author = {Zelkowitz, Marvin V and Yeh,R. and Hamlet,R.G. and Gannon,J. D and Basili, Victor R.} } @conference {18946, title = {Syntactic constraints and efficient parsability}, series = {ACL {\textquoteright}83}, year = {1983}, month = {1983///}, pages = {119 - 122}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {A central goal of linguistic theory is to explain why natural languages are the way they are. It has often been supposed that computational considerations ought to play a role in this characterization, but rigorous arguments along these lines have been difficult to come by. In this paper we show how a key "axiom" of certain theories of grammar, Subjacency, can be explained by appealing to general restrictions on on-line parsing plus natural constraints on the rule-writing vocabulary of grammars. The explanation avoids the problems with Marcus{\textquoteright} [1980] attempt to account for the same constraint. The argument is robust with respect to machine implementation, and thus avoids the problems that often arise when making detailed claims about parsing efficiency. It has the added virtue of unifying in the functional domain of parsing certain grammatically disparate phenomena, as well as making a strong claim about the way in which the grammar is actually embedded into an on-line sentence processor.}, doi = {10.3115/981311.981335}, url = {http://dx.doi.org/10.3115/981311.981335}, author = {Berwick,Robert C. and Weinberg, Amy} } @article {18143, title = {Complexity of finding k-path-free dominating sets in graphs}, journal = {INFO. PROC. LETT.}, volume = {14}, year = {1982}, month = {1982///}, pages = {228 - 232}, author = {Bar-Yehuda,R. and Vishkin, Uzi} } @book {17088, title = {Directions in human/computer interaction.}, year = {1982}, month = {1982///}, publisher = {ABLEX PUBL. CORP.}, organization = {ABLEX PUBL. CORP.}, address = {355 CHESTNUT ST., NORWOOD, NJ 07648, USA}, abstract = {This book presents current research in interactive system design and human information processing. The contributions offer a mixture of survey, theory, practical recommendations and experimental results reflecting the diversity of research efforts in human/computer interaction.}, author = {Badre,A. and Shneiderman, Ben} } @conference {15633, title = {Isomorphism of graphs with bounded eigenvalue multiplicity}, booktitle = {Proceedings of the fourteenth annual ACM symposium on Theory of computing}, series = {STOC {\textquoteright}82}, year = {1982}, month = {1982///}, pages = {310 - 324}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We investigate the connection between the spectrum of a graph, i.e. the eigenvalues of the adjacency matrix, and the complexity of testing isomorphism. In particular we describe two polynomial time algorithms which test isomorphism of undirected graphs whose eigenvalues have bounded multiplicity. If X and Y are graphs of eigenvalue multiplicity m, then the isomorphism of X and Y can be tested by an O(n4m+c) deterministic and by an O(n2m+c) Las Vegas algorithm, where n is the number of vertices of X and Y.}, isbn = {0-89791-070-2}, doi = {10.1145/800070.802206}, url = {http://doi.acm.org/10.1145/800070.802206}, author = {Babai,L{\'a}szl{\'o} and Grigoryev,D. Yu. and Mount, Dave} } @article {19002, title = {Structure and function of small ribonucleoproteins from eukaryotic cells}, journal = {Princess Takamatsu symposiaInt. Symp. Princess Takamatsu Cancer Res. Fund}, volume = {12}, year = {1982}, month = {1982///}, pages = {101 - 107}, abstract = {Autoantibodies from patients with systemic lupus erythematosus and other related diseases have been used to identify and study small RNA-protein complexes from mammalian cells. Properties of three previously described and several new classes of small ribonucleoproteins (RNPs) are reviewed. The sequence of Drosophila U1 RNA reveals that the region proposed to pair with 5{\textquoteright} splice junctions is conserved, while that proposed to interact with 3{\textquoteright} junctions diverges; this forces some revision of the model for U1 small nuclear (sn)RNP participation in hnRNA splicing. Further characterization of the Ro and La small RNPs has shown that the Ro small cytoplasmic (sc)RNPs are a subclass of La RNPs. Both tRNA and 5S rRNA precursors are at least transiently associated with the La protein. This raises the possibility that the La protein may be an RNA polymerase III transcription factor.}, keywords = {Antigen-Antibody Complex, Autoantibodies, HUMANS, Lupus Erythematosus, Systemic, Nucleoproteins, Ribonucleoproteins, RNA Polymerase III, Transcription, Genetic}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7166547}, author = {Steitz,J. A. and Berg,C and Gottlieb,E. and Hardin,J A and Hashimoto,C and Hendrick,J P and Hinterberger,M. and Krikeles,M and Lerner,M R and Mount, Stephen M.} } @conference {16635, title = {Bayesian classification in medicine: The transferability question}, booktitle = {Proceedings of the Fifth Annual Symposium on Computer Applications in Medical Care}, year = {1981}, month = {1981///}, pages = {250 - 252}, author = {Zagoria,R. and Reggia, James A. and Price,T. and Banko,M.} } @article {18967, title = {Are snRNPs involved in splicing?}, journal = {Nature}, volume = {283}, year = {1980}, month = {1980/01/10/}, pages = {220 - 224}, abstract = {Discrete, stable small RNA molecules are found in the nuclei of cells from a wide variety of eukaryotic organisms. Many of these small nuclear RNA (snRNA) species, which range in size from about 90 to 220 nucleotides, have been well-characterised biochemically, and some sequenced. However, their function has remained obscure. The most abundant snRNA species exist as a closely related set of RNA{\textendash}protein complexes called small nuclear ribonucleoproteins (snRNPs). snRNPs are the antigens recognised by antibodies from some patients with lupus erythematosus (LE), an autoimmune rheumatic disease. Anti-RNP antibodies from lupus sera selectively precipitate snRNP species containing Ula7 and Ulb9 RNAs from mouse Ehrlich ascites cell nuclei, whereas anti-Sm antibodies bind these snRNPs and four others containing U2, U4, US and U6 RNAs. Both antibody systems precipitate the same seven prominent nuclear proteins (molecular weight 12,000{\textendash}32,000). All molecules of the snRNAs U1, U2, U4, U5 and U6 appear to exist in the form of antigenic snRNPs9. The particles sediment at about 10S and each probably contains a single snRNA molecule. Indirect immunofluorescence studies using anti-RNP and anti-Sm sera confirm the nuclear (but non-nucleolar) location of the antigenic snRNPs. Here we present several lines of evidence that suggest a direct involvement of snRNPs in the splicing of hnRNA. Most intriguing is the observation that the nucleotide sequence at the 5' end of U1 RNA exhibits extensive complementarity to those across splice junctions in hnRNA molecules.}, doi = {10.1038/283220a0}, url = {http://www.nature.com/nature/journal/v283/n5743/abs/283220a0.html}, author = {Lerner,Michael R. and Boyle,John A. and Mount, Stephen M. and Wolin,Sandra L. and Steitz,Joan A.} } @article {18403, title = {Measuring software development characteristics in the local environment}, journal = {Computers \& Structures}, volume = {10}, year = {1979}, month = {1979/04//}, pages = {39 - 43}, abstract = {This paper discusses the characterization and analysis facilities being performed by the Software Engineering Laboratory which can be done with minimal effort on many projects. Some examples are given of the kinds of analyses that can be done to aid in managing, understanding and characterizing the development of software in a production environment.}, isbn = {0045-7949}, doi = {10.1016/0045-7949(79)90071-3}, url = {http://www.sciencedirect.com/science/article/pii/0045794979900713}, author = {Basili, Victor R. and Zelkowitz, Marvin V} } @conference {18375, title = {Analyzing medium-scale software development}, booktitle = {Proceedings of the 3rd international conference on Software engineering}, series = {ICSE {\textquoteright}78}, year = {1978}, month = {1978///}, pages = {116 - 123}, publisher = {IEEE Press}, organization = {IEEE Press}, address = {Piscataway, NJ, USA}, abstract = {The collection and analysis of data from programming projects is necessary for the appropriate evaluation of software engineering methodologies. Towards this end, the Software Engineering Laboratory was organized between the University of Maryland and NASA Goddard Space Flight Center. This paper describes the structure of the Laboratory and provides some data on project evaluation from some of the early projects that have been monitored. The analysis relates to resource forecasting using a model of the project life cycle based upon the Rayleigh equation and to error rates applying ideas developed by Belady and Lehman.}, url = {http://dl.acm.org/citation.cfm?id=800099.803200}, author = {Basili, Victor R. and Zelkowitz, Marvin V} } @conference {18407, title = {Operation of the Software Engineering Laboratory}, booktitle = {Proceedings of the Second US Army/IEEE Software Life Cycle Management Workshop. New York: Computer Societies Press}, year = {1978}, month = {1978///}, author = {Basili, Victor R. and Zelkowitz, Marvin V} } @article {17446, title = {Two experimental comparisons of relational and hierarchical database models}, journal = {International Journal of Man-Machine Studies}, volume = {10}, year = {1978}, month = {1978/11//}, pages = {625 - 637}, abstract = {The data model is a central feature which characterizes and distinguishes database management systems. This paper presents two experimental comparative studies of two prominent data models; the relational and hierarchical models. Comprehension, problem solving situation and memorization tasks were performed by undergraduate subjects. Significant effects were found for the data model, presentation order, subject background and tasks.}, isbn = {0020-7373}, doi = {10.1016/S0020-7373(78)80024-8}, url = {http://www.sciencedirect.com/science/article/pii/S0020737378800248}, author = {Brosey,Margaret and Shneiderman, Ben} } @conference {18443, title = {The software engineering laboratory: Objectives}, booktitle = {Proceedings of the fifteenth annual SIGCPR conference}, series = {SIGCPR {\textquoteright}77}, year = {1977}, month = {1977///}, pages = {256 - 269}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A great deal of time and money has been and will continue to be spent in developing software. Much effort has gone into the generation of various software development methodologies that are meant to improve both the process and the product ([MYER, 75], [BAKE, 74], [WOLV, 72]). Unfortunately, it has not always been clear what the underlying principles involved in the software development process are and what effect the methodologies have; it is not always clear what constitutes a better product. Thus progress in finding techniques that produce better, cheaper software depends on developing new deeper understandings of good software and the software development process through studying the underlying principles involved in software and the development process. At the same time we must continue to produce software. A better understanding of the factors that affect the development of software and their interrelationships is required in order to gain better insights into the underlying principles. The Software Engineering Laboratory has been established, in August 1976, at NASA Goddard Space Flight Center in cooperation with the University of Maryland to promote such understanding. The next section gives an overview of the research objectives and experiments being performed at the Laboratory. Section III contains the current list of factors that affect the software development process or product and are to be studied or neutralized. The data collection and data management activities are discussed in Section IV. The last section contains information on the current status and future plans for the Laboratory.}, doi = {10.1145/800100.803251}, url = {http://doi.acm.org/10.1145/800100.803251}, author = {Basili, Victor R. and Zelkowitz, Marvin V} } @inbook {15701, title = {A Generalized Conjugate Gradient Method for the Numerical Solution of Elliptic Partial Differential Equations}, booktitle = {Sparse Matrix ComputationsSparse Matrix Computations}, year = {1976}, month = {1976///}, pages = {309 - 332}, publisher = {Academic Press}, organization = {Academic Press}, address = {New York}, abstract = {We consider a generalized conjugate gradient method for solvingsparse, symmetric, positive-definite systems of linear equations, principally those arising from the discretization of boundary value problems for elliptic partial differential equations. The method is based on splitting off from the original coefficient matrix a symmetric, positive-definiteonethat corresponds to a more easily solvable system of equations, and then accelerating the associated iteration using conjugate gradients. Optimality and convergence properties are presented, and the relation to other methods is discussed. Several splittings for which the method seems particularly effective are also discussed, and for some, numerical examples are given }, author = {Concus,Paul and Golub, Gene H. and O{\textquoteright}Leary, Dianne P.}, editor = {Bunch,James R. and Rose,Donald J.} } @article {16973, title = {An internship in information systems: Combining computer science education with realistic problems}, journal = {SIGCSE Bull.}, volume = {8}, year = {1976}, month = {1976/07//}, pages = {80 - 83}, abstract = {Computer science graduates who become professional programmers will have a direct and substantial influence on the impact of applications, but little in traditional computer science training curriculum prepares them for this serious responsibility. Recognizing this situation, we designed a two term sequence for advanced undergraduates and masters students which would not only provide them with the required academic knowledge. The educational atmosphere that we tried to create resembles the internship phase followed in teacher training, medical schools, law schools, clinical psychology and other disciplines.}, isbn = {0097-8418}, doi = {10.1145/952991.804761}, url = {http://doi.acm.org/10.1145/952991.804761}, author = {Buck,John and Shneiderman, Ben} } @article {16724, title = {TORUS: A step towards bridging the gap between data bases and the casual user}, journal = {Information Systems}, volume = {2}, year = {1976}, month = {1976///}, pages = {49 - 64}, abstract = {This paper describes TORUS, a natural language understanding system that serves as a front end to a data base management system in order to facilitate communication with casual users. The system employs a semantic network to store knowledge about a data base of student files. This knowledge is used to find the meaning of each input statement, to decide what action to take with respect to the data base, and to select information that must be output in response to the input statement. A prototype version of TORUS has been implemented.}, isbn = {0306-4379}, doi = {16/0306-4379(76)90009-0}, url = {http://www.sciencedirect.com/science/article/pii/0306437976900090}, author = {Mylopoulos,J. and Borgida,A. and Cohen,P. and Roussopoulos, Nick and Tsotsos,J. and Wong,H.} } @conference {16721, title = {TORUS-a natural language understanding system for data management}, booktitle = {Proceedings of the Fourth International Conference on Artificial Intelligence}, year = {1975}, month = {1975///}, pages = {414 - 421}, author = {Mylopoulos,J. and Borgida,A. and Cohen,P. and Roussopoulos, Nick and Tsotsos,J. and Wong,H.} }