@article {19559, title = {System and Method for Optimal Verification of Operations on Dynamic Sets}, year = {Submitted}, abstract = {A system and method for cryptographically checking the correctness of outsourced set operations performed by an untrusted server over a dynamic collection of sets that are owned (and updated) by a trusted source is disclosed. The system and method provides new authentication mechanisms that allow any entity to publicly verify a proof attesting the correctness of primitive set operations such as intersection, union, subset and set difference. Based on a novel extension of the security properties of bilinear-map accumulators as well as on a primitive called accumulation tree, the system and method achieves optimal verification and proof complexity, as well as optimal update complexity, while incurring no extra asymptotic space overhead. The method provides an efficient proof construction, adding a logarithmic overhead to the computation of the answer of a set-operation query. Applications of interest include efficient verification of keyword search and database queries.}, url = {http://www.google.com/patents?id=mrcCAgAAEBAJ}, author = {Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikolaos} } @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 {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} } @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 {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 {20311, title = {Comparative Genomics of Escherichia coli Isolated from Skin and Soft Tissue and Other Extraintestinal Infections}, journal = {mBio}, year = {2017}, month = {Jun-09-2017}, abstract = {Escherichia coli, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs), meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs), and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic E. coli (ExPEC). It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive. In the study reported here, ExPEC E. coli isolated from SSTIs was characterized, including virulence and drug resistance profiles, and compared with isolates from patients suffering either pyelonephritis or septicemia. Results revealed that the majority of the isolates belonged to two pathogenic phylogroups, B2 and D. Approximately 67\% of the isolates were multidrug resistant (MDR), with 85\% producing extended-spectrum beta-lactamase (ESBL) and 6\% producing metallo-beta-lactamase (MBL). The blaCTX-M-15 genotype was observed in at least 70\% of the E. coli isolates in each category, conferring resistance to an extended range of beta-lactam antibiotics. Whole-genome sequencing and comparative genomics of the ExPEC isolates revealed that two of the four isolates from SSTIs, NA633 and NA643, belong to pandemic sequence type ST131, whereas functional characteristics of three of the ExPEC pathotypes revealed that they had equal capabilities to form biofilm and were resistant to human serum. Overall, the isolates from a variety of ExPEC infections demonstrated similar resistomes and virulomes and did not display any disease-specific functional or genetic coordinates. IMPORTANCE Infections caused by extraintestinal pathogenic E. coli (ExPEC) are of global concern as they result in significant costs to health care facilities management. The recent emergence of a multidrug-resistant pandemic clone, Escherichia coli ST131, is of primary concern as a global threat. In developing countries, such as India, skin and soft tissue infections (SSTIs) associated with E. coli are marginally addressed. In this study, we employed both genomic analysis and phenotypic assays to determine relationships, if any, among the ExPEC pathotypes. Similarity between antibiotic resistance and virulence profiles was observed, ST131 isolates from SSTIs were reported, and genomic similarities among strains isolated from different disease conditions were detected. This study provides functional molecular infection epidemiology insight into SSTI-associated E. coli compared with ExPEC pathotypes.}, doi = {10.1128/mBio.01070-17}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.01070-17}, author = {Ranjan, Amit and Shaik, Sabiha and Nandanwar, Nishant and Hussain, Arif and Tiwari, Sumeet K. and Semmler, Torsten and Jadhav, Savita and Wieler, Lothar H. and Alam, Munirul and Rita R Colwell and Ahmed, Niyaz}, editor = {Cossart, Pascale F.} } @article {20308, title = {Comprehensive benchmarking and ensemble approaches for metagenomic classifiers}, journal = {Genome Biology}, year = {2017}, month = {Jan-12-2017}, doi = {10.1186/s13059-017-1299-7}, url = {http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1299-7}, author = {McIntyre, Alexa B. R. and Ounit, Rachid and Afshinnekoo, Ebrahim and Prill, Robert J. and H{\'e}naff, Elizabeth and Alexander, Noah and Minot, Samuel S. and Danko, David and Foox, Jonathan and Ahsanuddin, Sofia and Tighe, Scott and Hasan, Nur A. and Subramanian, Poorani and Moffat, Kelly and Levy, Shawn and Lonardi, Stefano and Greenfield, Nick and Rita R Colwell and Rosen, Gail L. and Mason, Christopher E.} } @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 {20336, title = {Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed infection leading to necrotizing fasciitis}, journal = {Proceedings of the National Academy of Sciences}, volume = {11312161268}, year = {2016}, month = {Jul-01-2017}, pages = {722 - 727}, abstract = {Necrotizing fasciitis (NF) caused by flesh-eating bacteria is associated with high case fatality. In an earlier study, we reported infection of an immunocompetent individual with multiple strains of Aeromonas hydrophila (NF1{\textendash}NF4), the latter three constituted a clonal group whereas NF1 was phylogenetically distinct. To understand the complex interactions of these strains in NF pathophysiology, a mouse model was used, whereby either single or mixed A. hydrophila strains were injected intramuscularly. NF2, which harbors exotoxin A (exoA) gene, was highly virulent when injected alone, but its virulence was attenuated in the presence of NF1 (exoA-minus). NF1 alone, although not lethal to animals, became highly virulent when combined with NF2, its virulence augmented by cis-exoA expression when injected alone in mice. Based on metagenomics and microbiological analyses, it was found that, in mixed infection, NF1 selectively disseminated to mouse peripheral organs, whereas the other strains (NF2, NF3, and NF4) were confined to the injection site and eventually cleared. In vitro studies showed NF2 to be more effectively phagocytized and killed by macrophages than NF1. NF1 inhibited growth of NF2 on solid media, but ExoA of NF2 augmented virulence of NF1 and the presence of NF1 facilitated clearance of NF2 from animals either by enhanced priming of host immune system or direct killing via a contact-dependent mechanism.}, issn = {0027-8424}, doi = {10.1073/pnas.1523817113}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1523817113}, author = {Ponnusamy, Duraisamy and Kozlova, Elena V. and Sha, Jian and Erova, Tatiana E. and Azar, Sasha R. and Fitts, Eric C. and Kirtley, Michelle L. and Tiner, Bethany L. and Andersson, Jourdan A. and Grim, Christopher J. and Isom, Richard P. and Hasan, Nur A. and Rita R Colwell and Chopra, Ashok K.} } @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 {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} } @article {20347, title = {Hybrid Vibrio~cholerae El Tor Lacking SXT Identified as the Cause of a Cholera Outbreak in the Philippines}, journal = {mBio}, year = {2015}, month = {Jan-05-2015}, abstract = {Cholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died. Vibrio cholerae O1 was confirmed as the etiological agent. Source attribution is critical in cholera outbreaks for proper management of the disease, as well as to control spread. In this study, three V. cholerae O1 isolates from a Philippines cholera outbreak were sequenced and their genomes analyzed to determine phylogenetic relatedness to V. cholerae O1 isolates from recent outbreaks of cholera elsewhere. The Philippines V. cholerae O1 isolates were determined to be V. cholerae O1 hybrid El Tor belonging to the seventh-pandemic clade. They clustered tightly, forming a monophyletic clade closely related to V. cholerae O1 hybrid El Tor from Asia and Africa. The isolates possess a unique multilocus variable-number tandem repeat analysis (MLVA) genotype (12-7-9-18-25 and 12-7-10-14-21) and lack SXT. In addition, they possess a novel 15-kb genomic island (GI-119) containing a predicted type I restriction-modification system. The CTXΦ-RS1 array of the Philippines isolates was similar to that of V. cholerae O1 MG116926, a hybrid El Tor strain isolated in Bangladesh in 1991. Overall, the data indicate that the Philippines V. cholerae O1 isolates are unique, differing from recent V. cholerae O1 isolates from Asia, Africa, and Haiti. Furthermore, the results of this study support the hypothesis that the Philippines isolates of V. cholerae O1 are indigenous and exist locally in the aquatic ecosystem of the Philippines.}, doi = {10.1128/mBio.00047-15}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00047-15}, author = {Klinzing, David C. and Choi, Seon Young and Hasan, Nur A. and Matias, Ronald R. and Tayag, Enrique and Geronimo, Josefina and Skowronski, Evan and Rashed, Shah M. and Kawashima, Kent and Rosenzweig, C. Nicole and Gibbons, Henry S. and Torres, Brian C. and Liles, Veni and Alfon, Alicia C. and Juan, Maria Luisa and Natividad, Filipinas F. and Cebula, Thomas A. and Rita R Colwell} } @article {20319, title = {Occurrence and Diversity of Clinically Important Vibrio Species in the Aquatic Environment of Georgia}, journal = {Frontiers in Public Health}, year = {2015}, month = {10/2015}, doi = {10.3389/fpubh.2015.00232}, url = {http://journal.frontiersin.org/Article/10.3389/fpubh.2015.00232/}, author = {Kokashvili, Tamar and Whitehouse, Chris A. and Tskhvediani, Ana and Grim, Christopher J. and Elbakidze, Tinatin and Mitaishvili, Nino and Janelidze, Nino and Jaiani, Ekaterine and Haley, Bradd J. and Lashkhi, Nino and Huq, Anwar and Rita R Colwell and Tediashvili, Marina} } @article {20344, title = {Rapid Proliferation of Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae during Freshwater Flash Floods in French Mediterranean Coastal Lagoons}, journal = {Applied and Environmental Microbiology}, year = {2015}, month = {Jan-11-2015}, pages = {7600 - 7609}, abstract = {Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae of the non-O1/non-O139 serotype are present in coastal lagoons of southern France. In these Mediterranean regions, the rivers have long low-flow periods followed by short-duration or flash floods during and after heavy intense rainstorms, particularly at the end of the summer and in autumn. These floods bring large volumes of freshwater into the lagoons, reducing their salinity. Water temperatures recorded during sampling (15 to 24{\textdegree}C) were favorable for the presence and multiplication of vibrios. In autumn 2011, before heavy rainfalls and flash floods, salinities ranged from 31.4 to 36.1{\textperthousand} and concentrations of V. parahaemolyticus, V. vulnificus, and V. cholerae varied from 0 to 1.5 {\texttimes} 103 most probable number (MPN)/liter, 0.7 to 2.1 {\texttimes} 103 MPN/liter, and 0 to 93 MPN/liter, respectively. Following heavy rainstorms that generated severe flash flooding and heavy discharge of freshwater, salinity decreased, reaching 2.2 to 16.4{\textperthousand} within 15 days, depending on the site, with a concomitant increase in Vibrio concentration to ca. 104 MPN/liter. The highest concentrations were reached with salinities between 10 and 20{\textperthousand} for V. parahaemolyticus, 10 and 15{\textperthousand} for V. vulnificus, and 5 and 12{\textperthousand} for V. cholerae. Thus, an abrupt decrease in salinity caused by heavy rainfall and major flooding favored growth of human-pathogenic Vibrio spp. and their proliferation in the Languedocian lagoons. Based on these results, it is recommended that temperature and salinity monitoring be done to predict the presence of these Vibrio spp. in shellfish-harvesting areas of the lagoons.}, issn = {0099-2240}, doi = {10.1128/AEM.01848-15}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01848-15}, author = {Esteves, Kevin and Hervio-Heath, Dominique and Mosser, Thomas and Rodier, Claire and Tournoud, Marie-George and Jumas-Bilak, Estelle and Rita R Colwell and Monfort, Patrick}, editor = {Wommack, K. E.} } @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 {20362, title = {Molecular diversity and predictability of Vibrio parahaemolyticus along the Georgian coastal zone of the Black Sea}, journal = {Frontiers in Microbiology}, volume = {5}, year = {2014}, month = {Jan-01-2014}, abstract = {Vibrio parahaemolyticus is a leading cause of seafood-related gastroenteritis and is also an autochthonous member of marine and estuarine environments worldwide. One-hundred seventy strains of V. parahaemolyticus were isolated from water and plankton samples collected along the Georgian coast of the Black Sea during 28 months of sample collection. All isolated strains were tested for presence of tlh, trh, and tdh. A subset of strains were serotyped and tested for additional factors and markers of pandemicity. Twenty-six serotypes, five of which are clinically relevant, were identified. Although all 170 isolates were negative for tdh, trh, and the Kanagawa Phenomenon, 7 possessed the GS-PCR sequence and 27 the 850 bp sequence of V. parahaemolyticus pandemic strains. The V. parahaemolyticus population in the Black Sea was estimated to be genomically heterogeneous by rep-PCR and the serodiversity observed did not correlate with rep-PCR genomic diversity. Statistical modeling was used to predict presence of V. parahaemolyticus as a function of water temperature, with strongest concordance observed for Green Cape site samples (Percent of total variance = 70, P < 0.001). Results demonstrate a diverse population of V. parahaemolyticus in the Black Sea, some of which carry pandemic markers, with increased water temperature correlated to an increase in abundance of V. parahaemolyticus.}, doi = {10.3389/fmicb.2014.00045}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2014.00045}, author = {Haley, Bradd J. and Kokashvili, Tamar and Tskshvediani, Ana and Janelidze, Nino and Mitaishvili, Nino and Grim, Christopher J. and Constantin_de_Magny, Guillaume and Chen, Arlene J. and Taviani, Elisa and Eliashvili, Tamar and Tediashvili, Marina and Whitehouse, Chris A. and Rita R Colwell and Huq, Anwar} } @article {20357, title = {Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection}, journal = {mBio}, year = {2014}, month = {Jul-12-2016}, abstract = {Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy.}, doi = {10.1128/mBio.01824-14}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.01824-14}, author = {Azarian, Taj and Ali, Afsar and Johnson, Judith A. and Mohr, David and Prosperi, Mattia and Veras, Nazle M. and Jubair, Mohammed and Strickland, Samantha L. and Rashid, Mohammad H. and Alam, Meer T. and Weppelmann, Thomas A. and Katz, Lee S. and Tarr, Cheryl L. and Rita R Colwell and Morris, J. Glenn and Salemi, Marco} } @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 {20370, title = {Distribution of Virulence Genes in Clinical and Environmental Vibrio cholerae Strains in Bangladesh}, journal = {Applied and Environmental Microbiology}, year = {2013}, month = {Mar-09-2014}, pages = {5782 - 5785}, abstract = {Vibrio cholerae, an environmental organism, is a facultative human pathogen. Here, we report the virulence profiles, comprising 18 genetic markers, of 102 clinical and 692 environmental V. cholerae strains isolated in Bangladesh between March 2004 and January 2006, showing the variability of virulence determinants within the context of public health. }, issn = {0099-2240}, doi = {10.1128/AEM.01113-13}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01113-13}, author = {Hasan, Nur A. and Ceccarelli, Daniela and Grim, Christopher J. and Taviani, Elisa and Choi, Jinna and Sadique, Abdus and Alam, Munirul and Siddique, Abul K. and Sack, R. Bradley and Huq, Anwar and Rita R Colwell} } @article {20367, title = {Drug response and genetic properties of Vibrio cholerae associated with endemic cholera in north-eastern Thailand, 2003-2011}, journal = {Journal of Medical Microbiology}, year = {2013}, month = {Jan-04-2013}, pages = {599 - 609}, abstract = {Cholera, caused by Vibrio cholerae, results in significant morbidity and mortality worldwide, including Thailand. Representative V. cholerae strains associated with endemic cholera (n = 32), including strains (n = 3) from surface water sources, in Khon Kaen, Thailand (2003{\textendash}2011), were subjected to microbiological, molecular and phylogenetic analyses. According to phenotypic and related genetic data, all tested V. cholerae strains belonged to serogroup O1, biotype El Tor (ET), Inaba (IN) or Ogawa (OG). All of the strains were sensitive to gentamicin and ciprofloxacin, while multidrug-resistant (MDR) strains showing resistance to erythromycin, tetracycline, trimethoprim/sulfamethoxazole and ampicillin were predominant in 2007. V. cholerae strains isolated before and after 2007 were non-MDR. All except six diarrhoeal strains possessed ctxA and ctxB genes and were toxigenic altered ET, confirmed by MAMA-PCR and DNA sequencing. Year-wise data revealed that V. cholerae INET strains isolated between 2003 and 2004, plus one strain isolated in 2007, lacked the RS1 sequence (rstC) and toxin-linked cryptic plasmid (TLC)-specific genetic marker, but possessed CTXCL prophage genes ctxB CL and rstR CL. A sharp genetic transition was noted, namely the majority of V. cholerae strains in 2007 and all in 2010 and 2011 were not repressor genotype rstR CL but instead were rstR ET, and all ctx + strains possessed RS1 and TLC-specific genetic markers. DNA sequencing data revealed that strains isolated since 2007 had a mutation in the tcpA gene at amino acid position 64 (N{\textrightarrow}S). Four clonal types, mostly of environmental origin, including subtypes, reflected genetic diversity, while distinct signatures were observed for clonally related, altered ET from Thailand, Vietnam and Bangladesh, confirmed by distinct subclustering patterns observed in the PFGE (NotI)-based dendrogram, suggesting that endemic cholera is caused by V. cholerae indigenous to Khon Kaen.}, issn = {0022-2615}, doi = {10.1099/jmm.0.053801-0}, url = {http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.053801-0}, author = {Chomvarin, C. and Johura, F.-T. and Mannan, S. B. and Jumroenjit, W. and Kanoktippornchai, B. and Tangkanakul, W. and Tantisuwichwong, N. and Huttayananont, S. and Watanabe, H. and Hasan, N. A. and Huq, A. and Cravioto, A. and Rita R Colwell and Alam, M.} } @article {19587, title = {From Principles to Practice with Class in the First Year}, journal = {arXiv:1306.4713 [cs]}, year = {2013}, month = {2013/06/19/}, abstract = {We propose a bridge between functional and object-oriented programming in the first-year curriculum. Traditionally, curricula that begin with functional programming transition to a professional, usually object-oriented, language in the second course. This transition poses obstacles for students, and often results in confusing the details of development environments, syntax, and libraries with the fundamentals of OO programming that the course should focus on. Instead, we propose to begin the second course with a sequence of custom teaching languages which minimize the transition from the first course, and allow students to focus on core ideas. After working through the sequence of pedagogical languages, we then transition to Java, at which point students have a strong command of the basic principles. We have 3 years of experience with this course, with notable success.}, keywords = {Computer Science - Programming Languages}, url = {http://arxiv.org/abs/1306.4713}, author = {Tobin-Hochstadt, Sam and David Van Horn} } @inbook {19603, title = {Signatures of Correct Computation}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2013}, month = {2013/01/01/}, pages = {222 - 242}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We introduce Signatures of Correct Computation (SCC), a new model for verifying dynamic computations in cloud settings. In the SCC model, a trusted source outsources a function f to an untrusted server, along with a public key for that function (to be used during verification). The server can then produce a succinct signature σ vouching for the correctness of the computation of f, i.e., that some result v is indeed the correct outcome of the function f evaluated on some point a. There are two crucial performance properties that we want to guarantee in an SCC construction: (1) verifying the signature should take asymptotically less time than evaluating the function f; and (2) the public key should be efficiently updated whenever the function changes. We construct SCC schemes (satisfying the above two properties) supporting expressive manipulations over multivariate polynomials, such as polynomial evaluation and differentiation. Our constructions are adaptively secure in the random oracle model and achieve optimal updates, i.e., the function{\textquoteright}s public key can be updated in time proportional to the number of updated coefficients, without performing a linear-time computation (in the size of the polynomial). We also show that signatures of correct computation imply Publicly Verifiable Computation (PVC), a model recently introduced in several concurrent and independent works. Roughly speaking, in the SCC model, any client can verify the signature σ and be convinced of some computation result, whereas in the PVC model only the client that issued a query (or anyone who trusts this client) can verify that the server returned a valid signature (proof) for the answer to the query. Our techniques can be readily adapted to construct PVC schemes with adaptive security, efficient updates and without the random oracle model.}, 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_13}, author = {Charalampos Papamanthou and Shi, Elaine and Tamassia, Roberto}, editor = {Sahai, Amit} } @inbook {19613, title = {Streaming Authenticated Data Structures}, booktitle = {Advances in Cryptology {\textendash} EUROCRYPT 2013}, series = {Lecture Notes in Computer Science}, year = {2013}, month = {2013/01/01/}, pages = {353 - 370}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We consider the problem of streaming verifiable computation, where both a verifier and a prover observe a stream of n elements x 1,x 2,{\textellipsis},x n and the verifier can later delegate some computation over the stream to the prover. The prover must return the output of the computation, along with a cryptographic proof to be used for verifying the correctness of the output. Due to the nature of the streaming setting, the verifier can only keep small local state (e.g., logarithmic) which must be updatable in a streaming manner and with no interaction with the prover. Such constraints make the problem particularly challenging and rule out applying existing verifiable computation schemes. We propose streaming authenticated data structures, a model that enables efficient verification of data structure queries on a stream. Compared to previous work, we achieve an exponential improvement in the prover{\textquoteright}s running time: While previous solutions have linear prover complexity (in the size of the stream), even for queries executing in sublinear time (e.g., set membership), we propose a scheme with O(logM logn)O(\log M\ log n) prover complexity, where n is the size of the stream and M is the size of the universe of elements. Our schemes support a series of expressive queries, such as (non-)membership, successor, range search and frequency queries, over an ordered universe and even in higher dimensions. The central idea of our construction is a new authentication tree, called generalized hash tree. We instantiate our generalized hash tree with a hash function based on lattices assumptions, showing that it enjoys suitable algebraic properties that traditional Merkle trees lack. We exploit such properties to achieve our results.}, keywords = {Algorithm Analysis and Problem Complexity, Data Encryption, Discrete Mathematics in Computer Science, Systems and Data Security}, isbn = {978-3-642-38347-2, 978-3-642-38348-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-38348-9_22}, author = {Charalampos Papamanthou and Shi, Elaine and Tamassia, Roberto and Yi, Ke}, editor = {Johansson, Thomas and Nguyen, Phong Q.} } @article {12433, title = {A Blur-robust Descriptor with Applications to Face Recognition}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {PP}, year = {2012}, month = {2012/01/10/}, pages = {1 - 1}, abstract = {Understanding the effect of blur is an important problem in unconstrained visual analysis. We address this problem in the context of image-based recognition, by a fusion of image-formation models, and differential geometric tools. First, we discuss the space spanned by blurred versions of an image and then under certain assumptions, provide a differential geometric analysis of that space. More specifically, we create a subspace resulting from convolution of an image with a complete set of orthonormal basis functions of a pre-specified maximum size (that can represent an arbitrary blur kernel within that size), and show that the corresponding subspaces created from a clean image and its blurred versions are equal under the ideal case of zero noise, and some assumptions on the properties of blur kernels. We then study the practical utility of this subspace representation for the problem of direct recognition of blurred faces, by viewing the subspaces as points on the Grassmann manifold and present methods to perform recognition for cases where the blur is both homogenous and spatially varying. We empirically analyze the effect of noise, as well as the presence of other facial variations between the gallery and probe images, and provide comparisons with existing approaches on standard datasets.}, keywords = {Blur, convolution, Face, face recognition, Grassmann manifold, Kernel, Manifolds, NOISE, PROBES}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2012.15}, author = {Gopalan,R. and Taheri, S. and Turaga,P. and Chellapa, Rama} } @article {12853, title = {Conversion of viable but nonculturable enteric bacteria to culturable by co-culture with eukaryotic cells}, journal = {Microbiology and Immunology}, volume = {56}, year = {2012}, month = {2012/04/27/}, pages = {342 - 345}, abstract = {Viable but nonculturable (VBNC) Vibrio cholerae non-O1/non-O139, V. parahaemolyticus, enterohemorrhagic Escherichia coli, enterotoxigenic E. coli, enteropathogenic E. coli, Shigella flexneri, and Salmonella enterica were converted to the culturable state by co-culture with selected eukaryotic cells, e.g., HT-29, Caco-2, T84, HeLa, Intestine 407, and CHO cells.}, keywords = {conversion to culturability, enteric bacteria, viable but nonculturable}, isbn = {1348-0421}, doi = {10.1111/j.1348-0421.2012.00440.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2012.00440.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Senoh,Mitsutoshi and Ghosh-Banerjee,Jayeeta and Ramamurthy,Thandavarayan and Rita R Colwell and Miyoshi,Shin-ichi and Nair,G. Balakrish and Takeda,Yoshifumi} } @article {19128, title = {Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease}, journal = {PloS one}, volume = {7}, year = {2012}, month = {2012}, abstract = {The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ~90\%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.}, author = {Liu,B. and Faller, L.L. and Klitgord, N. and Mazumdar, V. and Ghodsi,M. and Sommer, D.D. and Gibbons, T.R. and Treangen, T.J. and Chang, Y.C. and Li,S.} } @article {20376, title = {Detection, Isolation, and Identification of Vibrio cholerae from the Environment}, journal = {Current Protocols in Microbiology}, volume = {26}, year = {2012}, month = {08/2012}, publisher = {John Wiley \& Sons, Inc.}, chapter = {Unit 6A.5}, address = {Hoboken, NJ, USA}, abstract = {Recent molecular advances in microbiology have greatly improved the detection of bacterial pathogens in the environment. These improvements and a downward trend in the cost of molecular detection methods have contributed to increased frequency of detection of pathogenic microorganisms where traditional culture-based detection methods have failed. Culture methods also have been greatly improved, and the confluence of the two suites of methods provides a powerful tool for detection, isolation, and characterization of pathogens. While molecular detection provides data on the presence and type of pathogens, culturing methods allow a researcher to preserve the organism of interest for {\textquotedblleft}-omics{\textquotedblright} studies, such as genomic, metabolomic, secretomic, and transcriptomic analysis, which are rapidly becoming more affordable. This has yielded a clearer understanding of the ecology and epidemiology of microorganisms that cause disease. In this unit, we present commonly accepted methods for isolation, detection, and characterization of V. cholerae, providing more extensive knowledge of the ecology and epidemiology of this organism. This unit has been fully revised and updated from the earlier version with the latest knowledge and additional information not previously included. Curr. Protoc. Microbiol. 26:6A.5.1-6A.5.51. {\textcopyright} 2012 by John Wiley \& Sons, Inc. }, doi = {10.1002/9780471729259.mc06a05s26}, url = {http://doi.wiley.com/10.1002/9780471729259.mc06a05s26}, author = {Huq, Anwar and Haley, Bradd J. and Taviani, Elisa and Chen, Arlene and Hasan, Nur A. and Rita R Colwell}, editor = {Coico, Richard and Kowalik, Tim and Quarles, John and Stevenson, Brian and Taylor, Ron} } @article {19612, title = {Efficient Verification of Web-content Searching Through Authenticated Web Crawlers}, journal = {Proc. VLDB Endow.}, volume = {5}, year = {2012}, month = {2012/06//}, pages = {920 - 931}, abstract = {We consider the problem of verifying the correctness and completeness of the result of a keyword search. We introduce the concept of an authenticated web crawler and present its design and prototype implementation. An authenticated web crawler is a trusted program that computes a specially-crafted signature over the web contents it visits. This signature enables (i) the verification of common Internet queries on web pages, such as conjunctive keyword searches---this guarantees that the output of a conjunctive keyword search is correct and complete; (ii) the verification of the content returned by such Internet queries---this guarantees that web data is authentic and has not been maliciously altered since the computation of the signature by the crawler. In our solution, the search engine returns a cryptographic proof of the query result. Both the proof size and the verification time are proportional only to the sizes of the query description and the query result, but do not depend on the number or sizes of the web pages over which the search is performed. As we experimentally demonstrate, the prototype implementation of our system provides a low communication overhead between the search engine and the user, and fast verification of the returned results by the user.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=2336664.2336666}, author = {Goodrich, Michael T. and Charalampos Papamanthou and Nguyen, Duy and Tamassia, Roberto and Lopes, Cristina Videira and Ohrimenko, Olga and Triandopoulos, Nikos} } @conference {Ture:2012:ECT:2382029.2382088, title = {Encouraging consistent translation choices}, booktitle = {Proceedings of the 2012 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies}, series = {NAACL HLT {\textquoteright}12}, year = {2012}, pages = {417{\textendash}426}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, isbn = {978-1-937284-20-6}, url = {http://dl.acm.org/citation.cfm?id=2382029.2382088}, author = {Ture, Ferhan and Oard, Douglas and Resnik, Philip} } @article {16266, title = {GAGE: A Critical Evaluation of Genome Assemblies and Assembly Algorithms}, journal = {Genome Research}, volume = {22}, year = {2012}, month = {2012}, pages = {557 - 567}, abstract = {New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previously unsequenced organisms. The lowest-cost technology can generate deep coverage of most species, including mammals, in just a few days. The sequence data generated by one of these projects consist of millions or billions of short DNA sequences (reads) that range from 50 to 150 nt in length. These sequences must then be assembled de novo before most genome analyses can begin. Unfortunately, genome assembly remains a very difficult problem, made more difficult by shorter reads and unreliable long-range linking information. In this study, we evaluated several of the leading de novo assembly algorithms on four different short-read data sets, all generated by Illumina sequencers. Our results describe the relative performance of the different assemblers as well as other significant differences in assembly difficulty that appear to be inherent in the genomes themselves. Three overarching conclusions are apparent: first, that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome; second, that the degree of contiguity of an assembly varies enormously among different assemblers and different genomes; and third, that the correctness of an assembly also varies widely and is not well correlated with statistics on contiguity. To enable others to replicate our results, all of our data and methods are freely available, as are all assemblers used in this study.}, doi = {10.1101/gr.131383.111}, url = {http://genome.cshlp.org/content/22/3/557}, author = {Salzberg,Steven L. and Phillippy,Adam M and Zimin,Aleksey and Puiu,Daniela and Magoc,Tanja and Koren,Sergey and Treangen,Todd J and Schatz,Michael C and Delcher,Arthur L. and Roberts,Michael and Mar{\c c}ais,Guillaume and Pop, Mihai and Yorke,James A.} } @article {20384, title = {Genomic analysis of ICE Vch Ban8: An atypical genetic element in Vibrio cholerae}, journal = {FEBS Letters}, year = {2012}, month = {Apr-06-2012}, pages = {1617 - 1621}, abstract = {Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non-toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.}, doi = {10.1016/j.febslet.2012.03.064}, url = {http://doi.wiley.com/10.1016/j.febslet.2012.03.064}, author = {Taviani, Elisa and Spagnoletti, Matteo and Ceccarelli, Daniela and Haley, Bradd J. and Hasan, Nur A. and Chen, Arlene and Colombo, Mauro M. and Huq, Anwar and Rita R Colwell} } @article {20386, title = {Genomic diversity of 2010 Haitian cholera outbreak strains}, journal = {Proceedings of the National Academy of Sciences}, year = {2012}, month = {05/2012}, pages = {E2010 - E2017}, issn = {0027-8424}, doi = {10.1073/pnas.1207359109}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1207359109}, author = {Hasan, N. A. and Choi, S. Y. and Eppinger, M. and Clark, P. W. and Chen, A. and Alam, M. and Haley, B. J. and Taviani, E. and Hine, E. and Su, Q. and Tallon, L. J. and Prosper, J. B. and Furth, K. and Hoq, M. M. and Li, H. and Fraser-Liggett, C. M. and Cravioto, A. and Huq, A. and Ravel, J. and Cebula, T. A. and Rita R Colwell} } @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 {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 {14492, title = {Privacy in Social Networks}, journal = {Synthesis Lectures on Data Mining and Knowledge Discovery}, volume = {3}, year = {2012}, month = {2012///}, pages = {1 - 85}, author = {Zheleva,E. and Terzi,E. and Getoor, Lise} } @article {16030, title = {Querying event sequences by exact match or similarity search: Design and empirical evaluation}, journal = {Interacting with Computers}, volume = {24}, year = {2012}, month = {2012/03//}, pages = {55 - 68}, abstract = {Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Most graphical user interfaces for database search use an exact match approach, which is often effective, but near misses may also be of interest. We describe a new similarity search interface, in which users specify a query by simply placing events on a blank timeline and retrieve a similarity-ranked list of results. Behind this user interface is a new similarity measure for event sequences which the users can customize by four decision criteria, enabling them to adjust the impact of missing, extra, or swapped events or the impact of time shifts. We describe a use case with Electronic Health Records based on our ongoing collaboration with hospital physicians. A controlled experiment with 18 participants compared exact match and similarity search interfaces. We report on the advantages and disadvantages of each interface and suggest a hybrid interface combining the best of both.}, keywords = {Event sequence, Similan, similarity measure, Similarity Search, temporal categorical data, Temporal query interface}, isbn = {0953-5438}, doi = {10.1016/j.intcom.2012.01.003}, url = {http://www.sciencedirect.com/science/article/pii/S0953543812000124}, author = {Wongsuphasawat,Krist and Plaisant, Catherine and Taieb-Maimon,Meirav and Shneiderman, Ben} } @inbook {18597, title = {Re-wiring Activity of Malicious Networks}, booktitle = {Passive and Active MeasurementPassive and Active Measurement}, series = {Lecture Notes in Computer Science}, volume = {7192}, year = {2012}, month = {2012///}, pages = {116 - 125}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper studies the AS-level re-wiring dynamics (changes in the connectivity) of malicious networks. Anecdotal evidence suggests that some malicious ASes that are primarily involved in nefarious activities on the Internet, were sequentially de-peered by providers before their final cut-off (as occurred in the well-publicized cases of Atrivo/Intercage). We present the first systematic study of the re-wiring dynamics of malicious ASes. We tracked the ASes that were listed by Hostexploit over the last two years and compared their AS-level re-wiring dynamics with non-reported ASes. Using a publicly available dataset of Customer-Provider (CP) relations in the Internet{\textquoteright}s AS graph, we studied how interconnection between autonomous systems evolves, both for ASes that provide connectivity for attackers and ASes that were not reported as malicious. We find that malicious networks are more aggressive both in forming links with providers and changing their upstream connectivity than other ASes. Our results indicate that the re-wiring dynamics of the networks that host attacks are stable over time, despite the evolving nature of the attacks themselves, which suggests that existing defense mechanisms could benefit from incorporating these features.}, keywords = {Computer science}, isbn = {978-3-642-28536-3}, url = {http://www.springerlink.com/content/95vn833728404877/abstract/}, author = {Konte,Maria and Feamster, Nick}, editor = {Taft,Nina and Ricciato,Fabio} } @article {14398, title = {TACI: Taxonomy-Aware Catalog Integration}, journal = {IEEE Transactions on Knowledge and Data Engineering (TKDE)}, year = {2012}, month = {2012///}, abstract = {A fundamental data integration task faced by online commercial portals and commerce search engines is the integration of products coming from multiple providers to their product catalogs. In this scenario, the commercial portal has its own taxonomy (the {\textquotedblleft}master taxonomy{\textquotedblright}), while each data provider organizes its products into a different taxonomy (the {\textquotedblleft}provider taxonomy{\textquotedblright}). In this paper, we consider the problem of categorizing products from the data providers into the master taxonomy, while making use of the provider taxonomy information. Our approach is based on a taxonomy-aware processing step that adjusts the results of a text-based classifier to ensure that products that are close together in the provider taxonomy remain close in the master taxonomy. We formulate this intuition as a structured prediction optimization problem. To the best of our knowledge, this is the first approach that leverages the structure of taxonomies in order to enhance catalog integration. We propose algorithms that are scalable and thus applicable to the large datasets that are typical on the Web. We evaluate our algorithms on real-world data and we show that taxonomy-aware classification provides a significant improvement over existing approaches.}, author = {Papadimitriou,P. and Tsaparas,P. and Fuxman,A. and Getoor, Lise} } @conference {16031, title = {Towards event sequence representation, reasoning and visualization for EHR data}, booktitle = {Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium}, series = {IHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {801 - 806}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Efficient analysis of event sequences and the ability to answer time-related, clinically important questions can accelerate clinical research in several areas such as causality assessments, decision support systems, and retrospective studies. The Clinical Narrative Temporal Reasoning Ontology (CNTRO)-based system is designed for semantically representing, annotating, and inferring temporal relations and constraints for clinical events in Electronic Health Records (EHR) represented in both structured and unstructured ways. The LifeFlow system is designed to support an interactive exploration of event sequences using visualization techniques. The combination of the two systems will provide a comprehensive environment for users to visualize inferred temporal relationships from EHR data. This paper discusses our preliminary efforts on connecting the two systems and the benefits we envision from such an environment.}, keywords = {ehr, semantic web, temporal relation reasoning, time trend visualization}, isbn = {978-1-4503-0781-9}, doi = {10.1145/2110363.2110461}, url = {http://doi.acm.org/10.1145/2110363.2110461}, author = {Tao,Cui and Wongsuphasawat,Krist and Clark,Kimberly and Plaisant, Catherine and Shneiderman, Ben and Chute,Christopher G.} } @article {15115, title = {Two-server password-only authenticated key exchange}, journal = {Journal of Computer and System Sciences}, volume = {78}, year = {2012}, month = {2012/03//}, pages = {651 - 669}, abstract = {Typical protocols for password-based authentication assume a single server that stores all the information (e.g., the password) necessary to authenticate a user. An inherent limitation of this approach, assuming low-entropy passwords are used, is that the user's password is exposed if this server is ever compromised. To address this issue, it has been suggested to share a user's password information among multiple servers, and to have these servers cooperate (possibly in a threshold manner) when the user wants to authenticate. We show here a two-server version of the password-only key-exchange protocol of Katz, Ostrovsky, and Yung (the KOY protocol). Our work gives the first secure two-server protocol for the password-only setting (in which the user need remember only a password, and not the servers' public keys), and is the first two-server protocol (in any setting) with a proof of security in the standard model. Our work thus fills a gap left by the work of MacKenzie et al. (2006) [31] and Di Raimondo and Gennaro (2006) [16]. As an additional benefit of our work, we show modifications that improve the efficiency of the original KOY protocol.}, keywords = {Key-exchange protocols, passwords}, isbn = {0022-0000}, doi = {10.1016/j.jcss.2011.09.005}, url = {http://www.sciencedirect.com/science/article/pii/S0022000011001048}, author = {Katz, Jonathan and MacKenzie,Philip and Taban,Gelareh and Gligor,Virgil} } @article {19618, title = {Verifying Search Results Over Web Collections}, journal = {arXiv:1204.5446 [cs]}, year = {2012}, month = {2012/04/24/}, abstract = {Searching accounts for one of the most frequently performed computations over the Internet as well as one of the most important applications of outsourced computing, producing results that critically affect users{\textquoteright} decision-making behaviors. As such, verifying the integrity of Internet-based searches over vast amounts of web contents is essential. We provide the first solution to this general security problem. We introduce the concept of an authenticated web crawler and present the design and prototype implementation of this new concept. An authenticated web crawler is a trusted program that computes a special "signature" $s$ of a collection of web contents it visits. Subject to this signature, web searches can be verified to be correct with respect to the integrity of their produced results. This signature also allows the verification of complicated queries on web pages, such as conjunctive keyword searches. In our solution, along with the web pages that satisfy any given search query, the search engine also returns a cryptographic proof. This proof, together with the signature $s$, enables any user to efficiently verify that no legitimate web pages are omitted from the result computed by the search engine, and that no pages that are non-conforming with the query are included in the result. An important property of our solution is that the proof size and the verification time both depend solely on the sizes of the query description and the query result, but not on the number or sizes of the web pages over which the search is performed. Our authentication protocols are based on standard Merkle trees and the more involved bilinear-map accumulators. As we experimentally demonstrate, the prototype implementation of our system gives a low communication overhead between the search engine and the user, and allows for fast verification of the returned results on the user side.}, keywords = {Computer Science - Cryptography and Security}, url = {http://arxiv.org/abs/1204.5446}, author = {Goodrich, Michael T. and Nguyen, Duy and Ohrimenko, Olga and Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikos and Lopes, Cristina Videira} } @article {19717, title = {Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.}, journal = {PLoS Negl Trop Dis}, volume = {6}, year = {2012}, month = {2012}, pages = {e1853}, abstract = {

The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.

}, keywords = {DNA, Bacterial, Evolution, Molecular, Gene Transfer, Horizontal, Genome, Bacterial, Genomic islands, HUMANS, Leptospira, Molecular Sequence Data, Multigene Family, Prophages, Sequence Analysis, DNA, Virulence factors}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0001853}, author = {Ricaldi, Jessica N and Fouts, Derrick E and Jeremy D Selengut and Harkins, Derek M and Patra, Kailash P and Moreno, Angelo and Lehmann, Jason S and Purushe, Janaki and Sanka, Ravi and Torres, Michael and Webster, Nicholas J and Vinetz, Joseph M and Matthias, Michael A} } @article {16241, title = {Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences}, journal = {BMC Genomics}, volume = {12}, year = {2011}, month = {2011/07/27/}, pages = {S4 - S4}, abstract = {A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-12-S2-S4}, url = {http://www.biomedcentral.com/1471-2164/12/S2/S4}, author = {Liu,Bo and Gibbons,Theodore and Ghodsi,Mohammad and Treangen,Todd and Pop, Mihai} } @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 {14192, title = {Active scene recognition with vision and language}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {810 - 817}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a novel approach to utilizing high level knowledge for the problem of scene recognition in an active vision framework, which we call active scene recognition. In traditional approaches, high level knowledge is used in the post-processing to combine the outputs of the object detectors to achieve better classification performance. In contrast, the proposed approach employs high level knowledge actively by implementing an interaction between a reasoning module and a sensory module (Figure 1). Following this paradigm, we implemented an active scene recognizer and evaluated it with a dataset of 20 scenes and 100+ objects. We also extended it to the analysis of dynamic scenes for activity recognition with attributes. Experiments demonstrate the effectiveness of the active paradigm in introducing attention and additional constraints into the sensing process.}, keywords = {accuracy, active scene recognition, classification performance, Cognition, Computer vision, Detectors, Equations, high level knowledge utilization, HUMANS, image classification, inference mechanisms, object detectors, Object recognition, reasoning module, sensing process, sensory module, support vector machines, Training}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126320}, author = {Yu,Xiaodong and Ferm{\"u}ller, Cornelia and Ching Lik Teo and Yezhou Yang and Aloimonos, J.} } @conference {16815, title = {Adapting a map query interface for a gesturing touch screen interface}, booktitle = {Proceedings of the 20th international conference companion on World wide web}, series = {WWW {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {257 - 260}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {NewsStand is an example application of a general framework that we are developing to enable searching for information using a map query interface, where the information results from monitoring the output of over 8,000 RSS news sources and is available for retrieval within minutes of publication. The user interface of NewsStand was recently adapted so that NewsStand can execute on mobile and tablet devices with a gesturing touch screen interface such as the iPhone, iPod Touch, and iPad. This action led to a discovery of some shortcomings of current mapping APIs as well as devising some interesting new widgets. These issues are discussed, and the realization can be seen by a demo at http://newsstand.umiacs.umd.edu on any of the above Apple devices as well as other devices that support gestures such as an Android phone.}, keywords = {map query interface, newsstand, touch screen gesturing interface}, isbn = {978-1-4503-0637-9}, doi = {10.1145/1963192.1963303}, url = {http://doi.acm.org/10.1145/1963192.1963303}, author = {Samet, Hanan and Teitler,Benjamin E. and Adelfio,Marco D. and Lieberman,Michael D.} } @article {12461, title = {Advances in Video-Based Biometrics}, journal = {Advances in Imaging and Electron Physics}, volume = {83}, year = {2011}, month = {2011///}, pages = {183 - 203}, author = {Chellapa, Rama and Turaga,P.} } @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 {13423, title = {Ant Colony Optimization in a Changing Environment}, booktitle = {2011 AAAI Fall Symposium Series}, year = {2011}, month = {2011/03/11/}, abstract = {Ant colony optimization (ACO) algorithms are computational problem-solving methods that are inspired by the complex behaviors of ant colonies; specifically, the ways in which ants interact with each other and their environment to optimize the overall performance of the ant colony. Our eventual goal is to develop and experiment with ACO methods that can more effectively adapt to dynamically changing environments and problems. We describe biological ant systems and the dynamics of their environments and behaviors. We then introduce a family of dynamic ACO algorithms that can handle dynamic modifications of their inputs. We report empirical results, showing that dynamic ACO algorithms can effectively adapt to time-varying environments.}, url = {http://www.aaai.org/ocs/index.php/FSS/FSS11/paper/viewPaper/4223}, author = {Seymour,John Jefferson and Tuzo,Joseph and desJardins, Marie} } @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.} } @conference {13069, title = {AVSS 2011 demo session: A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Advanced Video and Signal-Based Surveillance (AVSS), 2011 8th IEEE International Conference on}, year = {2011}, month = {2011/09/30/2}, pages = {527 - 528}, abstract = {We introduce to the surveillance community the VIRAT Video Dataset[1], which is a new large-scale surveillance video dataset designed to assess the performance of event recognition algorithms in realistic scenes1.}, doi = {10.1109/AVSS.2011.6027400}, author = {Oh,Sangmin and Hoogs,Anthony and Perera,Amitha and Cuntoor,Naresh and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,Saurajit and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,Eran and Wang,Xiaoyang and Ji,Qiang and Reddy,Kishore and Shah,Mubarak and Vondrick,Carl and Pirsiavash,Hamed and Ramanan,Deva and Yuen,Jenny and Torralba,Antonio and Song,Bi and Fong,Anesco and Roy-Chowdhury,Amit and Desai,Mita} } @article {19114, title = {Bambus 2: scaffolding metagenomes}, journal = {Bioinformatics}, volume = {27}, year = {2011}, month = {2011}, pages = {2964 - 2971}, author = {Koren, S. and Treangen, T.J. and Pop, Mihai} } @conference {12435, title = {Blurring-invariant Riemannian metrics for comparing signals and images}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {1770 - 1775}, publisher = {IEEE}, organization = {IEEE}, abstract = {We propose a novel Riemannian framework for comparing signals and images in a manner that is invariant to their levels of blur. This framework uses a log-Fourier representation of signals/images in which the set of all possible Gaussian blurs of a signal, i.e. its orbits under semigroup action of Gaussian blur functions, is a straight line. Using a set of Riemannian metrics under which the group actions are by isometries, the orbits are compared via distances between orbits. We demonstrate this framework using a number of experimental results involving 1D signals and 2D images.}, keywords = {blurring-invariant Riemannian metrics, Estimation, Fourier transforms, Gaussian blur function, Gaussian processes, image representation, log-Fourier representation, measurement, Orbits, Polynomials, signal representation, Space vehicles, vectors}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126442}, author = {Zhengwu Zhang and Klassen, E. and Srivastava, A. and Turaga,P. and Chellapa, Rama} } @article {18510, title = {Broadband internet performance: A view from the gateway}, journal = {SIGCOMM-Computer Communication Review}, volume = {41}, year = {2011}, month = {2011///}, pages = {134 - 134}, abstract = {We present the first study of network access link performance mea-sured directly from home gateway devices. Policymakers, ISPs, and users are increasingly interested in studying the performance of Internet access links. Because of many confounding factors in a home network or on end hosts, however, thoroughly understanding access network performance requires deploying measurement in- frastructure in users{\textquoteright} homes as gateway devices. In conjunction with the Federal Communication Commission{\textquoteright}s study of broad- band Internet access in the United States, we study the throughput and latency of network access links using longitudinal measure- ments from nearly 4,000 gateway devices across 8 ISPs from a de- ployment of over 4,200 devices. We study the performance users achieve and how various factors ranging from the user{\textquoteright}s choice of modem to the ISP{\textquoteright}s traffic shaping policies can affect performance. Our study yields many important findings about the characteristics of existing access networks. Our findings also provide insights into the ways that access network performance should be measured and presented to users, which can help inform ongoing broader efforts to benchmark the performance of access networks. }, author = {Sundaresan,S. and de Donato,W. and Feamster, Nick and Teixeira,R. and Crawford,S. and Pescap{\`e},A.} } @article {19369, title = {Cell cycle dependent TN-C promoter activity determined by live cell imaging.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {79}, year = {2011}, month = {2011 Mar}, pages = {192-202}, abstract = {The extracellular matrix protein tenascin-C plays a critical role in development, wound healing, and cancer progression, but how it is controlled and how it exerts its physiological responses remain unclear. By quantifying the behavior of live cells with phase contrast and fluorescence microscopy, the dynamic regulation of TN-C promoter activity is examined. We employ an NIH 3T3 cell line stably transfected with the TN-C promoter ligated to the gene sequence for destabilized green fluorescent protein (GFP). Fully automated image analysis routines, validated by comparison with data derived from manual segmentation and tracking of single cells, are used to quantify changes in the cellular GFP in hundreds of individual cells throughout their cell cycle during live cell imaging experiments lasting 62 h. We find that individual cells vary substantially in their expression patterns over the cell cycle, but that on average TN-C promoter activity increases during the last 40\% of the cell cycle. We also find that the increase in promoter activity is proportional to the activity earlier in the cell cycle. This work illustrates the application of live cell microscopy and automated image analysis of a promoter-driven GFP reporter cell line to identify subtle gene regulatory mechanisms that are difficult to uncover using population averaged measurements.}, keywords = {Animals, cell cycle, Gene Expression Regulation, Green Fluorescent Proteins, Image Processing, Computer-Assisted, Mice, Microscopy, Fluorescence, Microscopy, Phase-Contrast, NIH 3T3 Cells, Promoter Regions, Genetic, Tenascin}, issn = {1552-4930}, doi = {10.1002/cyto.a.21028}, author = {Halter, Michael and Sisan, Daniel R and Chalfoun, Joe and Stottrup, Benjamin L and Cardone, Antonio and Dima,Alden A. and Tona, Alessandro and Plant,Anne L. and Elliott, John T} } @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} } @article {19647, title = {A computational statistics approach for estimating the spatial range of morphogen gradients}, journal = {Development}, volume = {138}, year = {2011}, month = {2011/11/15/}, pages = {4867 - 4874}, abstract = {A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.}, keywords = {Computational Biology, Confidence interval, Dorsal gradient, Drosophila embryo, Morphogen gradient, Statistics}, isbn = {0950-1991, 1477-9129}, url = {http://dev.biologists.org/content/138/22/4867}, author = {Kanodia, Jitendra S. and Kim, Yoosik and Tomer, Raju and Zia Khan and Chung, Kwanghun and Storey, John D. and Lu, Hang and Keller, Philipp J. and Shvartsman, Stanislav Y.} } @article {15698, title = {A Constraint-Reduced Variant of Mehrotra{\textquoteright}s Predictor-Corrector Algorithm}, journal = {Computational Optimization and Applications}, year = {2011}, month = {2011/01/19/36 pa}, doi = {DOI: 10.1007/s10589-010-9389-4}, author = {Winternitz,Luke B. and Nicholls,Stacey O. and Tits,Andr\&$\#$x65;\&$\#$x0301; and O{\textquoteright}Leary, Dianne P.} } @conference {14183, title = {A Corpus-Guided Framework for Robotic Visual Perception}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, author = {Teo,C.L. and Yang, Y. and Daum{\'e}, Hal and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {14832, title = {A deformation and lighting insensitive metric for face recognition based on dense correspondences}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {2353 - 2360}, abstract = {Face recognition is a challenging problem, complicated by variations in pose, expression, lighting, and the passage of time. Significant work has been done to solve each of these problems separately. We consider the problems of lighting and expression variation together, proposing a method that accounts for both variabilities within a single model. We present a novel deformation and lighting insensitive metric to compare images, and we present a novel framework to optimize over this metric to calculate dense correspondences between images. Typical correspondence cost patterns are learned between face image pairs and a Nai $\#$x0308;ve Bayes classifier is applied to improve recognition accuracy. Very promising results are presented on the AR Face Database, and we note that our method can be extended to a broad set of applications.}, keywords = {$\#$x0308;ve, Bayes, classifier;pose, comparison;lighting, correspondences;expression, deformation;dense, estimation;, insensitive, methods;face, metric;nai, recognition;image, recognition;pose, variation;Bayes, variation;face}, doi = {10.1109/CVPR.2011.5995431}, author = {Jorstad,A. and Jacobs, David W. and Trouve,A.} } @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} } @conference {19441, title = {A Dive into Online Community Properties}, booktitle = {CSCW {\textquoteright}11}, series = {CSCW {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {725 - 728}, publisher = {ACM}, organization = {ACM}, abstract = {As digital communities grow in size their feature sets also grow with them. Different users have different experiences with the same tools and communities. Enterprises and other organizations seeking to leverage these communities need a straightforward way to analyze and compare a variety of salient attributes of these communities. We describe a taxonomy and tool for crowd-sourcing user based evaluations of enterprise relevant attributes of digital communities and present the results of a small scale study on its usefulness and stability across multiple raters.}, keywords = {enterprise, Online communities, Taxonomy, Visualization}, isbn = {978-1-4503-0556-3}, url = {http://doi.acm.org/10.1145/1958824.1958955}, author = {Wagstrom, Patrick and Martino, Jacquelyn and von Kaenel, Juerg and Marshini Chetty and Thomas, John and Jones, Lauretta} } @article {15263, title = {Energy efficient monitoring in sensor networks}, journal = {Algorithmica}, volume = {59}, year = {2011}, month = {2011///}, pages = {94 - 114}, abstract = {We study a set of problems related to efficient battery energy utilization for monitoring applications in a wireless sensor network with the goal to increase the sensor network lifetime. We study several generalizations of a basic problem called Set k-Cover. The problem can be described as follows: we are given a set of sensors, and a set of targets to be monitored. Each target 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 set of sensors in a different time-slot, thus extending the battery life of the sensors by a factor of k. The goal is to find a partitioning that maximizes the total coverage of the targets for a given k. This problem is known to be NP-hard. We develop an improved approximation algorithm for this problem using a reduction to Max k-Cut. Moreover, we are able to demonstrate that this algorithm is efficient, and yields almost optimal solutions in practice.We also consider generalizations of this problem in several different directions. First, we allow each sensor to be active in α different sets (time-slots). This means that the battery life is extended by a factor of k, and allows for a richer space of solutions. We also consider different coverage requirements, such as requiring that all targets, or at least a certain number of targets, be covered in each time slot. In the Set k-Cover formulation, there is no requirement that a target be monitored at all, or in any number of time slots. We develop a randomized rounding algorithm for this problem. We also consider extensions where each sensor can monitor only a bounded number of targets in any time-slot, and not all the targets adjacent to it. This kind of problem may arise when a sensor has a directional camera, or some other physical constraint might prevent it from monitoring all adjacent targets even when it is active. We develop the first approximation algorithms for this problem. }, doi = {10.1007/s00453-010-9407-z}, author = {Deshpande, Amol and Khuller, Samir and Malekian,A. and Toossi,M.} } @conference {12450, title = {Entropy rate superpixel segmentation}, booktitle = {2011 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2011}, month = {2011/06/20/25}, pages = {2097 - 2104}, publisher = {IEEE}, organization = {IEEE}, abstract = {We propose a new objective function for superpixel segmentation. This objective function consists of two components: entropy rate of a random walk on a graph and a balancing term. The entropy rate favors formation of compact and homogeneous clusters, while the balancing function encourages clusters with similar sizes. We present a novel graph construction for images and show that this construction induces a matroid - a combinatorial structure that generalizes the concept of linear independence in vector spaces. The segmentation is then given by the graph topology that maximizes the objective function under the matroid constraint. By exploiting submodular and mono-tonic properties of the objective function, we develop an efficient greedy algorithm. Furthermore, we prove an approximation bound of {\textonehalf} for the optimality of the solution. Extensive experiments on the Berkeley segmentation benchmark show that the proposed algorithm outperforms the state of the art in all the standard evaluation metrics.}, keywords = {balancing function, Berkeley segmentation benchmark, Complexity theory, Entropy, entropy rate, graph construction, graph theory, graph topology, greedy algorithm, Greedy algorithms, homogeneous clusters, Image edge detection, Image segmentation, matrix algebra, matroid constraint, measurement, pattern clustering, Random variables, standard evaluation metrics, superpixel segmentation, vector spaces}, isbn = {978-1-4577-0394-2}, doi = {10.1109/CVPR.2011.5995323}, author = {Ming-Yu Liu and Tuzel, O. and Ramalingam, S. and Chellapa, Rama} } @article {12440, title = {Example-Driven Manifold Priors for Image Deconvolution}, journal = {Image Processing, IEEE Transactions on}, volume = {20}, year = {2011}, month = {2011/11//}, pages = {3086 - 3096}, abstract = {Image restoration methods that exploit prior information about images to be estimated have been extensively studied, typically using the Bayesian framework. In this paper, we consider the role of prior knowledge of the object class in the form of a patch manifold to address the deconvolution problem. Specifically, we incorporate unlabeled image data of the object class, say natural images, in the form of a patch-manifold prior for the object class. The manifold prior is implicitly estimated from the given unlabeled data. We show how the patch-manifold prior effectively exploits the available sample class data for regularizing the deblurring problem. Furthermore, we derive a generalized cross-validation (GCV) function to automatically determine the regularization parameter at each iteration without explicitly knowing the noise variance. Extensive experiments show that this method performs better than many competitive image deconvolution methods.}, keywords = {Bayesian, cross-validation, data;Bayes, deconvolution;image, determination;deblurring, estimation;, framework;GCV, function;automatic, function;image, image, image;patch-manifold, manifold, method;iteration, method;natural, methods;deconvolution;image, methods;natural, parameter, prior;generalized, prior;unlabeled, problem, regularization, regularization;example-driven, restoration, restoration;iterative, scenes;parameter}, isbn = {1057-7149}, doi = {10.1109/TIP.2011.2145386}, author = {Ni,Jie and Turaga,P. and Patel, Vishal M. and Chellapa, Rama} } @inbook {12460, title = {Face Tracking and Recognition in Video}, booktitle = {Handbook of Face RecognitionHandbook of Face Recognition}, year = {2011}, month = {2011///}, pages = {323 - 351}, publisher = {Springer London}, organization = {Springer London}, abstract = {In this chapter, we describe the utility of videos in enhancing performance of image-based recognition tasks. We discuss a joint tracking-recognition framework that allows for using the motion information in a video to better localize and identify the person in the video using still galleries. We discuss how to jointly capture facial appearance and dynamics to obtain a parametric representation for video-to-video recognition. We discuss recognition in multi-camera networks where the probe and gallery both consist of multi-camera videos. Concluding remarks and directions for future research are provided.}, isbn = {978-0-85729-932-1}, url = {http://dx.doi.org/10.1007/978-0-85729-932-1_13}, author = {Chellapa, Rama and Du,Ming and Turaga,Pavan and Zhou,Shaohua Kevin}, editor = {Li,Stan Z. and Jain,Anil K.} } @article {14155, title = {Fast solvers for models of ICEO microfluidic flows}, journal = {International Journal for Numerical Methods in Fluids}, volume = {65}, year = {2011}, month = {2011///}, pages = {383 - 404}, author = {Shuttleworth, R. R and Elman, Howard and Long, K. R and Templeton, J. A} } @article {17180, title = {Graph Analytics-Lessons Learned and Challenges Ahead}, volume = {31}, year = {2011}, month = {2011///}, pages = {18 - 29}, abstract = {Graph analytics is one of the most influential and important R\&D topics in the visual analytics community. Researchers with diverse backgrounds from information visualization, human-computer interaction, computer graphics, graph drawing, and data mining have pursued graph analytics from scientific, technical, and social approaches. These studies have addressed both distinct and common challenges. Past successes and mistakes can provide valuable lessons for revising the research agenda. In this article, six researchers from four academic and research institutes identify graph analytics{\textquoteright} fundamental challenges and present both insightful lessons learned from their experience and good practices in graph analytics research. The goal is to critically assess those lessons and shed light on how they can stimulate research and draw attention to grand challenges for graph analytics. The article also establishes principles that could lead to measurable standards and criteria for research.}, keywords = {citation analysis, citespace, Computer Graphics, document analysis, graphics and multimedia, greengrid, jigsaw system, modeling, power grid analysis, semantic substrates, simulation, social networks, text analysis, Visualization}, isbn = {0272-1716}, author = {Wong,Pak Chung and Chen,Chaomei and Gorg,Carsten and Shneiderman, Ben and Stasko,John and Thomas,Jim} } @conference {19452, title = {Helping Users Shop for ISPs with Internet Nutrition Labels}, booktitle = {ACM SIGCOMM Workshop on Home Networks {\textquoteright}11}, series = {HomeNets {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {13 - 18}, publisher = {ACM}, organization = {ACM}, abstract = {When purchasing home broadband access from Internet service providers (ISPs), users must decide which service plans are most appropriate for their needs. Today, ISPs advertise their available service plans using only generic upload and download speeds. Unfortunately, these metrics do not always accurately reflect the varying performance that home users will experience for a wide range of applications. In this paper, we propose that each ISP service plan carry a "nutrition label" that conveys more comprehensive information about network metrics along many dimensions, including various aspects of throughput, latency, loss rate, and jitter. We first justify why these metrics should form the basis of a network nutrition label. Then, we demonstrate that current plans that are superficially similar with respect to advertised download rates may have different performance according to the label metrics. We close with a discussion of the challenges involved in presenting a nutrition label to users in a way that is both accurate and easy to understand.}, keywords = {access networks, benchmarking, bismark, broadband networks, gateway measurements}, isbn = {978-1-4503-0798-7}, url = {http://doi.acm.org/10.1145/2018567.2018571}, author = {Sundaresan, Srikanth and Feamster, Nick and Teixeira, Renata and Tang, Anthony and Edwards, W. Keith and Grinter, Rebecca E. and Marshini Chetty and de Donato, Walter} } @article {19588, title = {Higher-Order Symbolic Execution via Contracts}, journal = {arXiv:1103.1362 [cs]}, year = {2011}, month = {2011/03/07/}, abstract = {We present a new approach to automated reasoning about higher-order programs by extending symbolic execution to use behavioral contracts as symbolic values, enabling symbolic approximation of higher-order behavior. Our approach is based on the idea of an abstract reduction semantics that gives an operational semantics to programs with both concrete and symbolic components. Symbolic components are approximated by their contract and our semantics gives an operational interpretation of contracts-as-values. The result is a executable semantics that soundly predicts program behavior, including contract failures, for all possible instantiations of symbolic components. We show that our approach scales to an expressive language of contracts including arbitrary programs embedded as predicates, dependent function contracts, and recursive contracts. Supporting this feature-rich language of specifications leads to powerful symbolic reasoning using existing program assertions. We then apply our approach to produce a verifier for contract correctness of components, including a sound and computable approximation to our semantics that facilitates fully automated contract verification. Our implementation is capable of verifying contracts expressed in existing programs, and of justifying valuable contract-elimination optimizations.}, keywords = {Computer Science - Programming Languages}, url = {http://arxiv.org/abs/1103.1362}, author = {Tobin-Hochstadt, Sam and David Van Horn} } @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} } @conference {14226, title = {Language Models for Semantic Extraction and Filtering in Video Action Recognition}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011/08/24/}, abstract = {The paper addresses the following issues: (a) how to represent semantic information from natural language so that a vision model can utilize it? (b) how to extract the salient textual information relevant to vision? For a given domain, we present a new model of semantic extraction that takes into account word relatedness as well as word disambiguation in order to apply to a vision model. We automatically process the text transcripts and perform syntactic analysis to extract dependency relations. We then perform semantic extraction on the output to filter semantic entities related to actions. The resulting data are used to populate a matrix of co-occurrences utilized by the vision processing modules. Results show that explicitly modeling the co-occurrence of actions and tools significantly improved performance.}, url = {https://www.aaai.org/ocs/index.php/WS/AAAIW11/paper/viewPaper/3919}, author = {Tzoukermann,Evelyne and Neumann, Jan and Kosecka,Jana and Ferm{\"u}ller, Cornelia and Perera,Ian and Ferraro,Frank and Sapp,Ben and Chaudhry,Rizwan and Singh,Gautam} } @conference {13074, title = {A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {3153 - 3160}, abstract = {We introduce a new large-scale video dataset designed to assess the performance of diverse visual event recognition algorithms with a focus on continuous visual event recognition (CVER) in outdoor areas with wide coverage. Previous datasets for action recognition are unrealistic for real-world surveillance because they consist of short clips showing one action by one individual [15, 8]. Datasets have been developed for movies [11] and sports [12], but, these actions and scene conditions do not apply effectively to surveillance videos. Our dataset consists of many outdoor scenes with actions occurring naturally by non-actors in continuously captured videos of the real world. The dataset includes large numbers of instances for 23 event types distributed throughout 29 hours of video. This data is accompanied by detailed annotations which include both moving object tracks and event examples, which will provide solid basis for large-scale evaluation. Additionally, we propose different types of evaluation modes for visual recognition tasks and evaluation metrics along with our preliminary experimental results. We believe that this dataset will stimulate diverse aspects of computer vision research and help us to advance the CVER tasks in the years ahead.}, keywords = {algorithm;evaluation, CVER, databases;, databases;video, dataset;moving, event, metrics;large-scale, object, recognition, recognition;diverse, recognition;video, scenes;surveillance, surveillance;visual, tasks;computer, tracks;outdoor, video, video;computer, vision;continuous, vision;image, visual}, doi = {10.1109/CVPR.2011.5995586}, author = {Oh,Sangmin and Hoogs, A. and Perera,A. and Cuntoor, N. and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,S. and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,E. and Wang,Xioyang and Ji,Qiang and Reddy,K. and Shah,M. and Vondrick,C. and Pirsiavash,H. and Ramanan,D. and Yuen,J. and Torralba,A. and Song,Bi and Fong,A. and Roy-Chowdhury, A. and Desai,M.} } @conference {16036, title = {LifeFlow: visualizing an overview of event sequences}, booktitle = {Proceedings of the 2011 annual conference on Human factors in computing systems}, series = {CHI {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {1747 - 1756}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Event sequence analysis is an important task in many domains: medical researchers may study the patterns of transfers within the hospital for quality control; transportation experts may study accident response logs to identify best practices. In many cases they deal with thousands of records. While previous research has focused on searching and browsing, overview tasks are often overlooked. We introduce a novel interactive visual overview of event sequences called \emph{LifeFlow}. LifeFlow is scalable, can summarize all possible sequences, and represents the temporal spacing of the events within sequences. Two case studies with healthcare and transportation domain experts are presented to illustrate the usefulness of LifeFlow. A user study with ten participants confirmed that after 15 minutes of training novice users were able to rapidly answer questions about the prevalence and temporal characteristics of sequences, find anomalies, and gain significant insight from the data.}, keywords = {Information Visualization, overview visualization, temporal categorical data, timestamped event sequences}, isbn = {978-1-4503-0228-9}, doi = {10.1145/1978942.1979196}, url = {http://doi.acm.org/10.1145/1978942.1979196}, author = {Wongsuphasawat,Krist and Guerra G{\'o}mez,John Alexis and Plaisant, Catherine and Wang,Taowei David and Taieb-Maimon,Meirav and Shneiderman, Ben} } @conference {17280, title = {LifeFlow: visualizing an overview of event sequences (video preview)}, booktitle = {Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {507 - 510}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Event sequence analysis is an important task in many domains: medical researchers may study the patterns of transfers within the hospital for quality control; transportation experts may study accident response logs to identify best practices. In many cases they deal with thousands of records. While previous research has focused on searching and browsing, overview tasks are often overlooked. We introduce a novel interactive visual overview of event sequences called LifeFlow. LifeFlow is scalable, can summarize all possible sequences, and represents the temporal spacing of the events within sequences. In this video, we show an example of patient transfer data and briefly demonstrate how to analyze them with LifeFlow. Please see [11] or visit http:www.cs.umd.eduhcillifeflow for more detail.}, keywords = {emergency room, healthcare, Information Visualization, overview visualization, temporal categorical data, timestamped event sequences}, isbn = {978-1-4503-0268-5}, doi = {10.1145/1979742.1979557}, url = {http://doi.acm.org/10.1145/1979742.1979557}, author = {Wongsuphasawat,Krist and Guerra G{\'o}mez,John Alexis and Plaisant, Catherine and Wang,Taowei and Taieb-Maimon,Meirav and Shneiderman, Ben} } @article {13380, title = {Lightweight Graphical Models for Selectivity Estimation Without Independence Assumptions}, journal = {Proceedings of the VLDB Endowment}, volume = {4}, year = {2011}, month = {2011///}, abstract = {As a result of decades of research and industrial development, mod-ern query optimizers are complex software artifacts. However, the quality of the query plan chosen by an optimizer is largely deter- mined by the quality of the underlying statistical summaries. Small selectivity estimation errors, propagated exponentially, can lead to severely sub-optimal plans. Modern optimizers typically maintain one-dimensional statistical summaries and make the attribute value independence and join uniformity assumptions for efficiently esti- mating selectivities. Therefore, selectivity estimation errors in to- day{\textquoteright}s optimizers are frequently caused by missed correlations be- tween attributes. We present a selectivity estimation approach that does not make the independence assumptions. By carefully using concepts from the field of graphical models, we are able to fac- tor the joint probability distribution of all the attributes in the data- base into small, usually two-dimensional distributions. We describe several optimizations that can make selectivity estimation highly efficient, and we present a complete implementation inside Post- greSQL{\textquoteright}s query optimizer. Experimental results indicate an order of magnitude better selectivity estimates, while keeping optimiza- tion time in the range of tens of milliseconds. }, author = {Tzoumas,K. and Deshpande, Amol and Jensen,C. S} } @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} } @conference {13454, title = {Model AI Assignments 2011}, booktitle = {Second AAAI Symposium on Educational Advances in Artificial Intelligence}, year = {2011}, month = {2011/04/08/}, abstract = {The Model AI Assignments session seeks to gather and disseminate the best assignment designs of the Artificial Intelligence (AI) Education community. Recognizing that assignments form the core of student learning experience, we here present abstracts of three AI assignments from the 2011 session that are easily adoptable, playfully engaging, and flexible for a variety of instructor needs.}, url = {http://www.aaai.org/ocs/index.php/EAAI/EAAI11/paper/viewPaper/3452}, author = {Neller,Todd William and desJardins, Marie and Oates,Tim and Taylor,Matthew E} } @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} } @article {14709, title = {MultiOtter: Multiprocess Symbolic Execution}, journal = {Technical Reports of the Computer Science Department}, year = {2011}, month = {2011///}, abstract = {Symbolic execution can be an effective technique for exploring large numbers of program paths, but it has generally been applied to programs running in isolation, whose inputs are files or command-line arguments. Programs that take inputs from other programs---servers, for example---have been beyond the reach of symbolic execution. To address this, we developed a multiprocess symbolic executor called MultiOtter, along with an implementation of many of the POSIX functions, such as socket and select, that interactive programs usually rely on. However, that is just a first step. Next, we must determine what symbolic inputs to feed to an interactive program to make multiprocess symbolic execution effective. Providing completely unconstrained symbolic values causes symbolic execution to spend too much time exploring uninteresting paths, such as paths to handle invalid inputs. MultiOtter allows us to generate inputs that conform to a context-free grammar, similar to previous work, but it also enables new input generation capabilities because we can now run arbitrary programs concurrently with the program being studied. As examples, we symbolically executed a key-value store server, redis, and an FTP server, vsftpd, each with a variety of inputs, including symbolic versions of tests from redis{\textquoteright}s test suite and wget as a client for vsftpd. We report the coverage provided by symbolic execution with various forms of symbolic input, showing that different testing goals require different degrees of symbolic inputs.}, author = {Turpie,J. and Reisner,E. and Foster, Jeffrey S. and Hicks, Michael W.} } @conference {17306, title = {NetVisia: Heat Map \& Matrix Visualization of Dynamic Social Network Statistics \& Content}, 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 = {19 - 26}, publisher = {IEEE}, organization = {IEEE}, abstract = {Visualizations of static networks in the form of node-link diagrams have evolved rapidly, though researchers are still grappling with how best to show evolution of nodes over time in these diagrams. This paper introduces NetVisia, a social network visualization system designed to support users in exploring temporal evolution in networks by using heat maps to display node attribute changes over time. NetVisia{\textquoteright}s novel contributions to network visualizations are to (1) cluster nodes in the heat map by similar metric values instead of by topological similarity, and (2) align nodes in the heat map by events. We compare NetVisia to existing systems and describe a formative user evaluation of a NetVisia prototype with four participants that emphasized the need for tool tips and coordinated views. Despite the presence of some usability issues, in 30-40 minutes the user evaluation participants discovered new insights about the data set which had not been discovered using other systems. We discuss implemented improvements to NetVisia, and analyze a co-occurrence network of 228 business intelligence concepts and entities. This analysis confirms the utility of a clustered heat map to discover outlier nodes and time periods.}, keywords = {business intelligence concept, business intelligence entity, competitive intelligence, data visualisation, dynamic networks, dynamic social network, heat map, Heating, Image color analysis, Information Visualization, Layout, matrix visualization, measurement, NetVisia system, network evolution, network visualization, node-link diagrams, outlier node, social network content, Social network services, social network statistics, social networking (online), social networks, static network visualization, time period, topological similarity, Training, usability, user evaluation, User interfaces}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.216}, author = {Gove,R. and Gramsky,N. and Kirby,R. and Sefer,E. and Sopan,A. and Dunne,C. and Shneiderman, Ben and Taieb-Maimon,M.} } @article {19111, title = {Next Generation Sequence Assembly with AMOS}, journal = {Current Protocols in Bioinformatics}, volume = {11}, year = {2011}, month = {2011}, pages = {1 - 11}, author = {Treangen, T.J. and Sommer, D.D. and Angly, F.E. and Koren, S. and Pop, Mihai} } @inbook {19600, title = {Optimal Verification of Operations on Dynamic Sets}, booktitle = {Advances in Cryptology {\textendash} CRYPTO 2011}, series = {Lecture Notes in Computer Science}, year = {2011}, month = {2011/01/01/}, pages = {91 - 110}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We study the design of protocols for set-operation verification, namely the problem of cryptographically checking the correctness of outsourced set operations performed by an untrusted server over a dynamic collection of sets that are owned (and updated) by a trusted source. We present new authenticated data structures that allow any entity to publicly verify a proof attesting the correctness of primitive set operations such as intersection, union, subset and set difference. Based on a novel extension of the security properties of bilinear-map accumulators as well as on a primitive called accumulation tree, our protocols achieve optimal verification and proof complexity (i.e., only proportional to the size of the query parameters and the answer), as well as optimal update complexity (i.e., constant), while incurring no extra asymptotic space overhead. The proof construction is also efficient, adding a logarithmic overhead to the computation of the answer of a set-operation query. In contrast, existing schemes entail high communication and verification costs or high storage costs. Applications of interest include efficient verification of keyword search and database queries. The security of our protocols is based on the bilinear q-strong Diffie-Hellman assumption.}, keywords = {Computer Communication Networks, computers and society, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-642-22791-2, 978-3-642-22792-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-22792-9_6}, author = {Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikos}, editor = {Rogaway, Phillip} } @article {18349, title = {Photo-based mobile deixis system and related techniques}, volume = {10/762,941}, year = {2011}, month = {2011/01/18/}, abstract = {A mobile deixis device includes a camera to capture an image and a wireless handheld device, coupled to the camera and to a wireless network, to communicate the image with existing databases to find similar images. The mobile deixis device further includes a processor, coupled to the device, to process found database records related to similar images and a display to view found database records that include web pages including images. With such an arrangement, users can specify a location of interest by simply pointing a camera-equipped cellular phone at the object of interest and by searching an image database or relevant web resources, users can quickly identify good matches from several close ones to find an object of interest.}, url = {http://www.google.com/patents?id=jeXwAAAAEBAJ}, author = {Darrell,Trevor J and Tom Yeh and Tollmar,Konrad}, editor = {Massachusetts Institute of Technology} } @article {18521, title = {Practical Data-Leak Prevention for Legacy Applications in Enterprise Networks}, volume = {GT-CS-11-01}, year = {2011}, month = {2011///}, institution = {Georgia Institute of Technology}, abstract = {Organizations must control where private information spreads; this problem is referred to in the industry as data leak prevention. Commercial solutions for DLP are based on scanning content; these impose high overhead and are easily evaded. Research solutions for this problem, information flow control, require rewriting applications or running a custom operating system, which makes these approaches difficult to deploy. They also typically enforce information flow control on a single host, not across a network, making it difficult to implement an information flow control policy for a network of machines. This paper presents Pedigree, which enforces information flow control across a network for legacy applications. Pedigree allows enterprise administrators and users to associate a label with each file and process; a small, trusted module on the host uses these labels to determine whether two processes on the same host can communicate. When a process attempts to communicate across the network, Pedigree tracks these information flows and enforces information flow control either at end-hosts or at a network switch. Pedigree allows users and operators to specify network-wide information flow policies rather than having to specify and implement policies for each host. Enforcing information flow policies in the network allows Pedigree to operate in networks with heterogeneous devices and operating systems. We present the design and implementation of Pedigree, show that it can prevent data leaks, and investigate its feasibility and usability in common environments.}, url = {http://hdl.handle.net/1853/36612}, author = {Mundada,Y. and Ramachandran,A. and Tariq,M.B. and Feamster, Nick} } @article {18783, title = {Real-time dynamics simulation of unmanned sea surface vehicle for virtual environments}, journal = {Journal of Computing and Information Science in Engineering}, volume = {11}, year = {2011}, month = {2011///}, pages = {031005 - 031005}, author = {Thakur,A. and Gupta,S.K.} } @conference {12453, title = {Recent advances in age and height estimation from still images and video}, booktitle = {2011 IEEE International Conference on Automatic Face \& Gesture Recognition and Workshops (FG 2011)}, year = {2011}, month = {2011/03/21/25}, pages = {91 - 96}, publisher = {IEEE}, organization = {IEEE}, abstract = {Soft-biometrics such as gender, age, race, etc have been found to be useful characterizations that enable fast pre-filtering and organization of data for biometric applications. In this paper, we focus on two useful soft-biometrics - age and height. We discuss their utility and the factors involved in their estimation from images and videos. In this context, we highlight the role that geometric constraints such as multiview-geometry, and shape-space geometry play. Then, we present methods based on these geometric constraints for age and height-estimation. These methods provide a principled means by fusing image-formation models, multi-view geometric constraints, and robust statistical methods for inference.}, keywords = {age estimation, biometrics (access control), Calibration, Estimation, Geometry, height estimation, HUMANS, image fusion, image-formation model fusion, Legged locomotion, multiview-geometry, Robustness, SHAPE, shape-space geometry, soft-biometrics, statistical analysis, statistical methods, video signal processing}, isbn = {978-1-4244-9140-7}, doi = {10.1109/FG.2011.5771367}, author = {Chellapa, Rama and Turaga,P.} } @article {16038, title = {Reducing Missed Laboratory Results: Defining Temporal Responsibility, Generating User Interfaces for Test Process Tracking, and Retrospective Analyses to Identify Problems}, journal = {AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc}, volume = {2011}, year = {2011}, month = {2011///}, pages = {1382 - 1391}, abstract = {Researchers have conducted numerous case studies reporting the details on how laboratory test results of patients were missed by the ordering medical providers. Given the importance of timely test results in an outpatient setting, there is limited discussion of electronic versions of test result management tools to help clinicians and medical staff with this complex process. This paper presents three ideas to reduce missed results with a system that facilitates tracking laboratory tests from order to completion as well as during follow-up: (1) define a workflow management model that clarifies responsible agents and associated time frame, (2) generate a user interface for tracking that could eventually be integrated into current electronic health record (EHR) systems, (3) help identify common problems in past orders through retrospective analyses.}, isbn = {1942-597X}, author = {Tarkan,Sureyya and Plaisant, Catherine and Shneiderman, Ben and Hettinger,A. Zachary} } @article {14639, title = {Regulation of Lung Endoderm Progenitor Cell Behavior by miR302/367}, journal = {DevelopmentDevelopment}, volume = {138}, year = {2011}, month = {2011/04/01/}, pages = {1235 - 1245}, abstract = {The temporal and spatial control of organ-specific endoderm progenitor development is poorly understood. miRNAs affect cell function by regulating programmatic changes in protein expression levels. We show that the miR302/367 cluster is a target of the transcription factor Gata6 in mouse lung endoderm and regulates multiple aspects of early lung endoderm progenitor development. miR302/367 is expressed at early stages of lung development, but its levels decline rapidly as development proceeds. Gain- and loss-of-function studies show that altering miR302/367 expression disrupts the balance of lung endoderm progenitor proliferation and differentiation, as well as apical-basal polarity. Increased miR302/367 expression results in the formation of an undifferentiated multi-layered lung endoderm, whereas loss of miR302/367 activity results in decreased proliferation and enhanced lung endoderm differentiation. miR302/367 coordinates the balance between proliferation and differentiation, in part, through direct regulation of Rbl2 and Cdkn1a, whereas apical-basal polarity is controlled by regulation of Tiam1 and Lis1. Thus, miR302/367 directs lung endoderm development by coordinating multiple aspects of progenitor cell behavior, including proliferation, differentiation and apical-basal polarity.}, keywords = {Lung, MicroRNA, mouse, Progenitor}, isbn = {0950-1991, 1477-9129}, doi = {10.1242/dev.061762}, url = {http://dev.biologists.org/content/138/7/1235}, author = {Tian,Ying and Zhang,Yuzhen and Hurd,Laura and Hannenhalli, Sridhar and Liu,Feiyan and Lu,Min Min and Morrisey,Edward E.} } @inbook {19643, title = {Secure Efficient Multiparty Computing of Multivariate Polynomials and Applications}, booktitle = {Applied Cryptography and Network Security}, series = {Lecture Notes in Computer Science}, year = {2011}, month = {2011/01/01/}, pages = {130 - 146}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a robust secure methodology for computing functions that are represented as multivariate polynomials where parties hold different variables as private inputs. Our generic efficient protocols are fully black-box and employ threshold additive homomorphic encryption; they do not assume honest majority, yet are robust in detecting any misbehavior. We achieve solutions that take advantage of the algebraic structure of the polynomials, and are polynomial-time in all parameters (security parameter, polynomial size, polynomial degree, number of parties). We further exploit a {\textquotedblleft}round table{\textquotedblright} communication paradigm to reduce the complexity in the number of parties. A large collection of problems are naturally and efficiently represented as multivariate polynomials over a field or a ring: problems from linear algebra, statistics, logic, as well as operations on sets represented as polynomials. In particular, we present a new efficient solution to the multi-party set intersection problem, and a solution to a multi-party variant of the polynomial reconstruction problem.}, keywords = {additive homomorphic encryption, Algorithm Analysis and Problem Complexity, Computer Communication Networks, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, multiparty set intersection, multivariate polynomial evaluation, secret sharing, secure multiparty computation, Systems and Data Security, threshold cryptosystems}, isbn = {978-3-642-21553-7, 978-3-642-21554-4}, url = {http://link.springer.com/chapter/10.1007/978-3-642-21554-4_8}, author = {Dana Dachman-Soled and Malkin, Tal and Raykova, Mariana and Yung, Moti}, editor = {Lopez, Javier and Tsudik, Gene} } @article {19594, title = {Semantic Solutions to Program Analysis Problems}, journal = {arXiv:1105.0106 [cs]}, year = {2011}, month = {2011/04/30/}, abstract = {Problems in program analysis can be solved by developing novel program semantics and deriving abstractions conventionally. For over thirty years, higher-order program analysis has been sold as a hard problem. Its solutions have required ingenuity and complex models of approximation. We claim that this difficulty is due to premature focus on abstraction and propose a new approach that emphasizes semantics. Its simplicity enables new analyses that are beyond the current state of the art.}, keywords = {Computer Science - Programming Languages}, url = {http://arxiv.org/abs/1105.0106}, author = {Tobin-Hochstadt, Sam and David Van Horn} } @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 {12439, title = {Statistical Computations on Grassmann and Stiefel Manifolds for Image and Video-Based Recognition}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {33}, year = {2011}, month = {2011/11//}, pages = {2273 - 2286}, abstract = {In this paper, we examine image and video-based recognition applications where the underlying models have a special structure-the linear subspace structure. We discuss how commonly used parametric models for videos and image sets can be described using the unified framework of Grassmann and Stiefel manifolds. We first show that the parameters of linear dynamic models are finite-dimensional linear subspaces of appropriate dimensions. Unordered image sets as samples from a finite-dimensional linear subspace naturally fall under this framework. We show that an inference over subspaces can be naturally cast as an inference problem on the Grassmann manifold. To perform recognition using subspace-based models, we need tools from the Riemannian geometry of the Grassmann manifold. This involves a study of the geometric properties of the space, appropriate definitions of Riemannian metrics, and definition of geodesics. Further, we derive statistical modeling of inter and intraclass variations that respect the geometry of the space. We apply techniques such as intrinsic and extrinsic statistics to enable maximum-likelihood classification. We also provide algorithms for unsupervised clustering derived from the geometry of the manifold. Finally, we demonstrate the improved performance of these methods in a wide variety of vision applications such as activity recognition, video-based face recognition, object recognition from image sets, and activity-based video clustering.}, keywords = {activity based video clustering, activity recognition, computational geometry, Computational modeling, Data models, face recognition, feature representation, finite dimensional linear subspaces, geometric properties, Geometry, Grassmann Manifolds, Grassmann., HUMANS, Image and video models, image recognition, linear dynamic models, linear subspace structure, Manifolds, maximum likelihood classification, maximum likelihood estimation, Object recognition, Riemannian geometry, Riemannian metrics, SHAPE, statistical computations, statistical models, Stiefel, Stiefel Manifolds, unsupervised clustering, video based face recognition, video based recognition, video signal processing}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2011.52}, author = {Turaga,P. and Veeraraghavan,A. and Srivastava, A. and Chellapa, Rama} } @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.} } @inbook {16046, title = {Temporal Visualization of Social Network Dynamics: Prototypes for Nation of Neighbors}, booktitle = {Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction}, series = {Lecture Notes in Computer Science}, volume = {6589}, year = {2011}, month = {2011///}, pages = {309 - 316}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Information visualization is a powerful tool for analyzing the dynamic nature of social communities. Using Nation of Neighbors community network as a testbed, we propose five principles of implementing temporal visualizations for social networks and present two research prototypes: NodeXL and TempoVis. Three different states are defined in order to visualize the temporal changes of social networks. We designed the prototypes to show the benefits of the proposed ideas by letting users interactively explore temporal changes of social networks.}, isbn = {978-3-642-19655-3}, url = {http://dx.doi.org/10.1007/978-3-642-19656-0_43}, author = {Ahn,Jae-wook and Taieb-Maimon,Meirav and Sopan,Awalin and Plaisant, Catherine and Shneiderman, Ben}, editor = {Salerno,John and Yang,Shanchieh and Nau, Dana S. and Chai,Sun-Ki} } @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} } @conference {12452, title = {Towards view-invariant expression analysis using analytic shape manifolds}, booktitle = {2011 IEEE International Conference on Automatic Face \& Gesture Recognition and Workshops (FG 2011)}, year = {2011}, month = {2011/03/21/25}, pages = {306 - 313}, publisher = {IEEE}, organization = {IEEE}, abstract = {Facial expression analysis is one of the important components for effective human-computer interaction. However, to develop robust and generalizable models for expression analysis one needs to break the dependence of the models on the choice of the coordinate frame of the camera i.e. expression models should generalize across facial poses. To perform this systematically, one needs to understand the space of observed images subject to projective transformations. However, since the projective shape-space is cumbersome to work with, we address this problem by deriving models for expressions on the affine shape-space as an approximation to the projective shape-space by using a Riemannian interpretation of deformations that facial expressions cause on different parts of the face. We use landmark configurations to represent facial deformations and exploit the fact that the affine shape-space can be studied using the Grassmann manifold. This representation enables us to perform various expression analysis and recognition algorithms without the need for the normalization as a preprocessing step. We extend some of the available approaches for expression analysis to the Grassmann manifold and experimentally show promising results, paving the way for a more general theory of view-invariant expression analysis.}, keywords = {Databases, Deformable models, Face, face recognition, facial expression analysis, Geometry, Gold, Human-computer interaction, Manifolds, projective transformation, Riemannian interpretation, SHAPE, view invariant expression analysis}, isbn = {978-1-4244-9140-7}, doi = {10.1109/FG.2011.5771415}, author = {Taheri, S. and Turaga,P. and Chellapa, Rama} } @conference {18794, title = {Trajectory planning with look-ahead for Unmanned Sea Surface Vehicles to handle environmental disturbances}, year = {2011}, month = {2011///}, pages = {1154 - 1159}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6048670}, author = {Svec,P. and Schwartz,M. and Thakur,A. and Gupta,S.K.} } @article {17445, title = {Tutorial-Graph Analytics {\textemdash} Lessons Learned and Challenges Ahead}, journal = {IEEE Computer Graphics and Applications}, volume = {31}, year = {2011}, month = {2011///}, pages = {18 - 18}, author = {Wong,P.C. and Chen,C. and G{\"o}rg,C. and Shneiderman, Ben and Stasko,J. and Thomas,J.} } @article {15193, title = {Universally composable synchronous computation}, year = {2011}, month = {2011///}, institution = {Cryptology ePrint Archive, Report 2011/310, 2011. http://eprint. iacr. org}, abstract = {In synchronous networks, protocols can achieve security guarantees that are not possible in an asynchronousworld: i.e., they can simultaneously achieve input completeness (all honest parties{\textquoteright} inputs are included in the computation) and guaranteed termination (honest parties do not {\textquotedblleft}hang{\textquotedblright} indefinitely). In practice truly syn- chronous networks rarely exist, but synchrony can be emulated if channels have (known) latency and parties have loosely synchronized clocks. The framework of universal composability (UC) is inherently asynchronous, but several approaches for adding synchrony to the framework have been proposed. However, we show that the existing proposals do not provide the expected guarantees. Given this, we propose a {\textquotedblleft}clean slate{\textquotedblright} approach to defining synchrony in the UC framework by introducing functionalities exactly meant to model, respectively, bounded-delay networks and loosely synchronized clocks. We show that the expected guarantees of synchronous computation can be realized given these functionalities, and that previous models can all be expressed within our new framework. }, author = {Katz, Jonathan and Maurer,U. and Tackmann,B. and Zikas,V.} } @conference {13476, title = {Using Agent-Based Simulation to Determine an Optimal Lane-Changing Strategy on a Multi-Lane Highway}, booktitle = {2011 AAAI Fall Symposium Series}, year = {2011}, month = {2011///}, author = {Tuzo,J. and Seymour,J. and desJardins, Marie and others} } @article {17487, title = {Visual Exploration across Biomedical Databases}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, year = {2011}, month = {2011/04//March}, pages = {536 - 550}, abstract = {Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database exploration. A new approach is offered for visualizing and exploring a query-based subset of multiple heterogeneous biomedical databases. Databases are modeled as an entity-relation graph containing nodes (database records) and links (relationships between records). Users specify a keyword search string to retrieve an initial set of nodes, and then explore intra- and interdatabase links. Results are visualized with user-defined semantic substrates to take advantage of the rich set of attributes usually present in biomedical data. Comments from domain experts indicate that this visualization method is potentially advantageous for biomedical knowledge exploration.}, keywords = {Bioinformatics, Biomedical computing, biomedical databases, cross-database exploration, Data exploration and discovery, Data visualization, database management systems, Databases, Factual, DNA, graph theory, Information Storage and Retrieval, information visualization., Keyword search, medical computing, natural language processing, Proteins, semantic networks, semantics, sequences, text mining, User-Computer Interface, user-defined semantics, visual databases}, isbn = {1545-5963}, doi = {10.1109/TCBB.2010.1}, author = {Lieberman,M.D. and Taheri, S. and Guo,Huimin and Mirrashed,F. and Yahav,I. and Aris,A. and Shneiderman, Ben} } @article {15262, title = {Achieving anonymity via clustering}, journal = {ACM Trans. Algorithms}, volume = {6}, year = {2010}, month = {2010/07//}, pages = {49:1{\textendash}49:19 - 49:1{\textendash}49:19}, abstract = {Publishing data for analysis from a table containing personal records, while maintaining individual privacy, is a problem of increasing importance today. The traditional approach of deidentifying records is to remove identifying fields such as social security number, name, etc. However, recent research has shown that a large fraction of the U.S. population can be identified using nonkey attributes (called quasi-identifiers) such as date of birth, gender, and zip code. The k-anonymity model protects privacy via requiring that nonkey attributes that leak information are suppressed or generalized so that, for every record in the modified table, there are at least k-1 other records having exactly the same values for quasi-identifiers. We propose a new method for anonymizing data records, where quasi-identifiers of data records are first clustered and then cluster centers are published. To ensure privacy of the data records, we impose the constraint that each cluster must contain no fewer than a prespecified number of data records. This technique is more general since we have a much larger choice for cluster centers than k-anonymity. In many cases, it lets us release a lot more information without compromising privacy. We also provide constant factor approximation algorithms to come up with such a clustering. This is the first set of algorithms for the anonymization problem where the performance is independent of the anonymity parameter k. We further observe that a few outlier points can significantly increase the cost of anonymization. Hence, we extend our algorithms to allow an ε fraction of points to remain unclustered, that is, deleted from the anonymized publication. Thus, by not releasing a small fraction of the database records, we can ensure that the data published for analysis has less distortion and hence is more useful. Our approximation algorithms for new clustering objectives are of independent interest and could be applicable in other clustering scenarios as well.}, keywords = {anonymity, Approximation algorithms, clustering, privacy}, isbn = {1549-6325}, doi = {10.1145/1798596.1798602}, url = {http://doi.acm.org/10.1145/1798596.1798602}, author = {Aggarwal,Gagan and Panigrahy,Rina and Feder,Tom{\'a}s and Thomas,Dilys and Kenthapadi,Krishnaram and Khuller, Samir and Zhu,An} } @article {15707, title = {Adaptive Constraint Reduction for Convex Quadratic Programming}, journal = {Computational Optimization and Applications}, year = {2010}, month = {2010/03//}, abstract = {We propose an adaptive, constraint-reduced, primal-dual interior-point algorithm for convex quadratic programming with many more inequality constraints than variables. We reduce the computational effort by assembling, instead of the exact normal-equation matrix, an approximate matrix from a well chosen index set which includes indices of constraints that seem to be most critical. Starting with a large portion of the constraints, our proposed scheme excludes more unnecessary constraints at later iterations. We provide proofs for the global convergence and the quadratic local convergence rate of an affine-scaling variant. Numerical experiments on random problems, on a data-fitting problem, and on a problem in array pattern synthesis show the effectiveness of the constraint reduction in decreasing the time per iteration without significantly affecting the number of iterations. We note that a similar constraint-reduction approach can be applied to algorithms of Mehrotra{\textquoteright}s predictor-corrector type, although no convergence theory is supplied.}, doi = {DOI:10.1007/s10589-010-9324-8}, author = {Jung,Jin Hyuk and O{\textquoteright}Leary, Dianne P. and Tits,Andre{\textquoteright} L.} } @inbook {12498, title = {Advances in Video-Based Human Activity Analysis: Challenges and Approaches}, booktitle = {Advances in ComputersAdvances in Computers}, volume = {Volume 80}, year = {2010}, month = {2010///}, pages = {237 - 290}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {Videos play an ever increasing role in our everyday lives with applications ranging from news, entertainment, scientific research, security, and surveillance. Coupled with the fact that cameras and storage media are becoming less expensive, it has resulted in people producing more video content than ever before. Analysis of human activities in video is important for several important applications. Interpretation and identification of human activities requires approaches that address the following questions (a) what are the appropriate atomic primitives for human activities, (b) how to combine primitives to produce complex activities, (c) what are the required invariances for inference algorithms, and (d) how to build computational models for each of these. In this chapter, we provide a broad overview and discussion of these issues. We shall review state-of-the-art computer vision algorithms that address these issues and then provide a unified perspective from which specific algorithms can be derived. We will then present supporting experimental results.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245810800075}, author = {Turaga,Pavan and Chellapa, Rama and Veeraraghavan,Ashok}, editor = {Zelkowitz, Marvin V} } @article {19627, title = {Applications of Parameterized st-Orientations}, journal = {Journal of Graph Algorithms and Applications}, volume = {14}, year = {2010}, month = {2010///}, pages = {337 - 365}, isbn = {1526-1719}, url = {http://emis.um.ac.ir/journals/JGAA/getPaper-96.html?id=212}, author = {Charalampos Papamanthou and Tollis, Ioannis G.} } @inbook {12504, title = {Articulation-Invariant Representation of Non-planar Shapes}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6313}, year = {2010}, month = {2010///}, pages = {286 - 299}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Given a set of points corresponding to a 2D projection of a non-planar shape, we would like to obtain a representation invariant to articulations (under no self-occlusions). It is a challenging problem since we need to account for the changes in 2D shape due to 3D articulations, viewpoint variations, as well as the varying effects of imaging process on different regions of the shape due to its non-planarity. By modeling an articulating shape as a combination of approximate convex parts connected by non-convex junctions, we propose to preserve distances between a pair of points by (i) estimating the parts of the shape through approximate convex decomposition, by introducing a robust measure of convexity and (ii) performing part-wise affine normalization by assuming a weak perspective camera model, and then relating the points using the inner distance which is insensitive to planar articulations. We demonstrate the effectiveness of our representation on a dataset with non-planar articulations, and on standard shape retrieval datasets like MPEG-7.}, isbn = {978-3-642-15557-4}, url = {http://dx.doi.org/10.1007/978-3-642-15558-1_21}, author = {Gopalan,Raghuraman and Turaga,Pavan and Chellapa, Rama}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @article {12983, title = {Broader incorporation of bioinformatics in education: opportunities and challenges}, journal = {Brief Bioinform}, volume = {11}, year = {2010}, month = {2010///}, abstract = {The major opportunities for broader incorporation of bioinformatics in education can be placed into three general categories: general applicability of bioinformatics in life science and related curricula; inherent fit of bioinformatics for promoting student learning in most biology programs; and the general experience and associated comfort students have with computers and technology. Conversely, the major challenges for broader incorporation of bioinformatics in education can be placed into three general categories: required infrastructure and logistics; instructor knowledge of bioinformatics and continuing education; and the breadth of bioinformatics, and the diversity of students and educational objectives. Broader incorporation of bioinformatics at all education levels requires overcoming the challenges to using transformative computer- requiring learning activities, assisting faculty in collecting assessment data on mastery of student learning outcomes, as well as creating more faculty development opportunities that span diverse skill levels, with an emphasis placed on providing resource materials that are kept up-to-date as the field and tools change.}, author = {Cummings, Michael P. and Temple,GG} } @conference {18932, title = {Building an IT Taxonomy with Co-occurrence Analysis, Hierarchical Clustering, and Multidimensional Scaling}, year = {2010}, month = {2010///}, abstract = {Different information technologies (ITs) are related in complex ways. How can the relationships among a large number of ITs be described and analyzed in a representative, dynamic, and scalable way? In this study, we employed co-occurrence analysis to explore the relationships among 50 information technologies discussed in six magazines over ten years (1998-2007). Using hierarchical clustering and multidimensional scaling, we have found that the similarities of the technologies can be depicted in hierarchies and two-dimensional plots, and that similar technologies can be classified into meaningful categories. The results imply reasonable validity of our approach for understanding technology relationships and building an IT taxonomy. The methodology that we offer not only helps IT practitioners and researchers make sense of numerous technologies in the iField but also bridges two related but thus far largely separate research streams in iSchools - information management and IT management.}, url = {https://www.ideals.illinois.edu/handle/2142/14918}, author = {Tsui,C. and Wang,P. and Fleischmann,K.R. and Sayeed,A. B. and Weinberg, Amy} } @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 {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} } @article {12870, title = {Comparative Genomics of Clinical and Environmental Vibrio Mimicus}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {107}, year = {2010}, month = {2010/12/07/}, pages = {21134 - 21139}, abstract = {Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has been the subject of taxonomic controversy. A genomic analysis was undertaken to resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I (C-I) predominantly contains genes necessary for growth and viability, whereas chromosome II (C-II) bears genes for adaptation to environmental change. C-I harbors many virulence genes, including some not previously reported in V. mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2 (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes. Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution and genesis of speciation for the genus Vibrio. The number of virulence regions discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron integrase, IntI4) with no notable difference in potential virulence genes between clinical and environmental strains suggests these genes also may play a role in the environment and that pathogenic strains may arise in the environment. Significant genome synteny with prototypic pre-seventh pandemic strains of V. cholerae was observed, and the results of phylogenetic analysis support the hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged from a common ancestor with a prototypic sixth pandemic genomic backbone.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.1013825107}, url = {http://www.pnas.org/content/107/49/21134}, author = {Hasan,Nur A. and Grim,Christopher J. and Haley,Bradd J. and Jongsik Chun and Alam,Munirul and Taviani,Elisa and Mozammel Hoq and Munk,A. Christine 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 {16254, title = {Computational Approaches for Genome Assembly Validation}, journal = {Biological Data Mining}, year = {2010}, month = {2010///}, pages = {163 - 163}, author = {Choi,J.H. and Tang,H. and Kim,S. and Pop, Mihai} } @conference {18797, title = {A Computational Framework for Real-Time Unmanned Sea Surface Vehicle Motion Simulation}, volume = {3}, year = {2010}, month = {2010///}, pages = {51 - 61}, publisher = {ASME}, organization = {ASME}, address = {Montreal, Quebec, Canada}, abstract = {Unmanned Sea Surface Vehicle (USSV) motion simulation in time domain is an important component of USSV design and operation. This capability is needed for hull design, operator training, controller synthesis and testing. Many applications such as simulators for operator training require real-time performance. Traditional approaches based on strip theory, although fast, abstract hulls into slender bodies, making the simulation results insensitive to changes in geometry. Computational fluid dynamics (CFD) based approaches are accurate but very slow. Potential flow based approaches are sensitive to hull geometry and take lesser amount of time than CFD based approaches. The motion simulation using potential flow theory involves following four main operations: (1) computation of dynamic pressure head due to fluid flow around the hull under the ocean wave, (2) computation of wet surface, (3) computing surface integral of dynamic pressure head over wet surface, and (4) solving the rigid body dynamics equation. First three operations depend upon the boat geometry complexity and need to be performed at each time step, making the simulation run very slow. In this paper, we investigate the problem of model simplification for real-time simulation of USSV model in time domain using potential flow theory, with arbitrary geometry under ocean waves with inviscid and irrotational flow. Using clustering based simplification scheme and parallel computing we obtained real time simulation performance.}, isbn = {978-0-7918-4411-3}, doi = {10.1115/DETC2010-28526}, url = {http://link.aip.org/link/ASMECP/v2010/i44113/p51/s1\&Agg=doi}, author = {Thakur,Atul and Gupta, Satyandra K.} } @article {12873, title = {Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co-culture with eukaryotic cells}, journal = {Microbiology and Immunology}, volume = {54}, year = {2010}, month = {2010/06/14/}, pages = {502 - 507}, abstract = {VBNC Vibrio cholerae O139 VC-280 obtained by incubation in 1\% solution of artificial sea water IO at 4{\textdegree}C for 74 days converted to the culturable state when co-cultured with CHO cells. Other eukaryotic cell lines, including HT-29, Caco-2, T84, HeLa, and Intestine 407, also supported conversion of VBNC cells to the culturable state. Conversion of VBNC V. cholerae O1 N16961 and V. cholerae O139 VC-280/pG13 to the culturable state, under the same conditions, was also confirmed. When VBNC V. cholerae O139 VC-280 was incubated in 1\% IO at 4{\textdegree}C for up to 91 days, the number of cells converted by co-culture with CHO cells declined with each additional day of incubation and after 91 days conversion was not observed.}, keywords = {conversion to culturability, co-culture, eukaryotic cell, viable but nonculturable (VBNC) Vibrio cholerae}, isbn = {1348-0421}, doi = {10.1111/j.1348-0421.2010.00245.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2010.00245.x/full}, author = {Senoh,Mitsutoshi and Ghosh-Banerjee,Jayeeta and Ramamurthy,Thandavarayan and Hamabata,Takashi and Kurakawa,Takashi and Takeda,Makoto and Rita R Colwell and Nair,G. Balakrish and Takeda,Yoshifumi} } @conference {18559, title = {Decoupling policy from configuration in campus and enterprise networks}, booktitle = {Local and Metropolitan Area Networks (LANMAN), 2010 17th IEEE Workshop on}, year = {2010}, month = {2010/05//}, pages = {1 - 6}, abstract = {This paper surveys our ongoing work on the use of software-defined networking to simplify two acute policy problems in campus and enterprise network operations: access control and information flow control. We describe how the current coupling of high-level policy with low-level configuration makes these problems challenging today. We describe the specific policy problems faced by campus and enterprise network operators; illustrate our approach, which leverages recent trends in separating the network{\textquoteright}s $\#$x201C;control plane $\#$x201D; from the data plane; and show how this approach can be applied to simplify these two enterprise network management tasks. We also describe our ongoing deployment efforts to build a campus network testbed where trial designs can be deployed and evaluated. We close with a summary of current and future research challenges for solving challenges within enterprise networks within the context of this new paradigm.}, keywords = {Access control, Business communication, campus network, decoupling policy, enterprise network management tasks, enterprise network operator, information flow control, software defined network, software radio, telecommunication network management, telecommunication security}, doi = {10.1109/LANMAN.2010.5507162}, author = {Feamster, Nick and Nayak,A. and Kim,Hyojoon and Clark,R. and Mundada,Y. and Ramachandran,A. and bin Tariq,M.} } @article {12874, title = {Discovery of novel Vibrio cholerae VSP-II genomic islands using comparative genomic analysis}, journal = {FEMS Microbiology Letters}, volume = {308}, year = {2010}, month = {2010/05/06/}, pages = {130 - 137}, abstract = {This report describes Vibrio seventh pandemic island II (VSP-II) and three novel variants revealed by comparative genomics of 23 Vibrio cholerae strains and their presence among a large and diverse collection of V. cholerae isolates. Three VSP-II variants were reported previously and our results demonstrate the presence of three novel VSP-II in clinical and environmental V. cholerae marked by major deletions and genetic rearrangements. A new VSP-II cluster was found in the seventh pandemic V. cholerae O1 El Tor strain CIRS101, which is dominant (95\%) among the recent (2004{\textendash}2007) seven pandemic V. cholerae O1 El Tor isolates from two endemic sites, but was not found in older strains from the same region. Two other variants were found in V. cholerae TMA21 and RC385, two environmental strains from coastal Brazil and the Chesapeake Bay, respectively, the latter being prevalent among environmental V. cholerae non-O1/non-O139 and Vibrio mimicus. The results of this study indicate that the VSP-II island has undergone significant rearrangement through a complex evolutionary pathway in V. cholerae. Interestingly, one of the new VSP-II revealed the presence of {\textquoteleft}old{\textquoteright} and {\textquoteleft}new{\textquoteright}V. cholerae O1 El Tor pandemic clones circulating in some of the areas where cholera is endemic.}, keywords = {Vibrio cholerae, Vibrio mimicus, VPS-II}, isbn = {1574-6968}, doi = {10.1111/j.1574-6968.2010.02008.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2010.02008.x/full}, author = {Taviani,Elisa and Grim,Christopher J. and Choi,Jinna and Jongsik Chun and Haley,Bradd and Hasan,Nur A. and Huq,Anwar and Rita R Colwell} } @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} } @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} } @article {17152, title = {Exploring distributions: design and evaluation}, journal = {University of Maryland, Human-Computer Interaction Lab Tech Report HCIL-2010-01}, year = {2010}, month = {2010///}, abstract = {Visual overviews of tables of numerical and categorical data have been proposed for tables with a single value per cell.In this paper we address the problem of exploring tables including columns consisting of distributions, e.g. the distributions of movie ratings or trust ratings in recommender systems, age distributions in demographic data, usage distributions in logs of telephone calls etc. We propose a novel way of displaying and interacting with distribution data, and present the results of a usability study that demonstrates the benefits of the interface in providing an overview of the data and facilitating the discovery of interesting clusters, patterns, outliers and relationships between columns. }, author = {Sopan,A. and Freire,M. and Taieb-Maimon,M. and Golbeck,J. and Shneiderman, Ben} } @conference {15874, title = {Exploring the Relationships among ICTs: A Scalable Computational Approach Using KL Divergence and Hierarchical Clustering}, booktitle = {Hawaii International Conference on System Sciences}, year = {2010}, month = {2010///}, pages = {1 - 10}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Different information and communication technologies (ICTs) are related in complex ways and, accordingly, their diffusion trajectories are related, too. How can the relationships among multiple ICTs be described and analyzed in a scalable way? In this study, we offer a scalable methodology, based on computational analysis of discourse, to examine the relationships among ICTs. Specifically, we employed Kullback-Leibler (KL) divergence to compare the semantic similarity of forty-seven ICTs discussed in the trade magazine InformationWeek over a decade. Using hierarchical clustering, we have found that the similarity of the technologies can be mapped in a hierarchy and similar technologies demonstrated similar discourses. The results establish the validity of our approach and demonstrate its scalability and richness. This analytical approach not only enables diffusion researchers to undertake multi-innovation, multi-source, and multi-period studies, but also helps practitioners effectively adopt and efficiently use new ICTs in their organizations.}, isbn = {978-0-7695-3869-3}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2010.203}, author = {Tsui,Chia-jung and Wang,Ping and Fleischmann,Kenneth R. and Oard, Douglas and Sayeed,Asad B.} } @conference {12483, title = {Fast directional chamfer matching}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {1696 - 1703}, abstract = {We study the object localization problem in images given a single hand-drawn example or a gallery of shapes as the object model. Although many shape matching algorithms have been proposed for the problem over the decades, chamfer matching remains to be the preferred method when speed and robustness are considered. In this paper, we significantly improve the accuracy of chamfer matching while reducing the computational time from linear to sublinear (shown empirically). Specifically, we incorporate edge orientation information in the matching algorithm such that the resulting cost function is piecewise smooth and the cost variation is tightly bounded. Moreover, we present a sublinear time algorithm for exact computation of the directional chamfer matching score using techniques from 3D distance transforms and directional integral images. In addition, the smooth cost function allows to bound the cost distribution of large neighborhoods and skip the bad hypotheses within. Experiments show that the proposed approach improves the speed of the original chamfer matching upto an order of 45 $\#$x00D7;, and it is much faster than many state of art techniques while the accuracy is comparable.}, keywords = {3D, algorithm;edge, algorithms;single, chamfer, cost, detection;image, directional, distance, distribution;cost, example;smooth, function;sublinear, hand-drawn, images;edge, information;fast, integral, localization, MATCHING, matching;gallery, matching;transforms;, model;piecewise, of, orientation, problem;object, score;directional, shapes;object, smooth;shape, TIME, time;cost, transforms;computational, variation;directional}, doi = {10.1109/CVPR.2010.5539837}, author = {Ming-Yu Liu and Tuzel, O. and Veeraraghavan,A. and Chellapa, Rama} } @conference {17988, title = {General-purpose vs. gpu: Comparison of many-cores on irregular workloads}, booktitle = {Proceedings of the Second Usenix Workshop on Hot Topics in Parallelism}, year = {2010}, month = {2010///}, pages = {14 - 15}, abstract = {XMT1 is a general-purpose many-core parallel architec-ture. The foremost design objective for XMT was to meet the highest standards for ease of parallel programming. GPUs, on the other hand, have acquired a strong reputa- tion on performance, sometimes at the expense of ease- of-programming. The current paper presents a perfor- mance comparison on diverse workloads between XMT and an NVIDIA CUDA-enabled GPU. Configured with roughly the same amount of chip resources as the GPU, XMT achieves an average speedup of 6.05x on irregu- lar applications, while incurring an average slowdown of 2.07x on regular ones. Namely, XMT comes ahead for significant applications without having to pay a (possibly worthwhile) price for easier programming. This surpris- ing result suggests a yet untapped opportunity: A high- performance easy-to-program general-purpose 1000-core computer. }, author = {Caragea,G.C. and Keceli,F. and Tzannes,A. and Vishkin, Uzi} } @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 {19094, title = {Genomic characterization of the Yersinia genus}, journal = {Genome biology}, volume = {11}, year = {2010}, month = {2010}, author = {Chen, P.E. and Cook, C. and Stewart, A.C. and Nagarajan,N. and Sommer, D.D. and Pop, Mihai and Thomason, B. and Thomason, M.P.K. and Lentz, S. and Nolan, N. and others} } @article {14622, title = {Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation}, journal = {Developmental Cell}, volume = {19}, year = {2010}, month = {2010/09/14/}, pages = {450 - 459}, abstract = {SummaryRegulation of chromatin structure via histone modification has recently received intense attention. Here,~we demonstrate that the chromatin-modifying enzyme histone deacetylase 2 (Hdac2) functions with a small homeodomain factor, Hopx, to mediate deacetylation of Gata4, which is expressed by cardiac progenitor cells and plays critical roles in the regulation of cardiogenesis. In the absence of Hopx and Hdac2 in mouse embryos, Gata4 hyperacetylation is associated with a marked increase in~cardiac myocyte proliferation, upregulation of Gata4 target genes, and perinatal lethality. Hdac2 physically interacts with Gata4, and this interaction is stabilized by Hopx. The ability of Gata4 to transactivate cell cycle genes is impaired by Hopx/Hdac2-mediated deacetylation, and this effect is abrogated by loss of Hdac2-Gata4 interaction. These results suggest that Gata4 is a nonhistone target of Hdac2-mediated deacetylation and that Hdac2, Hopx, and Gata4 coordinately regulate cardiac myocyte proliferation during embryonic development. }, isbn = {1534-5807}, doi = {10.1016/j.devcel.2010.08.012}, url = {http://www.sciencedirect.com/science/article/pii/S1534580710003874}, author = {Trivedi,Chinmay M. and Zhu,Wenting and Wang,Qiaohong and Jia,Cheng and Kee,Hae Jin and Li,Li and Hannenhalli, Sridhar and Epstein,Jonathan A.} } @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} } @article {15883, title = {Investigating multi-label classification for human values}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {47}, year = {2010}, month = {2010///}, pages = {1 - 4}, author = {Ishita,E. and Oard, Douglas and Fleischmann,K.R. and Cheng,A.S. and Templeton,T.C.} } @conference {18578, title = {Joint analysis of network incidents and intradomain routing changes}, booktitle = {Network and Service Management (CNSM), 2010 International Conference on}, year = {2010}, month = {2010/10//}, pages = {198 - 205}, abstract = {This paper studies how intradomain routing instability relates to events in network trouble tickets for two networks: a VPN provider and the Internet2 backbone network. Our goal in performing this joint analysis of routing and trouble tickets is to better understand the likely underlying causes of intradomain routing instability. We develop a method to correlate trouble tickets with instability events and find that, although unplanned events last longer than scheduled maintenance, there is no single underlying cause for most instability, and that these causes differ across networks. In comparison to a similar study from Labovitz et al. from ten years ago, we find that, while certain causes of instability such as maintenance and circuit problems remain significant, power issues have become much less prevalent, and software-related problems have become more common.}, keywords = {correlation method, Internet, Internet2 backbone network, intradomain routing instability, network maintenance, network routing joint analysis, telecommunication network routing, Virtual private networks, VPN provider}, doi = {10.1109/CNSM.2010.5691306}, author = {Medem,A. and Teixeira,R. and Feamster, Nick and Meulle,M.} } @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} } @article {14421, title = {Learning algorithms for link prediction based on chance constraints}, journal = {Machine Learning and Knowledge Discovery in Databases}, year = {2010}, month = {2010///}, pages = {344 - 360}, abstract = {In this paper, we consider the link prediction problem, where we are given a partial snapshot of a network at some time and the goal is to predict the additional links formed at a later time. The accuracy of current prediction methods is quite low due to the extreme class skew and the large number of potential links. Here, we describe learning algorithms based on chance constrained programs and show that they exhibit all the properties needed for a good link predictor, namely, they allow preferential bias to positive or negative class; handle skewness in the data; and scale to large networks. Our experimental results on three real-world domains{\textemdash}co-authorship networks, biological networks and citation networks{\textemdash}show significant performance improvement over baseline algorithms. We conclude by briefly describing some promising future directions based on this work.}, doi = {10.1007/978-3-642-15880-3_28}, author = {Doppa,J. and Yu,J. and Tadepalli,P. and Getoor, Lise} } @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 {12479, title = {Moving vistas: Exploiting motion for describing scenes}, booktitle = {2010 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2010}, month = {2010/06/13/18}, pages = {1911 - 1918}, publisher = {IEEE}, organization = {IEEE}, abstract = {Scene recognition in an unconstrained setting is an open and challenging problem with wide applications. In this paper, we study the role of scene dynamics for improved representation of scenes. We subsequently propose dynamic attributes which can be augmented with spatial attributes of a scene for semantically meaningful categorization of dynamic scenes. We further explore accurate and generalizable computational models for characterizing the dynamics of unconstrained scenes. The large intra-class variation due to unconstrained settings and the complex underlying physics present challenging problems in modeling scene dynamics. Motivated by these factors, we propose using the theory of chaotic systems to capture dynamics. Due to the lack of a suitable dataset, we compiled a dataset of {\textquoteleft}in-the-wild{\textquoteright} dynamic scenes. Experimental results show that the proposed framework leads to the best classification rate among other well-known dynamic modeling techniques. We also show how these dynamic features provide a means to describe dynamic scenes with motion-attributes, which then leads to meaningful organization of the video data.}, keywords = {Application software, Automation, Chaos, chaotic system, Computational modeling, Computer vision, dynamic scene categorization, Educational institutions, HUMANS, image recognition, in the wild dynamic scene, Layout, motion attribute, natural scenes, Physics, probability, scene recognition, Snow, video data}, isbn = {978-1-4244-6984-0}, doi = {10.1109/CVPR.2010.5539864}, author = {Shroff, N. and Turaga,P. and Chellapa, Rama} } @conference {12499, title = {Nearest-neighbor search algorithms on non-Euclidean manifolds for computer vision applications}, booktitle = {Proceedings of the Seventh Indian Conference on Computer Vision, Graphics and Image Processing}, series = {ICVGIP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {282 - 289}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Nearest-neighbor searching is a crucial component in many computer vision applications such as face recognition, object recognition, texture classification, and activity recognition. When large databases are involved in these applications, it is also important to perform these searches in a fast manner. Depending on the problem at hand, nearest neighbor strategies need to be devised over feature and model spaces which in many cases are not Euclidean in nature. Thus, metrics that are tuned to the geometry of this space are required which are also known as geodesics. In this paper, we address the problem of fast nearest neighbor searching in non-Euclidean spaces, where in addition to dealing with the large size of the dataset, the significant computational load involves geodesic computations. We study the applicability of the various classes of nearest neighbor algorithms toward this end. Exact nearest neighbor methods that rely solely on the existence of a metric can be extended, albeit with a huge computational cost. We derive an approximate method of searching via approximate embeddings using the logarithmic map. We study the error incurred in such an embedding and show that it performs well in real experiments.}, keywords = {Grassmann manifold, hashing, manifold, nearest-neighbor, region covariance, shapes}, isbn = {978-1-4503-0060-5}, doi = {10.1145/1924559.1924597}, url = {http://doi.acm.org/10.1145/1924559.1924597}, author = {Turaga,Pavan and Chellapa, Rama} } @article {14513, title = {Object Classification Using Taxonomies}, volume = {12/414,065}, year = {2010}, month = {2010/07/22/}, abstract = {As provided herein objects from a source catalog, such as a provider{\textquoteright}s catalog, can be added to a target catalog, such as an enterprise master catalog, in a scalable manner utilizing catalog taxonomies. A baseline classifier determines probabilities for source objects to target catalog classes. Source objects can be assigned to those classes with probabilities that meet a desired threshold and meet a desired rate. A classification cost for target classes can be determined for respective unassigned source objects, which can comprise determining an assignment cost and separation cost for the source objects for respective desired target classes. The separation and assignment costs can be combined to determine the classification cost, and the unassigned source objects can be assigned to those classes having a desired classification cost.}, url = {http://www.google.com/patents?id=oXDSAAAAEBAJ}, author = {Tsaparas,Panayiotis and Papadimitriou,Panagiotis and Fuxman,Ariel D. and Getoor, Lise and Agrawal,Rakesh}, editor = {Microsoft Corporation} } @conference {12481, title = {Object Dependent Manifold Priors for Image Deconvolution}, booktitle = {Digital Image Processing and Analysis}, series = {OSA Technical Digest (CD)}, year = {2010}, month = {2010/06/07/}, pages = {DMC2 - DMC2}, publisher = {Optical Society of America}, organization = {Optical Society of America}, abstract = {In this paper we propose a manifold based deconvolution algorithm by estimating a manifold from a set of natural images that exploits the availability of the sample class data for regularizing the deblurring problem.}, keywords = {Deconvolution, IMAGE PROCESSING, Inverse problems}, url = {http://www.opticsinfobase.org/abstract.cfm?URI=DIPA-2010-DMC2}, author = {Ni,Jie and Turaga,Pavan and M.Patel,Vishal and Chellapa, Rama} } @article {12879, title = {Occurrence of the Vibrio cholerae seventh pandemic VSP-I island and a new variant}, journal = {OMICS: A Journal of Integrative Biology}, volume = {14}, year = {2010}, month = {2010/02//}, pages = {1 - 7}, isbn = {1536-2310, 1557-8100}, doi = {10.1089/omi.2009.0087}, url = {http://online.liebertpub.com/doi/abs/10.1089/omi.2009.0087}, author = {Grim,Christopher J. and Choi,Jinna and Jongsik Chun and Jeon,Yoon-Seong and Taviani,Elisa and Hasan,Nur A. and Haley,Bradd and Huq,Anwar and Rita R Colwell} } @inbook {19604, title = {Optimal Authenticated Data Structures with Multilinear Forms}, booktitle = {Pairing-Based Cryptography - Pairing 2010}, series = {Lecture Notes in Computer Science}, year = {2010}, month = {2010/01/01/}, pages = {246 - 264}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Cloud computing and cloud storage are becoming increasingly prevalent. In this paradigm, clients outsource their data and computations to third-party service providers. Data integrity in the cloud therefore becomes an important factor for the functionality of these web services.Authenticated data structures, implemented with various cryptographic primitives, have been widely studied as a means of providing efficient solutions to data integrity problems (e.g., Merkle trees). In this paper, we introduce a new authenticated dictionary data structure that employs multilinear forms, a cryptographic primitive proposed by Silverberg and Boneh in 2003 [10], the construction of which, however, remains an open problem to date. Our authenticated dictionary is optimal, that is, it does not add any extra asymptotic cost to the plain dictionary data structure, yielding proofs of constant size, i.e., asymptotically equal to the size of the answer, while maintaining other relevant complexities logarithmic. Instead, solutions based on cryptographic hashing (e.g., Merkle trees) require proofs of logarithmic size [40]. Because multilinear forms are not known to exist yet, our result can be viewed from a different angle: if one could prove that optimal authenticated dictionaries cannot exist in the computational model, irrespectively of cryptographic primitives, then our solution would imply that cryptographically interesting multilinear form generators cannot exist as well (i.e., it can be viewed as a reduction). Thus, we provide an alternative avenue towards proving the nonexistence of multilinear form generators in the context of general lower bounds for authenticated data structures [40] and for memory checking [18], a model similar to the authenticated data structures model.}, keywords = {Algorithm Analysis and Problem Complexity, authenticated dictionary, Coding and Information Theory, Computer Communication Networks, Data Encryption, Discrete Mathematics in Computer Science, multilinear forms, Systems and Data Security}, isbn = {978-3-642-17454-4, 978-3-642-17455-1}, url = {http://link.springer.com/chapter/10.1007/978-3-642-17455-1_16}, author = {Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikos}, editor = {Joye, Marc and Miyaji, Atsuko and Otsuka, Akira} } @article {18708, title = {Perturbing the Ubiquitin Pathway Reveals How Mitosis Is Hijacked to Denucleate and Regulate Cell Proliferation and Differentiation In Vivo}, journal = {PLoS ONEPLoS ONE}, volume = {5}, year = {2010}, month = {2010/10/20/}, pages = {e13331 - e13331}, abstract = {BackgroundThe eye lens presents a unique opportunity to explore roles for specific molecules in cell proliferation, differentiation and development because cells remain in place throughout life and, like red blood cells and keratinocytes, they go through the most extreme differentiation, including removal of nuclei and cessation of protein synthesis. Ubiquitination controls many critical cellular processes, most of which require specific lysines on ubiquitin (Ub). Of the 7 lysines (K) least is known about effects of modification of K6. Methodology and Principal Findings We replaced K6 with tryptophan (W) because K6 is the most readily modified K and W is the most structurally similar residue to biotin. The backbone of K6W-Ub is indistinguishable from that of Wt-Ub. K6W-Ub is effectively conjugated and deconjugated but the conjugates are not degraded via the ubiquitin proteasome pathways (UPP). Expression of K6W-ubiquitin in the lens and lens cells results in accumulation of intracellular aggregates and also slows cell proliferation and the differentiation program, including expression of lens specific proteins, differentiation of epithelial cells into fibers, achieving proper fiber cell morphology, and removal of nuclei. The latter is critical for transparency, but the mechanism by which cell nuclei are removed has remained an age old enigma. This was also solved by expressing K6W-Ub. p27kip, a UPP substrate accumulates in lenses which express K6W-Ub. This precludes phosphorylation of nuclear lamin by the mitotic kinase, a prerequisite for disassembly of the nuclear membrane. Thus the nucleus remains intact and DNAseIIβ neither gains entry to the nucleus nor degrades the DNA. These results could not be obtained using chemical proteasome inhibitors that cannot be directed to specific tissues. Conclusions and Significance K6W-Ub provides a novel, genetic means to study functions of the UPP because it can be targeted to specific cells and tissues. A fully functional UPP is required to execute most stages of lens differentiation, specifically removal of cell nuclei. In the absence of a functional UPP, small aggregate prone, cataractous lenses are formed. }, doi = {10.1371/journal.pone.0013331}, url = {http://dx.doi.org/10.1371/journal.pone.0013331}, author = {Caceres,Andrea and Shang,Fu and Wawrousek,Eric and Liu,Qing and Avidan,Orna and Cvekl,Ales and Yang,Ying and Haririnia,Aydin and Storaska,Andrew and Fushman, David and Kuszak,Jer and Dudek,Edward and Smith,Donald and Taylor,Allen} } @conference {12486, title = {Pose estimation in heavy clutter using a multi-flash camera}, booktitle = {Robotics and Automation (ICRA), 2010 IEEE International Conference on}, year = {2010}, month = {2010/05//}, pages = {2028 - 2035}, abstract = {We propose a novel solution to object detection, localization and pose estimation with applications in robot vision. The proposed method is especially applicable when the objects of interest may not be richly textured and are immersed in heavy clutter. We show that a multi-flash camera (MFC) provides accurate separation of depth edges and texture edges in such scenes. Then, we reformulate the problem, as one of finding matches between the depth edges obtained in one or more MFC images to the rendered depth edges that are computed offline using 3D CAD model of the objects. In order to facilitate accurate matching of these binary depth edge maps, we introduce a novel cost function that respects both the position and the local orientation of each edge pixel. This cost function is significantly superior to traditional Chamfer cost and leads to accurate matching even in heavily cluttered scenes where traditional methods are unreliable. We present a sub-linear time algorithm to compute the cost function using techniques from 3D distance transforms and integral images. Finally, we also propose a multi-view based pose-refinement algorithm to improve the estimated pose. We implemented the algorithm on an industrial robot arm and obtained location and angular estimation accuracy of the order of 1 mm and 2 $\#$x00B0; respectively for a variety of parts with minimal texture.}, keywords = {3D, algorithm;object, based, camera;multiview, depth, detection;object, detection;pose, distance, edge, edges;cameras;image, edges;integral, estimation;binary, estimation;multiflash, estimation;robot, function;depth, images;location, localization;pose, maps, matching;cost, matching;image, pose-refinement, texture;object, transforms;angular, vision;texture, vision;transforms;}, doi = {10.1109/ROBOT.2010.5509897}, author = {Ming-Yu Liu and Tuzel, O. and Veeraraghavan,A. and Chellapa, Rama and Agrawal,A. and Okuda, H.} } @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} } @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} } @article {18711, title = {Reversible Post-Translational Carboxylation Modulates the Enzymatic Activity of N-Acetyl-l-ornithine Transcarbamylase}, journal = {Biochemistry}, volume = {49}, year = {2010}, month = {2010///}, pages = {6887 - 6895}, abstract = {N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis.N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis. }, isbn = {0006-2960}, doi = {10.1021/bi1007386}, url = {http://dx.doi.org/10.1021/bi1007386}, author = {Li,Yongdong and Yu,Xiaolin and Ho,Jeremy and Fushman, David and Allewell,Norma M. and Tuchman,Mendel and Shi,Dashuang} } @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} } @inbook {12507, title = {Semantic Video Content Analysis}, booktitle = {Video Search and MiningVideo Search and Mining}, series = {Studies in Computational Intelligence}, volume = {287}, year = {2010}, month = {2010///}, pages = {147 - 176}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In recent years, there has been significant interest in the area of automatically recognizing activities occurring in a camera{\textquoteright}s field of view and detecting abnormalities. The practical applications of such a system could include airport tarmac monitoring, or monitoring of activities in secure installations, to name a few. The difficulty of the problem is compounded by several factors: detection of primitive actions in spite of changes in illumination, occlusions and noise; complexmultiagent interaction;mapping of higher-level activities to lower-level primitive actions; variations in which the same semantic activity can be performed. In this chapter, we develop a theory of semantic activity analysis that addresses each of these issues in an integrated manner. Specifically, we discuss ontological representations of knowledge of a domain, integration of domain knowledge and statistical models for achieving semantic mappings, definition of logical languages to describe activities, and design of frameworks which integrate all the above aspects in a coherent way, thus laying the foundations of effective Semantic Video Content Analysis systems.}, isbn = {978-3-642-12899-8}, url = {http://dx.doi.org/10.1007/978-3-642-12900-1_6}, author = {Albanese,Massimiliano and Turaga,Pavan and Chellapa, Rama and Pugliese,Andrea and Subrahmanian,V.}, editor = {Schonfeld,Dan and Shan,Caifeng and Tao,Dacheng and Wang,Liang} } @article {13404, title = {Sharing-aware horizontal partitioning for exploiting correlations during query processing}, journal = {Proc. VLDB Endow.}, volume = {3}, year = {2010}, month = {2010/09//}, pages = {542 - 553}, abstract = {Optimization of join queries based on average selectivities is suboptimal in highly correlated databases. In such databases, relations are naturally divided into partitions, each partition having substantially different statistical characteristics. It is very compelling to discover such data partitions during query optimization and create multiple plans for a given query, one plan being optimal for a particular combination of data partitions. This scenario calls for the sharing of state among plans, so that common intermediate results are not recomputed. We study this problem in a setting with a routing-based query execution engine based on eddies [1]. Eddies naturally encapsulate horizontal partitioning and maximal state sharing across multiple plans. We define the notion of a conditional join plan, a novel representation of the search space that enables us to address the problem in a principled way. We present a low-overhead greedy algorithm that uses statistical summaries based on graphical models. Experimental results suggest an order of magnitude faster execution time over traditional optimization for high correlations, while maintaining the same performance for low correlations.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=1920841.1920911}, author = {Tzoumas,Kostas and Deshpande, Amol and Jensen,Christian S.} } @conference {15921, title = {Sparse representations and Random Projections for robust and cancelable biometrics}, booktitle = {Control Automation Robotics Vision (ICARCV), 2010 11th International Conference on}, year = {2010}, month = {2010/12//}, pages = {1 - 6}, abstract = {In recent years, the theories of Sparse Representation (SR) and Compressed Sensing (CS) have emerged as powerful tools for efficiently processing data in non-traditional ways. An area of promise for these theories is biome $\#$x0301;trie identification. In this paper, we review the role of sparse representation and CS for efficient biome $\#$x0301;trie identification. Algorithms to perform identification from face and iris data are reviewed. By applying Random Projections it is possible to purposively hide the biome $\#$x0301;trie data within a template. This procedure can be effectively employed for securing and protecting personal biome $\#$x0301;trie data against theft. Some of the most compelling challenges and issues that confront research in biometrics using sparse representations and CS are also addressed.}, keywords = {Biometric identification, Cancelable Biometrics, Compressed sensing, face data, face recognition, iris data, iris recognition, personal biometric data, Random Projections, robust biometrics, sparse representations}, doi = {10.1109/ICARCV.2010.5707955}, author = {Patel, Vishal M. and Chellapa, Rama and Tistarelli,M.} } @inbook {12497, title = {Statistical Analysis on Manifolds and Its Applications to Video Analysis}, booktitle = {Video Search and MiningVideo Search and Mining}, series = {Studies in Computational Intelligence}, volume = {287}, year = {2010}, month = {2010///}, pages = {115 - 144}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The analysis and interpretation of video data is an important component of modern vision applications such as biometrics, surveillance, motionsynthesis and web-based user interfaces. A common requirement among these very different applications is the ability to learn statistical models of appearance and motion from a collection of videos, and then use them for recognizing actions or persons in a new video. These applications in video analysis require statistical inference methods to be devised on non-Euclidean spaces or more formally on manifolds. This chapter outlines a broad survey of applications in video analysis that involve manifolds. We develop the required mathematical tools needed to perform statistical inference on manifolds and show their effectiveness in real video-understanding applications.}, isbn = {978-3-642-12899-8}, url = {http://dx.doi.org/10.1007/978-3-642-12900-1_5}, author = {Turaga,Pavan and Veeraraghavan,Ashok and Srivastava,Anuj and Chellapa, Rama}, editor = {Schonfeld,Dan and Shan,Caifeng and Tao,Dacheng and Wang,Liang} } @conference {17987, title = {Is teaching parallel algorithmic thinking to high school students possible?: one teacher{\textquoteright}s experience}, booktitle = {Proceedings of the 41st ACM technical symposium on Computer science education}, series = {SIGCSE {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {290 - 294}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {All students at our high school are required to take at least one course in Computer Science prior to their junior year. They are also required to complete a year-long senior project associated with a specific in-house laboratory, one of which is the Computer Systems Lab. To prepare students for this experience the lab offers elective courses at the post-AP Computer Science level. Since the early 1990s one of these electives has focused on parallel computing. The course enrolls approximately 40 students each year for two semesters of instruction. The lead programming language is C and topics include a wide array of industry-standard and experimental tools. Since the 2007-2008 school year we have included a unit on parallel algorithmic thinking (PAT) using the Explicit Multi-Threading (XMT) system. We describe our experiences using this system after self-studying the approach from a publicly available tutorial. Overall, this article provides significant evidence regarding the unique teachability of the XMT PAT approach, and advocates using it broadly in Computer Science education.}, keywords = {high school, parallel algorithmic thinking, pram algorithms, XMT}, isbn = {978-1-4503-0006-3}, doi = {10.1145/1734263.1734363}, url = {http://doi.acm.org/10.1145/1734263.1734363}, author = {Torbert,Shane and Vishkin, Uzi and Tzur,Ron and Ellison,David J.} } @conference {19506, title = {To Upgrade or Not to Upgrade: Impact of Online Upgrades Across Multiple Administrative Domains}, booktitle = {OOPSLA{\textquoteright}10 Proceedings of the ACM International Conference on Object Oriented Programming Systems Languages and Applications}, series = {OOPSLA {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {865 - 876}, publisher = {ACM}, organization = {ACM}, abstract = {Online software upgrades are often plagued by runtime behaviors that are poorly understood and difficult to ascertain. For example, the interactions among multiple versions of the software expose the system to race conditions that can introduce latent errors or data corruption. Moreover, industry trends suggest that online upgrades are currently needed in large-scale enterprise systems, which often span multiple administrative domains (e.g., Web 2.0 applications that rely on AJAX client-side code or systems that lease cloud-computing resources). In such systems, the enterprise does not control all the tiers of the system and cannot coordinate the upgrade process, making existing techniques inadequate to prevent mixed-version races. In this paper, we present an analytical framework for impact assessment, which allows system administrators to directly compare the risk of following an online-upgrade plan with the risk of delaying or canceling the upgrade. We also describe an executable model that implements our formal impact assessment and enables a systematic approach for deciding whether an online upgrade is appropriate. Our model provides a method of last resort for avoiding undesirable program behaviors, in situations where mixed-version races cannot be avoided through other technical means.}, keywords = {mixed-version race, multiple administrative domains, online upgrade, risk assessment}, isbn = {978-1-4503-0203-6}, url = {http://doi.acm.org/10.1145/1869459.1869530}, author = {Tudor Dumitras and Narasimhan, Priya and Tilevich, Eli} } @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.} } @article {12464, title = {Video Pr{\'e}cis: Highlighting Diverse Aspects of Videos}, journal = {IEEE Transactions on Multimedia}, volume = {12}, year = {2010}, month = {2010/12//}, pages = {853 - 868}, abstract = {Summarizing long unconstrained videos is gaining importance in surveillance, web-based video browsing, and video-archival applications. Summarizing a video requires one to identify key aspects that contain the essence of the video. In this paper, we propose an approach that optimizes two criteria that a video summary should embody. The first criterion, {\textquotedblleft}coverage,{\textquotedblright} requires that the summary be able to represent the original video well. The second criterion, {\textquotedblleft}diversity,{\textquotedblright} requires that the elements of the summary be as distinct from each other as possible. Given a user-specified summary length, we propose a cost function to measure the quality of a summary. The problem of generating a précis is then reduced to a combinatorial optimization problem of minimizing the proposed cost function. We propose an efficient method to solve the optimization problem. We demonstrate through experiments (on KTH data, unconstrained skating video, a surveillance video, and a YouTube home video) that optimizing the proposed criterion results in meaningful video summaries over a wide range of scenarios. Summaries thus generated are then evaluated using both quantitative measures and user studies.}, keywords = {$K$-means, CAMERAS, combinatorial mathematics, combinatorial optimization, Cost function, data compression, Exemplar selection, Image segmentation, Internet, Iron, Length measurement, multimedia systems, Ncut, optimisation, Optimization methods, original video, Permission, shot segmentation, Surveillance, user specified summary length, video précis, Video sharing, video signal processing, Video summarization}, isbn = {1520-9210}, doi = {10.1109/TMM.2010.2058795}, author = {Shroff, N. and Turaga,P. and Chellapa, Rama} } @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} } @article {16820, title = {A Web Database for Computer-Aided Detection and Diagnosis of Medical Images}, journal = {Digital Mammography}, year = {2010}, month = {2010///}, pages = {265 - 272}, author = {Tahmoush,D. and Samet, Hanan} } @article {18524, title = {Which Factors Affect Access Network Performance?}, volume = {GT-CS-10-04}, year = {2010}, month = {2010///}, institution = {Georgia Institute of Technology}, abstract = {This paper presents an analysis of the performance of residential access networks using over four months of round-trip, download, and upload measurements from more than 7,000 users across four ADSL and cable providers in France. Previous studies have characterized residential access network performance, but this paper presents the first study of how access network performance relates to other factors, such as choice of access provider, service-level agreement, and geographic location. We first explore the extent to which user performance matches the capacity advertised by an access provider, and whether the ability to achieve this capacity depends on the user{\textquoteright}s access network. We then analyze the extent to which various factors influence the performance that users experience. Finally, we explore how different groups of users experience simultaneous performance anomalies and analyze the common characteristics of users that share fate (e.g., whether users that experience simultaneous performance degradation share the same provider, city). Our analysis informs both users and designers of networked services who wish to improve the reliability and performance of access networks through multihoming and may also assist operators with troubleshooting network issues by narrowing down likely causes.}, url = {http://hdl.handle.net/1853/37336}, author = {Sundaresan,S. and Feamster, Nick and Dicioccio,L. and Teixeira,R.} } @article {12527, title = {3D Face Recognition: Technology and Applications}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {217 - 246}, author = {Tistarelli,M. and Li, S.Z. and Chellapa, Rama and Akarun, L.} } @article {12528, title = {Advanced Technologies for Touchless Fingerprint Recognition}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {83 - 109}, author = {Tistarelli,M. and Li, S.Z. and Chellapa, Rama} } @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.} } @article {14480, title = {Chance-constrained programs for link prediction}, journal = {Proceedings of Workshop on Analyzing Networks and Learning with Graphs at NIPS Conference}, year = {2009}, month = {2009///}, abstract = {In this paper, we consider the link prediction problem, where we are given a par-tial snapshot of a network at some time and the goal is to predict additional links at a later time. The accuracy of the current prediction methods is quite low due to the extreme class skew and the large number of potential links. In this paper, we describe learning algorithms based on chance constrained programs and show that they exhibit all the properties needed for a good link predictor, namely, al- low preferential bias to positive or negative class; handle skewness in the data; and scale to large networks. Our experimental results on three real-world co- authorship networks show significant improvement in prediction accuracy over baseline algorithms. }, author = {Doppa,J.R. and Yu,J. and Tadepalli,P. and Getoor, Lise} } @article {14482, title = {Common effect of antipsychotics on the biosynthesis and regulation of fatty acids and cholesterol supports a key role of lipid homeostasis in schizophrenia}, journal = {Schizophrenia Research}, volume = {108}, year = {2009}, month = {2009/03//}, pages = {134 - 142}, abstract = {For decades, the dopamine hypothesis has gained the most attention in an attempt to explain the origin and the symptoms of schizophrenia. While this hypothesis offers an explanation for the relationship between psychotic symptoms and dopamine kinetics, it does not provide a direct explanation of the etiology of schizophrenia which remains poorly understood. Consequently, current antipsychotics that target neurotransmitter receptors, have limited and inconsistent efficacy. To gain insights into the mechanism of action of these drugs, we studied the expression profile of 12,490 human genes in a cell line treated with 18 antipsychotics, and compared it to that of a library of 448 other compounds used in a variety of disorders. Analysis reveals a common effect of antipsychotics on the biosynthesis and regulation of fatty acids and cholesterol, which is discussed in the context of a lipid hypothesis where alterations in lipid homeostasis might underlie the pathogenesis of schizophrenia. This finding may help research aimed at the development of novel treatments for this devastating disease.}, keywords = {Antipsychotic action, Gene expression, Lipid homeostasis, Pathogenesis}, isbn = {0920-9964}, doi = {10.1016/j.schres.2008.11.025}, url = {http://www.sciencedirect.com/science/article/pii/S0920996408005306}, author = {Polymeropoulos,Mihael H. and Licamele,Louis and Volpi,Simona and Mack,Kendra and Mitkus,Shruti N. and Carstea,Eugene D. and Getoor, Lise and Thompson,Andrew and Lavedan,Christian} } @article {12895, title = {Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae}, journal = {Proceedings of the National Academy of Sciences}, volume = {106}, year = {2009}, month = {2009///}, pages = {15442 - 15447}, 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 sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a {\textquotedblleft}shift{\textquotedblright} between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a {\textquotedblleft}drift{\textquotedblright} between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics 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.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0907787106}, url = {http://www.pnas.org/content/106/36/15442}, author = {Chun,J. and Grim,C. J. and Hasan,N. A. and Lee,J. H. and Choi,S. Y. and Haley,B. J. and Taviani,E. and Jeon,Y. S. and Kim,D.W. and Lee,J. H. and Rita R Colwell} } @article {12883, title = {Detection of toxigenic Vibrio cholerae O1 in freshwater lakes of the former Soviet Republic of Georgia}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2009}, month = {2009/09/03/}, pages = {2 - 6}, abstract = {Three freshwater lakes, Lisi Lake, Kumisi Lake and Tbilisi Sea, near Tbilisi, Georgia, were studied from January 2006 to December 2007 to determine the presence of Vibrio cholerae employing both bacteriological culture method and direct detection methods, namely PCR and direct fluorescent antibody (DFA). For PCR, DNA extracted from water samples was tested for presence of V. cholerae and genes coding for selected virulence factors. Vibrio cholerae non-O1/non-O139 was routinely isolated by culture from all three lakes; whereas V. cholerae O1 and O139 were not. Water samples collected during the summer months from Lisi Lake and Kumisi Lake were positive for both V. cholerae and V. cholerae ctxA, tcpA, zot, ompU and toxR by PCR. Water samples collected during the same period from both Lisi and Kumisi Lake were also positive for V. cholerae serogroup O1 by DFA. All of the samples were negative for V. cholerae serotype O139. The results of this study provide evidence for an environmental presence of toxigenic V. cholerae O1, which may represent a potential source of illness as these lakes serve as recreational water in Tbilisi, Georgia.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2009.00073.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2009.00073.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Grim,Christopher J. and Jaiani,Ekaterina and Whitehouse,Chris A. and Janelidze,Nino and Kokashvili,Tamuna and Tediashvili,Marina and Rita R Colwell and Huq,Anwar} } @article {18519, title = {Determining the causes of intradomain routing changes}, year = {2009}, month = {2009///}, institution = {University Pierre and Marie Curie}, abstract = {This paper studies how intradomain routinginstability relates to events in network trouble tickets for two networks: a VPN provider and the Internet2 backbone network. Our goal in performing this joint analysis of routing and trouble tickets is to better understand the likely underlying causes of intradomain routing instability. We develop a method to correlate trouble tickets with instability events and find that, although unplanned events last longer than scheduled maintenance, there is no single underlying cause for most instability, and that these causes differ across networks. In comparison to a similar study from Labovitz et al. from ten years ago, we find that, while certain causes of instability such as maintenance and circuit problems remain significant, power issues have become much less prevalent, and software-related problems have become more common. }, author = {Medem,A. and Teixeira,R. and Feamster, Nick and Meulle,M.} } @conference {19597, title = {Dynamic Provable Data Possession}, booktitle = {CCS {\textquoteright}09 Proceedings of the 16th ACM Conference on Computer and Communications Security }, series = {CCS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {213 - 222}, publisher = {ACM}, organization = {ACM}, abstract = {We consider the problem of efficiently proving the integrity of data stored at untrusted servers. In the provable data possession (PDP) model, the client preprocesses the data and then sends it to an untrusted server for storage, while keeping a small amount of meta-data. The client later asks the server to prove that the stored data has not been tampered with or deleted (without downloading the actual data). However, the original PDP scheme applies only to static (or append-only) files. We present a definitional framework and efficient constructions for dynamic provable data possession (DPDP), which extends the PDP model to support provable updates to stored data. We use a new version of authenticated dictionaries based on rank information. The price of dynamic updates is a performance change from O(1) to O(logn) (or O(nεlog n), for a file consisting of n blocks, while maintaining the same (or better, respectively) probability of misbehavior detection. Our experiments show that this slowdown is very low in practice (e.g. 415KB proof size and 30ms computational overhead for a 1GB file). We also show how to apply our DPDP scheme to outsourced file systems and version control systems (e.g. CVS).}, keywords = {authenticated data structures, Authentication, integrity checking, outsourced storage, proof of retrievability, provable data possession, skip list}, isbn = {978-1-60558-894-0}, url = {http://doi.acm.org/10.1145/1653662.1653688}, author = {Erway, Chris and K{\"u}p\cc{\"u}, Alptekin and Charalampos Papamanthou and Tamassia, Roberto} } @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} } @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} } @inbook {19605, title = {Graph Drawing for Security Visualization}, booktitle = {Graph Drawing}, series = {Lecture Notes in Computer Science}, year = {2009}, month = {2009/01/01/}, pages = {2 - 13}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {With the number of devices connected to the internet growing rapidly and software systems being increasingly deployed on the web, security and privacy have become crucial properties for networks and applications. Due the complexity and subtlety of cryptographic methods and protocols, software architects and developers often fail to incorporate security principles in their designs and implementations. Also, most users have minimal understanding of security threats. While several tools for developers, system administrators and security analysts are available, these tools typically provide information in the form of textual logs or tables, which are cumbersome to analyze. Thus, in recent years, the field of security visualization has emerged to provide novel ways to display security-related information so that it is easier to understand. In this work, we give a preliminary survey of approaches to the visualization of computer security concepts that use graph drawing techniques.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Graphics, Data structures, Discrete Mathematics in Computer Science}, isbn = {978-3-642-00218-2, 978-3-642-00219-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-00219-9_2}, author = {Tamassia, Roberto and Palazzi, Bernardo and Charalampos Papamanthou}, editor = {Tollis, Ioannis G. and Patrignani, Maurizio} } @article {16759, title = {GrouPeer: Dynamic clustering of P2P databases}, journal = {Information Systems}, volume = {34}, year = {2009}, month = {2009/03//}, pages = {62 - 86}, abstract = {Sharing structured data in a P2P network is a challenging problem, especially in the absence of a mediated schema. The standard practice of answering a consecutively rewritten query along the propagation path often results in significant loss of information. On the opposite, the use of mediated schemas requires human interaction and global agreement, both during creation and maintenance. In this paper we present GrouPeer, an adaptive, automated approach to both issues in the context of unstructured P2P database overlays. By allowing peers to individually choose which rewritten version of a query to answer and evaluate the received answers, information-rich sources left hidden otherwise are discovered. Gradually, the overlay is restructured as semantically similar peers are clustered together. Experimental results show that our technique produces very accurate answers and builds clusters that are very close to the optimal ones by contacting a very small number of nodes in the overlay.}, keywords = {Peer-to-Peer databases, Query reformulation in P2P databases, Semantics in P2P query answering, Structured data in unstructured P2P overlays}, isbn = {0306-4379}, doi = {16/j.is.2008.04.002}, url = {http://www.sciencedirect.com/science/article/pii/S0306437908000252}, author = {Kantere,Verena and Tsoumakos,Dimitrios and Sellis,Timos and Roussopoulos, Nick} } @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} } @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.} } @conference {12516, title = {Locally time-invariant models of human activities using trajectories on the grassmannian}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {2435 - 2441}, abstract = {Human activity analysis is an important problem in computer vision with applications in surveillance and summarization and indexing of consumer content. Complex human activities are characterized by non-linear dynamics that make learning, inference and recognition hard. In this paper, we consider the problem of modeling and recognizing complex activities which exhibit time-varying dynamics. To this end, we describe activities as outputs of linear dynamic systems (LDS) whose parameters vary with time, or a time-varying linear dynamic system (TV-LDS). We discuss parameter estimation methods for this class of models by assuming that the parameters are locally time-invariant. Then, we represent the space of LDS models as a Grassmann manifold. Then, the TV-LDS model is defined as a trajectory on the Grassmann manifold. We show how trajectories on the Grassmannian can be characterized using appropriate distance metrics and statistical methods that reflect the underlying geometry of the manifold. This results in more expressive and powerful models for complex human activities. We demonstrate the strength of the framework for activity-based summarization of long videos and recognition of complex human actions on two datasets.}, keywords = {action, activity, analysis;local, analysis;video, content, dynamic, Estimation, estimation;statistical, Grassmann, indexing;distance, linear, manifold;activity-based, method;statistical, method;surveillance;time-varying, metrics;human, model;parameter, recognition;human, recognition;indexing;parameter, summarization;computer, surveillance;, system;computer, time-invariant, vision;consumer, vision;image}, doi = {10.1109/CVPR.2009.5206710}, author = {Turaga,P. and Chellapa, Rama} } @conference {18581, title = {Measurement methods for fast and accurate blackhole identification with binary tomography}, booktitle = {Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference}, series = {IMC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {254 - 266}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Binary tomography - the process of identifying faulty network links through coordinated end-to-end probes - is a promising method for detecting failures that the network does not automatically mask (e.g., network "blackholes"). Because tomography is sensitive to the quality of the input, however, na{\"\i}ve end-to-end measurements can introduce inaccuracies. This paper develops two methods for generating inputs to binary tomography algorithms that improve their inference speed and accuracy. Failure confirmation is a per-path probing technique to distinguish packet losses caused by congestion from persistent link or node failures. Aggregation strategies combine path measurements from unsynchronized monitors into a set of consistent observations. When used in conjunction with existing binary tomography algorithms, our methods identify all failures that are longer than two measurement cycles, while inducing relatively few false alarms. In two wide-area networks, our techniques decrease the number of alarms by as much as two orders of magnitude. Compared to the state of the art in binary tomography, our techniques increase the identification rate and avoid hundreds of false alarms.}, keywords = {diagnosis, network tomography, troubleshooting}, isbn = {978-1-60558-771-4}, doi = {10.1145/1644893.1644924}, url = {http://doi.acm.org/10.1145/1644893.1644924}, author = {Cunha,{\'I}talo and Teixeira,Renata and Feamster, Nick and Diot,Christophe} } @conference {18513, title = {Measuring vlan-induced dependencies on a campus network}, booktitle = {Proceedings of the ACM SIGCOMM Internet measurement conference}, year = {2009}, month = {2009///}, abstract = {Many enterprise, campus, and data-center networks have complexlayer-2 virtual LANs ({\textquotedblleft}VLANs{\textquotedblright}) underlying the layer-3 network. The interac- tion between layer-2 and layer-3 topologies can introduce dependencies that are not visible when analyzed solely from layer 3; this paper studies the extent and impact of these dependencies. We first present EtherTrace, a tool that 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 the two topologies. Our comparison yields some striking initial findings: 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 has significant implications for both robustness and for network tomography. 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 tomography is performed at layer 2. }, author = {Mansy,A. and Tariq,M.B. and Feamster, Nick and Ammar,M.} } @article {17917, title = {Modeling and visualization of human activities for multicamera networks}, journal = {EURASIP Journal on Image and Video Processing}, volume = {2009}, year = {2009}, month = {2009///}, author = {Sankaranarayanan,A. C and Patro,R. and Turaga,P. and Varshney, Amitabh and Chellapa, Rama} } @article {18534, title = {A Narrow Waist for Multipath Routing}, year = {2009}, month = {2009///}, institution = {School of Computer Science, Georgia Tech}, abstract = {Many applications can use multipath routing to improvereliability or throughput, and many multipath routing pro- tocols exist. Despite this diversity of mechanisms and applications, no common interface exists to allow an ap- plication to select these paths. This paper presents a de- sign for such a common interface, called path bits. Path bits are a small string of opaque, semantic-free bits in a packet header; these bits have a simple property: changing a packet{\textquoteright}s path bits should, with high probability, result in the packet taking a different path to the destination. This paper presents the design of path bits and demonstrates that they are simple enough to be easily implemented in both hardware and software and expressive enough to sup- port a variety of applications that can benefit from mul- tipath routing. We present both hardware and software implementations of multipath routing protocols that im- plement the path bits abstraction, as well as implementa- tions of applications that can use this abstraction with only small modifications. }, author = {Motiwala,M. and bin Tariq,M. and Anwer,B. and Andersen,D. and Feamster, Nick} } @conference {15258, title = {Online allocation of display advertisements subject to advanced sales contracts}, booktitle = {Proceedings of the Third International Workshop on Data Mining and Audience Intelligence for Advertising}, series = {ADKDD {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {69 - 77}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper we propose a utility model that accounts for both sales and branding advertisers. We first study the computational complexity of optimization problems related to both online and offline allocation of display advertisements. Next, we focus on a particular instance of the online allocation problem, and design a simple online algorithm with provable approximation guarantees. Our algorithm is near optimal as is shown by a matching lower bound. Finally, we report on experiments to establish actual case behavior on some real datasets, with encouraging results.}, keywords = {display advertising, modeling, online algorithms, OPTIMIZATION, simulation}, isbn = {978-1-60558-671-7}, doi = {10.1145/1592748.1592758}, url = {http://doi.acm.org/10.1145/1592748.1592758}, author = {Alaei,Saeed and Arcaute,Esteban and Khuller, Samir and Ma,Wenjing and Malekian,Azarakhsh and Tomlin,John} } @article {15704, title = {A Polynomial-Time Interior-Point Method for Conic Optimization, with Inexact Barrier Evaluations}, journal = {SIAM Journal on Optimization}, volume = {20}, year = {2009}, month = {2009///}, pages = {548 - 571}, doi = {DOI: 10.1137/080722825}, author = {Schurr,Simon P. and O{\textquoteright}Leary, Dianne P. and Tits,Andre{\textquoteright} L.} } @article {14640, title = {Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians}, journal = {Clinical Endocrinology}, volume = {70}, year = {2009}, month = {2009/05/01/}, pages = {698 - 705}, abstract = {Objective Resistin causes insulin resistance and diabetes in mice whereas in humans it is linked to inflammation and atherosclerosis. Few human genetic studies of resistin in inflammation and atherosclerosis have been performed. We hypothesized that the {\textendash}420C>G putative gain-of-function resistin variant would be associated with inflammatory markers and atherosclerosis but not with metabolic syndrome or adipokines in humans.Design and methods We examined the association of three resistin polymorphisms, {\textendash}852A>G, {\textendash}420C>G and +157C>T, and related haplotypes with plasma resistin, cytokines, C-reactive protein (CRP), adipokines, plasma lipoproteins, metabolic syndrome and coronary artery calcification (CAC) in nondiabetic Caucasians (n~=~851). Results Resistin levels were higher, dose-dependently, with the {\textendash}420G allele (CC 5{\textperiodcentered}9~{\textpm}~2{\textperiodcentered}7~ng/ml, GC 6{\textperiodcentered}5~{\textpm}~4{\textperiodcentered}0~ng/ml and GG 7{\textperiodcentered}2~{\textpm}~4{\textperiodcentered}8~ng/ml, trend P~=~0{\textperiodcentered}04) after age and gender adjustment [fold higher for GC~+~GG vs. CC; 1{\textperiodcentered}07~(1{\textperiodcentered}00{\textendash}1{\textperiodcentered}15), P~<~0{\textperiodcentered}05)]. The {\textendash}852A>G single nucleotide polymorphism (SNP) was associated with higher soluble tumour necrosis factor-receptor~2 (sol-TNFR2) levels in fully adjusted models [1{\textperiodcentered}06~(95\%~CI 1{\textperiodcentered}01{\textendash}1{\textperiodcentered}11), P~=~0{\textperiodcentered}01)]. The estimated resistin haplotype (GGT) was associated with sol-TNFR2 (P~=~0{\textperiodcentered}04) and the AGT haplotype was related to CRP (P~=~0{\textperiodcentered}04) in the fully adjusted models. Resistin SNPs and haplotypes were not associated with body mass index (BMI), fasting glucose, insulin resistance, metabolic syndrome, adipokines or CAC scores. Conclusions Despite modest associations with plasma resistin and inflammatory biomarkers, resistin 5' variants were not associated with metabolic parameters or coronary calcification. This suggests that resistin is an inflammatory cytokine in humans but has little influence on adiposity, metabolic syndrome or atherosclerosis. }, isbn = {1365-2265}, doi = {10.1111/j.1365-2265.2008.03375.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2265.2008.03375.x/abstract;jsessionid=3EAA174C4993EDEE1267334CDA36E086.d01t01}, author = {Qasim,Atif N and Metkus,Thomas S and Tadesse,Mahlet and Lehrke,Michael and Restine,Stephanie and Wolfe,Megan L and Hannenhalli, Sridhar and Cappola,Thomas and Rader,Daniel J and Reilly,Muredach P} } @conference {19502, title = {Second ACM Workshop on Hot Topics in Software Upgrades (HotSWUp 2009)}, series = {OOPSLA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {705 - 706}, publisher = {ACM}, organization = {ACM}, abstract = {The goal of HotSWUp is to identify cutting-edge research ideas for implementing software upgrades. In the presence of modified user requirements, deployment environments, and bug fixes, actively-used software must be upgraded continuously to ensure its utility and safety. The upgrades incorporate changes to the structure, behavior, configuration, data, or topology of a computer system. Whether applied offline or directly to a live system, such upgrades may have a significant impact on the performance and reliability of the software. Indeed, recent studies and a large body of anecdotal evidence suggest that, in practice, upgrades are failure-prone and can lead to outages, data corruption or latent errors. These problems not only inconvenience end users - they create a significant burden for organizations due to the associated downtime and high administrative costs.}, keywords = {software, upgrades}, isbn = {978-1-60558-768-4}, url = {http://doi.acm.org/10.1145/1639950.1639974}, author = {Tudor Dumitras and Neamtiu, Iulian and Tilevich, Eli} } @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.} } @article {18921, title = {Task decomposition on abstract states, for planning under nondeterminism}, journal = {Artificial Intelligence}, volume = {173}, year = {2009}, month = {2009/04//}, pages = {669 - 695}, abstract = {Although several approaches have been developed for planning in nondeterministic domains, solving large planning problems is still quite difficult. In this work, we present a new planning algorithm, called Yoyo, for solving planning problems in fully observable nondeterministic domains. Yoyo combines an HTN-based mechanism for constraining its search and a Binary Decision Diagram (BDD) representation for reasoning about sets of states and state transitions.We provide correctness theorems for Yoyo, and an experimental comparison of it with MBP and ND-SHOP2, the two previously-best algorithms for planning in nondeterministic domains. In our experiments, Yoyo could easily deal with problem sizes that neither MBP nor ND-SHOP2 could scale up to, and could solve problems about 100 to 1000 times faster than MBP and ND-SHOP2. }, keywords = {Binary decision diagrams, Hierarchical task-network (HTN) planning, Planning in nondeterministic domains}, isbn = {0004-3702}, doi = {10.1016/j.artint.2008.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S0004370208001987}, author = {Kuter,Ugur and Nau, Dana S. and Pistore,Marco and Traverso,Paolo} } @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} } @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 {16830, title = {TwitterStand: news in tweets}, booktitle = {Proceedings of the 17th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {42 - 51}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Twitter is an electronic medium that allows a large user populace to communicate with each other simultaneously. Inherent to Twitter is an asymmetrical relationship between friends and followers that provides an interesting social network like structure among the users of Twitter. Twitter messages, called tweets, are restricted to 140 characters and thus are usually very focused. We investigate the use of Twitter to build a news processing system, called TwitterStand, from Twitter tweets. The idea is to capture tweets that correspond to late breaking news. The result is analogous to a distributed news wire service. The difference is that the identities of the contributors/reporters are not known in advance and there may be many of them. Furthermore, tweets are not sent according to a schedule: they occur as news is happening, and tend to be noisy while usually arriving at a high throughput rate. Some of the issues addressed include removing the noise, determining tweet clusters of interest bearing in mind that the methods must be online, and determining the relevant locations associated with the tweets.}, keywords = {geotagging, news, online clustering, Twitter}, isbn = {978-1-60558-649-6}, doi = {10.1145/1653771.1653781}, url = {http://doi.acm.org/10.1145/1653771.1653781}, author = {Sankaranarayanan,Jagan and Samet, Hanan and Teitler,Benjamin E. and Lieberman,Michael D. and Sperling,Jon} } @article {16292, title = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/03/04/}, pages = {R25 - R25}, abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-3-r25}, url = {http://genomebiology.com/2009/10/3/R25}, author = {Langmead,Ben and Trapnell,Cole and Pop, Mihai and Salzberg,Steven L.} } @article {15843, title = {Understanding IT Innovations Through Computational Analysis of Discourse}, journal = {ICIS 2009 Proceedings}, year = {2009}, month = {2009/01/01/}, url = {http://aisel.aisnet.org/icis2009/102}, author = {Tsui,Chia-jung and Wang,Ping and Fleischmann,Kenneth and Oard, Douglas and Sayeed,Asad} } @article {12523, title = {Unsupervised view and rate invariant clustering of video sequences}, journal = {Computer Vision and Image Understanding}, volume = {113}, year = {2009}, month = {2009/03//}, pages = {353 - 371}, abstract = {Videos play an ever increasing role in our everyday lives with applications ranging from news, entertainment, scientific research, security and surveillance. Coupled with the fact that cameras and storage media are becoming less expensive, it has resulted in people producing more video content than ever before. This necessitates the development of efficient indexing and retrieval algorithms for video data. Most state-of-the-art techniques index videos according to the global content in the scene such as color, texture, brightness, etc. In this paper, we discuss the problem of activity-based indexing of videos. To address the problem, first we describe activities as a cascade of dynamical systems which significantly enhances the expressive power of the model while retaining many of the computational advantages of using dynamical models. Second, we also derive methods to incorporate view and rate-invariance into these models so that similar actions are clustered together irrespective of the viewpoint or the rate of execution of the activity. We also derive algorithms to learn the model parameters from a video stream and demonstrate how a single video sequence may be clustered into different clusters where each cluster represents an activity. Experimental results for five different databases show that the clusters found by the algorithm correspond to semantically meaningful activities.}, keywords = {Affine invariance, Cascade of linear dynamical systems, Rate invariance, Summarization, Surveillance, Video clustering, View invariance}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2008.08.009}, url = {http://www.sciencedirect.com/science/article/pii/S1077314208001367}, author = {Turaga,Pavan and Veeraraghavan,Ashok and Chellapa, Rama} } @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.} } @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 {14323, title = {Activity sensing in the wild: a field trial of ubifit garden}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {1797 - 1806}, author = {Consolvo,S. and McDonald,D.W. and Toscos,T. and Chen,M.Y. and Jon Froehlich and Harrison,B. and Klasnja,P. and LaMarca,A. and LeGrand,L. and Libby,R. and others} } @article {15708, title = {Adaptive Constraint Reduction for Training Support Vector Machines}, journal = {Electronic Transactions on Numerical Analysis}, volume = {31}, year = {2008}, month = {2008///}, pages = {156 - 177}, url = {http://etna.mcs.kent.edu/vol.31.2008/pp156-177.dir/pp156-177.pdfhttp://etna.mcs.kent.edu/vol.31.2008/pp156-177.dir/pp156-177.pdf}, author = {Jung,Jin Hyuk and O{\textquoteright}Leary, Dianne P. and Tits,Andre{\textquoteright} L.} } @article {19608, title = {Algorithms for computing a parameterized st-orientation}, journal = {Theoretical Computer Science}, volume = {408}, year = {2008}, month = {2008/11/28/}, pages = {224 - 240}, abstract = {s t -orientations ( s t -numberings) or bipolar orientations of undirected graphs are central to many graph algorithms and applications. Several algorithms have been proposed in the past to compute an s t -orientation of a biconnected graph. In this paper, we present new algorithms that compute such orientations with certain (parameterized) characteristics in the final s t -oriented graph, such as the length of the longest path. This work has many applications, including Graph Drawing and Network Routing, where the length of the longest path is vital in deciding certain features of the final solution. This work applies to other difficult problems as well, such as graph coloring and of course longest path. We present extended theoretical and experimental results which show that our technique is efficient and performs well in practice.}, keywords = {Graph algorithms, Longest path, Planar graphs, s t -numberings}, isbn = {0304-3975}, url = {http://www.sciencedirect.com/science/article/pii/S0304397508005653}, author = {Charalampos Papamanthou and Tollis, Ioannis G.} } @inbook {19602, title = {Algorithms for Location Estimation Based on RSSI Sampling}, booktitle = {Algorithmic Aspects of Wireless Sensor Networks}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {72 - 86}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {In this paper, we re-examine the RSSI measurement model for location estimation and provide the first detailed formulation of the probability distribution of the position of a sensor node. We also show how to use this probabilistic model to efficiently compute a good estimation of the position of the sensor node by sampling multiple readings from the beacons (where we do not merely use the mean of the samples) and then minimizing a function with an acceptable computational effort. The results of the simulation of our method in TOSSIM indicate that the location of the sensor node can be computed in a small amount of time and that the quality of the solution is competitive with previous approaches.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Communication Networks, Data structures, Discrete Mathematics in Computer Science, Information Systems and Communication Service}, isbn = {978-3-540-92861-4, 978-3-540-92862-1}, url = {http://link.springer.com/chapter/10.1007/978-3-540-92862-1_7}, author = {Charalampos Papamanthou and Preparata, Franco P. and Tamassia, Roberto}, editor = {Fekete, S{\'a}ndor P.} } @conference {18546, title = {Answering what-if deployment and configuration questions with wise}, booktitle = {Proceedings of the ACM SIGCOMM 2008 conference on Data communication}, series = {SIGCOMM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {99 - 110}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Designers of content distribution networks often need to determine how changes to infrastructure deployment and configuration affect service response times when they deploy a new data center, change ISP peering, or change the mapping of clients to servers. Today, the designers use coarse, back-of-the-envelope calculations, or costly field deployments; they need better ways to evaluate the effects of such hypothetical "what-if" questions before the actual deployments. This paper presents What-If Scenario Evaluator (WISE), a tool that predicts the effects of possible configuration and deployment changes in content distribution networks. WISE makes three contributions: (1) an algorithm that uses traces from existing deployments to learn causality among factors that affect service response-time distributions; (2) an algorithm that uses the learned causal structure to estimate a dataset that is representative of the hypothetical scenario that a designer may wish to evaluate, and uses these datasets to predict future response-time distributions; (3) a scenario specification language that allows a network designer to easily express hypothetical deployment scenarios without being cognizant of the dependencies between variables that affect service response times. Our evaluation, both in a controlled setting and in a real-world field deployment at a large, global CDN, shows that WISE can quickly and accurately predict service response-time distributions for many practical What-If scenarios.}, keywords = {content distribution networks, performance modeling, what-if scenario evaluation}, isbn = {978-1-60558-175-0}, doi = {10.1145/1402958.1402971}, url = {http://doi.acm.org/10.1145/1402958.1402971}, author = {Tariq,Mukarram and Zeitoun,Amgad and Valancius,Vytautas and Feamster, Nick and Ammar,Mostafa} } @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.} } @article {19619, title = {Athos: Efficient Authentication of Outsourced File Systems: Information Security}, journal = {Lecture Notes in Computer Science}, year = {2008}, month = {2008///}, pages = {80 - 96}, isbn = {03029743}, author = {Triandopoulos, Nikolaos and Goodrich, Michael T. and Charalampos Papamanthou and Tamassia, Roberto} } @conference {19598, title = {Authenticated Hash Tables}, booktitle = {CCS {\textquoteright}08 Proceedings of the 15th ACM Conference on Computer and Communications Security }, series = {CCS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {437 - 448}, publisher = {ACM}, organization = {ACM}, abstract = {Hash tables are fundamental data structures that optimally answer membership queries. Suppose a client stores n elements in a hash table that is outsourced at a remote server so that the client can save space or achieve load balancing. Authenticating the hash table functionality, i.e., verifying the correctness of queries answered by the server and ensuring the integrity of the stored data, is crucial because the server, lying outside the administrative control of the client, can be malicious. We design efficient and secure protocols for optimally authenticating membership queries on hash tables: for any fixed constants 0 < ε < 1 and κ > 1/ε, the server can provide a proof of integrity of the answer to a (non-)membership query in constant time, requiring O(nε/logκε--1 n) time to treat updates, yet keeping the communication and verification costs constant. This is the first construction for authenticating a hash table with constant query cost and sublinear update cost. Our solution employs the RSA accumulator in a nested way over the stored data, strictly improving upon previous accumulator-based solutions. Our construction applies to two concrete data authentication models and lends itself to a scheme that achieves different trade-offs---namely, constant update time and O(nε/logκε n) query time for fixed ε > 0 and κ > 0. An experimental evaluation of our solution shows very good scalability.}, keywords = {Authentication, hash tables, rsa accumulator, verification}, isbn = {978-1-59593-810-7}, url = {http://doi.acm.org/10.1145/1455770.1455826}, author = {Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikos} } @article {12567, title = {Computational Vision Approaches for Event Modeling}, journal = {Understanding Events}, volume = {1}, year = {2008}, month = {2008///}, pages = {473 - 522}, abstract = {Event modeling systems provide a semantic interpretation of sequences of pixels that are captured by a video camera. The design of a practical system has to take into account the following three main factors: low-level preprocessing limitations, computational and storage complexity of the event model, and user interaction. The hidden Markov model (HMM) and its variants have been widely used to model both speech and video signals. Computational efficiency of the Baum-Welch and the Viterbi algorithms has been a leading reason for the popularity of the HMM. Since the objective is to detect events in video sequences that are meaningful to humans, one might want to provide space in the design loop for a user who can specify events of interest. This chapter explores this using semantic approaches that not only use features extracted from raw video streams but also incorporate metadata and ontologies of activities. It presents three approaches for applications such as event recognition: anomaly detection, temporal segmentation, and ontology evaluation. The three approaches discussed are statistical methods based on HMMs, formal grammars, and ontologies. The effectiveness of these approaches is illustrated using video sequences captured both indoors and outdoors: the indoor UCF human action dataset, the TSA airport tarmac surveillance dataset, and the bank monitoring dataset.}, author = {Chellapa, Rama and Cuntoor, N.P. and Joo, S.W. and V.S. Subrahmanian and Turaga,P.} } @article {12549, title = {A Constrained Probabilistic Petri Net Framework for Human Activity Detection in Video}, journal = {Multimedia, IEEE Transactions on}, volume = {10}, year = {2008}, month = {2008/10//}, pages = {982 - 996}, abstract = {Recognition of human activities in restricted settings such as airports, parking lots and banks is of significant interest in security and automated surveillance systems. In such settings, data is usually in the form of surveillance videos with wide variation in quality and granularity. Interpretation and identification of human activities requires an activity model that a) is rich enough to handle complex multi-agent interactions, b) is robust to uncertainty in low-level processing and c) can handle ambiguities in the unfolding of activities. We present a computational framework for human activity representation based on Petri nets. We propose an extension-Probabilistic Petri Nets (PPN)-and show how this model is well suited to address each of the above requirements in a wide variety of settings. We then focus on answering two types of questions: (i) what are the minimal sub-videos in which a given activity is identified with a probability above a certain threshold and (ii) for a given video, which activity from a given set occurred with the highest probability? We provide the PPN-MPS algorithm for the first problem, as well as two different algorithms (naive PPN-MPA and PPN-MPA) to solve the second. Our experimental results on a dataset consisting of bank surveillance videos and an unconstrained TSA tarmac surveillance dataset show that our algorithms are both fast and provide high quality results.}, keywords = {activity, dataset;automated, detection;human, interactions;security, net;human, nets;image, Petri, probabilistic, processing;multiagent, processing;video, representation;low-level, representation;video, signal, Surveillance, surveillance;, systems;constrained, systems;surveillance, tarmac, TSA, videos;Petri}, isbn = {1520-9210}, doi = {10.1109/TMM.2008.2001369}, author = {Albanese, M. and Chellapa, Rama and Moscato, V. and Picariello, A. and V.S. Subrahmanian and Turaga,P. and Udrea,O.} } @article {17581, title = {Cost-Sharing Mechanisms for Network Design}, journal = {Algorithmica}, volume = {50}, year = {2008}, month = {2008///}, pages = {98 - 119}, abstract = {We consider a single-source network design problem from a game-theoretic perspective. Gupta, Kumar and Roughgarden (Proc. 35th Annual ACM STOC, pp. 365{\textendash}372, 2003 ) developed a simple method for a single-source rent-or-buy problem that also yields the best-known approximation ratio for the problem. We show how to use a variant of this method to develop an approximately budget-balanced and group strategyproof cost-sharing method for the problem. The novelty of our approach stems from our obtaining the cost-sharing methods for the rent-or-buy problem by carefully combining cost-shares for the simpler Steiner tree problem. Our algorithm is conceptually simpler than the previous such cost-sharing method due to P{\'a}l and Tardos (Proc. 44th Annual FOCS, pp. 584{\textendash}593, 2003 ), and improves the previously-known approximation factor of 15 to 4.6.}, isbn = {0178-4617}, url = {http://dx.doi.org/10.1007/s00453-007-9065-y}, author = {Gupta,Anupam and Srinivasan, Aravind and Tardos,{\'E}va} } @conference {18565, title = {Distinguishing persistent failures from transient losses}, booktitle = {Proceedings of the 2008 ACM CoNEXT Conference}, series = {CoNEXT {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {50:1{\textendash}50:2 - 50:1{\textendash}50:2}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network tomography is a promising technique to identify the location of of IP faults. The goal of tomography is to infer the status of network internal characteristics based on end-to-end observations. In particular, binary tomography identifies the set of failed links from end-to-end path meausrments. Upon detecting the failure of one or more of the monitored paths, a monitor sends its measurements to a central coordinator. The coordinator then runs the binary tomography algorithm, which takes as input the topology of the network and the status (i.e., up or down) of all monitored paths and finds the minimum set of links that explain the observations.}, isbn = {978-1-60558-210-8}, doi = {10.1145/1544012.1544062}, url = {http://doi.acm.org/10.1145/1544012.1544062}, author = {Cunha,{\'I}talo and Teixeira,Renata and Feamster, Nick and Diot,Christophe} } @inbook {19607, title = {Effective Visualization of File System Access-Control}, booktitle = {Visualization for Computer Security}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {18 - 25}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {In this paper, we present a visual representation of access control permissions in a standard hierarchical file system. Our visualization of file permissions leverages treemaps, a popular graphical representation of hierarchical data. In particular, we present a visualization of access control for the NTFS file system that can help a non-expert user understand and manipulate file system permissions in a simple and effective way. While our examples are based on NTFS, our approach can be used for many other hierarchical file systems as well.}, keywords = {Computer Communication Networks, Computer Imaging, Vision, Pattern Recognition and Graphics, data mining and knowledge discovery, Data Structures, Cryptology and Information Theory, Visualization}, isbn = {978-3-540-85931-4, 978-3-540-85933-8}, url = {http://link.springer.com/chapter/10.1007/978-3-540-85933-8_2}, author = {Heitzmann, Alexander and Palazzi, Bernardo and Charalampos Papamanthou and Tamassia, Roberto}, editor = {Goodall, John R. and Conti, Gregory and Ma, Kwan-Liu} } @conference {19601, title = {Efficient Integrity Checking of Untrusted Network Storage}, booktitle = {StorageSS {\textquoteright}08 Proceedings of the 4th ACM International Workshop on Storage Security and Survivability }, series = {StorageSS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {43 - 54}, publisher = {ACM}, organization = {ACM}, abstract = {Outsourced storage has become more and more practical in recent years. Users can now store large amounts of data in multiple servers at a relatively low price. An important issue for outsourced storage systems is to design an efficient scheme to assure users that their data stored at remote servers has not been tampered with. This paper presents a general method and a practical prototype application for verifying the integrity of files in an untrusted network storage service. The verification process is managed by an application running in a trusted environment (typically on the client) that stores just one cryptographic hash value of constant size, corresponding to the "digest" of an authenticated data structure. The proposed integrity verification service can work with any storage service since it is transparent to the storage technology used. Experimental results show that our integrity verification method is efficient and practical for network storage systems.}, keywords = {authenticated data structures, data integrity, Security, untrusted outsourced storage}, isbn = {978-1-60558-299-3}, url = {http://doi.acm.org/10.1145/1456469.1456479}, author = {Heitzmann, Alexander and Palazzi, Bernardo and Charalampos Papamanthou and Tamassia, Roberto} } @article {17132, title = {Enabling teachers to explore grade patterns to identify individual needs and promote fairer student assessment}, journal = {Computers \& Education}, volume = {51}, year = {2008}, month = {2008/12//}, pages = {1467 - 1485}, abstract = {Exploring student test, homework, and other assessment scores is a challenge for most teachers, especially when attempting to identify cross-assessment weaknesses and produce final course grades. During the course, teachers need to identify subject weaknesses in order to help students who are struggling with a particular topic. This identification often needs to happen across multiple assessment data points and should be considered in comparison to the class{\textquoteright}s progress as a whole. When determining grades, fairness to all is essential, but there are special needs for students who did poorly on one exam or had a steadily increasing grasp of the subject. We present eduViz, a visualization tool designed to help teachers explore and assign grades. Teachers can see the trajectory of student scores, the relationship of a particular student to the class, and use categories they have defined in order to filter their assessment information. Query response is immediate and all logical comparisons are possible. Teachers can easily compare their query to the class or per student average as well as view scores by raw point total or percentage. Additionally, eduViz provides a grade assignment interface which allows teachers to view sorted student scores in a scatterplot. This scatterplot is coupled with a unique partition slider which allows users to move color coordinated bands on the scatterplot to indicate grade ranges. As these grade ranges are set, a histogram is updated to show the number of students assigned to each grade range. These features give teachers new and powerful ways to explore and assign grades so that they can better understand student strengths and weaknesses and make the most of the time they have available. Interviews with 16 expert teachers indicate that eduViz is a success across fields, provides teachers with a useful tool to understand and help their classes, and encourages reflective practice.}, keywords = {Evaluation methodologies, Human{\textendash}computer interface, Improving classroom teaching, Pedagogical issues, Teaching/learning strategies}, isbn = {0360-1315}, doi = {10.1016/j.compedu.2008.01.005}, url = {http://www.sciencedirect.com/science/article/pii/S0360131508000353}, author = {Friedler,Sorelle A. and Tan,Yee Lin and Peer,Nir J. and Shneiderman, Ben} } @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 {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.} } @article {16066, title = {Evaluating Visual Analytics at the 2007 VAST Symposium Contest}, journal = {Computer Graphics and Applications, IEEE}, volume = {28}, year = {2008}, month = {2008/04//march}, pages = {12 - 21}, abstract = {In this article, we report on the contest{\textquoteright}s data set and tasks, the judging criteria, the winning tools, and the overall lessons learned in the competition. We believe that by organizing these contests, we{\textquoteright}re creating useful resources for researchers and are beginning to understand how to better evaluate VA tools. Competitions encourage the community to work on difficult problems, improve their tools, and develop baselines for others to build or improve upon. We continue to evolve a collection of data sets, scenarios, and evaluation methodologies that reflect the richness of the many VA tasks and applications.}, keywords = {2007, analytics, analytics;data, and, Contest;Visual, Science, Symposium, Technology;data, VAST, visualisation;, visualization;visual}, isbn = {0272-1716}, doi = {10.1109/MCG.2008.27}, author = {Plaisant, Catherine and Grinstein,G. and Scholtz,J. and Whiting,M. and O{\textquoteright}Connell,T. and Laskowski,S. and Chien,L. and Tat,A. and Wright,W. and Gorg,C. and Zhicheng Liu and Parekh,N. and Singhal,K. and Stasko,J.} } @article {13128, title = {Event modeling and recognition using markov logic networks}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {610 - 623}, abstract = {We address the problem of visual event recognition in surveillance where noise and missing observations are serious problems. Common sense domain knowledge is exploited to overcome them. The knowledge is represented as first-order logic production rules with associated weights to indicate their confidence. These rules are used in combination with a relaxed deduction algorithm to construct a network of grounded atoms, the Markov Logic Network. The network is used to perform probabilistic inference for input queries about events of interest. The system{\textquoteright}s performance is demonstrated on a number of videos from a parking lot domain that contains complex interactions of people and vehicles.}, author = {Tran,S. and Davis, Larry S.} } @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 {14432, title = {Exploiting Prior Knowledge in Intelligent Assistants: Combining Relational Models with Hierarchies}, journal = {Probabilistic, Logical and Relational Learning - A Further Synthesis}, year = {2008}, month = {2008///}, abstract = {Statitsical relational models have been successfully used to model static probabilistic relationships between the entities of the domain. In this talk, we illustrate their use in a dynamic decison-theoretic setting where the task is to assist a user by inferring his intentional structure and taking appropriate assistive actions. We show that the statistical relational models can be used to succintly express the system{\textquoteright}s prior knowledge about the user{\textquoteright}s goal-subgoal structure and tune it with experience. As the system is better able to predict the user{\textquoteright}s goals, it improves the effectiveness of its assistance. We show through experiments that both the hierarchical structure of the goals and the parameter sharing facilitated by relational models significantly improve the learning speed.}, author = {Natarajan,S. and Tadepalli,P. and Fern,A. and De Raedt,L. and Dietterich,T. and Getoor, Lise and Kersting,K. and Muggleton,S. H} } @conference {18212, title = {Extended abstract: A hardware-assisted data hiding based approach in building high performance secure execution systems}, booktitle = {Hardware-Oriented Security and Trust, 2008. HOST 2008. IEEE International Workshop on}, year = {2008}, month = {2008/06//}, pages = {93 - 96}, abstract = {Recently, a novel data hiding technique was proposed to embed information into compiled binary codes in order to enhance system performance. Using this technique as a vehicle, we propose a framework to build high-performance secure execution systems by embedding data for security and trust purposes. We illustrate this approach in a mobile computing environment by an instruction-block level data hiding technique, which can be used to defend against malicious attacks (such as Trojan injection). This improves the trustworthiness of mobile codes. It also protects the code providerpsilas intellectual property because the code can be executed only on the designated device. When combined with the existing approach in [4], the proposed data hiding framework can provide trust and high-performance simultaneously. Finally, we conduct a proof-of-the-concept FPGA prototyping to validate the data hiding technique and evaluate the hardware cost in terms of gate count, power consumption, and gate delay.}, keywords = {arrays;invasive, attacks;mobile, codes;data, codes;mobile, computing;, computing;power, consumption;proof-of-the-concept, count;gate, data, delay;hardware-assisted, embedding;gate, embedding;instruction-block, encapsulation;distributed, execution, FPGA, gate, hiding;information, injection;binary, level;malicious, programmable, programming;field, prototyping;secure, software;mobile, systems;binary, Trojan}, doi = {10.1109/HST.2008.4559062}, author = {Taylor,M. and Yin,Chi-En and M. Wu and Gang Qu} } @inbook {14698, title = {Formalizing Soundness of Contextual Effects}, booktitle = {Theorem Proving in Higher Order LogicsTheorem Proving in Higher Order Logics}, series = {Lecture Notes in Computer Science}, volume = {5170}, year = {2008}, month = {2008///}, pages = {262 - 277}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A contextual effect system generalizes standard type and effect systems: where a standard effect system computes the effect of an expression e , a contextual effect system additionally computes the prior and future effect of e , which characterize the behavior of computation prior to and following, respectively, the evaluation of e . This paper describes the formalization and proof of soundness of contextual effects, which we mechanized using the Coq proof assistant. Contextual effect soundness is an unusual property because the prior and future effect of a term e depends not on e itself (or its evaluation), but rather on the evaluation of the context in which e appears. Therefore, to state and prove soundness we must {\textquotedblleft}match up{\textquotedblright} a subterm in the original typing derivation with the possibly-many evaluations of that subterm during the evaluation of the program, in a way that is robust under substitution. We do this using a novel typed operational semantics. We conjecture that our approach could prove useful for reasoning about other properties of derivations that rely on the context in which that derivation appears.}, isbn = {978-3-540-71065-3}, url = {http://dx.doi.org/10.1007/978-3-540-71067-7_22}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W. and Neamtiu,Iulian}, editor = {Mohamed,Otmane and Mu{\~n}oz,C{\'e}sar and Tahar,Sofi{\`e}ne} } @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.} } @article {12563, title = {From Videos to Verbs: Mining Videos for Activities using a cascade of dynamical systems (Supplemental Material)}, journal = {Relation}, volume = {10}, year = {2008}, month = {2008///}, pages = {9944 - 9944}, author = {Turaga, P.K. and Veeraraghavan,A. and Chellapa, Rama} } @conference {19448, title = {Getting to Green: Understanding Resource Consumption in the Home}, booktitle = {UbiComp {\textquoteright}08}, series = {UbiComp {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {242 - 251}, publisher = {ACM}, organization = {ACM}, abstract = {Rising global energy demands, increasing costs and limited natural resources mean that householders are more conscious about managing their domestic resource consumption. Yet, the question of what tools Ubicomp researchers can create for residential resource management remains open. To begin to address this omission, we present a qualitative study of 15 households and their current management practices around the water, electricity and natural gas systems in the home. We find that in-the-moment resource consumption is mostly invisible to householders and that they desire more real-time information to help them save money, keep their homes comfortable and be environmentally friendly. Designing for domestic sustainability therefore turns on improving the visibility of resource production and consumption costs as well as supporting both individuals and collectives in behavior change. Domestic sustainability also highlights the caveat of potentially creating a green divide by making resource management available only to those who can afford the technologies to support being green. Finally, we suggest that the Ubicomp community can contribute to the domestic and broader sustainability agenda by incorporating green values in designs and highlight the challenge of collecting data on being green.}, keywords = {domestic conservation, residential resource consumption, Sustainability}, isbn = {978-1-60558-136-1}, url = {http://doi.acm.org/10.1145/1409635.1409668}, author = {Marshini Chetty and Tran, David and Grinter, Rebecca E.} } @article {14788, title = {Hardware monitors for dynamic page migration}, journal = {Journal of Parallel and Distributed Computing}, volume = {68}, year = {2008}, month = {2008/09//}, pages = {1186 - 1200}, abstract = {In this paper, we first introduce a profile-driven online page migration scheme and investigate its impact on the performance of multithreaded applications. We use centralized lightweight, inexpensive plug-in hardware monitors to profile the memory access behavior of an application, and then migrate pages to memory local to the most frequently accessing processor. We also investigate the use of several other potential sources of data gathered from hardware monitors and compare their effectiveness to using data from centralized hardware monitors. In particular, we investigate the effectiveness of using cache miss profiles, Translation Lookaside Buffer (TLB) miss profiles and the content of the on-chip TLBs using the valid bit information. Moreover, we also introduce a modest hardware feature, called Address Translation Counters (ATC), and compare its effectiveness with other sources of hardware profiles.Using the Dyninst runtime instrumentation combined with hardware monitors, we were able to add page migration capabilities to a Sun Fire 6800 server without having to modify the operating system kernel, or to re-compile application programs. Our dynamic page migration scheme reduced the total number of non-local memory accesses of applications by up to 90\% and improved the execution times up to 16\%. We also conducted a simulation based study and demonstrated that cache miss profiles gathered from on-chip CPU monitors, which are typically available in current microprocessors, can be effectively used to guide dynamic page migrations in applications. }, keywords = {Address translation counters, cc-NUMA systems, Dynamic page migration, Full system simulation, Hardware performance monitors, High performance computing, Multiprocessor systems, OpenMP applications, Runtime optimization}, isbn = {0743-7315}, doi = {16/j.jpdc.2008.05.006}, url = {http://www.sciencedirect.com/science/article/pii/S0743731508001020}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K} } @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 {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} } @conference {16836, title = {High-Dimensional Similarity Retrieval Using Dimensional Choice}, booktitle = {Similarity Search and Applications, 2008. SISAP 2008. First International Workshop on}, year = {2008}, month = {2008/04//}, pages = {35 - 42}, abstract = {There are several pieces of information that can be utilized in order to improve the efficiency of similarity searches on high-dimensional data. The most commonly used information is the distribution of the data itself but the use of dimensional choice based on the information in the query as well as the parameters of the distribution can provide an effective improvement in the query processing speed and storage. The use of this method can produce dimension reduction by as much as a factor of n, the number of data points in the database, over sequential search. We demonstrate that the curse of dimensionality is not based on the dimension of the data itself, but primarily upon the effective dimension of the distance function. We also introduce a new distance function that utilizes fewer dimensions of the higher dimensional space to produce a maximal lower bound distance in order to approximate the full distance function. This work has demonstrated significant dimension reduction, up to 70\% reduction with an improvement in accuracy or over 99\% with only a 6\% loss in accuracy on a prostate cancer data set.}, keywords = {data, database, function;high-dimensional, management, processing;, processing;sequential, reduction;database, reduction;distance, retrieval;query, search;data, search;similarity, similarity, system;dimension, systems;query}, doi = {10.1109/SISAP.2008.20}, author = {Tahmoush,D. and Samet, Hanan} } @conference {12543, title = {Learning action dictionaries from video}, booktitle = {Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on}, year = {2008}, month = {2008/10//}, pages = {1704 - 1707}, abstract = {Summarizing the contents of a video containing human activities is an important problem in computer vision and has important applications in automated surveillance systems. Summarizing a video requires one to identify and learn a {\textquoteright}vocabulary{\textquoteright} of action-phrases corresponding to specific events and actions occurring in the video. We propose a generative model for dynamic scenes containing human activities as a composition of independent action-phrases - each of which is derived from an underlying vocabulary. Given a long video sequence, we propose a completely unsupervised approach to learn the vocabulary. Once the vocabulary is learnt, a video segment can be decomposed into a collection of phrases for summarization. We then describe methods to learn the correlations between activities and sequentiality of events. We also propose a novel method for building invariances to spatial transforms in the summarization scheme.}, keywords = {(artificial, action, action-phrases;learning, automated, decomposition;video, dictionaries;spatial, intelligence);video, segment, segmentation;learning, sequence;computer, Surveillance, surveillance;, systems;computer, transforms;video, vision;image, vision;independent}, doi = {10.1109/ICIP.2008.4712102}, author = {Turaga,P. and Chellapa, Rama} } @article {12542, title = {Machine Recognition of Human Activities: A Survey}, journal = {Circuits and Systems for Video Technology, IEEE Transactions on}, volume = {18}, year = {2008}, month = {2008/11//}, pages = {1473 - 1488}, abstract = {The past decade has witnessed a rapid proliferation of video cameras in all walks of life and has resulted in a tremendous explosion of video content. Several applications such as content-based video annotation and retrieval, highlight extraction and video summarization require recognition of the activities occurring in the video. The analysis of human activities in videos is an area with increasingly important consequences from security and surveillance to entertainment and personal archiving. Several challenges at various levels of processing-robustness against errors in low-level processing, view and rate-invariant representations at midlevel processing and semantic representation of human activities at higher level processing-make this problem hard to solve. In this review paper, we present a comprehensive survey of efforts in the past couple of decades to address the problems of representation, recognition, and learning of human activities from video and related applications. We discuss the problem at two major levels of complexity: 1) "actions" and 2) "activities." "Actions" are characterized by simple motion patterns typically executed by a single human. "Activities" are more complex and involve coordinated actions among a small number of humans. We will discuss several approaches and classify them according to their ability to handle varying degrees of complexity as interpreted above. We begin with a discussion of approaches to model the simplest of action classes known as atomic or primitive actions that do not require sophisticated dynamical modeling. Then, methods to model actions with more complex dynamics are discussed. The discussion then leads naturally to methods for higher level representation of complex activities.}, keywords = {activity;low-level, annotation;human, cameras;video, content-based, factors;image, processing;machine, processing;rate-invariant, recognition;image, recognition;midlevel, representation;image, representation;video, representations;semantic, retrieval;human, sequences;, summarization;content-based, video}, isbn = {1051-8215}, doi = {10.1109/TCSVT.2008.2005594}, author = {Turaga,P. and Chellapa, Rama and V.S. Subrahmanian and Udrea,O.} } @article {14921, title = {The Maryland Large-Scale Integrated Neurocognitive Architecture}, year = {2008}, month = {2008/03//}, institution = {University of Maryland College Park}, abstract = {Recent progress in neural computation, high performance computing, neuroscience and cognitive science suggests that an effort to produce a general-purpose, adaptive machine intelligence is likely to yield a qualitatively more powerful system than those currently existing. Here we outline our progress in developing a framework for creating such a large-scale machine intelligence, or neurocognitive architecture that is based on the modularity, dynamics and plasticity of the human brain. We successfully implemented three intermediate-scale parts of such a system, and these are described. Based on this experience, we concluded that for the short term, optimal results would be obtained by using a hybrid design including neural, symbolic AI, and artificial life methods. We propose a three-tiered architecture that integrates these different methods, and describe a prototype mini-Roboscout that we implemented and evaluated based on this architecture. We also examined, via computational experiments, the effectiveness of genetic programming as a design tool for recurrent neural networks, and the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for proceeding.}, keywords = {*COMPUTATIONS, *HYBRID SYSTEMS, *NEURAL NETS, *NEUROCOGNITIVE ARCHITECTURE, ADAPTIVE SYSTEMS, Artificial intelligence, BRAIN, Cognition, COMPUTER PROGRAMMING, COMPUTER PROGRAMMING AND SOFTWARE, HYBRID AI, Machine intelligence, MECHANICAL ORGANS, MODULAR CONSTRUCTION, NERVOUS SYSTEM, PE61101E, PLASTIC PROPERTIES, PROCESSING EQUIPMENT, RECURRENT NEURAL NETWORK}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA481261}, author = {Reggia, James A. and Tagamets,M. and Contreras-Vidal,J. and Jacobs, David W. and Weems,S. and Naqvi,W. and Yang,C.} } @article {12976, title = {A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13}, journal = {J Mol Evol}, volume = {67}, year = {2008}, month = {2008/12//}, pages = {581 - 593}, abstract = {The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42\%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss and possible limb re-evolution.}, doi = {10.1007/s00239-008-9156-7}, author = {Kohlsdorf,T and Cummings, Michael P. and Lynch,VJ and Stopper,GF and Takahashi,K and Wagner,GP} } @conference {13117, title = {Multi-resolution Tracking in Space and Time}, booktitle = {Computer Vision, Graphics Image Processing, 2008. ICVGIP {\textquoteright}08. Sixth Indian Conference on}, year = {2008}, month = {2008/12//}, pages = {352 - 358}, abstract = {This paper proposes efficient and robust methods for tracking a moving object at multiple spatial and temporal resolution levels. The efficiency comes from optimising the amounts of spatial and temporal data processed. The robustness results from multi-level coarse-to-fine state-space searching. Tracking across resolution levels incurs an accuracy-versus-speed trade-off. For example, tracking at higher resolutions incurs greater processing cost, while maintaining higher accuracy in estimating the position of the moving object. We propose a novel spatial multi-scale tracker that tracks at the optimal accuracy-versus-speed operating point. Next, we relax this requirement to propose a multi-resolution tracker that operates at a minimum acceptable performance level. Finally, we extend these ideas to a multi-resolution spatio-temporal tracker. We show results of extensive experimentation in support of the proposed approaches.}, keywords = {analysis;image, coarse-to-fine, detection;, estimation;spatial, MOTION, moving, multiscale, object, resolution;object, searching;multiresolution, state-space, tracker;image, tracker;spatio-temporal, tracking;multilevel, tracking;position}, doi = {10.1109/ICVGIP.2008.74}, author = {Roy,S.D. and Tran,S.D. and Davis, Larry S. and Vikram,B.S.} } @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 {18502, title = {NANO: Network Access Neutrality Observatory}, volume = {GT-CS-08-03}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {This paper tackles a technical problem that is of growing interest in light of the ongoing network neutrality debate: We aim to develop a system that can reliably determine whether particular ISP is discriminating against a service using only passive measurements from end-hosts. This problem presents significant challenges because many types of discrimination can often resemble commonplace performance degradations (e.g., resulting from failure or misconfiguration). To distinguish discrimination from degradation, we propose a statistical method to estimate causal effect and develop a system, NANO, based on this method. NANO aggregates passive measurements from end-hosts, stratifies the measurements to account for possible confounding factors, and distinguishes when an ISP is discriminating against a particular service or group of clients. Preliminary simulation results demonstrate the promise of NANO for both detecting various types of discrimination and absolving an ISP when it is not discriminating.}, url = {http://hdl.handle.net/1853/25461}, author = {Tariq,M.B. and Motiwala,M. and Feamster, Nick} } @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} } @conference {16839, title = {NewsStand: a new view on news}, booktitle = {Proceedings of the 16th ACM SIGSPATIAL international conference on Advances in geographic information systems}, series = {GIS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {18:1{\textendash}18:10 - 18:1{\textendash}18:10}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {News articles contain a wealth of implicit geographic content that if exposed to readers improves understanding of today{\textquoteright}s news. However, most articles are not explicitly geotagged with their geographic content, and few news aggregation systems expose this content to users. A new system named NewsStand is presented that collects, analyzes, and displays news stories in a map interface, thus leveraging on their implicit geographic content. NewsStand monitors RSS feeds from thousands of online news sources and retrieves articles within minutes of publication. It then extracts geographic content from articles using a custom-built geotagger, and groups articles into story clusters using a fast online clustering algorithm. By panning and zooming in NewsStand{\textquoteright}s map interface, users can retrieve stories based on both topical significance and geographic region, and see substantially different stories depending on position and zoom level.}, keywords = {clustering, geotagging, knowledge discovery, text mining}, isbn = {978-1-60558-323-5}, doi = {10.1145/1463434.1463458}, url = {http://doi.acm.org/10.1145/1463434.1463458}, author = {Teitler,Benjamin E. and Lieberman,Michael D. and Panozzo,Daniele and Sankaranarayanan,Jagan and Samet, Hanan and Sperling,Jon} } @article {12910, title = {Occurrence and Expression of Luminescence in Vibrio Cholerae}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {74}, year = {2008}, month = {2008/02/01/}, pages = {708 - 715}, abstract = {Several species of the genus Vibrio, including Vibrio cholerae, are bioluminescent or contain bioluminescent strains. Previous studies have reported that only 10\% of V. cholerae strains are luminescent. Analysis of 224 isolates of non-O1/non-O139 V. cholerae collected from Chesapeake Bay, MD, revealed that 52\% (116/224) were luminescent when an improved assay method was employed and 58\% (130/224) of isolates harbored the luxA gene. In contrast, 334 non-O1/non-O139 V. cholerae strains isolated from two rural provinces in Bangladesh yielded only 21 (6.3\%) luminescent and 35 (10.5\%) luxA+ isolates. An additional 270 clinical and environmental isolates of V. cholerae serogroups O1 and O139 were tested, and none were luminescent or harbored luxA. These results indicate that bioluminescence may be a trait specific for non-O1/non-O139 V. cholerae strains that frequently occur in certain environments. Luminescence expression patterns of V. cholerae were also investigated, and isolates could be grouped based on expression level. Several strains with defective expression of the lux operon, including natural K variants, were identified.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01537-07}, url = {http://aem.asm.org/content/74/3/708}, author = {Grim,Christopher J. and Taviani,Elisa and Alam,Munirul and Huq,Anwar and Sack,R. Bradley and Rita R Colwell} } @conference {12570, title = {An ontology based approach for activity recognition from video}, booktitle = {Proceedings of the 16th ACM international conference on Multimedia}, series = {MM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {709 - 712}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Representation and recognition of human activities is an important problem for video surveillance and security applications. Considering the wide variety of settings in which surveillance systems are being deployed, it is necessary to create a common knowledge-base or ontology of human activities. Most current attempts at ontology design in computer vision for human activities have been empirical in nature. In this paper, we present a more systematic approach to address the problem of designing ontologies for visual activity recognition. We draw on general ontology design principles and adapt them to the specific domain of human activity ontologies. Then, we discuss qualitative evaluation principles and provide several examples from existing ontologies and how they can be improved upon. Finally, we demonstrate quantitatively in terms of recognition performance, the efficacy and validity of our approach for bank and airport tarmac surveillance domains.}, keywords = {activity ontologies, visual surveillance}, isbn = {978-1-60558-303-7}, doi = {10.1145/1459359.1459466}, url = {http://doi.acm.org/10.1145/1459359.1459466}, author = {Akdemir,Umut and Turaga,Pavan and Chellapa, Rama} } @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} } @article {18594, title = {Practical issues with using network tomography for fault diagnosis}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {38}, year = {2008}, month = {2008/09//}, pages = {53 - 58}, abstract = {This paper investigates the practical issues in applying network tomography to monitor failures. We outline an approach for selecting paths to monitor, detecting and confirming the existence of a failure, correlating multiple independent observations into a single failure event, and applying existing binary networking tomography algorithms to identify failures. We evaluate the ability of network tomography algorithms to correctly detect and identify failures in a controlled environment on the VINI testbed.}, keywords = {Environment, Fault detection, network tomography}, isbn = {0146-4833}, doi = {10.1145/1452335.1452343}, url = {http://doi.acm.org/10.1145/1452335.1452343}, author = {Huang,Yiyi and Feamster, Nick and Teixeira,Renata} } @article {12564, title = {Recognition of Humans and their Activities using Statistical analysis on Stiefel and Grassmann Manifolds}, journal = {Red}, volume = {7}, year = {2008}, month = {2008///}, pages = {643 - 643}, abstract = {Many applications in computer vision involve learning and recognition of patterns from exemplars which lie on certainmanifolds. Given a database of examples and a query, the following two questions are usually addressed {\textendash} a) what is the {\textquoteleft}closest{\textquoteright} example to the query in the database ? b) what is the {\textquoteleft}most probable{\textquoteright} class to which the query belongs ? The answer to the first question involves study of the geometric properties of the manifold, which then leads to appropriate definitions of distance metrics on the manifold (geodesics etc). The answer to the second question involves statistical modeling of inter- and intra-class variations on the manifold. In this paper, we concern ourselves with two related manifolds that often appear in several vision applications {\textendash} the Stiefel Manifold and the Grassmann Manifold. We describe statistical modeling and inference tools on these manifolds which result in significant improvements in performance over traditional distance-based classifiers. We illustrate applications to video-based face recognition and activity recognition. }, author = {Turaga,P. and Veeraraghavan,A. and Chellapa, Rama} } @inbook {13634, title = {Review of Classifier Combination Methods}, booktitle = {Studies in Computational Intelligence: Machine Learning in Document Analysis and RecognitionStudies in Computational Intelligence: Machine Learning in Document Analysis and Recognition}, year = {2008}, month = {2008///}, pages = {361 - 386}, publisher = {Springer}, organization = {Springer}, abstract = {Classifier combination methods have proved to be an effective tool to increase the performance of pattern recognition applications. In this chapter we review and categorize major advancements in this field. Despite a significant number of publications describing successful classifier combination implementations, the theoretical basis is still missing and achieved improvements are inconsistent. By introducing different categories of classifier combinations in this review we attempt to put forward more specific directions for future theoretical research.We also introduce a retraining effect and effects of locality based training as important properties of classifier combinations. Such effects have significant influence on the performance of combinations, and their study is necessary for complete theoretical understanding of combination algorithms.}, author = {Tulyakov,Sergey and Jaeger,Stefan and Govindaraju,Venu and David Doermann}, editor = {Simone Marinai,Hiromichi Fujisawa} } @article {12907, title = {Seasonal Cholera from Multiple Small Outbreaks, Rural Bangladesh}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {14}, year = {2008}, month = {2008/05//}, pages = {831 - 833}, abstract = {Clinical and environmental Vibrio cholerae organisms collected from February 2004 through April 2005 were systematically isolated from 2 rural Bangladeshi locales. Their genetic relatedness was evaluated at 5 loci that contained a variable number of tandem repeats (VNTR). The observed minimal overlap in VNTR patterns between the 2 communities was consistent with sequential, small outbreaks from local sources.}, isbn = {1080-6040}, doi = {10.3201/eid1405.071116}, author = {Stine,O. Colin and Alam,Munirul and Tang,Li and Nair,G. Balakrish and Siddique,A. Kasem and Faruque,Shah M. and Huq,Anwar and Rita R Colwell and Sack,R. Bradley and Morris,J. Glenn} } @article {18509, title = {Securing enterprise networks using traffic tainting}, journal = {Special Interest Group on Data Communication}, year = {2008}, month = {2008///}, abstract = {Enterprise networks are vulnerable to attacks ranging from dataleaks to the spread of malware to insider threats. Previous defenses have largely focused on securing hosts; unfortunately, when hosts are compromised, these defenses become ineffective. Rather than attempting to harden the host against every possible attack (which is impractical) or constraining the software that can run on a host (which is inconvenient), we place a small amount of trusted code on the host to assist with tracking the provenance of network traf- fic, moving the rest of the trust and function to the network. We present Pedigree, a system that tracks information flow across pro- cesses and hosts within a network by annotating traffic with taints that reflect the process that generated the traffic and the inputs that process has taken (we call this function traffic tainting). A tagger on the host annotates network traffic with information about the {\textquotedblleft}taints{\textquotedblright} that the sending process has acquired. Network devices act as arbiters to take appropriate actions (e.g., blocking) based on the taints associated with the traffic and the enterprise network{\textquoteright}s secu- rity policy. We have implemented Pedigree{\textquoteright}s host-based tagger as a Linux kernel module and the arbiter using the OpenFlow platform. This demonstration presents a prototype deployment of Pedigree that identifies and prevents both sensitive data leaks and the spread of malware in a typical enterprise network setting. The demon- stration will show that Pedigree can defend against these attacks without significant overhead at the host or the filtering device. }, author = {Ramachandran,A. and Mundada,Y. and Tariq,M.B. and Feamster, Nick} } @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.} } @conference {12551, title = {Statistical analysis on Stiefel and Grassmann manifolds with applications in computer vision}, booktitle = {Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on}, year = {2008}, month = {2008/06//}, pages = {1 - 8}, abstract = {Many applications in computer vision and pattern recognition involve drawing inferences on certain manifold-valued parameters. In order to develop accurate inference algorithms on these manifolds we need to a) understand the geometric structure of these manifolds b) derive appropriate distance measures and c) develop probability distribution functions (pdf) and estimation techniques that are consistent with the geometric structure of these manifolds. In this paper, we consider two related manifolds - the Stiefel manifold and the Grassmann manifold, which arise naturally in several vision applications such as spatio-temporal modeling, affine invariant shape analysis, image matching and learning theory. We show how accurate statistical characterization that reflects the geometry of these manifolds allows us to design efficient algorithms that compare favorably to the state of the art in these very different applications. In particular, we describe appropriate distance measures and parametric and non-parametric density estimators on these manifolds. These methods are then used to learn class conditional densities for applications such as activity recognition, video based face recognition and shape classification.}, keywords = {algorithm;learning, analysis;computer, analysis;statistical, analysis;video, based, classification;image, classification;spatio-temporal, distribution, distributions;, Face, functions;shape, Grassmann, invariant, manifold;activity, manifold;Stiefel, matching;inference, matching;spatiotemporal, measures;estimation, modeling;statistical, parameters;pattern, phenomena;statistical, recognition;affine, recognition;computer, recognition;probability, SHAPE, structure;image, technique;geometric, theory;manifold-valued, vision;distance, vision;image}, doi = {10.1109/CVPR.2008.4587733}, author = {Turaga,P. and Veeraraghavan,A. and Chellapa, Rama} } @article {14419, title = {Structured machine learning: the next ten years}, journal = {Machine Learning}, volume = {73}, year = {2008}, month = {2008///}, pages = {3 - 23}, abstract = {The field of inductive logic programming (ILP) has made steady progress, since the first ILP workshop in 1991, based on a balance of developments in theory, implementations and applications. More recently there has been an increased emphasis on Probabilistic ILP and the related fields of Statistical Relational Learning (SRL) and Structured Prediction. The goal of the current paper is to consider these emerging trends and chart out the strategic directions and open problems for the broader area of structured machine learning for the next 10 years.}, doi = {10.1007/s10994-008-5079-1}, author = {Dietterich,T. G and Domingos,P. and Getoor, Lise and Muggleton,S. and Tadepalli,P.} } @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.} } @article {13127, title = {UMD_VDT, an Integration of Detection and Tracking Methods for Multiple Human Tracking}, journal = {Multimodal Technologies for Perception of Humans}, year = {2008}, month = {2008///}, pages = {179 - 190}, abstract = {This paper presents a cooperative body part labeling and tracking algorithm for locating body parts in a videoimage sequence. The body part labeling procedure is used to initialize the tracking procedure and to prevent tracking from getting lost; and the tracking procedure is used to analyze frames that cannot be handled reliably by the labeling procedure. This results in an automatic and robust body part tracking system. Unlike previous work that always start tracking from the first frame which may be difficult to analyze, our tracking procedure starts with some key frames in which body parts can be located reliably. Key frames are selected based on a labeling confidence measure which evaluates the similarity between the human model and the image features. The labeled body parts are tracked in-between frames based on such cues as shape, color, and location interpolated between key frames iteratively. The proposed algorithm has been applied to analyze NASA videotapes in which crew members present challenging postures of bending, twisting, and rotating in a space station. The experimental results demonstrate the effectiveness of the proposed algorithm. }, author = {Tran,S. and Lin,Z. and Harwood,D. and Davis, Larry S.} } @article {14829, title = {Using specularities in comparing 3D models and 2D images}, journal = {Computer Vision and Image Understanding}, volume = {111}, year = {2008}, month = {2008/09//}, pages = {275 - 294}, abstract = {We aim to create systems that identify and locate objects by comparing known, 3D shapes to intensity images that they have produced. To do this we focus on verification methods that determine whether a known model in a specific pose is consistent with an image. We build on prior work that has done this successfully for Lambertian objects, to handle a much broader class of shiny objects that produce specular highlights. Our core contribution is a novel method for determining whether a known 3D shape is consistent with the 2D shape of a possible highlight found in an image. We do this using only a qualitative description of highlight formation that is consistent with most models of specular reflection, so no specific knowledge of an object{\textquoteright}s specular reflectance properties is needed. This allows us to treat non-Lambertian image effects as a positive source of information about object identity, rather than treating them as a potential source of noise. We then show how to integrate information about highlights into a system that also checks the consistency of Lambertian reflectance effects. Also, we show how to model Lambertian reflectance using a reference image, rather than albedos, which can be difficult to measure in shiny objects. We test each aspect of our approach using several different data sets. We demonstrate the potential value of our method of handling specular highlights by building a system that can locate shiny, transparent objects, such as glassware, on table tops. We demonstrate our hybrid methods on pottery, and our use of reference images with face recognition experiments.}, keywords = {illumination, Object recognition, Specularity}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2007.12.004}, url = {http://www.sciencedirect.com/science/article/pii/S1077314207001713}, author = {Osadchy,Margarita and Jacobs, David W. and Ramamoorthi,Ravi and Tucker,David} } @article {15350, title = {Assessment of WENO methods with shock-confining filtering for LES of compressible turbulence}, journal = {AIAA Paper 2007}, volume = {4198}, year = {2007}, month = {2007///}, author = {Grube,N. E and Taylor,E. M and Martin, M.P} } @conference {14808, title = {Automatic software interference detection in parallel applications}, booktitle = {Proceedings of the 2007 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {14:1{\textendash}14:12 - 14:1{\textendash}14:12}, publisher = {ACM}, organization = {ACM}, address = {Reno, Nevada}, abstract = {We present an automated software interference detection methodology for Single Program, Multiple Data (SPMD) parallel applications. Interference comes from the system and unexpected processes. If not detected and corrected such interference may result in performance degradation. Our goal is to provide a reliable metric for software interference that can be used in soft-failure protection and recovery systems. A unique feature of our algorithm is that we measure the relative timing of application events (i.e. time between MPI calls) rather than system level events such as CPU utilization. This approach lets our system automatically accommodate natural variations in an application{\textquoteright}s utilization of resources. We use performance irregularities and degradation as signs of software interference. However, instead of relying on temporal changes in performance, our system detects spatial performance degradation across multiple processors. We also include a case study that demonstrates our technique{\textquoteright}s effectiveness, resilience and robustness.}, isbn = {978-1-59593-764-3}, doi = {10.1145/1362622.1362642}, author = {Tabatabaee, Vahid and Hollingsworth, Jeffrey K} } @article {16998, title = {Browsing large online data tables using generalized query previews}, journal = {Information Systems}, volume = {32}, year = {2007}, month = {2007/05//}, pages = {402 - 423}, abstract = {Companies, government agencies, and other organizations are making their data available to the world over the Internet. They often use large online relational tables for this purpose. Users query such tables with front-ends that typically use menus or form fillin interfaces, but these interfaces rarely give users information about the contents and distribution of the data. Such a situation leads users to waste time and network/server resources posing queries that have zero- or mega-hit results. Generalized query previews enable efficient browsing of large online data tables by supplying data distribution information to users. The data distribution information provides continuous feedback about the size of the result set as the query is being formed. Our paper presents a new user interface architecture and discusses three controlled experiments (with 12, 16, and 48 participants). Our prototype systems provide flexible user interfaces for research and testing of the ideas. The user studies show that for exploratory querying tasks, generalized query previews can speed user performance for certain user domains and can reduce network/server load.}, keywords = {Information Visualization, Internet, Online querying, World-wide web}, isbn = {0306-4379}, doi = {10.1016/j.is.2005.12.006}, url = {http://www.sciencedirect.com/science/article/pii/S0306437905001213}, author = {Tanin,Egemen and Shneiderman, Ben and Xie,Hairuo} } @inbook {19606, title = {On the Cost of Persistence and Authentication in Skip Lists}, booktitle = {Experimental Algorithms}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {94 - 107}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present an extensive experimental study of authenticated data structures for dictionaries and maps implemented with skip lists. We consider realizations of these data structures that allow us to study the performance overhead of authentication and persistence. We explore various design decisions and analyze the impact of garbage collection and virtual memory paging, as well. Our empirical study confirms the efficiency of authenticated skip lists and offers guidelines for incorporating them in various applications.}, keywords = {Algorithm Analysis and Problem Complexity, algorithms, Computer Graphics, Data structures, Discrete Mathematics in Computer Science, Numeric Computing}, isbn = {978-3-540-72844-3, 978-3-540-72845-0}, url = {http://link.springer.com/chapter/10.1007/978-3-540-72845-0_8}, author = {Goodrich, Michael T. and Charalampos Papamanthou and Tamassia, Roberto}, editor = {Demetrescu, Camil} } @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} } @conference {16079, title = {Discovering interesting usage patterns in text collections: integrating text mining with visualization}, booktitle = {Proceedings of the sixteenth ACM conference on Conference on information and knowledge management}, series = {CIKM {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {213 - 222}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper addresses the problem of making text mining results more comprehensible to humanities scholars, journalists, intelligence analysts, and other researchers, in order to support the analysis of text collections. Our system, FeatureLens1, visualizes a text collection at several levels of granularity and enables users to explore interesting text patterns. The current implementation focuses on frequent itemsets of n-grams, as they capture the repetition of exact or similar expressions in the collection. Users can find meaningful co-occurrences of text patterns by visualizing them within and across documents in the collection. This also permits users to identify the temporal evolution of usage such as increasing, decreasing or sudden appearance of text patterns. The interface could be used to explore other text features as well. Initial studies suggest that FeatureLens helped a literary scholar and 8 users generate new hypotheses and interesting insights using 2 text collections.}, keywords = {digital humanities, frequent closed itemsets, n-grams, text mining, user interface}, isbn = {978-1-59593-803-9}, doi = {10.1145/1321440.1321473}, url = {http://doi.acm.org/10.1145/1321440.1321473}, author = {Don,Anthony and Zheleva,Elena and Gregory,Machon and Tarkan,Sureyya and Auvil,Loretta and Clement,Tanya and Shneiderman, Ben and Plaisant, Catherine} } @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 {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.} } @conference {15327, title = {Evaluation of Traditional and Shock-Confining LES Filters using DNS Data of Compressible Turbulence}, booktitle = {Proceedings of 18th AIAA Computational Fluid Dynamics Conference}, year = {2007}, month = {2007///}, abstract = {Uniformly high-order-accurate filtering of fluid flow properties in the presence of shocksand shocklets is theoretically susceptible to the same problem that afflicts uniformly high- order-accurate numerical methods for approximating the convective terms of the Navier- Stokes equations: the introduction of new, non-physical extrema near discontinuities. Ex- tensive investigations have been conducted into myriad types of shock-capturing methods, which adaptively decrease their order of accuracy within shock-containing regions in order to maintain accuracy and stability over time. Inspired by such work, Grube et al. (AIAA 2007-4198) have proposed the conceptually similar idea of {\textquotedblleft}shock-confining{\textquotedblright} filtering (SCF) for compressible large-eddy simulations (LES), in which a class of linear filters is subject to adaptive adjustments based on smoothness information provided by a weighted essen- tially non-oscillatory (WENO) method. In the current work, we utilize the turbulent flow fields produced by direct numerical simulations (DNS) of shock/isotropic-turbulence inter- action to perform preliminary a priori testing of these shock-confining filters against the corresponding linear filters. Although additional study, both a priori and a posteriori, is required to verify the necessity and suitability of SCF for LES, we conclude that linear filtering can indeed create serious qualitative discrepancies in global flow characteristics, discrepancies that are avoided by the use of SCF. }, author = {Taylor,E. M and Grube,N. E and Martin, M.P} } @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} } @conference {12583, title = {From Videos to Verbs: Mining Videos for Activities using a Cascade of Dynamical Systems}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {Clustering video sequences in order to infer and extract activities from a single video stream is an extremely important problem and has significant potential in video indexing, surveillance, activity discovery and event recognition. Clustering a video sequence into activities requires one to simultaneously recognize activity boundaries (activity consistent subsequences) and cluster these activity subsequences. In order to do this, we build a generative model for activities (in video) using a cascade of dynamical systems and show that this model is able to capture and represent a diverse class of activities. We then derive algorithms to learn the model parameters from a video stream and also show how a single video sequence may be clustered into different clusters where each cluster represents an activity. We also propose a novel technique to build affine, view, rate invariance of the activity into the distance metric for clustering. Experiments show that the clusters found by the algorithm correspond to semantically meaningful activities.}, keywords = {activities, clustering;image, clustering;video, extraction;dynamical, mining;video, processing;, sequence, sequences;pattern, signal, stream;video, systems;single, video}, doi = {10.1109/CVPR.2007.383170}, author = {Turaga, P.K. and Veeraraghavan,A. and Chellapa, Rama} } @article {16590, title = {Functional connectivity in fMRI: A modeling approach for estimation and for relating to local circuits}, journal = {Neuroimage}, volume = {34}, year = {2007}, month = {2007///}, pages = {1093 - 1107}, author = {Winder,R. and Cortes,C. R and Reggia, James A. and Tagamets,M. A} } @inbook {14411, title = {Graphical Models in a Nutshell}, booktitle = {Introduction to Statistical Relational LearningIntroduction to Statistical Relational Learning}, year = {2007}, month = {2007///}, pages = {13 - 13}, author = {Koller,D. and Friedman,N. and Getoor, Lise and Taskar,B.} } @article {17905, title = {High-throughput sequence alignment using Graphics Processing Units}, journal = {BMC Bioinformatics}, volume = {8}, year = {2007}, month = {2007///}, pages = {474 - 474}, isbn = {1471-2105}, doi = {10.1186/1471-2105-8-474}, url = {http://www.biomedcentral.com/1471-2105/8/474}, author = {Schatz,Michael C and Trapnell,Cole and Delcher,Arthur L. and Varshney, Amitabh} } @article {16848, title = {An improved asymmetry measure to detect breast cancer}, journal = {Proceedings of SPIE}, volume = {6514}, year = {2007}, month = {2007/03/08/}, pages = {65141Q-65141Q-9 - 65141Q-65141Q-9}, abstract = {Radiologists can use the differences between the left and right breasts, or asymmetry, in mammograms to help detect certain malignant breast cancers. An image similarity method has been improved to make use of this knowledge base to recognize breast cancer. Image similarity is determined using computer-aided detection (CAD) prompts as the features, and then a cluster comparison is done to determine whether there is asymmetry. We develop the analysis through a combination of clustering and supervised learning of model parameters. This process correctly classifies cancerous mammograms 95\% of the time, and all mammograms 84\% of the time, and thus asymmetry is a measure that can play an important role in significantly improving computer-aided breast cancer detection systems. This technique represents an improvement in accuracy of 121\% over commercial techniques on non-cancerous cases. Most computer-aided detection (CAD) systems are tested on images which contain cancer on the assumption that images without cancer would produce the same number of false positives. However, a pre-screening system is designed to remove the normal cases from consideration, and so the inclusion of a pre-screening system into CAD dramatically reduces the number of false positives reported by the CAD system. We define three methods for the inclusion of pre-screening into CAD, and improve the performance of the CAD system by over 70\% at low levels of false positives.}, isbn = {0277786X}, doi = {doi:10.1117/12.708327}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/6514/1/65141Q_1?isAuthorized=no}, author = {Tahmoush,Dave and Samet, Hanan} } @book {19350, title = {Introduction to Statistical Relational Learning}, year = {2007}, month = {2007}, pages = {602}, publisher = {MIT Press}, organization = {MIT Press}, abstract = {Handling inherent uncertainty and exploiting compositional structure are fundamental to understanding and designing large-scale systems. Statistical relational learning builds on ideas from probability theory and statistics to address uncertainty while incorporating tools from logic, databases and programming languages to represent structure. In Introduction to Statistical Relational Learning, leading researchers in this emerging area of machine learning describe current formalisms, models, and algorithms that enable effective and robust reasoning about richly structured systems and data. The early chapters provide tutorials for material used in later chapters, offering introductions to representation, inference and learning in graphical models, and logic. The book then describes object-oriented approaches, including probabilistic relational models, relational Markov networks, and probabilistic entity-relationship models as well as logic-based formalisms including Bayesian logic programs, Markov logic, and stochastic logic programs. Later chapters discuss such topics as probabilistic models with unknown objects, relational dependency networks, reinforcement learning in relational domains, and information extraction. By presenting a variety of approaches, the book highlights commonalities and clarifies important differences among proposed approaches and, along the way, identifies important representational and algorithmic issues. Numerous applications are provided throughout.Lise Getoor is Assistant Professor in the Department of Computer Science at the University of Maryland. Ben Taskar is Assistant Professor in the Computer and Information Science Department at the University of Pennsylvania.}, keywords = {Computers / Logic Design, Computers / Machine Theory, Education / Statistics}, isbn = {9780262072885}, author = {Getoor,Lise and Taskar,Ben} } @conference {18855, title = {Investigation of Revolute Joint Clearances Created by an In-Mold Assembly Process}, year = {2007}, month = {2007/07//}, pages = {112 - 117}, abstract = {Revolute joints are frequently used in articulated structures. Traditionally, such a joint is formed by assembling two components. As an alternative, revolute joints can be created inside the mold using an in-mold assembly process. This process eliminates the need for post-molding assembly, thus significantly reducing the cycle time and part count. The functional performance of a revolute joint depends on the clearance in the joint. The clearance in turn depends on the part shrinkage and the mold deformation during the molding process. The presence of a polymer part during the second molding stage makes an in-mold assembly process significantly different from the traditional molding process due to the difference in heat transfer and deformation characteristics. This paper presents experimental data and a preliminary model to explain the differences in clearance produced by an aluminum mold and an Aluminum mold with an Acrylonitrile butadiene styrene (ABS) insert. Our data indicates that there is a significant difference between the clearances observed from these two different types of molds. We believe that clearances produced depend strongly on the thermal history of the parts.}, keywords = {acrylonitrile butadiene styrene insert, aluminum mold, assembling, couplings, cycle time reduction, heat transfer, injection moulding, inmold assembly process, mold deformation, molding process, moulding equipment, part count reduction, plastics industry, revolute joint clearances}, doi = {10.1109/ISAM.2007.4288458}, author = {Ananthanarayanan,A. and Thamire,C. and Gupta,S.K.} } @article {14129, title = {Least squares preconditioners for stabilized discretizations of the Navier-Stokes equations}, journal = {SIAM J. Sci. Comput}, volume = {30}, year = {2007}, month = {2007///}, pages = {290 - 311}, author = {Elman, Howard and Howle, V. E and Shadid, J. and Silvester, D. and Tuminaro, R.} } @article {14586, title = {MetaProm: a neural network based meta-predictor for alternative human promoter prediction}, journal = {BMC Genomics}, volume = {8}, year = {2007}, month = {2007///}, pages = {374 - 374}, abstract = {BACKGROUND:De novo eukaryotic promoter prediction is important for discovering novel genes and understanding gene regulation. In spite of the great advances made in the past decade, recent studies revealed that the overall performances of the current promoter prediction programs (PPPs) are still poor, and predictions made by individual PPPs do not overlap each other. Furthermore, most PPPs are trained and tested on the most-upstream promoters; their performances on alternative promoters have not been assessed.RESULTS:In this paper, we evaluate the performances of current major promoter prediction programs (i.e., PSPA, FirstEF, McPromoter, DragonGSF, DragonPF, and FProm) using 42,536 distinct human gene promoters on a genome-wide scale, and with emphasis on alternative promoters. We describe an artificial neural network (ANN) based meta-predictor program that integrates predictions from the current PPPs and the predicted promoters{\textquoteright} relation to CpG islands. Our specific analysis of recently discovered alternative promoters reveals that although only 41\% of the 3{\textquoteright} most promoters overlap a CpG island, 74\% of 5{\textquoteright} most promoters overlap a CpG island.CONCLUSION:Our assessment of six PPPs on 1.06 x 109 bps of human genome sequence reveals the specific strengths and weaknesses of individual PPPs. Our meta-predictor outperforms any individual PPP in sensitivity and specificity. Furthermore, we discovered that the 5{\textquoteright} alternative promoters are more likely to be associated with a CpG island.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-8-374}, url = {http://www.biomedcentral.com/1471-2164/8/374}, author = {Wang,Junwen and Ungar,Lyle and Tseng,Hung and Hannenhalli, Sridhar} } @conference {16851, title = {A new database for medical images and information}, booktitle = {Proceedings of SPIE-Medical Imaging}, year = {2007}, month = {2007///}, abstract = {We present a medical image and medical record database for the storage, research,transmission, and evaluation of medical images, as well as tele-medicine applications. Any medical image from a source that supports the DICOM standard can be stored and accessed, as well as associated analysis and annotations. Information and image retrieval can be done based on patient info, date, doctor{\textquoteright}s annotations, features in the images, or a spatial combination of features. Secure access and transmission is addressed for tele- medicine applications. This database application follows all HIPAA regulations. }, author = {Tahmoush,D. and Samet, Hanan} } @conference {13143, title = {Object Tracking at Multiple Levels of Spatial Resolutions}, booktitle = {Image Analysis and Processing, 2007. ICIAP 2007. 14th International Conference on}, year = {2007}, month = {2007/09//}, pages = {149 - 154}, abstract = {Tracking is usually performed at a single level of data resolution. This paper describes a multi-resolution tracking framework developed with efficiency and robustness in mind. Efficiency is achieved by processing low resolution data whenever possible. Robustness results from multiple level coarse-to-fine searching in the tracking state space. We combine sequential filtering both in time and resolution levels into a probabilistic framework. A color blob tracker is implemented and the tracking results are evaluated in a number of experiments.}, keywords = {coarse-to-fine, detection;tracking;, filtering;spatial, framework;object, levels;tracking, multiple, resolution;multiresolution, resolutions, searching;data, space;computer, state, tracking, tracking;sequential, vision;object}, doi = {10.1109/ICIAP.2007.4362772}, author = {Tran,S.D. and Davis, Larry S.} } @article {15338, title = {Optimization of nonlinear error for weighted essentially non-oscillatory methods in direct numerical simulations of compressible turbulence}, journal = {Journal of Computational Physics}, volume = {223}, year = {2007}, month = {2007///}, pages = {384 - 397}, abstract = {Weighted essentially non-oscillatory (WENO) methods have been developed to simultaneously provide robust shock-capturing in compressible fluid flow and avoid excessive damping of fine-scale flow features such as turbulence. Under certain conditions in compressible turbulence, however, numerical dissipation remains unacceptably high even after optimization of the linear component that dominates in smooth regions. We therefore construct and evaluate WENO schemes that also reduce dissipation due to one source of nonlinear error: the smoothness measurement that governs the application of stencil adaptation away from the linear optimal stencil. Direct numerical simulations (DNS) include a one-dimensional Euler solution and three-dimensional compressible isotropic turbulence. We find that the smoothness measurement modifications that we call the {\textquotedblleft}relative smoothness limiter{\textquotedblright} and the {\textquotedblleft}relative total variation limiter{\textquotedblright} each significantly enhance thez grid-convergence properties of WENO schemes while generating, respectively, small and moderate additional computational expense. Moreover, we observe these techniques to be broadly effective regardless of flow configuration.}, keywords = {Compressible turbulence, direct numerical simulation, Limiters, Linear dissipation, Non-linear dissipation, Numerical dissipation, Shock capturing}, isbn = {0021-9991}, doi = {10.1016/j.jcp.2006.09.010}, url = {http://www.sciencedirect.com/science/article/pii/S0021999106004426}, author = {Taylor,Ellen M. and Wu,Minwei and Martin, M.P} } @inbook {19623, title = {Parameterized st-Orientations of Graphs: Algorithms and Experiments}, booktitle = {Graph Drawing}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {220 - 233}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {st-orientations (st-numberings) or bipolar orientations of undirected graphs are central to many graph algorithms and applications. Several algorithms have been proposed in the past to compute an st-orientation of a biconnected graph. However, as indicated in [1], the computation of more than one st-orientation is very important for many applications in multiple research areas, such as this of Graph Drawing. In this paper we show how to compute such orientations with certain (parameterized) characteristics in the final st-oriented graph, such as the length of the longest path. Apart from Graph Drawing, this work applies in other areas such as Network Routing and in tackling difficult problems such as Graph Coloring and Longest Path. We present primary approaches to the problem of computing longest path parameterized st-orientations of graphs, an analytical presentation (together with proof of correctness) of a new O(mlog5 n) (O(mlogn) for planar graphs) time algorithm that computes such orientations (and which was used in [1]) and extensive computational results that reveal the robustness of the algorithm.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Graphics, Data structures, Discrete Mathematics in Computer Science}, isbn = {978-3-540-70903-9, 978-3-540-70904-6}, url = {http://link.springer.com/chapter/10.1007/978-3-540-70904-6_22}, author = {Charalampos Papamanthou and Tollis, Ioannis G.}, editor = {Kaufmann, Michael and Wagner, Dorothea} } @inbook {14410, title = {Probabilistic Relational Models}, booktitle = {Introduction to Statistical Relational LearningIntroduction to Statistical Relational Learning}, year = {2007}, month = {2007///}, pages = {129 - 129}, author = {Getoor, Lise and Friedman,N. and Koller,D. and Pfeffer,A. and Taskar,B.} } @conference {13137, title = {Robust Object Tracking with Regional Affine Invariant Features}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {We present a tracking algorithm based on motion analysis of regional affine invariant image features. The tracked object is represented with a probabilistic occupancy map. Using this map as support, regional features are detected and probabilistically matched across frames. The motion of pixels is then established based on the feature motion. The object occupancy map is in turn updated according to the pixel motion consistency. We describe experiments to measure the sensitivities of our approach to inaccuracy in initialization, and compare it with other approaches.}, keywords = {affine, algorithm;feature, analysis;image, analysis;pixel, consistency;regional, detection;motion, detection;tracking;, extraction;image, feature, features;robust, invariant, matching;image, MOTION, object, resolution;object, tracking}, doi = {10.1109/ICCV.2007.4408948}, author = {Tran,Son and Davis, Larry S.} } @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 {15777, title = {On Sensitivity of Gauss-Christoffel Quadrature}, journal = {Numerische Mathematik}, volume = {107}, year = {2007}, month = {2007///}, pages = {147 - 174}, abstract = {In numerical computations the question how much does a function change under perturbations of its arguments is of central importance. In this work, we investigate sensitivity of Gauss{\textendash}Christoffel quadrature with respect to small perturbations of the distribution function. In numerical quadrature, a definite integral is approximated by a finite sum of functional values evaluated at given quadrature nodes and multiplied by given weights. Consider a sufficiently smooth integrated function uncorrelated with the perturbation of the distribution function. Then it seems natural that given the same number of function evaluations, the difference between the quadrature approximations is of the same order as the difference between the (original and perturbed) approximated integrals. That is perhaps one of the reasons why, to our knowledge, the sensitivity question has not been formulated and addressed in the literature, though several other sensitivity problems, motivated, in particular, by computation of the quadrature nodes and weights from moments, have been thoroughly studied by many authors. We survey existing particular results and show that even a small perturbation of a distribution function can cause large differences in Gauss{\textendash}Christoffel quadrature estimates. We then discuss conditions under which the Gauss{\textendash}Christoffel quadrature is insensitive under perturbation of the distribution function, present illustrative examples, and relate our observations to known conjectures on some sensitivity problems.}, url = {doi:10.1007/s00211-007-0078-xdoi:10.1007/s00211-007-0078-x}, author = {O{\textquoteright}Leary, Dianne P. and Strako{\v s},Zden{\v e}k and Tich{\'y},Petr} } @article {15325, title = {Stencil adaptation properties of a WENO scheme in direct numerical simulations of compressible turbulence}, journal = {Journal of Scientific Computing}, volume = {30}, year = {2007}, month = {2007///}, pages = {533 - 554}, author = {Taylor,E. M and Martin, M.P} } @inbook {19622, title = {Time and Space Efficient Algorithms for Two-Party Authenticated Data Structures}, booktitle = {Information and Communications Security}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {1 - 15}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Authentication is increasingly relevant to data management. Data is being outsourced to untrusted servers and clients want to securely update and query their data. For example, in database outsourcing, a client{\textquoteright}s database is stored and maintained by an untrusted server. Also, in simple storage systems, clients can store very large amounts of data but at the same time, they want to assure their integrity when they retrieve them. In this paper, we present a model and protocol for two-party authentication of data structures. Namely, a client outsources its data structure and verifies that the answers to the queries have not been tampered with. We provide efficient algorithms to securely outsource a skip list with logarithmic time overhead at the server and client and logarithmic communication cost, thus providing an efficient authentication primitive for outsourced data, both structured (e.g., relational databases) and semi-structured (e.g., XML documents). In our technique, the client stores only a constant amount of space, which is optimal. Our two-party authentication framework can be deployed on top of existing storage applications, thus providing an efficient authentication service. Finally, we present experimental results that demonstrate the practical efficiency and scalability of our scheme.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Communication Networks, computers and society, Data Encryption, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-540-77047-3, 978-3-540-77048-0}, url = {http://link.springer.com/chapter/10.1007/978-3-540-77048-0_1}, author = {Charalampos Papamanthou and Tamassia, Roberto}, editor = {Qing, Sihan and Imai, Hideki and Wang, Guilin} } @article {14746, title = {Toward Specifying and Validating Cross-Domain Policies}, journal = {Technical Reports from UMIACS}, year = {2007}, month = {2007/04/17/undef}, abstract = {Formal security policies are extremely useful for two related reasons. First, they allow a policy to be considered in isolation, separate from programs under the purview of the policy and separate from the implementation of the policy{\textquoteright}s enforcement. Second, policies can be checked for compliance against higher-level security goals by using automated analyses. By contrast, ad hoc enforcement mechanisms (for which no separate policies are specified) enjoy neither benefit, and non-formal policies enjoy the first but not the second. We would like to understand how best to define (and enforce) multi-level security policies when information must be shared across domains that have varying levels of trust (the so-called "cross domain" problem). Because we wish to show such policies meet higher-level security goals with high assurance, we are interested in specifying cross domain policies formally, and then reasoning about them using automated tools. In this report, we briefly survey work that presents formal security policies with cross-domain concerns, in particular with respect to the problem of downgrading. We also describe correctness properties for such policies, all based on noninterference. Finally, we briefly discuss recently-developed tools for analyzing formal security policies; though no existing tools focus on the analysis of downgrading-oriented policies, existing research points the way to providing such support.}, author = {Hicks, Michael W. and Swamy,N. and Tsang,S.} } @article {15827, title = {Universal Duality in Conic Convex Optimization}, journal = {Mathematical Programming A}, volume = {109}, year = {2007}, month = {2007///}, pages = {69 - 88}, abstract = {Given a primal-dual pair of linear programs, it is well known that if their optimal values are viewed as lying on the extended real line, then the duality gap is zero, unless both problems are infeasible, in which case the optimal values are +$\infty$ and -$\infty$. In contrast, for optimization problems over nonpolyhedral convex cones, a nonzero duality gap can exist when either the primal or the dual is feasible.For a pair of dual conic convex programs, we provide simple conditions on the {\textquoteleft}{\textquoteleft}constraint matrices{\textquoteright}{\textquoteright} and cone under which the duality gap is zero for every choice of linear objective function and constraint right-hand side. We refer to this property as {\textquoteleft}{\textquoteleft}universal duality{\textquoteright}{\textquoteright}. Our conditions possess the following properties: (i) they are necessary and sufficient, in the sense that if (and only if) they do not hold, the duality gap is nonzero for some linear objective function and constraint right-hand side; (ii) they are metrically and topologically generic; and (iii) they can be verified by solving a single conic convex program. We relate to universal duality the fact that the feasible sets of a primal convex program and its dual cannot both be bounded, unless they are both empty. Finally we illustrate our theory on a class of semidefinite programs that appear in control theory applications. }, author = {Schurr,Simon P. and Tits,Andr{\'e} and O{\textquoteright}Leary, Dianne P.} } @article {16846, title = {Using a distributed quadtree index in peer-to-peer networks}, journal = {The VLDB Journal}, volume = {16}, year = {2007}, month = {2007/04//}, pages = {165 - 178}, abstract = {Peer-to-peer (P2P) networks have become a powerful means for online data exchange. Currently, users are primarily utilizing these networks to perform exact-match queries and retrieve complete files. However, future more data intensive applications, such as P2P auction networks, P2P job-search networks, P2P multiplayer games, will require the capability to respond to more complex queries such as range queries involving numerous data types including those that have a spatial component. In this paper, a distributed quadtree index that adapts the MX-CIF quadtree is described that enables more powerful accesses to data in P2P networks. This index has been implemented for various prototype P2P applications and results of experiments are presented. Our index is easy to use, scalable, and exhibits good load-balancing properties. Similar indices can be constructed for various multidimensional data types with both spatial and non-spatial components.}, keywords = {Distributed data structures, peer-to-peer networks, quadtrees, spatial data structures}, isbn = {1066-8888}, doi = {10.1007/s00778-005-0001-y}, url = {http://dx.doi.org/10.1007/s00778-005-0001-y}, author = {Tanin,Egemen and Harwood,Aaron and Samet, Hanan} } @conference {14755, title = {Verified Enforcement of Security Policies for Cross-Domain Information Flows}, booktitle = {IEEE Military Communications Conference, 2007. MILCOM 2007}, year = {2007}, month = {2007/10/29/31}, pages = {1 - 7}, publisher = {IEEE}, organization = {IEEE}, abstract = {We describe work in progress that uses program analysis to show that security-critical programs, such as cross-domain guards, correctly enforce cross-domain security policies. We are enhancing existing techniques from the field of Security-oriented Programming Languages to construct a new language for the construction of secure networked applications, SELINKS. In order to specify and enforce expressive and fine-grained policies, we advocate dynamically associating security labels with sensitive entities. Programs written in SELINKS are statically guaranteed to correctly manipulate an entity{\textquoteright}s security labels and to ensure that the appropriate policy checks mediate all operations that are performed on the entity. We discuss the design of our main case study : a web-based Collaborative Planning Application that will permit a collection of users, with varying security requirements and clearances, to access sensitive data sources and collaboratively create documents based on these sources.}, keywords = {Collaboration, Computer languages, Data security, Educational institutions, Government, Information analysis, Information filtering, Information filters, Information security, Vehicles}, isbn = {978-1-4244-1513-7}, doi = {10.1109/MILCOM.2007.4455189}, author = {Swamy,Nikhil and Hicks, Michael W. and Tsang,Simon} } @conference {16852, title = {A web collaboration system for content-based image retrieval of medical images}, booktitle = {Proceedings of SPIE{\textendash}Medical Imaging}, volume = {6516}, year = {2007}, month = {2007///}, abstract = {Building effective content-based image retrieval (CBIR) systemsinvolves the combination of image creation, storage, security, transmission, analysis, evaluation feature extraction, and feature combination in order to store and retrieve medical images effectively. This requires the involvement of a large community of experts across several fields. We have created a CBIR system called Archimedes which integrates the community together without requiring disclosure of sensitive details. Archimedes{\textquoteright} system design enables researchers to upload their feature sets and quickly compare the effectiveness of their methods against other stored feature sets. Additionally, research into the techniques used by radiologists is possible in Archimedes through double- blind radiologist comparisons based on their annotations and feature markups. This research archive contains the essential technologies of secure transmission and storage, textual and feature searches, spatial searches, annotation searching, filtering of result sets, feature creation, and bulk loading of features, while creating a repository and testbed for the community. }, author = {Tahmoush,D. and Samet, Hanan} } @article {13172, title = {3d surface reconstruction using graph cuts with surface constraints}, journal = {Computer Vision{\textendash}ECCV 2006}, year = {2006}, month = {2006///}, pages = {219 - 231}, abstract = {We describe a graph cut algorithm to recover the 3D object surface using both silhouette and foreground color information. The graph cut algorithm is used for optimization on a color consistency field. Constraints are added to improve its performance. These constraints are a set of predetermined locations that the true surface of the object is likely to pass through. They are used to preserve protrusions and to pursue concavities respectively in the first and the second phase of the algorithm. We also introduce a method for dealing with silhouette uncertainties arising from background subtraction on real data. We test the approach on synthetic data with different numbers of views (8, 16, 32, 64) and on a real image set containing 30 views of a toy squirrel.}, author = {Tran,S. and Davis, Larry S.} } @conference {15244, title = {Achieving anonymity via clustering}, booktitle = {Proceedings of the twenty-fifth ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems}, series = {PODS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {153 - 162}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Publishing data for analysis from a table containing personal records, while maintaining individual privacy, is a problem of increasing importance today. The traditional approach of de-identifying records is to remove identifying fields such as social security number, name etc. However, recent research has shown that a large fraction of the US population can be identified using non-key attributes (called quasi-identifiers) such as date of birth, gender, and zip code [15]. Sweeney [16] proposed the k-anonymity model for privacy where non-key attributes that leak information are suppressed or generalized so that, for every record in the modified table, there are at least k-1 other records having exactly the same values for quasi-identifiers. We propose a new method for anonymizing data records, where quasi-identifiers of data records are first clustered and then cluster centers are published. To ensure privacy of the data records, we impose the constraint that each cluster must contain no fewer than a pre-specified number of data records. This technique is more general since we have a much larger choice for cluster centers than k-Anonymity. In many cases, it lets us release a lot more information without compromising privacy. We also provide constant-factor approximation algorithms to come up with such a clustering. This is the first set of algorithms for the anonymization problem where the performance is independent of the anonymity parameter k. We further observe that a few outlier points can significantly increase the cost of anonymization. Hence, we extend our algorithms to allow an ε fraction of points to remain unclustered, i.e., deleted from the anonymized publication. Thus, by not releasing a small fraction of the database records, we can ensure that the data published for analysis has less distortion and hence is more useful. Our approximation algorithms for new clustering objectives are of independent interest and could be applicable in other clustering scenarios as well.}, keywords = {anonymity, Approximation algorithms, clustering, privacy}, isbn = {1-59593-318-2}, doi = {10.1145/1142351.1142374}, url = {http://doi.acm.org/10.1145/1142351.1142374}, author = {Aggarwal,Gagan and Feder,Tom{\'a}s and Kenthapadi,Krishnaram and Khuller, Samir and Panigrahy,Rina and Thomas,Dilys and Zhu,An} } @article {16731, title = {An adaptive probabilistic replication method for unstructured p2p networks}, journal = {On the Move to Meaningful Internet Systems 2006: CoopIS, DOA, GADA, and ODBASE}, year = {2006}, month = {2006///}, pages = {480 - 497}, author = {Tsoumakos,D. and Roussopoulos, Nick} } @book {18365, title = {Advances in Computers: Computational Biology and Bioinformatics}, year = {2006}, month = {2006/11/22/}, publisher = {Academic Press}, organization = {Academic Press}, abstract = {The field of bioinformatics and computational biology arose due to the need to apply techniques from computer science, statistics, informatics, and applied mathematics to solve biological problems. Scientists have been trying to study biology at a molecular level using techniques derived from biochemistry, biophysics, and genetics. Progress has greatly accelerated with the discovery of fast and inexpensive automated DNA sequencing techniques. As the genomes of more and more organisms are sequenced and assembled, scientists are discovering many useful facts by tracing the evolution of organisms by measuring changes in their DNA, rather than through physical characteristics alone. This has led to rapid growth in the related fields of phylogenetics, the study of evolutionary relatedness among various groups of organisms, and comparative genomics, the study of the correspondence between genes and other genomic features in different organisms. Comparing the genomes of organisms has allowed researchers to better understand the features and functions of DNA in individual organisms, as well as provide insights into how organisms evolve over time. The first four chapters of this book focus on algorithms for comparing the genomes of different organisms. Possible concrete applications include identifying the basis for genetic diseases and tracking the development and spread of different forms of Avian flu. As researchers begin to better understand the function of DNA, attention has begun shifting towards the actual proteins produced by DNA. The final two chapters explore proteomic techniques for analyzing proteins directly to identify their presence and understand their physical structure.- Written by active PhD researchers in computational biology and bioinformatics}, keywords = {Bioinformatics, Computational Biology, Computers / Bioinformatics, Computers / Computer Science, Computers / Data Processing, Computers / Information Theory, Computers / Interactive \& Multimedia, Computers / Programming / General, Computers / Reference, Computers / Software Development \& Engineering / General, Mathematics / Applied, Science / Life Sciences / Biology}, isbn = {9780120121687}, author = {Zelkowitz, Marvin V and Tseng,Chau-Wen} } @inbook {19624, title = {Applications of Parameterized st-Orientations in Graph Drawing Algorithms}, booktitle = {Graph Drawing}, series = {Lecture Notes in Computer Science}, year = {2006}, month = {2006/01/01/}, pages = {355 - 367}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Many graph drawing algorithms use st-numberings (st-orien-tations or bipolar orientations) as a first step. An st-numbering of a biconnected undirected graph defines a directed graph with no cycles, one single source s and one single sink t. As there exist exponentially many st-numberings that correspond to a certain undirected graph G, using different st-numberings in various graph drawing algorithms can result in aesthetically different drawings with different area bounds. In this paper, we present results concerning new algorithms for parameterized st-orientations, their impact on graph drawing algorithms and especially in visibility representations.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Graphics, Data structures, Discrete Mathematics in Computer Science}, isbn = {978-3-540-31425-7, 978-3-540-31667-1}, url = {http://link.springer.com/chapter/10.1007/11618058_32}, author = {Charalampos Papamanthou and Tollis, Ioannis G.}, editor = {Healy, Patrick and Nikolov, Nikola S.} } @conference {16868, title = {Archimedes, an archive of medical images}, booktitle = {American Medical Informatics Association 2006 Annual Symposium Proceedings Biomedical and Health Informatics: From Foundations to Applications to Policy, Washington, DC, DW Bates, JH Holmes, and G. Kuperman, editors}, year = {2006}, month = {2006///}, abstract = {We present a medical image and medical recorddatabase for the storage, research, transmission, and evaluation of medical images. Medical images from any source that supports the DICOM standard can be stored and accessed, as well as associated analysis and annotations. Retrieval is based on patient info, date, doctor{\textquoteright}s annotations, features in the images, or a spatial combination. This database supports the secure transmission of sensitive data for tele-medicine and follows all HIPPA regulations. }, author = {Tahmoush,D. and Samet, Hanan} } @article {14140, title = {Block preconditioners based on approximate commutators}, journal = {SIAM Journal on Scientific Computing}, volume = {27}, year = {2006}, month = {2006///}, pages = {1651 - 1668}, author = {Elman, Howard and Howle, V. E and Shadid, J. and Shuttleworth, R. and Tuminaro, R.} } @article {16866, title = {Building and querying a P2P virtual world}, journal = {Geoinformatica}, volume = {10}, year = {2006}, month = {2006///}, pages = {91 - 116}, abstract = {Peer-to-Peer (P2P) systems are known to provide excellent scalability in a networked environment. One peer is introduced to the system by each participant. However current P2P applications can only provide file sharing and other forms of relatively simple data communications, and, in this paper, we demonstrate how this limitation can be bridged by indexing and querying a 3D virtual-world on a dynamic distributed network. We present an algorithm for 3D range queries as well as an algorithm for nearest neighbor queries. We also show how to build such a complex application from the ground level of a P2P routing algorithm.}, doi = {10.1007/s10707-005-4887-8}, author = {Tanin,E. and Harwood,A. and Samet, Hanan and Nayar,D. and Nutanong,S.} } @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.} } @article {14924, title = {Cast shadows and linear subspaces for object recognition}, volume = {10/085,750}, year = {2006}, month = {2006/02/28/}, abstract = {The present invention is a method of deriving a reflectance function that analytically approximates the light reflected from an object model in terms of the spherical harmonic components of light. The reflectance function depends upon the intensity of light incident at each point on the model, but excludes light originating from below a local horizon, therefore not contributing to the reflectance because of the cast shadows. This reflectance function is used in the process of machine vision, by allowing a machine to optimize the reflectance function and arrive at an optimal rendered image of the object model, relative to an input image. Therefore, the recognition of an image produced under variable lighting conditions is more robust. The reflectance function of the present invention also has applicability in other fields, such as computer graphics.}, url = {http://www.google.com/patents?id=io54AAAAEBAJ}, author = {Thornber,Karvel K and Jacobs, David W.}, editor = {NEC Laboratories America, Inc.} } @article {17042, title = {Creativity Support Tools: Report From a U.S. National Science Foundation Sponsored Workshop}, journal = {International Journal of Human-Computer Interaction}, volume = {20}, year = {2006}, month = {2006///}, pages = {61 - 77}, abstract = {Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools.Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools. }, isbn = {1044-7318}, doi = {10.1207/s15327590ijhc2002_1}, url = {http://www.tandfonline.com/doi/abs/10.1207/s15327590ijhc2002_1}, author = {Shneiderman, Ben and Fischer,Gerhard and Czerwinski,Mary and Resnick,Mitch and Myers,Brad and Candy,Linda and Edmonds,Ernest and Eisenberg,Mike and Giaccardi,Elisa and Hewett,Tom and Jennings,Pamela and Kules,Bill and Nakakoji,Kumiyo and Nunamaker,Jay and Pausch,Randy and Selker,Ted and Sylvan,Elisabeth and Terry,Michael} } @article {14920, title = {Development of a Large-Scale Integrated Neurocognitive Architecture - Part 2: Design and Architecture}, volume = {UMIACS-TR-2006-43}, year = {2006}, month = {2006/10//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In Part 1 of this report, we outlined a framework for creating an intelligent agentbased upon modeling the large-scale functionality of the human brain. Building on those results, we begin Part 2 by specifying the behavioral requirements of a large-scale neurocognitive architecture. The core of our long-term approach remains focused on creating a network of neuromorphic regions that provide the mechanisms needed to meet these requirements. However, for the short term of the next few years, it is likely that optimal results will be obtained by using a hybrid design that also includes symbolic methods from AI/cognitive science and control processes from the field of artificial life. We accordingly propose a three-tiered architecture that integrates these different methods, and describe an ongoing computational study of a prototype {\textquoteright}mini-Roboscout{\textquoteright} based on this architecture. We also examine the implications of some non-standard computational methods for developing a neurocognitive agent. This examination included computational experiments assessing the effectiveness of genetic programming as a design tool for recurrent neural networks for sequence processing, and experiments measuring the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit (GPU) rather than a conventional CPU. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for achieving this goal. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/3957}, author = {Reggia, James A. and Tagamets,M. and Contreras-Vidal,J. and Jacobs, David W. and Weems,S. and Naqvi,W. and Winder,R. and Chabuk,T. and Jung,J. and Yang,C.} } @article {14922, title = {Development of a Large-Scale Integrated Neurocognitive Architecture Part 1: Conceptual Framework}, volume = {UMIACS-TR-2006-33}, year = {2006}, month = {2006/06/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The idea of creating a general purpose machine intelligence that capturesmany of the features of human cognition goes back at least to the earliest days of artificial intelligence and neural computation. In spite of more than a half-century of research on this issue, there is currently no existing approach to machine intelligence that comes close to providing a powerful, general-purpose human-level intelligence. However, substantial progress made during recent years in neural computation, high performance computing, neuroscience and cognitive science suggests that a renewed effort to produce a general purpose and adaptive machine intelligence is timely, likely to yield qualitatively more powerful approaches to machine intelligence than those currently existing, and certain to lead to substantial progress in cognitive science, AI and neural computation. In this report, we outline a conceptual framework for the long-term development of a large-scale machine intelligence that is based on the modular organization, dynamics and plasticity of the human brain. Some basic design principles are presented along with a review of some of the relevant existing knowledge about the neurobiological basis of cognition. Three intermediate-scale prototypes for parts of a larger system are successfully implemented, providing support for the effectiveness of several of the principles in our framework. We conclude that a human-competitive neuromorphic system for machine intelligence is a viable long- term goal, but that for the short term, substantial integration with more standard symbolic methods as well as substantial research will be needed to make this goal achievable. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/3665}, author = {Reggia, James A. and Tagamets,Malle and Contreras-Vidal,Jose and Weems,Scott and Jacobs, David W. and Winder,Ransom and Chabuk,Timur} } @inbook {12634, title = {Early Recognition Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {35 - 43}, abstract = {The earliest approaches concerned recognition within small populations, with the volume of data limited largely by the computational resources available then. As illustrated by Fig. 4.1, many sought to derive a human silhouette from an image and, as common in pattern recognition, and then to derive a description which can be associated with the identity of the subject. This gives a {\textquoteleft}statistical{\textquoteright} approach to automatic gait recognition wherein the image sequence is described as a whole, and neither by a model- nor by a motion-based approach, but one which describes the motion content. Given that techniques to separate a moving object from its background have been developed for many years (especially in surveillance) there existed a selection of approaches to derive the silhouette of the moving subject, an example silhouette extraction from the image of Fig. 4.1(a) is shown in Fig. 4.1(b). What was then needed was approaches to process the sequence of silhouettes so as to derive a gait signature {\textemdash} a set of numbers to represent a subject{\textquoteright}s identity. A selection of signatures is shown in Fig. 4.1(c) which are displayed in a 3-dimensional space for visualization purposes only (the signature usually has more dimensions than this). These signatures represent ten of walking subjects with four instances of each subject. In this case the signatures derived from the four instances mostly cluster well, representing a good recognition rate. Accordingly, the target of the early approaches was to process video data of the form of Fig. 4.1(a) to obtain silhouettes of the form of Fig. 4.1(b) so as to derive signatures for recognition performance analysis.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @article {13160, title = {Edge affinity for pose-contour matching}, journal = {Computer Vision and Image Understanding}, volume = {104}, year = {2006}, month = {2006/10//}, pages = {36 - 47}, abstract = {We present an approach for whole-body pose-contour matching. Contour matching in natural images in the absence of foreground{\textendash}background segmentation is difficult. Usually an asymmetric approach is adopted, where a contour is said to match well if it aligns with a subset of the image{\textquoteright}s gradients. This leads to problems as the contour can match with a portion of an object{\textquoteright}s outline and ignore the remainder. We present a model for using edge continuity to address this issue. Pairs of edge elements in the image are linked with affinities if they are likely to belong to the same object. A contour that matches with a set of image gradients is constrained to also match with other gradients having high affinities with the chosen ones. Experimental results show that this improves matching performance.}, keywords = {Contour matching, Edge continuity}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2006.06.008}, url = {http://www.sciencedirect.com/science/article/pii/S1077314206000737}, author = {Prasad,V. S.N and Davis, Larry S. and Tran,Son Dinh and Elgammal,Ahmed} } @article {14611, title = {Functional Analysis of Hes-1 in Preadipocytes}, journal = {Molecular EndocrinologyMolecular Endocrinology}, volume = {20}, year = {2006}, month = {2006/03/01/}, pages = {698 - 705}, abstract = {Notch signaling blocks differentiation of 3T3-L1 preadipocytes, and this can be mimicked by constitutive expression of the Notch target gene Hes-1. Although considered initially to function only as a repressor, recent evidence indicates that Hes-1 can also activate transcription. We show here that the domains of Hes-1 needed to block adipogenesis coincide with those necessary for transcriptional repression. HRT1, another basic-helix-loop-helix protein and potential Hes-1 partner, was also induced by Notch in 3T3-L1 cells but did not block adipogenesis, suggesting that Hes-1 functions primarily as a homodimer or possibly as a heterodimer with an unknown partner. Purification of Hes-1 identified the Groucho/transducin-like enhancer of split family of corepressors as the only significant Hes-1 interacting proteins in vivo. An evaluation of global gene expression in preadipocytes identified approximately 200 Hes-1-responsive genes comprising roughly equal numbers of up-regulated and down-regulated genes. However, promoter analyses indicated that the down-regulated genes were significantly more likely to contain Hes-1 binding sites, indicating that Hes-1 is more likely to repress transcription of its direct targets. We conclude that Notch most likely blocks adipogenesis through the induction of Hes-1 homodimers, which repress transcription of key target genes.}, isbn = {0888-8809, 1944-9917}, doi = {10.1210/me.2005-0325}, url = {http://mend.endojournals.org/content/20/3/698}, author = {Ross,David A and Hannenhalli, Sridhar and Tobias,John W and Cooch,Neil and Shiekhattar,Ramin and Kadesch,Tom} } @inbook {12635, title = {Further Gait Developments}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {135 - 149}, abstract = {Human gait characteristics are best analyzed when presented in its canonical view (side view). The dynamics behind an individual{\textquoteright}s gait, the quasi-periodicity of an individual{\textquoteright}s gait etc. which contribute significantly towards establishing his/her identity are more evident when the canonical view of human gait is presented. Thus, the availability of such a canonical view is crucial to the success of many gait recognition systems. We observe that in surveillance applications a non-canonical view of an individual{\textquoteright}s gait is captured more often and this necessitates developing gait recognition algorithms that are view invariant. When individuals walk at an angle oblique to the camera, the performance of gait recognition systems suffers due to the gradual change in the individual{\textquoteright}s height and stride length as captured by the camera.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @inbook {12631, title = {Future Challenges}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {151 - 170}, abstract = {Although a large number of gait recognition algorithms have been reported, it should be noted that gait recognition is still in its infancy. This is because previous work was mainly implemented under some simplified and controlled conditions, e.g., no occlusion during human walking, relatively plain background, the lack of view generality except [142, 103, 102], etc (see Table 8.1). Although reporting good recognition performance, most existing algorithms were usually evaluated on a small and non-realistic database. Further, recognition rates have not yet far reached a possible upper bound even under the above two conditions.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @inbook {12632, title = {Gait Databases}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {17 - 34}, abstract = {Naturally, the success and evolution of a new application relies largely on the dataset used for evaluation. The early gait databases were collected about 10 years before the time of writing. Then, computers had little power and memory costs were comparatively high. Clearly, this was before digital video and acquisition was based on analogue camcorder technology which resulted in frames being digitized individually. Since techniques were in their infancy, as in face recognition, early databases only had few subjects. The idea then was to determine whether recognition could be achieved at all {\textemdash} or not. At that stage we were not interested in the ramifications of recognition. There were two early databases which were developed independently: the UCSD data was recorded outdoors and the Southampton data was indoors, with subjects wearing special trousers. The current databases are considerably more advanced, but certainly benefited in their development for the early approaches.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @book {12628, title = {Human identification based on gait}, year = {2006}, month = {2006///}, publisher = {Springer Science \& Business}, organization = {Springer Science \& Business}, abstract = {Biometrics now affect many people{\textquoteright}s lives, and is the focus of much academic research and commercial development. Gait is one of the most recent biometrics, with its own unique advantages. Gait recognizes people by the way they walk and run, analyzes movement, which in turn implies analyzing sequences of images. This professional book introduces developments from the laboratories of very distinguished researchers within this relatively new area of biometrics and clearly establishes human gait as a biometric. Human Identification Based on Gait provides a snapshot of all the biometric work in human identification by gait (all major centers for research are indicated in this book). To complete the picture, studies are included from medicine, psychology and other areas wherein we find not only justification for the use of gait as a biometric, but also pointers to techniques and to analysis. Human Identification Based on Gait is designed for a professional audience, composed of researchers and practitioners in industry. This book is also suitable as a secondary text for graduate-level students in computer science.}, keywords = {Biometric identification, Computers / Computer Graphics, Computers / Computer Science, Computers / Computer Vision \& Pattern Recognition, Computers / General, Computers / Information Technology, Computers / Programming / Software Development, Computers / Software Development \& Engineering / Systems Analysis \& Design, Gait in humans, Medical / Physiology, Social Science / Anthropology / Physical}, isbn = {9780387244242}, author = {Nixon,Mark S. and Tan,Tieniu and Chellapa, Rama} } @article {18345, title = {IDiexis: Mobile image-based search on world wide web-a picture is worth a thousand keywords}, journal = {Proc. of Mobisys}, year = {2006}, month = {2006///}, abstract = {Images of objects as queries is a new approach to searchfor information on the web. Image-based information retrieval goes beyond only matching images, as information in other modalities also can be extracted from data collections using image search. We demonstrate a new system that uses images to search for web-based information. We introduce a point-by-photograph paradigm, where users can specify an object simply by taking pictures. Our technique uses content-based image retrieval methods to search the web or other databases for matching images and their source pages to find relevant location-based information. We have developed a prototype on a camera phone and conducted user studies to demonstrate the efficacy of our approach compared to other alternatives. }, author = {Tollmar,K. and Tom Yeh and Darrell,T.} } @article {16867, title = {Image Similarity and Asymmetry to Improve Computer-Aided Detection of Breast Cancer}, journal = {Digital Mammography}, year = {2006}, month = {2006///}, pages = {221 - 228}, abstract = {An improved image similarity method is introduced to recognize breast cancer, and it is incorporated into a computer-aided breast cancer detection system through Bayes Theorem. Radiologists can use the differences between the left and right breasts, or asymmetry, in mammograms to help detect certain malignant breast cancers. Image similarity is used to determine asymmetry using a contextual and then a spatial comparison. The mammograms are filtered to find the most contextually significant points, and then the resulting point set is analyzed for spatial similarity. We develop the analysis through a combination of modeling and supervised learning of model parameters. This process correctly classifies mammograms 84\% of the time, and significantly improves the accuracy of a computer-aided breast cancer detection system by 71\%.}, doi = {10.1007/11783237_31}, author = {Tahmoush,D. and Samet, Hanan} } @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} } @conference {14706, title = {Managing policy updates in security-typed languages}, booktitle = {19th IEEE Computer Security Foundations Workshop, 2006}, year = {2006}, month = {2006///}, pages = {13 pp.-216 - 13 pp.-216}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents Rx, a new security-typed programming language with features intended to make the management of information-flow policies more practical. Security labels in Rx, in contrast to prior approaches, are defined in terms of owned roles, as found in the RT role-based trust-management framework. Role-based security policies allow flexible delegation, and our language Rx provides constructs through which programs can robustly update policies and react to policy updates dynamically. Our dynamic semantics use statically verified transactions to eliminate illegal information flows across updates, which we call transitive flows. Because policy updates can be observed through dynamic queries, policy updates can potentially reveal sensitive information. As such, Rx considers policy statements themselves to be potentially confidential information and subject to information-flow metapolicies}, keywords = {Access control, Computer languages, Data security, Database systems, dynamic queries, dynamic semantics, Educational institutions, high level languages, Information security, information-flow policy management, Lattices, Network servers, Operating systems, policy update management, Robustness, role-based security policies, RT role-based trust-management framework, Rx security-typed programming language, security of data, statically verified transactions, transitive flows}, isbn = {0-7695-2615-2}, doi = {10.1109/CSFW.2006.17}, author = {Swamy,N. and Hicks, Michael W. and Tse,S. and Zdancewic,S.} } @article {16276, title = {Metagenomic Analysis of the Human Distal Gut Microbiome}, journal = {Science}, volume = {312}, year = {2006}, month = {2006/06/02/}, pages = {1355 - 1359}, abstract = {The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ({\textquotedblleft}microbiome{\textquotedblright}) contains at least 100 times as many genes as our own genome. We analyzed \~{}78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction{\textendash}amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway{\textendash}mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1124234}, url = {http://www.sciencemag.org/content/312/5778/1355}, author = {Gill,Steven R. and Pop, Mihai and DeBoy,Robert T. and Eckburg,Paul B and Turnbaugh,Peter J and Samuel,Buck S and Gordon,Jeffrey I and Relman,David A and Fraser-Liggett,Claire M and Nelson,Karen E.} } @inbook {12633, title = {Model-Based Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {107 - 133}, abstract = {The model based approaches aim to derive the movement of the torso and/or the legs. The distinction of a structural approach is one which uses static parameters illustrated in Fig. 6.1(a) whereas a model can be the (relative) motion of the angles (α, β, and ϕ) between the limbs, shown in Fig. 6.1(b). As earlier, these angles can also be measured relative to vertical.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @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 {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.} } @inbook {12629, title = {Silhouette-Based Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {45 - 105}, abstract = {Of the current approaches, most are based on analysis of silhouettes. This is like the earlier analysis which concerned abstracting a walking subject from the background and then deriving set of measurements that describe the shape and motion of that silhouette in a sequence of images. This is similar in approach the classic computer vision approach to recognize objects by using shape descriptions of objects derived, say, by optimal thresholding.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @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 {12630, title = {Subjects Allied to Gait}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {5 - 15}, abstract = {There is considerable support for the notion that each person{\textquoteright}s gait is unique. As we shall see, it has been observed in literature that people can be recognized by the way they walk. The same notion has been observed in medicine and biomechanics, though not in the context of biometrics but more as an assertion of individuality. Perhaps driven by these notions, though without reference to them, there has been work in psychology on the human ability to recognize each other by using gait. Those suffering myopia often state that they can use gait as a way of recognizing people. There is other evidence too, which suggests that each person{\textquoteright}s gait is unique. People have also studied walking from medical and biomechanical perspectives, and this gives insight into how its properties can change which is of general interest in any biometrie deployment. We shall start with literature, with definitions of meaning.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @conference {15352, title = {On Synchronization of Weighted Essentially Non-Oscillatory Methods}, booktitle = {36th AIAA Fluid Dynamics Conference and Exhibit}, year = {2006}, month = {2006///}, address = {San Francisco, CA}, abstract = {Weighted essentially non-oscillatory (WENO) methods have been developed to simul-taneously provide robust shock-capturing in compressible fluid flow and avoid excessive damping of fine-scale flow features such as turbulence. Under certain conditions in com- pressible turbulence, however, numerical dissipation remains unacceptably high even after optimization of the linear component that dominates in smooth regions. We demonstrate that a significant nonlinear source of dissipation error is due to a WENO implementa- tion defect that we call the {\textquotedblleft}synchronization deficiency,{\textquotedblright} and we develop and evaluate a preliminary technique to mitigate its effects. Direct numerical simulations (DNS) include one-dimensional test cases and three-dimensional compressible isotropic turbulence. Al- though we find the current formulation of our mitigation technique to be quite successful for the one-dimensional problems, its efficacy is more modest in the turbulence simulations, and its cost-to-benefit ratio is uncomfortably high. We believe, however, that with further work it will be possible to alleviate these drawbacks. }, author = {Taylor,E. M and Martin, M.P} } @conference {16869, title = {Using image similarity and asymmetry to detect breast cancer}, booktitle = {Proc. of SPIE Vol}, volume = {6144}, year = {2006}, month = {2006///}, pages = {61441S{\textendash}1 - 61441S{\textendash}1}, abstract = {Radiologists can use the differences between the left and right breasts, or asymmetry, in mammograms to helpdetect certain malignant breast cancers. An image similarity method is introduced to make use of this knowledge base to recognize breast cancer. Image similarity is determined using a contextual and then a spatial comparison. The mammograms are filtered to find the most contextually significant points, and then the resulting point set is analyzed for spatial similarity. We develop the analysis through a combination of modeling and supervised learning of model parameters. This process correctly classifies mammograms 80\% of the time and thus asymmetry is a measure that can play an important role in significantly improving computer-aided breast cancer detection systems. }, author = {Tahmoush,D. and Samet, Hanan} } @inbook {19610, title = {3D Visualization of Semantic Metadata Models and Ontologies}, booktitle = {Graph Drawing}, series = {Lecture Notes in Computer Science}, year = {2005}, month = {2005/01/01/}, pages = {377 - 388}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We propose an algorithm for the 3D visualization of general ontology models used in many applications, such as semantic web, entity-relationship diagrams and other database models. The visualization places entities in the 3D space. Previous techniques produce drawings that are 2-dimensional, which are often complicated and hard to comprehend. Our technique uses the third dimension almost exclusively for the display of the isa relationships (links) while the property relationships (links) are placed on some layer (plane). Thus the semantic difference between isa links and property links, which should be as vertical or as horizontal as possible respectively, is emphasized. Special reference is made on a certain model, the CIDOC Conceptual Reference Model.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Graphics, Data structures, Discrete Mathematics in Computer Science}, isbn = {978-3-540-24528-5, 978-3-540-31843-9}, url = {http://link.springer.com/chapter/10.1007/978-3-540-31843-9_38}, author = {Charalampos Papamanthou and Tollis, Ioannis G. and Doerr, Martin}, editor = {Pach, J{\'a}nos} } @article {18168, title = {Anti-collusion forensics of multimedia fingerprinting using orthogonal modulation}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/06//}, pages = {804 - 821}, abstract = {Digital fingerprinting is a method for protecting digital data in which fingerprints that are embedded in multimedia are capable of identifying unauthorized use of digital content. A powerful attack that can be employed to reduce this tracing capability is collusion, where several users combine their copies of the same content to attenuate/remove the original fingerprints. In this paper, we study the collusion resistance of a fingerprinting system employing Gaussian distributed fingerprints and orthogonal modulation. We introduce the maximum detector and the thresholding detector for colluder identification. We then analyze the collusion resistance of a system to the averaging collusion attack for the performance criteria represented by the probability of a false negative and the probability of a false positive. Lower and upper bounds for the maximum number of colluders Kmax are derived. We then show that the detectors are robust to different collusion attacks. We further study different sets of performance criteria, and our results indicate that attacks based on a few dozen independent copies can confound such a fingerprinting system. We also propose a likelihood-based approach to estimate the number of colluders. Finally, we demonstrate the performance for detecting colluders through experiments using real images.}, keywords = {Automated;Product Labeling;Signal Processing, Computer-Assisted;, Computer-Assisted;Multimedia;Patents as Topic;Pattern Recognition, Gaussian distribution;anticollusion forensic;colluder identification;collusion resistance;digital fingerprinting;false probability;likelihood-based approach;multimedia fingerprinting;orthogonal modulation;spread spectrum embedding;Gaussian distribution;fi}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.847284}, author = {Wang,Z.J. and M. Wu and Zhao,H.V. and Trappe,W. and Liu,K. J.R} } @conference {14325, title = {Are GSM phones THE solution for localization?}, booktitle = {Mobile Computing Systems and Applications, 2006. WMCSA{\textquoteright}06. Proceedings. 7th IEEE Workshop on}, year = {2005}, month = {2005///}, pages = {34 - 42}, author = {Varshavsky,A. and Chen,M.Y. and de Lara,E. and Jon Froehlich and Haehnel,D. and Hightower,J. and LaMarca,A. and Potter,F. and Sohn,T. and Tang,K. and others} } @article {15331, title = {Assessment of STBLI DNS data and comparison against experiments}, journal = {AIAA paper}, year = {2005}, month = {2005///}, author = {Wu,M. and Taylor,E. M and Martin, M.P} } @conference {18665, title = {Automated checking for Windows host vulnerabilities}, year = {2005}, month = {2005/11//}, pages = {10 pp. -148 - 10 pp. -148}, abstract = {Evaluation of computing system security requires knowledge of the vulnerabilities present in the system and of potential attacks against the system. Vulnerabilities can be classified based on their location as application vulnerabilities, network vulnerabilities, or host vulnerabilities. This paper describes Ferret-Windows, a new software tool for checking host vulnerabilities on the Windows platforms. This tool helps system administrators by quickly finding vulnerabilities that are present on a host. It is designed and implemented in a modular way: a plug-in module is used for each vulnerability checked, and each possible output format is specified by a plug-in module. Moreover, several vulnerability fixing plug-in modules exist to help users remove specific vulnerabilities. As a result, Ferret-Windows is extensible, and can easily be kept up-to-date through the addition of checks for new vulnerabilities as they are identified. Finally, Ferret-Windows is a freely available open-source software}, keywords = {application vulnerabilities, computing system security, Ferret-Windows software tool, host vulnerabilities, network vulnerabilities, open-source software, operating systems (computers), plug-in module, program diagnostics, security of data, software reliability, software tools, system attacks, Windows host vulnerability checking, Windows platforms}, doi = {10.1109/ISSRE.2005.11}, author = {Tamizi,M. and Weinstein,M. and Michel Cukier} } @article {15157, title = {Bounds on the efficiency of generic cryptographic constructions}, journal = {SIAM Journal on Computing}, volume = {35}, year = {2005}, month = {2005///}, pages = {217 - 217}, abstract = {A central focus of modern cryptography is the construction of efficient, {\textquotedblleft}high-level{\textquotedblright}cryptographic tools (e.g., encryption schemes) from weaker, {\textquotedblleft}low-level{\textquotedblright} cryptographic primitives (e.g., one-way functions). Of interest are both the existence of such construc- tions, and their efficiency. Here, we show essentially-tight lower bounds on the best possible efficiency of any black-box construction of some fundamental cryptographic tools from the most basic and widely-used cryptographic primitives. Our results hold in an extension of the model introduced by Impagliazzo and Rudich, and improve and extend earlier results of Kim, Simon, and Tetali. We focus on constructions of pseudorandom generators, universal one-way hash functions, and digital signatures based on one-way permutations, as well as constructions of public- and private-key encryption schemes based on trapdoor permutations. In each case, we show that any black-box construction beating our efficiency bound would yield the unconditional existence of a one-way function and thus, in particular, prove P \= NP }, author = {Gennaro,R. and Gertner,Y. and Katz, Jonathan and Trevisan,L.} } @article {16100, title = {Broadening Access to Large Online Databases by Generalizing Query Previews (2000)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, 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.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6474}, author = {Tanin,Egemen and Plaisant, Catherine and Shneiderman, Ben} } @article {16999, title = {Browsing Large Online Data Tables Using Generalized Query Previews (2001)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Companies, government agencies, and other organizations are making their data available to the world over the Internet. They often use large online relational tables for this purpose. Users query such tables with front-ends that typically use menus or form fillin interfaces, but these interfaces rarely give users information about the contents and distribution of the data. Such a situation leads users to waste time and network resources posing queries that have zero-hit or mega-hit results. Generalized query previews enable efficient browsing of large online databases by supplying data distribution information to the users. The data distribution information provides continuous feedback about the size of the result set as the query is being formed. Our paper presents a user interface architecture and discusses recent experimental findings. Our prototype system, ExpO, provides a flexible user interface for research and testing. The user study shows that for exploratory querying tasks, generalized query previews speed user performance and reduce network load.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6483}, author = {Tanin,Egemen and Shneiderman, Ben} } @article {16110, title = {The Challenge of Personal Information Management}, journal = {INTERACT{\textquoteright}05: Communicating Naturally through Computers (Adjunct Proceedings)}, year = {2005}, month = {2005///}, author = {Dix,A. and Jones,W. and Czerwinski,M. and Teevan,J. and Plaisant, Catherine and Moran,TP} } @article {18175, title = {Collusion resistance analysis of multimedia fingerprinting systems}, journal = {IEEE Tran. on Image Processing}, year = {2005}, month = {2005///}, author = {Wang,Z.J. and Wu,M. and Zhao,H.V. and Trappe,W. and Liu,K. J.R} } @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 {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 {16878, title = {A distributed quadtree index for peer-to-peer settings}, booktitle = {PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON DATA ENGINEERING}, volume = {21}, year = {2005}, month = {2005///}, pages = {254 - 254}, author = {Tanin,E. and Harwood,A. and Samet, Hanan} } @article {17097, title = {Dynamic Aggregation to Support Pattern Discovery: A Case Study with Web Logs (2001)}, year = {2005}, month = {2005///}, abstract = {Rapid growth of digital data collections is overwhelming the capabilities of humans to comprehend them without aid. The extraction of useful data from large raw data sets is something that humans do poorly because of the overwhelming amount of information. Aggregation is a technique that extracts important aspect from groups of data thus reducing the amount that the user has to deal with at one time, thereby enabling them to discover patterns, outliers, gaps, and clusters. Previous mechanisms for interactive exploration with aggregated data was either too complex to use or too limited in scope. This paper proposes a new technique for dynamic aggregation that can combine with dynamic queries to support most of the tasks involved in data manipulation.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6487}, author = {Tang,Lida and Shneiderman, Ben} } @article {14687, title = {Dynamic updating of information-flow policies}, journal = {Proceedings of the International Workshop on Foundations of Computer Security (FCS)}, year = {2005}, month = {2005///}, author = {Hicks, Michael W. and Tse,S. and Hicks,B. and Zdancewic,S.} } @conference {16877, title = {An efficient nearest neighbor algorithm for P2P settings}, booktitle = {Proceedings of the 2005 national conference on Digital government research}, series = {dg.o {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {21 - 28}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {New Peer-to-Peer (P2P) applications like P2P job-employee seeker networks and P2P virtual cities, for application domains such as collaborative urban planning and forming virtual communities, are about to emerge. An important component in these applications is spatial data, i.e., data with locational components. Many requests initiated on spatial data involve finding the spatial objects that are nearest to a query location. In this paper, we propose an efficient algorithm that finds the spatial objects that are nearest to a given query location on a P2P network in the order of their minimum distance to the query point. The proposed algorithm makes use of a distributed spatial index that does not rely on the use of a central server. The algorithm is designed to be more efficient by utilizing the parallel nature of the P2P network. A demonstration of the proposed algorithm was implemented as a prototype P2P application that finds events and places of interest in a city.}, keywords = {geographic information systems, nearest neighbor query, peer-to-peer networks, quadtree, spatial data}, url = {http://dl.acm.org/citation.cfm?id=1065226.1065237}, author = {Tanin,Egemen and Nayar,Deepa and Samet, Hanan} } @article {14763, title = {Efficient online computation of statement coverage}, journal = {Journal of Systems and Software}, volume = {78}, year = {2005}, month = {2005/11//}, pages = {146 - 165}, abstract = {Evaluation of statement coverage is the problem of identifying the statements of a program that execute in one or more runs of a program. The traditional approach for statement coverage tools is to use static code instrumentation. In this paper we present a new approach to dynamically insert and remove instrumentation code to reduce the runtime overhead of statement coverage measurement. We also explore the use of dominator tree information to reduce the number of instrumentation points needed. Our experiments show that our approach reduces runtime overhead by 38-90\% compared with purecov, a commercial statement coverage tool. Our tool is fully automated and available for download from the Internet.}, isbn = {0164-1212}, doi = {16/j.jss.2004.12.021}, url = {http://www.sciencedirect.com/science/article/pii/S0164121205000051}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K} } @inbook {16105, title = {Evaluation Methodologies for Visual Analytics}, booktitle = {Illuminating the Path: The Research and Development Agenda for Visual AnalyticsIlluminating the Path: The Research and Development Agenda for Visual Analytics}, year = {2005}, month = {2005///}, pages = {150 - 157}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, keywords = {file-import-09-03-18}, url = {http://nvac.pnl.gov/agenda.stm$\#$book}, author = {Laskowski,S. and Plaisant, Catherine}, editor = {Thomas,James and Cook,Kristin} } @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.} } @conference {18657, title = {An experimental evaluation to determine if port scans are precursors to an attack}, year = {2005}, month = {2005/07/01/june}, pages = {602 - 611}, abstract = {This paper describes an experimental approach to determine the correlation between port scans and attacks. Discussions in the security community often state that port scans should be considered as precursors to an attack. However, very few studies have been conducted to quantify the validity of this hypothesis. In this paper, attack data were collected using a test-bed dedicated to monitoring attackers. The data collected consist of port scans, ICMP scans, vulnerability scans, successful attacks and management traffic. Two experiments were performed to validate the hypothesis of linking port scans and vulnerability scans to the number of packets observed per connection. Customized scripts were then developed to filter the collected data and group them on the basis of scans and attacks between a source and destination IP address pair. The correlation of the filtered data groups was assessed. The analyzed data consists of forty-eight days of data collection for two target computers on a heavily utilized subnet.}, keywords = {attack data collection, computer crime, filtered data groups, ICMP scans, IP address, IP networks, management traffic, port scans, telecommunication security, Telecommunication traffic, vulnerability scans}, doi = {10.1109/DSN.2005.18}, author = {Panjwani,S. and Tan,S. and Jarrin,K.M. and Michel Cukier} } @article {13772, title = {Finite-State Language resources and Language Processing}, journal = {Machine Translation}, volume = {18}, year = {2005}, month = {2005///}, pages = {381 - 382}, author = {Hale,K. and Keyser,S.J. and Hutchins,W.J. and Habash,N. and Dorr, Bonnie J and Traum,D.} } @article {15385, title = {Forensic recovery of hard disk data by using the spin-stand imaging technique}, journal = {Proceedings of SPIE}, volume = {5778}, year = {2005}, month = {2005/05/20/}, pages = {595 - 606}, abstract = {An ex-situ technique for the drive-independent forensic recovery of data from failed hard drives has been developed.For drives which have suffered damage from a head crash or other mechanical problems and cannot be resuscitatedusing standard software, firmware, or part-replacement techniques, there is currently no commercially available meansto recover the data, even though the files are still stored on the magnetic disks. Here, we report on the results of a spinstandimaging based technology, where the failed disk is removed from its native drive, placed on a spin-stand, andscanned with a giant magnetoresistive head. After track centering, track following, signal detection, data decoding, errorcorrection, and sector mapping, the otherwise unrecoverable data can be retrieved to the computer operating system.Spin-stand based data imaging has the potential to provide recovery at data rates approaching those in the native driveand is a truly drive-independent method to recover hard disk data in a time-efficient manner.}, isbn = {0277786X}, doi = {doi:10.1117/12.602572}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/5778/1/595_1?isAuthorized=no}, author = {Tse,Chun and Krafft,Charles and Mayergoyz, Issak D and McAvoy,Patrick and Tseng,Chun-Yang} } @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 {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 {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} } @conference {18872, title = {A hierarchical task-network planner based on symbolic model checking}, year = {2005}, month = {2005///}, pages = {300 - 309}, abstract = {Although several approaches have been developed for planning in nondeterministic domains, solving large planning problems is still quite difficult. In this work, we present a novel algorithm, called YoYo, for planning in nondeterministic domains under the assumption of full observability. This algorithm enables us to combine the power of search-control strategies as in Planning with Hierarchical Task Networks (HTNs) with tech- niques from the Planning via Symbolic Model-Checking (SMC). Our experimental evaluation confirms the po- tentialities of our approach, demonstrating that it com- bines the advantages of these paradigms.}, url = {https://www.aaai.org/Papers/ICAPS/2005/ICAPS05-031.pdf}, author = {Kuter,U. and Nau, Dana S. and Pistore,M. and Traverso,P.} } @article {15757, title = {HOPE: A Homotopy Optimization Method for Protein Structure Prediction}, journal = {Journal of Computational Biology}, volume = {12}, year = {2005}, month = {2005/12//}, pages = {1275 - 1288}, abstract = {We use a homotopy optimization method, HOPE, to minimize the potential energy associated with a protein model. The method uses the minimum energy conformation of one protein as a template to predict the lowest energy structure of a query sequence. This objective is achieved by following a path of conformations determined by a homotopy between the potential energy functions for the two proteins. Ensembles of solutions are produced by perturbing conformations along the path, increasing the likelihood of predicting correct structures. Successful results are presented for pairs of homologous proteins, where HOPE is compared to a variant of Newton{\textquoteright}s method and to simulated annealing.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.2005.12.1275}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2005.12.1275}, author = {Dunlavy,Daniel M. and O{\textquoteright}Leary, Dianne P. and Klimov,Dmitri and Thirumalai,D.} } @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} } @conference {14814, title = {Parallel Parameter Tuning for Applications with Performance Variability}, booktitle = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {57{\textendash} - 57{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {In this paper, we present parallel on-line optimization algorithms for parameter tuning of parallel programs. We employ direct search algorithms that update parameters based on real-time performance measurements. We discuss the impact of performance variability on the accuracy and efficiency of the optimization algorithms and proposed modified versions of the direct search algorithms to cope with it. The modified version uses multiple samples instead of single sample to estimate the performance more accurately.We present preliminary results that the performance variability of applications on clusters is heavy tailed. Finally, we studay and demonstrate the performance ofthe proposed algorithms for real scientific application.}, keywords = {algorithms, compilers, design}, isbn = {1-59593-061-2}, doi = {http://dx.doi.org/10.1109/SC.2005.52}, url = {http://dx.doi.org/10.1109/SC.2005.52}, author = {Tabatabaee, Vahid and Tiwari, Ananta and Hollingsworth, Jeffrey K} } @conference {18329, title = {A picture is worth a thousand keywords: image-based object search on a mobile platform}, booktitle = {CHI {\textquoteright}05 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {2025 - 2028}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Finding information based on an object{\textquoteright}s visual appearance is useful when specific keywords for the object are not known. We have developed a mobile image-based search system that takes images of objects as queries and finds relevant web pages by matching them to similar images on the web. Image-based search works well when matching full scenes, such as images of buildings or landmarks, and for matching objects when the boundary of the object in the image is available. We demonstrate the effectiveness of a simple interactive paradigm for obtaining a segmented object boundary, and show how a shape-based image matching algorithm can use the object outline to find similar images on the web.}, keywords = {content-based image retrieval, interactive segmentation, mobile interface, Object recognition}, isbn = {1-59593-002-7}, doi = {10.1145/1056808.1057083}, url = {http://doi.acm.org/10.1145/1056808.1057083}, author = {Tom Yeh and Grauman,Kristen and Tollmar,Konrad and Darrell,Trevor} } @inbook {12666, title = {Pose-Encoded Spherical Harmonics for Robust Face Recognition Using a Single Image}, booktitle = {Analysis and Modelling of Faces and GesturesAnalysis and Modelling of Faces and Gestures}, series = {Lecture Notes in Computer Science}, volume = {3723}, year = {2005}, month = {2005///}, pages = {229 - 243}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Face recognition under varying pose is a challenging problem, especially when illumination variations are also present. Under Lambertian model, spherical harmonics representation has proved to be effective in modelling illumination variations for a given pose. In this paper, we extend the spherical harmonics representation to encode pose information. More specifically, we show that 2D harmonic basis images at different poses are related by close-form linear combinations. This enables an analytic method for generating new basis images at a different pose which are typically required to handle illumination variations at that particular pose. Furthermore, the orthonormality of the linear combinations is utilized to propose an efficient method for robust face recognition where only one set of front-view basis images per subject is stored. In the method, we directly project a rotated testing image onto the space of front-view basis images after establishing the image correspondence. Very good recognition results have been demonstrated using this method.}, isbn = {978-3-540-29229-6}, url = {http://dx.doi.org/10.1007/11564386_18}, author = {Yue,Zhanfeng and Zhao,Wenyi and Chellapa, Rama}, editor = {Zhao,Wenyi and Gong,Shaogang and Tang,Xiaoou} } @conference {15349, title = {Preliminary Study of the Turbulence Structure in Supersonic Boundary Layers using DNS Data}, booktitle = {35th AIAA Fluid Dynamics Conference}, year = {2005}, month = {2005///}, address = {Toronto, Canada}, abstract = {Direct numerical simulation data are used to visualize coherent structures in turbulentboundary layers at Mach numbers from 0.3 to 7. Different criteria to identify the three- dimensional turbulence structure are selected. We find that using the discriminant of the velocity gradient tensor, the swirling strength and the λ2 criteria give nearly identical results, with λ2 identifying more structures very close to the wall. }, author = {Taylor,E. M and Martin, M.P and Smits,A. J.} } @inbook {17793, title = {Probabilistic Ontologies and Relational Databases}, booktitle = {On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASEOn the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASE}, series = {Lecture Notes in Computer Science}, volume = {3760}, year = {2005}, month = {2005///}, pages = {1 - 17}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The relational algebra and calculus do not take the semantics of terms into account when answering queries. As a consequence, not all tuples that should be returned in response to a query are always returned, leading to low recall. In this paper, we propose the novel notion of a constrained probabilistic ontology (CPO). We developed the concept of a CPO-enhanced relation in which each attribute of a relation has an associated CPO. These CPOs describe relationships between terms occurring in the domain of that attribute. We show that the relational algebra can be extended to handle CPO-enhanced relations. This allows queries to yield sets of tuples, each of which has a probability of being correct.}, keywords = {Computer, Science}, isbn = {978-3-540-29736-9}, url = {http://dx.doi.org/10.1007/11575771_1}, author = {Udrea,Octavian and Yu,Deng and Hung,Edward and Subrahmanian,V.}, editor = {Meersman,Robert and Tari,Zahir} } @article {16094, title = {Robotic apparatus and wireless communication system}, volume = {10/085,821}, year = {2005}, month = {2005/05/17/}, abstract = {A robotic apparatus and system adapted to communicate with a wireless sensor. The apparatus may be either physical or virtual in nature and is adapted to communicate physical movements with a wireless sensor. Data received from the sensor and/or robotic apparatus may be reviewed in a real-time mode, or may be saved for review at a later time. In addition, the apparatus may be controlled through an operator that is in local or remote communication with the apparatus. The robotic system may include pre-programmed interactive platforms for enabling communication between a user and the apparatus in a dynamic mode. In addition, the system may allow an operator to program a game/story for use as an interactive platform. Accordingly, the apparatus and system provides a platform for rehabilitative exercise of a patient as well as an entertainment device.}, url = {http://www.google.com/patents?id=5-0VAAAAEBAJ}, author = {Lathan,Corinna E. and Tracey,Michael R. and Vice,Jack M. and Druin, Allison and Plaisant, Catherine} } @conference {16880, title = {Scalable data collection infrastructure for digital government applications}, booktitle = {Proceedings of the 2005 national conference on Digital government research}, series = {dg.o {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {305 - 306}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {Highlights are presented of a project on the development of a scalable data collection infrastructure of digital government applications. The approach takes advantage of both the distributed nature of the data and the distributed ways of interacting with it. The approach is three-parted having theoretical, systems, and application components. On the theoretical and systems levels, work has continued on the development of the BISTRO system. On the applications level, work has continued on the investigation of the use of peer-to-peer networks in a number of domains in which the proper handling of spatial data is important.}, url = {http://dl.acm.org/citation.cfm?id=1065226.1065333}, author = {Samet, Hanan and Tanin,Egemen and Golubchik,Leana} } @inbook {17656, title = {Scheduling on Unrelated Machines Under Tree-Like Precedence Constraints}, booktitle = {Approximation, Randomization and Combinatorial Optimization. Algorithms and TechniquesApproximation, Randomization and Combinatorial Optimization. Algorithms and Techniques}, series = {Lecture Notes in Computer Science}, volume = {3624}, year = {2005}, month = {2005///}, pages = {609 - 609}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present polylogarithmic approximations for the R | prec | C max and R | prec |∑ j w j C j problems, when the precedence constraints are {\textquotedblleft}treelike{\textquotedblright} {\textendash} i.e., when the undirected graph underlying the precedences is a forest. We also obtain improved bounds for the weighted completion time and flow time for the case of chains with restricted assignment {\textendash} this generalizes the job shop problem to these objective functions. We use the same lower bound of {\textquotedblleft}congestion+dilation{\textquotedblright}, as in other job shop scheduling approaches. The first step in our algorithm for the R | prec | C max problem with treelike precedences involves using the algorithm of Lenstra, Shmoys and Tardos to obtain a processor assignment with the congestion + dilation value within a constant factor of the optimal. We then show how to generalize the random delays technique of Leighton, Maggs and Rao to the case of trees. For the weighted completion time, we show a certain type of reduction to the makespan problem, which dovetails well with the lower bound we employ for the makespan problem. For the special case of chains, we show a dependent rounding technique which leads to improved bounds on the weighted completion time and new bicriteria bounds for the flow time.}, isbn = {978-3-540-28239-6}, url = {http://dx.doi.org/10.1007/11538462_13}, author = {Kumar, V. and Marathe,Madhav and Parthasarathy,Srinivasan and Srinivasan, Aravind}, editor = {Chekuri,Chandra and Jansen,Klaus and Rolim,Jos{\'e} and Trevisan,Luca} } @article {14923, title = {Torrance-sparrow off-specular reflection and linear subspaces for object recognition}, volume = {10/230,888}, year = {2005}, month = {2005/05/31/}, abstract = {The Torrance-Sparrow model of off-specular reflection is recast in a significantly simpler and more transparent form in order to render a spherical-harmonic decomposition more feasible. By assuming that a physical surface consists of small, reflecting facets whose surface normals satisfy a normal distribution, the model captures the off-specular enhancement of the reflected intensity distribution often observed at large angles of incidence and reflection, features beyond the reach of the phenomenological broadening models usually employed. In passing we remove a physical inconsistency in the original treatment, restoring reciprocity and correcting the dependence of reflectance on angle near grazing incidence. It is noted that the results predicted by the model are relatively insensitive to values of its one parameter, the width of the distribution of surface normals.}, url = {http://www.google.com/patents?id=LI4VAAAAEBAJ}, author = {Thornber,Karvel K and Jacobs, David W.}, editor = {NEC Laboratories America, Inc.} } @article {15098, title = {Two-server password-only authenticated key exchange}, journal = {Applied Cryptography and Network Security}, year = {2005}, month = {2005///}, pages = {175 - 206}, abstract = {Typical protocols for password-based authentication assume a single server which stores all the information (e.g.), the password necessary to authenticate a user. Unfortunately, an inherent limitation of this approach (assuming low-entropy passwords are used) is that the user{\textquoteright}s password is exposed if this server is ever compromised. To address this issue, a number of schemes have been proposed in which a user{\textquoteright}s password information is shared among multiple servers, and these servers cooperate in a threshold manner when the user wants to authenticate.We show here a two-server protocol for this task assuming public parameters available to everyone in the system (as well as the adversary). Ours is the first provably-secure two-server protocol for the important password-only setting (in which the user need remember only a password, and not the servers{\textquoteright} public keys), and is the first two-server protocol (in any setting) with a proof of security in the standard model. }, doi = {10.1007/11496137_1}, author = {Katz, Jonathan and MacKenzie,P. and Taban,G. and Gligor,V.} } @conference {16684, title = {The web in theoretical linguistics research: Two case studies using the Linguist{\textquoteright}s Search Engine}, booktitle = {31st Meeting of the Berkeley Linguistics Society}, year = {2005}, month = {2005///}, pages = {265 - 276}, author = {Resnik, Philip and Elkiss,A. and Lau,E. and Taylor,H.} } @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.} } @book {18895, title = {Automated Planning: Theory and Practice}, year = {2004}, month = {2004/05/03/}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {Automated planning technology now plays a significant role in a variety of demanding applications, ranging from controlling space vehicles and robots to playing the game of bridge. These real-world applications create new opportunities for synergy between theory and practice: observing what works well in practice leads to better theories of planning, and better theories lead to better performance of practical applications. Automated Planning mirrors this dialogue by offering a comprehensive, up-to-date resource on both the theory and practice of automated planning. The book goes well beyond classical planning, to include temporal planning, resource scheduling, planning under uncertainty, and modern techniques for plan generation, such as task decomposition, propositional satisfiability, constraint satisfaction, and model checking. The authors combine over 30 years experience in planning research and development to offer an invaluable text to researchers, professionals, and graduate students. *Comprehensively explains paradigms for automated planning. *Provides a thorough understanding of theory and planning practice, and how they relate to each other. *Presents case studies of applications in space, robotics, CAD/CAM, process control, emergency operations, and games.*Provides a thorough understanding of AI planning theory and practice, and how they relate to each other. *Covers all the contemporary topics of planning, as well as important practical applications of planning, such as model checking and game playing. *Presents case studies and applications in planning engineering, space, robotics, CAD/CAM, process control, emergency operations, and games.*Provides lecture notes, examples of programming assignments, pointers to downloadable planning systems and related information online.}, keywords = {Business \& Economics / Management, Computers / Intelligence (AI) \& Semantics, Production planning, Production planning/ Data processing, Technology \& Engineering / Robotics}, isbn = {9781558608566}, author = {Ghallab,Malik and Nau, Dana S. and Traverso,Paolo} } @conference {14550, title = {Bidimensional Parameters and Local Treewidth}, booktitle = {Latin 2004: Theoretical Informatics: 6th Latin American Symposium, Buenos Aires, Argentina, April 5-8, 2004: Proceedings}, year = {2004}, month = {2004///}, pages = {109 - 109}, author = {Fomin,E. D.D.F.V and Hajiaghayi, Mohammad T. and Thilikos,D. M} } @article {18176, title = {Collusion resistant multimedia fingerprinting: A unified framework}, journal = {Electronic Imaging Symposium: Security, Steganography, and Watermarking of Multimedia Contents VI, San Jose, CA, Proc. of SPIE}, volume = {5306}, year = {2004}, month = {2004///}, pages = {748 - 759}, abstract = {Digital fingerprints are unique labels inserted in different copies of the same content before distribution. Eachdigital fingerprint is assigned to an intended recipient, and can be used to trace the culprits who use their content for unintended purposes. Attacks mounted by multiple users, known as collusion attacks, provide a cost-effective method for attenuating the identifying fingerprint from each colluder, thus collusion poses a real challenge to protect the digital media data and enforce usage policies. This paper examines a few major design methodologies for collusion-resistant fingerprinting of multimedia, and presents a unified framework that helps highlight the common issues and the uniqueness of different fingerprinting techniques. }, author = {Wu,M. and Trappe,W. and Wang,Z.J. and Liu,K. J.R} } @article {18180, title = {Collusion-resistant fingerprinting for multimedia}, journal = {Signal Processing Magazine, IEEE}, volume = {21}, year = {2004}, month = {2004/03//}, pages = {15 - 27}, abstract = {Digital fingerprinting is a technology for enforcing digital rights policies whereby unique labels, known as digital fingerprints, are inserted into content prior to distribution. For multimedia content, fingerprints can be embedded using conventional watermarking techniques that are typically concerned with robustness against a variety of attacks mounted by an individual. These attacks, known as multiuser collusion attacks, provide a cost-effective method for attenuating each of the colluder{\textquoteright}s fingerprints and poses a real threat to protecting media data and enforcing usage policies. In this article, we review some major design methodologies for collusion-resistant fingerprinting of multimedia and highlight common and unique issues of different fingerprinting techniques. It also provides detailed discussions on the two major classes of fingerprinting strategies, namely, orthogonal fingerprinting and correlated fingerprinting.}, keywords = {attacks;, colluder, collusion, collusion-resistant, content;, correlated, data;, digital, fingerprinting;, identification;, multimedia, multiuser, of, orthogonal, policies;, rights, Security, systems;, techniques;, tracing;, watermarking, watermarking;}, isbn = {1053-5888}, doi = {10.1109/MSP.2004.1276103}, author = {M. Wu and Trappe,W. and Wang,Z.J. and Liu,K. J.R} } @book {15668, title = {Data Structures and Algorithms in C++}, year = {2004}, month = {2004///}, publisher = {John Wiley \& Sons Inc}, organization = {John Wiley \& Sons Inc}, author = {Goodrich,M. T and Tamassia,R. and Mount, Dave} } @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} } @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} } @article {14037, title = {FAST ALGORITHMS TO COMPUTE MATRIX-VECTOR PRODUCTS FOR PASCAL MATRICES}, journal = {Technical Reports from UMIACS UMIACS-TR-2004-08}, year = {2004}, month = {2004/03/25/}, abstract = {The Pascal matrix arises in a number of applications. We present a few waysto decompose the Pascal matrices of size $n \times n$ into products of matrices with structure. Based on these decompositions, we propose fast algorithms to compute the product of a Pascal matrix and a vector with omplexity $O(n\log n)$. We also present a strategy to stabilize the proposed algorithms. Finally, we also present some interesting properties of the Pascal matrices that help us to compute fast the product of the inverse of a Pascal matrix and a vector, and fast algorithms for generalized Pascal Matrices. UMIACS-TR-2004-08 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1338}, author = {Tang,Zhihui and Duraiswami, Ramani and Gumerov, Nail A.} } @conference {16742, title = {A Framework for Sharing Voluminous Content in P2P Systems}, booktitle = {PDPTA}, year = {2004}, month = {2004///}, pages = {1031 - 1036}, author = {Tsoumakos,D. and Roussopoulos, Nick} } @article {18220, title = {Group-oriented fingerprinting for multimedia forensics}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2004}, year = {2004}, month = {2004/01//}, pages = {2153 - 2173}, abstract = {Digital fingerprinting of multimedia data involves embedding information in the content signal and offers protection to the digital rights of the content by allowing illegitimate usage of the content to be identified by authorized parties. One potential threat to fingerprinting is collusion, whereby a group of adversaries combine their individual copies in an attempt to remove the underlying fingerprints. Former studies indicate that collusion attacks based on a few dozen independent copies can confound a fingerprinting system that employs orthogonal modulation. However, in practice an adversary is more likely to collude with some users than with other users due to geographic or social circumstances. To take advantage of prior knowledge of the collusion pattern, we propose a two-tier group-oriented fingerprinting scheme where users likely to collude with each other are assigned correlated fingerprints. Additionally, we extend our construction to represent the natural social and geographic hierarchical relationships between users by developing a more flexible tree-structure-based fingerprinting system. We also propose a multistage colluder identification scheme by taking advantage of the hierarchial nature of the fingerprints. We evaluate the performance of the proposed fingerprinting scheme by studying the collusion resistance of a fingerprinting system employing Gaussian-distributed fingerprints. Our results show that the group-oriented fingerprinting system provides the superior collusion resistance over a system employing orthogonal modulation when knowledge of the potential collusion pattern is available.}, keywords = {collusion resistance, group-oriented fingerprinting, multimedia fingerprinting, multimedia forensics, multistage colluder identification}, isbn = {1110-8657}, doi = {10.1155/S1110865704312151}, url = {http://dx.doi.org/10.1155/S1110865704312151}, author = {Wang,Z. Jane and M. Wu and Trappe,Wade and Liu,K. J.R} } @conference {18344, title = {IDeixis: image-based Deixis for finding location-based information}, booktitle = {CHI {\textquoteright}04 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {781 - 782}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We demonstrate an image-based approach to specifying location and finding location-based information from camera-equipped mobile devices. We introduce a point-by-photograph paradigm, where users can specify a location simply by taking pictures. Our technique uses content-based image retrieval methods to search the web or other databases for matching images and their source pages to find relevant location-based information. In contrast to conventional approaches to location detection, our method can refer to distant locations and does not require any physical infrastructure beyond mobile internet service. We have developed a prototype on a camera phone and conducted user studies to demonstrate the efficacy of our approach compared to other alternatives.}, keywords = {content-based image retrieval, context-aware computing, location-awareness, Mobile computing}, isbn = {1-58113-703-6}, doi = {10.1145/985921.985933}, url = {http://doi.acm.org/10.1145/985921.985933}, author = {Tom Yeh and Tollmar,Konrad and Darrell,Trevor} } @article {18342, title = {Ideixis-image-based deixis for finding location-based information}, journal = {Mobile HCI, Vienna, Austria, Pages}, year = {2004}, month = {2004///}, pages = {781 - 782}, author = {Tollmar,K. and Tom Yeh and Darrell,T.} } @article {18343, title = {IDeixis{\textendash}Searching the Web with Mobile Images for Location-Based Information}, journal = {Mobile Human-Computer Interaction{\textendash}MobileHCI 2004}, year = {2004}, month = {2004///}, pages = {61 - 125}, author = {Tollmar,K. and Tom Yeh and Darrell,T.} } @conference {16886, title = {Indexing distributed complex data for complex queries}, booktitle = {Proceedings of the 2004 annual national conference on Digital government research}, series = {dg.o {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {63:1{\textendash}63:10 - 63:1{\textendash}63:10}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {Peer-to-peer networks are becoming a common form of online data exchange. Querying data, mostly files, using keywords on peer-to-peer networks is well-known. But users cannot perform many types of queries on complex data and on many of the attributes of the data on such networks other than mostly exact-match queries. We introduce a distributed hashing-based index for enabling more powerful accesses on complex data over peer-to-peer networks that we expect to be commonly deployed for digital government applications. Preliminary experiments show that our index scales well and we believe that it can be extended to obtain similar indices for many other data types for performing various complex queries, such as range queries.}, url = {http://dl.acm.org/citation.cfm?id=1124191.1124254}, author = {Tanin,Egemen and Harwood,Aaron and Samet, Hanan} } @inbook {13795, title = {Interlingual Annotation for MT Development}, booktitle = {Machine Translation: From Real Users to ResearchMachine Translation: From Real Users to Research}, series = {Lecture Notes in Computer Science}, volume = {3265}, year = {2004}, month = {2004///}, pages = {236 - 245}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {MT systems that use only superficial representations, including the current generation of statistical MT systems, have been successful and useful. However, they will experience a plateau in quality, much like other {\textquotedblleft}silver bullet{\textquotedblright} approaches to MT. We pursue work on the development of interlingual representations for use in symbolic or hybrid MT systems. In this paper, we describe the creation of an interlingua and the development of a corpus of semantically annotated text, to be validated in six languages and evaluated in several ways. We have established a distributed, well-functioning research methodology, designed a preliminary interlingua notation, created annotation manuals and tools, developed a test collection in six languages with associated English translations, annotated some 150 translations, and designed and applied various annotation metrics. We describe the data sets being annotated and the interlingual (IL) representation language which uses two ontologies and a systematic theta-role list. We present the annotation tools built and outline the annotation process. Following this, we describe our evaluation methodology and conclude with a summary of issues that have arisen.}, isbn = {978-3-540-23300-8}, url = {http://dx.doi.org/10.1007/978-3-540-30194-3_26}, author = {Reeder,Florence and Dorr, Bonnie J and Farwell,David and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Levin,Lori and Mitamura,Teruko and Miller,Keith and Rambow,Owen and Siddharthan,Advaith}, editor = {Frederking,Robert and Taylor,Kathryn} } @conference {15347, title = {Local Adaption and Dissipation Properties of a Weighted Essentially Non-Oscillatory Scheme}, booktitle = {34th AIAA Fluid Dynamics Conference and Exhibit}, year = {2004}, month = {2004///}, address = {Portland, OR}, abstract = {We perform several direct numerical simulations (DNS) of decaying isotropic turbulencewith various initial turbulent mach numbers Mt using a modifiedi weighted essentially non-oscillatory (WENO) method. We then present a procedure for the identification of shock-containing and smooth regions where the WENO scheme should respectively engage its adaption mechanism and revert to its linear optimal stencil. Weirsi has previously proposed the centrality index CI and nonlinearity index NI as two quantitative measures of stencil adaption, and we analyze these values within the regions of interest in the DNS flow fields. Our preliminary results indicate that these indices are suitable for assessments of the local adaption and dissipation properties of the WENO method; however, further studies must be conducted over a wider range of compressible flow conditions. }, author = {Taylor,E. M and Martin, M.P and Weirs,V. G} } @article {15861, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, journal = {Computer Speech \& Language}, volume = {18}, year = {2004}, month = {2004/04//}, pages = {163 - 179}, abstract = {This paper describes the Mandarin{\^a}{\texteuro}{\textquotedblleft}English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English{\^a}{\texteuro}{\textquotedblleft}Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence, this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks {\^a}{\texteuro}{\textquotedblleft} multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {English{\^a}{\texteuro}{\textquotedblleft}Chinese cross-language spoken document retrieval, Multi-scale spoken document retrieval}, isbn = {0885-2308}, doi = {10.1016/j.csl.2003.09.003}, url = {http://www.sciencedirect.com/science/article/pii/S0885230803000524}, author = {Meng,Helen M. and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @article {16334, title = {Measuring HPC productivity}, journal = {International Journal of High Performance Computing Applications}, volume = {18}, year = {2004}, month = {2004///}, pages = {459 - 473}, author = {Faulk,S. and Gustafson,J. and Johnson,P. and Porter, Adam and Tichy,W. and Votta,L.} } @article {17626, title = {Modelling disease outbreaks in realistic urban social networks}, journal = {Nature}, volume = {429}, year = {2004}, month = {2004/05/13/}, pages = {180 - 184}, abstract = {Most mathematical models for the spread of disease use differential equations based on uniform mixing assumptions1 or ad hoc models for the contact process2, 3, 4. Here we explore the use of dynamic bipartite graphs to model the physical contact patterns that result from movements of individuals between specific locations. The graphs are generated by large-scale individual-based urban traffic simulations built on actual census, land-use and population-mobility data. We find that the contact network among people is a strongly connected small-world-like5 graph with a well-defined scale for the degree distribution. However, the locations graph is scale-free6, which allows highly efficient outbreak detection by placing sensors in the hubs of the locations network. Within this large-scale simulation framework, we then analyse the relative merits of several proposed mitigation strategies for smallpox spread. Our results suggest that outbreaks can be contained by a strategy of targeted vaccination combined with early detection without resorting to mass vaccination of a population.}, isbn = {0028-0836}, doi = {10.1038/nature02541}, url = {http://www.nature.com/nature/journal/v429/n6988/full/nature02541.html}, author = {Eubank,Stephen and Guclu,Hasan and Kumar,V. S. Anil and Marathe,Madhav V. and Srinivasan, Aravind and Toroczkai,Zolt|[aacute]|n and Wang,Nan} } @inbook {13830, title = {Multi-align: Combining Linguistic and Statistical Techniques to Improve Alignments for Adaptable MT}, booktitle = {Machine Translation: From Real Users to ResearchMachine Translation: From Real Users to Research}, series = {Lecture Notes in Computer Science}, volume = {3265}, year = {2004}, month = {2004///}, pages = {17 - 26}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {An adaptable statistical or hybrid MT system relies heavily on the quality of word-level alignments of real-world data. Statistical alignment approaches provide a reasonable initial estimate for word alignment. However, they cannot handle certain types of linguistic phenomena such as long-distance dependencies and structural differences between languages. We address this issue in Multi-Align, a new framework for incremental testing of different alignment algorithms and their combinations. Our design allows users to tune their systems to the properties of a particular genre/domain while still benefiting from general linguistic knowledge associated with a language pair. We demonstrate that a combination of statistical and linguistically-informed alignments can resolve translation divergences during the alignment process.}, isbn = {978-3-540-23300-8}, url = {http://dx.doi.org/10.1007/978-3-540-30194-3_3}, author = {Ayan,Necip and Dorr, Bonnie J and Habash,Nizar}, editor = {Frederking,Robert and Taylor,Kathryn} } @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 {15372, title = {A novel approach to removing intersymbol interference from spin-stand images}, journal = {Magnetics, IEEE Transactions on}, volume = {40}, year = {2004}, month = {2004/07//}, pages = {2197 - 2199}, abstract = {A novel intersymbol interference (ISI) removal technique based on the "response function" characterization of giant-magnetoresistive heads is presented. It is demonstrated that the ISI-free readback image that corresponds to the actual underlying magnetization patterns can be extracted from the ISI-distorted readback signal through deconvolution. A new image deconvolution algorithm has been implemented, and it has been shown that it effectively removes the ISI distortions.}, keywords = {algorithm;, characterization;, Deconvolution, function, function;, giant, giant-magnetoresistive, Head, heads;, image, image;, imaging;, Interference, interference;, intersymbol, ISI-distorted, ISI-free, magnetic, magnetization, magnetoresistance;, patterns;, readback, removal;, response, signal;, spin-stand, suppression;}, isbn = {0018-9464}, doi = {10.1109/TMAG.2004.830153}, author = {Mayergoyz, Issak D and Tse,C. and Krafft,C. and McAvoy,P.} } @article {12939, title = {Occurrence and distribution of Vibrio cholerae in the coastal environment of Peru}, journal = {Environmental Microbiology}, volume = {6}, year = {2004}, month = {2004/07/01/}, pages = {699 - 706}, abstract = {The occurrence and distribution of Vibrio cholerae in sea water and plankton along the coast of Peru were studied from October 1997 to June 2000, and included the 1997{\textendash}98 El Ni{\~n}o event. Samples were collected at four sites in coastal waters off Peru at monthly intervals. Of 178 samples collected and tested, V. cholerae O1 was cultured from 10 (5.6\%) samples, and V. cholerae O1 was detected by direct fluorescent antibody assay in 26 out of 159 samples tested (16.4\%). Based on the number of cholera cases reported in Peru from 1997 to 2000, a significant correlation was observed between cholera incidence and elevated sea surface temperature (SST) along the coast of Peru (P~<~0.001). From the results of this study, coastal sea water and zooplankton are concluded to be a reservoir for V. cholerae in Peru. The climate{\textendash}cholera relationship observed for the 1997{\textendash}98 El Ni{\~n}o year suggests that an early warning system for cholera risk can be established for Peru and neighbouring Latin American countries.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2004.00601.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2004.00601.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Gil,Ana I. and Louis,Val{\'e}rie R. and Rivera,Irma N. G. and Lipp,Erin and Huq,Anwar and Lanata,Claudio F. and Taylor,David N. and Russek-Cohen,Estelle and Choopun,Nipa and Sack,R. Bradley and Rita R Colwell} } @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.} } @inbook {18915, title = {Plan Databases: Model and Algebra}, booktitle = {Foundations of Information and Knowledge Systems}, series = {Lecture Notes in Computer Science}, volume = {2942}, year = {2004}, month = {2004///}, pages = {302 - 319}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Despite the fact that thousands of applications manipulate plans, there has been no work to date on managing large databases of plans. In this paper, we first propose a formal model of plan databases. We describe important notions of consistency and coherence for such databases. We then propose a set of operators similar to the relational algebra to query such databases of plans.}, keywords = {Computer science}, isbn = {978-3-540-20965-2}, url = {http://www.springerlink.com/content/yqhlqtu4te18q2e1/abstract/}, author = {Yaman,Fusun and Adali,Sibel and Nau, Dana S. and Sapino,Maria and Subrahmanian,V.}, editor = {Seipel,Dietmar and Turull-Torres,Jos{\'e}} } @conference {16774, title = {Querying structured data in an unstructured P2P system}, booktitle = {Proceedings of the 6th annual ACM international workshop on Web information and data management - WIDM {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {64 - 64}, address = {Washington DC, USA}, doi = {10.1145/1031453.1031466}, url = {http://dl.acm.org/citation.cfm?id=1031466}, author = {Kantere,Verena and Tsoumakos,Dimitrios and Roussopoulos, Nick} } @conference {18353, title = {Searching the web with mobile images for location recognition}, booktitle = {Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference on}, volume = {2}, year = {2004}, month = {2004///}, pages = {76 - 81}, publisher = {IEEE}, organization = {IEEE}, abstract = {We describe an approach to recognizing location from mobile devices using image-based Web search. We demonstrate the usefulness of common image search metrics applied on images captured with a camera-equipped mobile device to find matching images on the World Wide Web or other general-purpose databases. Searching the entire Web can be computationally overwhelming, so we devise a hybrid image-and-keyword searching technique. First, image-search is performed over images and links to their source Web pages in a database that indexes only a small fraction of the Web. Then, relevant keywords on these Web pages are automatically identified and submitted to an existing text-based search engine (e.g. Google) that indexes a much larger portion of the Web. Finally, the resulting image set is filtered to retain images close to the original query. It is thus possible to efficiently search hundreds of millions of images that are not only textually related but also visually relevant. We demonstrate our approach on an application allowing users to browse Web pages matching the image of a nearby location.}, isbn = {0-7695-2158-4}, doi = {10.1109/CVPR.2004.1315147}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1315147}, author = {Tom Yeh and Tollmar,K. and Darrell,T.} } @conference {16885, title = {A serverless 3D world}, booktitle = {Proceedings of the 12th annual ACM international workshop on Geographic information systems}, series = {GIS {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {157 - 165}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online multi-participant virtual-world systems have attracted significant interest from the Internet community but are hindered by their inability to efficiently support interactivity for a large number of participants. Current solutions divide a large virtual-world into a few mutually exclusive zones, with each zone controlled by a different server, and/or limit the number of participants per server or per virtual-world. Peer-to-Peer (P2P) systems are known to provide excellent scalability in a networked environment (one peer is introduced to the system by each participant), however current P2P applications can only provide file sharing and other forms of relatively simple data communications. In this paper, we present a generic 3D virtual-world application that runs on a P2P network with no central administration or server. Two issues are addressed by this paper to enable such a spatial application on a P2P network. First, we demonstrate how to index and query a 3D space on a dynamic distributed network. Second, we show how to build such a complex application from the ground level of a P2P routing algorithm. Our work leads to new directions for the development of online virtual-worlds that we believe can be used for many government, industry, and public domain applications.}, keywords = {distributed hash tables, peer-to-peer systems, spatial data, virtual-worlds}, isbn = {1-58113-979-9}, doi = {10.1145/1032222.1032246}, url = {http://doi.acm.org/10.1145/1032222.1032246}, author = {Tanin,Egemen and Harwood,Aaron and Samet, Hanan and Nutanong,Sarana and Truong,Minh Tri} } @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.} } @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 {18725, title = {Ubistatins Inhibit Proteasome-Dependent Degradation by Binding the Ubiquitin Chain}, journal = {Science}, volume = {306}, year = {2004}, month = {2004/10/01/}, pages = {117 - 120}, abstract = {To identify previously unknown small molecules that inhibit cell cycle machinery, we performed a chemical genetic screen in Xenopus extracts. One class of inhibitors, termed ubistatins, blocked cell cycle progression by inhibiting cyclin B proteolysis and inhibited degradation of ubiquitinated Sic1 by purified proteasomes. Ubistatins blocked the binding of ubiquitinated substrates to the proteasome by targeting the ubiquitin-ubiquitin interface of Lys48-linked chains. The same interface is recognized by ubiquitin-chain receptors of the proteasome, indicating that ubistatins act by disrupting a critical protein-protein interaction in the ubiquitin-proteasome system.}, doi = {10.1126/science.1100946}, url = {http://www.sciencemag.org/cgi/content/abstract/sci;306/5693/117}, author = {Verma,Rati and Peters,Noel R. and D{\textquoteright}Onofrio,Mariapina and Tochtrop,Gregory P. and Sakamoto,Kathleen M. and Varadan,Ranjani and Zhang,Mingsheng and Coffino,Philip and Fushman, David and Deshaies,Raymond J. and King,Randall W.} } @conference {14789, title = {Using Hardware Counters to Automatically Improve Memory Performance}, booktitle = {Proceedings of the 2004 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {46{\textendash} - 46{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {In this paper, we introduce a profile-driven online page migration scheme and investigate its impact on the performance of multithreaded applications. We use lightweight, inexpensive plug-in hardware counters to profile the memory access behavior of an application, and then migrate pages to memory local to the most frequently accessing processor. Using the Dyninst runtime instrumentation combined with hardware counters, we were able to add page migration capabilities to the system without having to modify the operating system kernel, or to re-compile application programs. This approach reduced the total number of non-local memory accesses of applications by up to 90\%. Even on a system with small remote to local memory access latency rations, this resulted in up to 16\% improvement in execution time.}, isbn = {0-7695-2153-3}, doi = {http://dx.doi.org/10.1109/SC.2004.64}, url = {http://dx.doi.org/10.1109/SC.2004.64}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K} } @article {12942, title = {Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains}, journal = {Microbiology and immunology}, volume = {48}, year = {2004}, month = {2004///}, pages = {773 - 777}, author = {Islam,M. S. and Talukder,K. A. and Khan,N. H. and Mahmud,Z. H. and Rahman,M. Z. and Nair,G. B. and Siddique,A. K. M. and Yunus,M. and Sack,D. A. and Sack,R. B. and Rita R Colwell} } @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} } @conference {16754, title = {Adaptive Probabilistic Search for Peer-to-Peer Networks}, booktitle = {Peer-to-Peer Computing, IEEE International Conference on}, year = {2003}, month = {2003///}, pages = {102 - 102}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Peer-to-Peer networks are gaining increasing attention from both the scientific and the large Internet user community. Popular applications utilizing this new technology offer many attractive features to a growing number of users. At the heart of such networks lies the search algorithm. Proposed methods either depend on the network-disastrous flooding and its variations or utilize various indices too expensive to maintain. In this paper, we describe an adaptive, bandwidth-efficient algorithm for search in unstructured Peer-to-Peer networks, the Adaptive Probabilistic Search method (APS). Our scheme utilizes feedback from previous searches to probabilistically guide future ones. It performs efficient object discovery while inducing zero overhead over dynamic network operations. Extensive simulation results show that APS achieves high success rates, increased number of discovered objects, very low bandwidth consumption and adaptation to changing topologies.}, isbn = {0-7695-2023-5}, doi = {http://doi.ieeecomputersociety.org/10.1109/PTP.2003.1231509}, author = {Tsoumakos,Dimitrios and Roussopoulos, Nick} } @article {18167, title = {Anti-collusion fingerprinting for multimedia}, journal = {Signal Processing, IEEE Transactions on}, volume = {51}, year = {2003}, month = {2003/04//}, pages = {1069 - 1087}, abstract = {Digital fingerprinting is a technique for identifying users who use multimedia content for unintended purposes, such as redistribution. These fingerprints are typically embedded into the content using watermarking techniques that are designed to be robust to a variety of attacks. A cost-effective attack against such digital fingerprints is collusion, where several differently marked copies of the same content are combined to disrupt the underlying fingerprints. We investigate the problem of designing fingerprints that can withstand collusion and allow for the identification of colluders. We begin by introducing the collusion problem for additive embedding. We then study the effect that averaging collusion has on orthogonal modulation. We introduce a tree-structured detection algorithm for identifying the fingerprints associated with K colluders that requires O(Klog(n/K)) correlations for a group of n users. We next develop a fingerprinting scheme based on code modulation that does not require as many basis signals as orthogonal modulation. We propose a new class of codes, called anti-collusion codes (ACCs), which have the property that the composition of any subset of K or fewer codevectors is unique. Using this property, we can therefore identify groups of K or fewer colluders. We present a construction of binary-valued ACC under the logical AND operation that uses the theory of combinatorial designs and is suitable for both the on-off keying and antipodal form of binary code modulation. In order to accommodate n users, our code construction requires only O( radic;n) orthogonal signals for a given number of colluders. We introduce three different detection strategies that can be used with our ACC for identifying a suspect set of colluders. We demonstrate the performance of our ACC for fingerprinting multimedia and identifying colluders through experiments using Gaussian signals and real images.}, keywords = {(mathematics);, additive, algorithm;, and, anti-collusion, attack;, averaging, binary, code, codes;, codevectors;, coding;, colluders, collusion;, combinatorial, communication;, compression;, correlation;, cost-effective, data, data;, design, DETECTION, detection;, digital, embedding;, fingerprinting;, Gaussian, identification;, image, images;, keying;, logical, mathematics;, Modulation, modulation;, multimedia, multimedia;, of, on-off, operation;, orthogonal, processes;, real, redistribution;, Security, signal, signals;, theory;, tree-structured, TREES, watermarking;}, isbn = {1053-587X}, doi = {10.1109/TSP.2003.809378}, author = {Trappe,W. and M. Wu and Wang,Z.J. and Liu,K. J.R} } @conference {18169, title = {Anti-collusion of group-oriented fingerprinting}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {2}, year = {2003}, month = {2003/07//}, pages = {II - 217-20 vol.2 - II - 217-20 vol.2}, abstract = {Digital fingerprinting of multimedia data involves embedding information in the content, and offers protection to the digital rights of the content by allowing illegitimate usage of the content to be identified by authorized parties. One potential threat to fingerprints is collusion, whereby a group of adversaries combine their individual copies in an attempt to remove the underlying fingerprints. Former studies indicate that collusion attacks based on a few dozen independent copies can confound a fingerprinting system that employs orthogonal modulation. However, since an adversary is more likely to collude with some users than other users, we propose a group-based fingerprinting scheme where users likely to collude with each other are assigned correlated fingerprints. We evaluate the performance of our group-based fingerprints by studying the collusion resistance of a fingerprinting system employing Gaussian distributed fingerprints. We compare the results to those of fingerprinting systems employing orthogonal modulation.}, keywords = {anticollusion, attacks;, collusion, communication;, data;, digital, distributed, distribution;, fingerprinting;, fingerprints;, Gaussian, group-oriented, Internet;, method;, modulation;, multimedia, orthogonal, security;, Telecommunication, watermarking;}, doi = {10.1109/ICME.2003.1221592}, author = {Wang,Z.J. and M. Wu and Trappe,W. and Liu,K. J.R} } @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 {12951, title = {Characterization of a Vibrio cholerae phage isolated from the coastal water of Peru}, journal = {Environmental Microbiology}, volume = {5}, year = {2003}, month = {2003/04/25/}, pages = {350 - 354}, abstract = {A Vibrio cholerae bacteriophage, family Myoviridae, was isolated from seawater collected from the coastal water of Lima, Peru. Genome size was estimated to be 29~kbp. The temperate phage was specific to V. cholerae and infected 12/13 V. cholerae O1 strains and half of the four non-O1/non-O139 strains tested in this study. Vibrio cholerae O139 strains were resistant to infection and highest infection rates were obtained in low nutrient media amended with NaCl or prepared using seawater as diluent.}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2003.00411.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2003.00411.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Talledo,Miguel and Rivera,Irma N. G. and Lipp,Erin K. and Neale,Angela and Karaolis,David and Huq,Anwar and Rita R Colwell} } @conference {14290, title = {Checking and inferring local non-aliasing}, booktitle = {ACM SIGPLAN Notices}, volume = {38}, year = {2003}, month = {2003///}, pages = {129 - 140}, author = {Aiken,A. and Foster, Jeffrey S. and Kodumal,J. and Terauchi,T.} } @conference {16760, title = {A comparison of peer-to-peer search methods}, booktitle = {Proceedings of the Sixth International Workshop on the Web and Databases}, year = {2003}, month = {2003///}, author = {Tsoumakos,D. and Roussopoulos, Nick} } @book {19346, title = {Data Structures and Algorithms in C++}, year = {2003}, month = {2003}, pages = {714}, publisher = {John Wiley \& Sons}, organization = {John Wiley \& Sons}, abstract = {* Provides a comprehensive introduction to data structures and algorithms, including their design, analysis, and implementation * Each data structure is presented using ADTs and their respective implementations * Helps provide an understanding of the wide spectrum of skills ranging from sound algorithm and data structure design to efficient implementation and coding of these designs in C++}, keywords = {Computers / Databases / General, Computers / Programming / Algorithms, Computers / Programming / General, Computers / Programming Languages / C, Fiction / General}, isbn = {9780471202080}, author = {Goodrich, Michael T. and Tamassia, Roberto and Mount, Dave} } @inbook {16142, title = {Database Discovery with Dynamic Queries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {1 - 1}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Fredrikson,A. and North,C. and Plaisant, Catherine and Shneiderman, Ben and Tanin,E. and Pkisant,C.} } @article {12952, title = {Emergence and Evolution of Vibrio Cholerae O139}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {100}, year = {2003}, month = {2003/02/04/}, pages = {1304 - 1309}, abstract = {The emergence of Vibrio cholerae O139 Bengal during 1992{\textendash}1993 was associated with large epidemics of cholera in India and Bangladesh and, initially, with a total displacement of the existing V. cholerae O1 strains. However, the O1 strains reemerged in 1994 and initiated a series of disappearance and reemergence of either of the two serogroups that was associated with temporal genetic and phenotypic changes sustained by the strains. Since the initial emergence of the O139 vibrios, new variants of the pathogen derived from multiple progenitors have been isolated and characterized. The clinical and epidemiological characteristics of these strains have been studied. Rapid genetic reassortment in O139 strains appears to be a response to the changing epidemiology of V. cholerae O1 and also a strategy for persistence in competition with strains of the O1 serogroup. The emergence of V. cholerae O139 has provided a unique opportunity to witness genetic changes in V. cholerae that may be associated with displacement of an existing serogroup by a newly emerging one and, thus, provide new insights into the epidemiology of cholera. The genetic changes and natural selection involving both environmental and host factors are likely to influence profoundly the genetics, epidemiology, and evolution of toxigenic V. cholerae, not only in the Ganges Delta region of India and Bangladesh, but also in other areas of endemic and epidemic cholera.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0337468100}, url = {http://www.pnas.org/content/100/3/1304}, author = {Faruque,Shah M. and Sack,David A. and Sack,R. Bradley and Rita R Colwell and Takeda,Yoshifumi and Nair,G. Balakrish} } @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 {13786, title = {Hybrid Natural Language Generation from Lexical Conceptual Structures}, journal = {Machine Translation}, volume = {18}, year = {2003}, month = {2003///}, pages = {81 - 128}, abstract = {This paper describes Lexogen, a system for generating natural-languagesentences from Lexical Conceptual Structure, an interlingualrepresentation. The system has been developed as part of aChinese{\textendash}English Machine Translation (MT) system; however, it isdesigned to be used for many other MT language pairs and naturallanguage applications. The contributions of this work include: (1)development of a large-scale Hybrid Natural Language Generation system withlanguage-independent components; (2) enhancements to an interlingualrepresentation and associated algorithm forgeneration from ambiguous input; (3) development of an efficientreusable language-independent linearization module with a grammardescription language that can be used with other systems; (4)improvements to an earlier algorithm forhierarchically mapping thematic roles to surface positions; and (5)development of a diagnostic tool for lexicon coverage and correctnessand use of the tool for verification of English, Spanish, and Chineselexicons. An evaluation of Chinese{\textendash}English translation quality showscomparable performance with a commercial translation system. Thegeneration system can also be extended to other languages and this isdemonstrated and evaluated for Spanish.}, isbn = {0922-6567}, url = {http://dx.doi.org/10.1023/B:COAT.0000020960.27186.18}, author = {Habash,Nizar and Dorr, Bonnie J and Traum,David} } @conference {16900, title = {Improving access to large volumes of online data}, booktitle = {Proceedings of the 2003 annual national conference on Digital government research}, series = {dg.o {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {1 - 6}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {The Internet has recently become the medium of interaction with large volumes of data. Enterprises in the public and private sectors made their databases available over the Internet. Working with such large volumes of online data is a challenging task. For efficient access to large data from remote locations we introduced APPOINT (an Approach for Peer-to-Peer Offloading the INTernet). In APPOINT, active clients of a client-server architecture act on the server{\textquoteright}s behalf and communicate with each other to transfer large volumes of online data more efficiently. In essence, a server is enabled to appoint alternatives and create a scalable collaborative virtual mirror from the active clients. Multiple parameters such as availability of clients and bandwidth information on clients are considered to decide on how to best forward a download request. APPOINT is built as an add-on to existing client-server systems. A library of functions, with a simple application programming interface (API) that can be used within an existing client-server system to improve the service, is developed. Our experimental findings show that APPOINT can dramatically improve the performance of existing client-server based database systems.}, url = {http://dl.acm.org/citation.cfm?id=1123196.1123260}, author = {Tanin,Egemen and Samet, Hanan} } @article {18980, title = {Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {31}, year = {2003}, month = {2003/10/01/}, pages = {5654 - 5666}, abstract = {The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the \~{}27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkg770}, url = {http://nar.oxfordjournals.org/content/31/19/5654}, author = {Haas,Brian J. and Delcher,Arthur L. and Mount, Stephen M. and Wortman,Jennifer R. and Jr,Roger K. Smith and Hannick,Linda I. and Maiti,Rama and Ronning,Catherine M. and Rusch,Douglas B and Town,Christopher D. and Salzberg,Steven L. and White,Owen} } @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 {12945, title = {Persistence of adhesive properties in Vibrio cholerae after long-term exposure to sea water}, journal = {Environmental Microbiology}, volume = {5}, year = {2003}, month = {2003/10/01/}, pages = {850 - 858}, abstract = {The effect of exposure to artificial sea water (ASW) on the ability of classical Vibrio cholerae O1 cells to interact with chitin-containing substrates and human intestinal cells was studied. Incubation of vibrios in ASW at 5{\textdegree}C and 18{\textdegree}C resulted in two kinds of cell responses: the viable but non-culturable (VBNC) state (i.e.~<0.1 colony forming unit ml-1) at 5{\textdegree}C, and starvation (i.e. maintenance of culturability of the population) at 18{\textdegree}C. The latter remained rod shaped and, after 40~days{\textquoteright} incubation, presented a 47{\textendash}58\% reduction in the number of cells attached to chitin, a 48{\textendash}53\% reduction in the number of bacteria adhering to copepods, and a 48{\textendash}54\% reduction in the number of bacteria adhering to human cultured intestinal cells, compared to control cells not suspended in ASW. Bacteria suspended in ASW at 5{\textdegree}C became coccoid and, after 40~days, showed 34{\textendash}42\% fewer cells attached to chitin, 52{\textendash}55\% fewer adhering to copep-ods, and 45{\textendash}48\% fewer cells adhering to intestinal cell monolayers, compared to controls. Sarkosyl-insoluble membrane proteins that bind chitin particles were isolated and analysed by SDS-PAGE. After 40~days incubation in ASW at both 5{\textdegree}C and 18{\textdegree}C vibrios expressed chitin-binding ligands similar to bacteria harvested in the stationary growth phase. It is concluded that as vibrios do not lose adhesive properties after long-term exposure to ASW, it is important to include methods for VBNC bacteria when testing environmental and clinical samples for purposes of public health safety.}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2003.00498.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2003.00498.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Pruzzo,Carla and Tarsi,Renato and Del Mar Lle{\`o},Maria and Signoretto,Caterina and Zampini,Massimiliano and Pane,Luigi and Rita R Colwell and Canepari,Pietro} } @article {16778, title = {Probabilistic knowledge discovery and management for P2P networks}, journal = {P2P Journal}, year = {2003}, month = {2003///}, pages = {15 - 20}, author = {Tsoumakos,D. and Roussopoulos, Nick} } @conference {17811, title = {Probabilistically survivable mass}, booktitle = {INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {18}, year = {2003}, month = {2003///}, pages = {789 - 795}, abstract = {Multiagent systems (MAS) can "go down" for alarge number of reasons, ranging from system mal- functions and power failures to malicious attacks. The placement of agents on nodes is called a de- ployment of the MAS. We develop a probabilis- tic model of survivability of a deployed MAS and provide two algorithms to compute the probability of survival of a deployed MAS. Our probabilistic model docs not make independence assumptions though such assumptions can be added if so de- sired. An optimal deployment of a MAS is one that maximizes its survival probability. We provide a mathematical answerto this question, an algorithm that computes an exact solution to this problem, as well as several algorithms that quickly compute approximate solutions to the problem. We have implemented our algorithms - our implementation demonstrates that computing deployments can be done scalably. }, author = {Kraus,S. and V.S. Subrahmanian and Tas,N. C} } @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.} } @conference {18266, title = {Resistance of orthogonal Gaussian fingerprints to collusion attacks}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {1}, year = {2003}, month = {2003/07//}, pages = {I - 617-20 vol.1 - I - 617-20 vol.1}, abstract = {Digital fingerprinting is a means to offer protection to digital data by which fingerprints embedded in the multimedia are capable of identifying unauthorized use of digital content. A powerful attack that can be employed to reduce this tracing capability is collusion. In this paper, we study the collusion resistance of a fingerprinting system employing Gaussian distributed fingerprints and orthogonal modulation. We propose a likelihood-based approach to estimate the number of colluders, and introduce the thresholding detector for colluder identification. We first analyze the collusion resistance of a system to the average attack by considering the probability of a false negative and the probability of a false positive when identifying colluders. Lower and upper bounds for the maximum number of colluders Kmax are derived. We then show that the detectors are robust to different attacks. We further study different sets of performance criteria.}, keywords = {approach;, attacks;, capability;, collusion, data, data;, digital, distributed, embedded, fingerprinting;, fingerprints;, Gaussian, likelihood-based, modulation;, multimedia, of, orthogonal, probability;, processes;, protection;, Security, systems;, tracing}, doi = {10.1109/ICME.2003.1220993}, author = {Wang,Z.J. and M. Wu and Zhao,Hong and Liu,K. J.R and Trappe,W.} } @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} } @article {18995, title = {Sex-lethal splicing autoregulation in vivo: interactions between SEX-LETHAL, the U1 snRNP and U2AF underlie male exon skipping}, journal = {DevelopmentDevelopment}, volume = {130}, year = {2003}, month = {2003/02/01/}, pages = {463 - 471}, abstract = {Alternative splicing of the Sex-lethal pre-mRNA has long served as a model example of a regulated splicing event, yet the mechanism by which the female-specific SEX-LETHAL RNA-binding protein prevents inclusion of the translation-terminating male exon is not understood. Thus far, the only general splicing factor for which there is in vivo evidence for a regulatory role in the pathway leading to male-exon skipping is sans-fille (snf), a protein component of the spliceosomal U1 and U2 snRNPs. Its role, however, has remained enigmatic because of questions about whether SNF acts as part of an intact snRNP or a free protein. We provide evidence that SEX-LETHAL interacts with SANS-FILLE in the context of the U1 snRNP, through the characterization of a point mutation that interferes with both assembly into the U1 snRNP and complex formation with SEX-LETHAL. Moreover, we find that SEX-LETHAL associates with other integral U1 snRNP components, and we provide genetic evidence to support the biological relevance of these physical interactions. Similar genetic and biochemical approaches also link SEX-LETHAL with the heterodimeric splicing factor, U2AF. These studies point specifically to a mechanism by which SEX-LETHAL represses splicing by interacting with these key splicing factors at both ends of the regulated male exon. Moreover, because U2AF and the U1 snRNP are only associated transiently with the pre-mRNA during the course of spliceosome assembly, our studies are difficult to reconcile with the current model that proposes that the SEX-LETHAL blocks splicing at the second catalytic step, and instead argue that the SEX-LETHAL protein acts after splice site recognition, but before catalysis begins.}, keywords = {Drosophila, SNF, Splicing regulation, SXL, U1 snRNP, U2AF}, isbn = {0950-1991, 1477-9129}, doi = {10.1242/dev.00274}, url = {http://dev.biologists.org/content/130/3/463}, author = {Nagengast,Alexis A. and Stitzinger,Shane M. and Tseng,Chin-Hsiu and Mount, Stephen M. and Salz,Helen K.} } @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.} } @article {18022, title = {Towards a first vertical prototyping of an extremely fine-grained parallel programming approach}, journal = {Theory of Computing Systems}, volume = {36}, year = {2003}, month = {2003///}, pages = {521 - 552}, abstract = {Explicit multithreading (XMT) is a parallel programming approach for exploiting on-chip parallelism. XMT introduces a computational framework with (1) a simple programming style that relies on fine-grained PRAM-style algorithms; (2) hardware support for low-overhead parallel threads, scalable load balancing, and efficient synchronization. The missing link between the algorithmic-programming level and the architecture level is provided by the first prototype XMT compiler. This paper also takes this new opportunity to evaluate the overall effectiveness of the interaction between the programming model and the hardware, and enhance its performance where needed, incorporating new optimizations into the XMT compiler. We present a wide range of applications, which written in XMT obtain significant speedups relative to the best serial programs. We show that XMT is especially useful for more advanced applications with dynamic, irregular access patterns, where for regular computations we demonstrate performance gains that scale up to much higher levels than have been demonstrated before for on-chip systems.}, author = {Naishlos,D. and Nuzman,J. and Tseng,C. W and Vishkin, Uzi} } @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} } @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 {14795, title = {Active Harmony: Towards Automated Performance Tuning}, booktitle = {Supercomputing, ACM/IEEE 2002 Conference}, year = {2002}, month = {2002/11//}, pages = {44 - 44}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we present the Active Harmony automated runtime tuning system. We describe the interface used by programs to make applications tunable. We present the Library Specification Layer which helps program library developers expose multiple variations of the same API using different algorithms.The Library Specification Language helps to select the most appropriate program library to tune the overall performance. We also present the optimization algorithm used to adjust parameters in the application and the libraries. Finally, we present results that show how the system is able to tune several real applications. The automated tuning system is able to tune the application parameers to within a few percent of the best value after evaluating only 11 out of over 1,700 possible configurations.}, keywords = {Application software, Automatic control, Computational modeling, Computer science, Computerized monitoring, Control systems, grid computing, Runtime library, software libraries, Specification languages}, isbn = {0-7695-1524-X}, doi = {10.1109/SC.2002.10062}, author = {Tapus, C. and I-Hsin Chung and Hollingsworth, Jeffrey K} } @conference {18166, title = {Anti-collusion codes: multi-user and multimedia perspectives}, booktitle = {Image Processing. 2002. Proceedings. 2002 International Conference on}, volume = {2}, year = {2002}, month = {2002///}, pages = {II-149 - II-152 vol.2 - II-149 - II-152 vol.2}, abstract = {Digital fingerprinting is an effective method to identify users who might try to redistribute multimedia content, such as images and video. These fingerprints are typically embedded into the content using watermarking techniques that are designed to be robust to a variety of attacks. A cheap and effective attack against such digital fingerprints is collusion, where several differently marked copies of the same content are averaged or combined to disrupt the underlying fingerprint. We present a construction of collusion-resistant fingerprints based upon anti-collusion codes (ACC) and binary code modulation. ACC have the property that the composition of any subset of K or fewer codevectors is unique. Using this property, we build fingerprints that allow for the identification of groups of K or less colluders. We present a construction of binary-valued ACC under the logical AND operation using the theory of combinatorial designs. Our code construction requires only Oscr;( radic;n) orthogonal signals to accommodate n users. We demonstrate the performance of our ACC for fingerprinting multimedia by identifying colluders through experiments using real images.}, keywords = {and, anti-collusion, authentication;, binary, code, codes;, coding;, combinatorial, computing;, content;, data, designs;, digital, embedding;, encapsulation;, fingerprinting;, image, images;, logical, mathematics;, message, Modulation, modulation;, multimedia, operation;, performance;, watermarking;}, doi = {10.1109/ICIP.2002.1039909}, author = {Trappe,W. and M. Wu and Liu,K. J.R} } @conference {16909, title = {APPOINT: an Approach for Peer-to-Peer Offloading the INTernet}, booktitle = {Proceedings of the 2002 annual national conference on Digital government research}, series = {dg.o {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {1 - 7}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {The Internet has recently become the medium of interaction with large volumes of online data. Enterprises in the public and private sectors made their data archives available over the Internet. Working with such large volumes of online data is a challenging task. APPOINT (an Approach for Peer-to-Peer Offloading the INTernet), a centralized peer-to-peer approach that helps users of the Internet transfer large volumes of online data efficiently, is introduced with this paper. In APPOINT, active clients of a 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. In essence, a server is enabled to appoint alternatives when needed and create a scalable collaborative virtual mirror from the active clients. Multiple parameters such as locality and availability to decide on how to best forward a download request are considered. The problems that can arise in symmetric upload requests are also addressed. APPOINT is an ongoing project and it is being built as an add-on to existing client-server systems. A library of functions, with a simple application programming interface (API) that can be used within an existing client-server system to improve the service, is currently being developed.}, url = {http://dl.acm.org/citation.cfm?id=1123098.1123102}, author = {Tanin,Egemen and Samet, Hanan} } @article {14538, title = {Approximating the head-related transfer function using simple geometric models of the head and torso}, journal = {The Journal of the Acoustical Society of America}, volume = {112}, year = {2002}, month = {2002///}, pages = {2053 - 2053}, author = {Algazi,V. R and Duda,R. O and Duraiswami, Ramani and Gumerov, Nail A. and Tang,Z.} } @conference {17009, title = {CHI@20: fighting our way from marginality to power}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {688 - 691}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The Special Interest Group on Computer Human Interaction (SIGCHI) has had a successful history of 20 years of growth in its numbers and influence. To help guide the continued evolution of the academic discipline and professional community, we invite several senior members to offer their visions for what the field of CHI actually accomplished over the past several decades, and what do we still need to accomplish? What do we need to do differently/ better/smarter? What haven{\textquoteright}t we tried because the technology, the money or the will wasn{\textquoteright}t there in the past, but perhaps is now.The CHI field is more than just technology. We understand that our work can have a profound effect on individuals, families, neighborhoods, corporations, and countries. We know that we can influence education, commerce, healthcare, and government. How can we contribute to bridging the digital divides in developed and developing countries? What agendas can we offer for the academic, research, industrial, and civic spheres for the next 20 years? How can we be more ambitious? How can we truly serve human needs.}, keywords = {education, future vision, Human-computer interaction, practice, professional, THEORY, usability engineering}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506548}, url = {http://doi.acm.org/10.1145/506443.506548}, author = {Shneiderman, Ben and Card,Stuart and Norman,Donald A. and Tremaine,Marilyn and Waldrop,M. Mitchell} } @conference {18179, title = {Collusion-resistant fingerprinting for multimedia}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-3309 -IV-3312 - IV-3309 -IV-3312}, abstract = {Digital fingerprinting is an effective method to identify users who might try to redistribute multimedia content, such as images and video. These fingerprints are typically embedded into the content using watermarking techniques that are designed to be robust to a variety of attacks. A cheap and effective attack against such digital fingerprints is collusion, where several differently marked copies of the same content are averaged or combined to disrupt the underlying fingerprint. In this paper, we study the problem of designing fingerprints that can withstand collusion, yet trace colluders. Since, in antipodal CDMA-type watermarking, the correlation contributions only decrease where watermarks differ, by constructing binary code vectors where any subset of k or fewer of these vectors have unique overlap, we may identify groups of k or less colluders. Our construction of such anti-collusion codes (ACC) uses the theory of combinatorial designs, and for n users requires O( $\#$x221A;n) bits. Further, we explore a block matrix structure for the ACC that reduces the computational complexity for identifying colluders and improves the detection capability when colluders belong to the same subgroup.}, doi = {10.1109/ICASSP.2002.5745361}, author = {Trappe,Wade and M. Wu and Liu,K. J.R} } @conference {14800, title = {Efficient instrumentation for code coverage testing}, booktitle = {ACM SIGSOFT Software Engineering Notes}, volume = {27}, year = {2002}, month = {2002///}, pages = {86 - 96}, author = {Tikir, M. M and Hollingsworth, Jeffrey K} } @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 {12843, title = {Evidence-based model checking}, booktitle = {Computer Aided Verification}, year = {2002}, month = {2002///}, pages = {641 - 680}, author = {Tan,L. and Cleaveland, Rance} } @inbook {14692, title = {Evolution in Action: Using Active Networking to Evolve Network Support for Mobility}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {2546}, year = {2002}, month = {2002///}, pages = {146 - 161}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A key early objective of Active Networking (AN) was to support on-the-fly network evolution. Although AN has been used relatively extensively to build application-customized protocols and even whole networking systems, demonstrations of evolution have been limited. This paper examines three AN mechanisms and how they enable evolution: active packets and plug-in extensions, well-known to the AN community, and update extensions, which are novel to AN. We devote our presentation to a series of demonstrations of how each type of evolution can be applied to the problem of adding support for mobility to a network. This represents the most large-scale demonstration of AN evolution to date. These demonstrations show what previous AN research has not: that AN technology can, in fact, support very significant changes to the network, even while the network is operational.}, isbn = {978-3-540-00223-9}, url = {http://dx.doi.org/10.1007/3-540-36199-5_12}, author = {Seong-Kyu,Song and Shannon,Stephen and Hicks, Michael W. and Nettles,Scott}, editor = {Sterbenz,James and Takada,Osamu and Tschudin,Christian and Plattner,Bernhard} } @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 {14551, title = {Exponential speedup of fixed-parameter algorithms on K 3, 3-minor-free or K 5-minor-free graphs}, journal = {Algorithms and Computation}, year = {2002}, month = {2002///}, pages = {277 - 287}, author = {Demaine,E. and Hajiaghayi, Mohammad T. and Thilikos,D.} } @article {14312, title = {Flow-sensitive type qualifiers}, journal = {ACM SIGPLAN Notices}, volume = {37}, year = {2002}, month = {2002///}, pages = {1 - 12}, author = {Foster, Jeffrey S. and Terauchi,T. and Aiken,A.} } @article {12963, title = {In vitro adhesion to human cells by viable but nonculturable Enterococcus faecalis}, journal = {Current microbiology}, volume = {45}, year = {2002}, month = {2002///}, pages = {105 - 110}, abstract = {The ability of viable but nonculturable (VBNC) Enterococcus faecalis to adhere to Caco-2 and Girardi heart cultured cells and to urinary tract epithelial cells (ECs) was studied. Enterococci were harvested during the vegetative growth phase (early exponential and stationary), in the VBNC state, and after recovery of the ability to divide. VBNC bacteria maintained their adherence capability but the efficiency of attachment was reduced by about 50 to 70\%, depending on the target cell employed. The decrease was transient, since enterococci that regained their culturability showed adherence values similar to those observed for actively growing cells. Analysis of the invasive properties of E. faecalis revealed that the VBNC state caused a decrease in the number of bacteria that entered the cultured HEK cells as a result of the reduction in the number of adhering bacteria. These results highlight the importance of studies of the VBNC phenomenon, with respect to both microbial survival in the environment and the impact on human health.}, doi = {10.1007/s00284-001-0089-2}, author = {Pruzzo,C. and Tarsi,R. and Lle{\`o},M. M. and Signoretto,C. and Zampini,M. and Rita R Colwell and Canepari,P.} } @article {18232, title = {Joint coding and embedding for collusion-resistant fingerprinting}, journal = {Proceedings of the European Signal Processing Conference, EUSIPCO}, year = {2002}, month = {2002///}, abstract = {An effective attack against fingerprints for multimedia is collusion,where several differently marked copies of the same content are av- eraged or combined to disrupt the underlying fingerprint. In this paper, we investigate the problem of designing fingerprints that can withstand collusion and allow for the identification of colluders. We begin by introducing the collusion problem for additive embedding, and introduce an efficient detection algorithm for orthogonal mod- ulation that identifies the fingerprints associated with K colluders and requires O(K log(n/K)) correlations for a group of n users. We present a construction of collusion-resistant fingerprints based upon anti-collusion codes (ACC) and binary code modulation. Us- ing ACC, we build fingerprints that identify groups of K or less colluders. We present a construction of binary-valued ACC un- der the logical AND operation using the theory of combinatorial designs. Our code construction requires only O(√n) orthogonal signals to accommodate n users. We demonstrate the performance of our ACC for fingerprinting multimedia and identifying colluders through experiments using Gaussian signals. }, author = {Trappe,W. and Wu,M. and Liu,K. J.R} } @article {16477, title = {Locating and accessing data repositories with WebSemantics}, journal = {The VLDB journal}, volume = {11}, year = {2002}, month = {2002///}, pages = {47 - 57}, author = {Mihaila,G. A and Raschid, Louiqa and Tomasic,A.} } @article {14507, title = {Method and apparatus for learning probabilistic relational models having attribute and link uncertainty and for performing selectivity estimation using probabilistic relational models}, volume = {09/922,324}, year = {2002}, month = {2002/08/01/}, abstract = {The invention comprises a method and apparatus for learning probabilistic models (PRM{\textquoteright}s) with attribute uncertainty. A PRM with attribute uncertainty defines a probability distribution over instantiations of a database. A learned PRM is useful for discovering interesting patterns and dependencies in the data. Unlike many existing techniques, the process is data-driven rather than hypothesis driven. This makes the technique particularly well-suited for exploratory data analysis. In addition, the invention comprises a method and apparatus for handling link uncertainty in PRM{\textquoteright}s. Link uncertainty is uncertainty over which entities are related in our domain. The invention comprises of two mechanisms for modeling link uncertainty: reference uncertainty and existence uncertainty. The invention includes learning algorithms for each form of link uncertainty. The third component of the invention is a technique for performing database selectivity estimation using probabilistic relational...}, url = {http://www.google.com/patents?id=FVqDAAAAEBAJ}, author = {Koller,Daphne and Getoor, Lise and Pfeffer,Avi and Friedman,Nir and Taskar,Ben} } @conference {14536, title = {Numerical study of the influence of the torso on the HRTF}, booktitle = {Acoustics, Speech, and Signal Processing, 1993. ICASSP-93., 1993 IEEE International Conference on}, volume = {2}, year = {2002}, month = {2002///}, pages = {II{\textendash}II - II{\textendash}II}, author = {Gumerov, Nail A. and Duraiswami, Ramani and Tang,Z.} } @article {15299, title = {Omnibase: Uniform access to heterogeneous data for question answering}, journal = {Natural Language Processing and Information Systems}, year = {2002}, month = {2002///}, pages = {230 - 234}, abstract = {Although the World Wide Web contains a tremendous amount of information, the lack of uniform structure makes finding the right knowledge difficult. A solution is to turn the Web into a {\textquotedblleft}virtual database{\textquotedblright} and to access it through natural language.We built Omnibase, a system that integrates heterogeneous data sources using an object- property-value model. With the help of Omnibase, our Start natural language system can now access numerous heterogeneous data sources on the Web in a uniform manner, and answers millions of user questions with high precision.}, doi = {10.1007/3-540-36271-1_23}, author = {Katz,B. and Felshin,S. and Yuret,D. and Ibrahim,A. and Jimmy Lin and Marton,G. and Jerome McFarland,A. and Temelkuran,B.} } @article {14163, title = {A Parallel Block Multi-level Preconditioner for the 3D Incompressible Navier--Stokes Equations}, volume = {UMIACS-TR-2002-95}, year = {2002}, month = {2002/10/25/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The development of robust and efficient algorithms for both steady-statesimulations and fully-implicit time integration of the Navier--Stokes equations is an active research topic. To be effective, the linear subproblems generated by these methods require solution techniques that exhibit robust and rapid convergence. In particular, they should be insensitive to parameters in the problem such as mesh size, time step, and Reynolds number. In this context, we explore a parallel preconditioner based on a block factorization of the coefficient matrix generated in an Oseen nonlinear iteration for the primitive variable formulation of the system. The key to this preconditioner is the approximation of a certain Schur complement operator by a technique first proposed by Kay, Loghin, and Wathen [25] and Silvester, Elman, Kay, and Wathen [45]. The resulting operator entails subsidiary computations (solutions of pressure Poisson and convection--diffusion subproblems) that are similar to those required for decoupled solution methods; however, in this case these solutions are applied as preconditioners to the coupled Oseen system. One important aspect of this approach is that the convection--diffusion and Poisson subproblems are significantly easier to solve than the entire coupled system, and a solver can be built using tools developed for the subproblems. In this paper, we apply smoothed aggregation algebraic multigrid to both subproblems. Previous work has focused on demonstrating the optimality of these preconditioners with respect to mesh size on serial, two-dimensional, steady-state computations employing geometric multi-grid methods; we focus on extending these methods to large-scale, parallel, three-dimensional, transient and steady-state simulations employing algebraic multigrid (AMG) methods. Our results display nearly optimal convergence rates for steady-state solutions as well as for transient solutions over a wide range of CFL numbers on the two-dimensional and three-dimensional lid-driven cavity problem. Also UMIACS-TR-2002-95 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1239}, author = {Elman, Howard and Howle, V. E and Shadid,John and Tuminaro,Ray} } @article {13459, title = {PASSAT: A user-centric planning framework}, journal = {Proceedings of the 3rd International NASA Workshop on Planning and Scheduling for Space}, year = {2002}, month = {2002///}, abstract = {We describe a plan-authoring system called PASSAT (Plan-Authoring System based on Sketches, Advice, and Templates) that combines interactive tools for constructing plans with a suite of automated and mixed-initiative capabilities designed to complement human planning skills. PASSAT is organized around a library of predefined templates that encode task networks describing standard operating procedures and previous cases. Users can select from these templates to apply during plan development, with the system providing various forms of automated assistance. A mixed-initiative plan sketch facility helps users refine outlines for plans to complete solutions, by detecting problems and proposing possible fixes. An advice capability enables user specification of high-level guidelines for plans that the system helps to enforce. Finally, PASSAT includes process facilitation mechanisms designed to help a user track and manage outstanding planning tasks and information requirements, as a means of improving the efficiency and effectiveness of the planning process. PASSAT is designed for applications for which a core of planning knowledge can be captured in predefined action models but where significant user control of the planning process is required. }, author = {Myers,K.L. and Tyson,W.M. and Wolverton,M.J. and Jarvis,P.A. and Lee,T.J. and desJardins, Marie} } @conference {14772, title = {Recompilation for debugging support in a JIT-compiler}, booktitle = {Proceedings of the 2002 ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, series = {PASTE {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {10 - 17}, publisher = {ACM}, organization = {ACM}, address = {Charleston, South Carolina, USA}, abstract = {A static Java compiler converts Java source code into a verifiably secure and compact architecture-neutral intermediate format, called Java byte codes. The Java byte codes can be either interpreted by a Java Virtual Machine or translated into native code by Java Just-In-Time compilers. Static Java compilers embed debug information in the Java class files to be used by the source level debuggers. However, the debug information is generated for architecture independent byte codes and most of the debug information is valid only when the byte codes are interpreted. Translating byte codes into native instructions puts a limitation on the amount of usable debug information that can be used by source level debuggers. In this paper, we present a new technique to generate valid debug information when Just-In-Time compilers are used. Our approach is based on the dynamic recompilation of Java methods by a fast code generator and lazily generates debug information when it is required. We also present three implementations for field watch support in the Java Virtual Machine Debugger Interface to investigate the runtime overhead and code size growth by our approach.}, keywords = {algorithms, debug information, debugging aids, dynamic recompilation, field access watch, java, java virtual machine debugger interface, just-in-time compilation, measurement, performance}, isbn = {1-58113-479-7}, doi = {10.1145/586094.586100}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K and Lueh,Guei-Yuan} } @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} } @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 {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.} } @inbook {15826, title = {Understanding Machine Performance in the Context of Human Performance for Multi-document Summarization}, booktitle = {DUC 02 Conference ProceedingsDUC 02 Conference Proceedings}, year = {2002}, month = {2002///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {We present a discussion of our summarization algorithm -- both single and multi-document -- along with a discussion of the evaluation experiments we have undertaken, what we have learned from them, and how we intend to utilize this information.}, url = {http://duc.nist.gov/http://duc.nist.gov/}, author = {Schlesinger,J.D. and Okurowski,M. E. and Conroy,J.M. and O{\textquoteright}Leary, Dianne P. and Taylor,A. and Hobbs,J. and Wilson,H. T.} } @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 {14067, title = {Analysis of a donor gene region for a variant surface glycoprotein and its expression site in African trypanosomes}, journal = {Nucleic acids research}, volume = {29}, year = {2001}, month = {2001///}, pages = {2012 - 2012}, author = {LaCount,D. J and El-Sayed, Najib M. and Kaul,S. and Wanless,D. and Turner,C. M.R and Donelson,J. E} } @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} } @conference {14293, title = {Detecting format string vulnerabilities with type qualifiers}, booktitle = {Proceedings of the 10th conference on USENIX Security Symposium-Volume 10}, year = {2001}, month = {2001///}, pages = {16 - 16}, author = {Shankar,U. and Talwar,K. and Foster, Jeffrey S. and Wagner,D.} } @article {17665, title = {The discrepancy of permutation families}, journal = {Unpublished manuscript}, year = {2001}, month = {2001///}, abstract = {In this note, we show that the discrepancy of any family of l permutations of[n] = {1,2,...,n} is O( √ llog n), improving on the O(llog n) bound due to Bohus (Random Structures \& Algorithms, 1:215{\textendash}220, 1990). In the case where l >= n, we show that the discrepancy is Θ(min{√nlog(2l/n),n}). }, author = {Spencer,JH and Srinivasan, Aravind and Tetali,P.} } @inbook {17096, title = {Dynamic Aggregation to Support Pattern Discovery: A Case Study with Web Logs}, booktitle = {Discovery ScienceDiscovery Science}, series = {Lecture Notes in Computer Science}, volume = {2226}, year = {2001}, month = {2001///}, pages = {464 - 469}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Rapid growth of digital data collections is overwhelming the capabilities of humans to comprehend them without aid. The extraction of useful data from large raw data sets is something that humans do poorly. Aggregation is a technique that extracts important aspect from groups of data thus reducing the amount that the user has to deal with at one time, thereby enabling them to discover patterns, outliers, gaps, and clusters. Previous mechanisms for interactive exploration with aggregated data were either too complex to use or too limited in scope. This paper proposes a new technique for dynamic aggregation that can combine with dynamic queries to support most of the tasks involved in data manipulation.}, isbn = {978-3-540-42956-2}, url = {http://dx.doi.org/10.1007/3-540-45650-3_42}, author = {Tang,Lida and Shneiderman, Ben}, editor = {Jantke,Klaus and Shinohara,Ayumi} } @article {13761, title = {Efficient Language Independent Generation from Lexical Conceptual Structure}, year = {2001}, month = {2001/09//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper describes a system for generating natural-language sentences from an interlingual representation, Lexical Conceptual Structure (LCS). The system has been developed as part of a Chinese-English Machine Translation system; however, it is designed to be used for many other MT language pairs and Natural Language applications. The contributions of this work include: (1) Development of a language-independent generation system that maximizes efficiency through the use of a hybrid rule-based/statistical module; (2) Enhancements to an interlingual representation and associated algorithms for interpretation of multiply ambiguous input sentences; (3) Development of an efficient reusable language-independent linearization module with a grammar description language that can be used with other systems; (4) Improvements to an earlier algorithm for hierarchically mapping thematic roles to surface positions; (5) Development of a diagnostic tool for lexicon coverage and correctness and use of the tool for verification of English, Spanish, and Chinese lexicons. An evaluation of translation quality shows comparable performance with commercial translation system. The generation system can also be straightforwardly extended to their languages and this is demonstrated and evaluated for Spanish.}, keywords = {*LEXICAL CONCEPTUAL STRUCTURE, *LEXICOGRAPHY, *MACHINE TRANSLATION, *VOCABULARY, *WORDS(LANGUAGE), algorithms, CHINA, COMMERCE, DIAGNOSTIC EQUIPMENT, efficiency, English language, grammars, INPUT, INTERLINGUAL, LANGUAGE, LANGUAGE-INDEPENDENT NLP., linguistics, MAPPING, natural language, QUALITY, SPANISH LANGUAGE, verification}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458756}, author = {Habash,Nizar and Dorr, Bonnie J and Traum,David} } @article {18027, title = {Evaluating the XMT parallel programming model}, journal = {High-Level Parallel Programming Models and Supportive Environments}, year = {2001}, month = {2001///}, pages = {95 - 108}, abstract = {Explicit-multithreading (XMT) is a parallel programming model designed for exploiting on-chip parallelism. Its features include a simple thread execution model and an efficient prefix-sum instruction for synchronizing shared data accesses. By taking advantage of low-overhead parallel threads and high on-chip memory bandwidth, the XMT model tries to reduce the burden on programmers by obviating the need for explicit task assignment and thread coarsening. This paper presents features of the XMT programming model, and evaluates their utility through experiments on a prototype XMT compiler and architecture simulator. We find the lack of explicit task assignment has slight effects on performance for the XMT architecture. Despite low thread overhead, thread coarsening is still necessary to some extent, but can usually be automatically applied by the XMT compiler. The prefix-sum instruction provides more scalable synchronization than traditional locks, and the simple run-untilcompletion thread execution model (no busy-waits) does not impair performance. Finally, the combination of features in XMT can encourage simpler parallel algorithms that may be more efficient than more traditional complex approaches.}, author = {Naishlos,D. and Nuzman,J. and Tseng,C. W and Vishkin, Uzi} } @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} } @article {17149, title = {Exploration of Large Online Data Tables Using Generalized Query Previews}, journal = {University of Maryland Computer Science Technical Report (June 2001)}, year = {2001}, month = {2001///}, abstract = {Companies, government agencies, and other organizations are making their data available to the world over the Internet. These organizations often store their data as large online relational database tables. Users query these databases with front-ends that mostly use menus or form fillin interfaces, but these interfaces rarely give users information about the contents and distribution of the data. This situation leads users to waste time and network resources posing queries that have zero-hit or mega-hit results. Generalized query previews form a user interface architecture for efficient browsing of large online databases by supplying data distribution information to the users. The data distribution information provides an overview of the data. Generalized query previews give continuous feedback about the size of the results as the query is being formed. This provides a preview of the results. This paper presents the generalized query previews user interface architecture and our experimental findings. Our user study shows that for exploratory querying tasks, generalized query previews speed user performance and reduce network load. Categories and Subject Descriptors: H.5.2 [Information Interfaces and Presentation]: User Interfaces - Graphical user interfaces (GUI), H.3.5 [Information Storage and Retrieval]: Online Information Services - Web-based services. General Terms: Design, Human Factors, Experimentation. Keywords: Visual Data Mining, Information Visualization, Graphical User Interfaces, Relational Databases, Database Querying, Online Databases, Dynamic Queries, Previews and Overviews.}, author = {Tanin,E. and Shneiderman, Ben} } @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.} } @article {13897, title = {KidStory: A technology design partnership with children}, journal = {Behaviour \& Information Technology}, volume = {20}, year = {2001}, month = {2001///}, pages = {119 - 125}, author = {Tax{\'e}n,G. and Druin, Allison and Fast,C. and Kjellin,M.} } @article {14422, title = {Learning probabilistic models of relational structure}, journal = {MACHINE LEARNING-INTERNATIONAL WORKSHOP}, year = {2001}, month = {2001///}, pages = {170 - 177}, abstract = {Most real-world data is stored in relational form. Incontrast, most statistical learning methods work with {\textquotedblleft}flat{\textquotedblright} data representations, forcing us to convert our data into a form that loses much of the relational struc- ture. The recently introduced framework of proba- bilistic relational models (PRMs) allows us to repre- sent probabilistic models over multiple entities that utilize the relations between them. In this paper, we propose the use of probabilistic models not only for the attributes in a relational model, but for the rela- tional structure itself. We propose two mechanisms for modeling structural uncertainty: reference uncertainty and existence uncertainty. We describe the appropriate conditions for using each model and present learning algorithms for each. We present experimental results showing that the learned models can be used to pre- dict relational structure and, moreover, the observed relational structure can be used to provide better pre- dictions for the attributes in the model. }, author = {Getoor, Lise and Friedman,N. and Koller,D. and Taskar,B.} } @conference {15899, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, booktitle = {Proceedings of the first international conference on Human language technology research}, series = {HLT {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {1 - 7}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper describes the Mandarin-English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English-Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks -- multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {cross-language, English-Chinese, spoken document retrieval}, doi = {10.3115/1072133.1072202}, url = {http://dx.doi.org/10.3115/1072133.1072202}, author = {Meng,Helen and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @conference {14400, title = {Probabilistic models of relational structure}, booktitle = {In Proc. ICML}, year = {2001}, month = {2001///}, abstract = {Most real-world data is stored in relational form. In contrast, most statistical learning methods work with {\textquotedblleft}flat {\textquotedblright} data representations, forcing us to convert our data into a form that loses much of the relational structure. The recently introduced framework of probabilistic relational models (PRMs) allows us to represent probabilistic models over multiple entities that utilize the relations between them. In this paper, we propose the use of probabilistic models not only for the attributes in a relational model, but for the relational structure itself. We propose two mechanisms for modeling structural uncertainty: reference uncertainty and existence uncertainty. We describe the appropriate conditions for using each model and present learning algorithms for each. We present experimental results showing that the learned models can be used to predict relational structure and, moreover, the observed relational structure can be used to provide better predictions for the attributes in the model.}, author = {Getoor, Lise and Friedman,N. and Taskar,B.} } @article {14399, title = {Probabilistic models of text and link structure for hypertext classification}, journal = {IJCAI workshop on text learning: beyond supervision}, year = {2001}, month = {2001///}, pages = {24 - 29}, abstract = {Most text classification methods treat each document as anindependent instance. However, in many text domains, doc- uments are linked and the topics of linked documents are cor- related. For example, web pages of related topics are often connected by hyperlinks and scientific papers from related fields are commonly linked by citations. We propose a unified probabilistic model for both the textual content and the link structure of a document collection. Our model is based on the recently introduced framework of Probabilistic Relational Models (PRMs), which allows us to capture cor- relations between linked documents. We show how to learn these models from data and use them efficiently for classifi- cation. Since exact methods for classification in these large models are intractable, we utilize belief propagation, an ap- proximate inference algorithm. Belief propagation automat- ically induces a very natural behavior, where our knowledge about one document helps us classify related ones, which in turn help us classify others. We present preliminary empiri- cal results on a dataset of university web pages. }, author = {Getoor, Lise and Segal,E. and Taskar,B. and Koller,D.} } @article {14364, title = {Selectivity estimation using probabilistic models}, journal = {ACM SIGMOD Record}, volume = {30}, year = {2001}, month = {2001/05//}, pages = {461 - 472}, abstract = {Estimating the result size of complex queries that involve selection on multiple attributes and the join of several relations is a difficult but fundamental task in database query processing. It arises in cost-based query optimization, query profiling, and approximate query answering. In this paper, we show how probabilistic graphical models can be effectively used for this task as an accurate and compact approximation of the joint frequency distribution of multiple attributes across multiple relations. Probabilistic Relational Models (PRMs) are a recent development that extends graphical statistical models such as Bayesian Networks to relational domains. They represent the statistical dependencies between attributes within a table, and between attributes across foreign-key joins. We provide an efficient algorithm for constructing a PRM front a database, and show how a PRM can be used to compute selectivity estimates for a broad class of queries. One of the major contributions of this work is a unified framework for the estimation of queries involving both select and foreign-key join operations. Furthermore, our approach is not limited to answering a small set of predetermined queries; a single model can be used to effectively estimate the sizes of a wide collection of potential queries across multiple tables. We present results for our approach on several real-world databases. For both single-table multi-attribute queries and a general class of select-join queries, our approach produces more accurate estimates than standard approaches to selectivity estimation, using comparable space and time.}, isbn = {0163-5808}, doi = {10.1145/376284.375727}, url = {http://doi.acm.org/10.1145/376284.375727}, author = {Getoor, Lise and Taskar,Benjamin and Koller,Daphne} } @article {12800, title = {Simulation revisited}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {2001}, month = {2001///}, pages = {480 - 495}, author = {Tan,L. and Cleaveland, Rance} } @conference {16156, title = {Therapeutic play with a storytelling robot}, booktitle = {CHI {\textquoteright}01 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {27 - 28}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We are developing a prototype storytelling robot for use with children in rehabilitation. Children can remotely control a furry robot by using a variety of body sensors adapted to their disability or rehabilitation goal. We believe this robot can motivate children and help them reach their therapy goals through therapeutic play, either by exercising muscles or joints (e.g. for physically challenged children) or by reflecting on the stories (e.g. for children with developmental disabilities). To develop this technology we use an innovative design methodology involving children as design partners.}, keywords = {children, design process, rehabilitation, robot, therapeutic play, user interface}, isbn = {1-58113-340-5}, doi = {10.1145/634067.634088}, url = {http://doi.acm.org/10.1145/634067.634088}, author = {Lathan,Corinna and Vice,Jack Maxwell and Tracey,Michael and Plaisant, Catherine and Druin, Allison and Edward,Kris and Montemayor,Jaime} } @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 {13737, title = {Chinese-English Semantic Resource Construction}, year = {2000}, month = {2000/06//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We describe an approach to large-scale construction of a semantic lexicon for Chinese verbs. We leverage off of three existing resources-- a classification of English verbs called EVCA (English Verbs Classes and Alternations), a Chinese conceptual database called HowNet, and a large-machine readable dictionary called Optilex. The resulting lexicon is used for determining appropriate word senses in applications such as machine translation and cross-language information retrieval.}, keywords = {*CHINESE LANGUAGE, *ENGLISH LANGUAGE, *LEXICONS, *SEMANTICS, *VERBS, *WORD SENSES, *WORDS(LANGUAGE), classification, CONCEPTS, CONSTRUCTION, Dictionaries, INFORMATION SCIENCE, linguistics, VERB CLASSES, Vocabulary}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458703}, author = {Dorr, Bonnie J and Levow,Gina-Anne and Lin,Dekang and Thomas,Scott} } @article {17576, title = {Combinatorial Problems Arising in Deregulated Electrical Power Industry: Survey and Future Directions}, journal = {NONCONVEX OPTIMIZATION AND ITS APPLICATIONS}, volume = {42}, year = {2000}, month = {2000///}, pages = {138 - 162}, author = {Cook,D. and Hicks,G. and Faber,V. and Marathe,M. V and Srinivasan, Aravind and Sussmann,Y. J and Thornquist,H.} } @conference {18192, title = {Data hiding in digital binary image}, booktitle = {Multimedia and Expo, 2000. ICME 2000. 2000 IEEE International Conference on}, volume = {1}, year = {2000}, month = {2000///}, pages = {393 -396 vol.1 - 393 -396 vol.1}, abstract = {This paper proposes a new method to embed data in binary images, including scanned text, figures and signatures. The method manipulates ldquo;flippable rdquo; pixels and uses shuffling to embed a significant amount of data without causing noticeable artifacts. The extraction of the hidden data does not require the original image. Potential applications include detecting unauthorized use of a digitized signature and authenticating binary documents}, keywords = {authentication;data, binary, data;, document, encapsulation;image, hiding;digital, image;digital, of, pixels;multimedia;scanned, processing;multimedia, signature;flippable, systems;security, text;shuffling;data, watermarking;digitized}, doi = {10.1109/ICME.2000.869623}, author = {M. Wu and Tang,E. and Lin, B.} } @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 {15148, title = {On the efficiency of local decoding procedures for error-correcting codes}, booktitle = {Proceedings of the thirty-second annual ACM symposium on Theory of computing}, series = {STOC {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {80 - 86}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-184-4}, doi = {10.1145/335305.335315}, url = {http://doi.acm.org/10.1145/335305.335315}, author = {Katz, Jonathan and Trevisan,Luca} } @conference {18031, title = {Evaluating multi-threading in the prototype XMT environment}, booktitle = {Proc. 4th Workshop on Multi-Threaded Execution, Architecture and Compliation (MTEAC2000)}, year = {2000}, month = {2000///}, abstract = {XMT is a multi-threaded programming model designed toexploit explicit specification of parallel threads. Its main features are a simple thread execution model and an efficient prefix-sum instruction for synchronizing shared data accesses. This paper presents and evaluates the performance of multi- threading in the XMT programming environment. A prototype XMT compiler converts parallel regions into procedure calls, which are then executed efficiently in XMT hardware. An architecture simulator similar to SimpleScalar is used to evaluate the performance of the XMT system for twelve benchmark codes. Results show the XMT architecture generally succeeds in providing low-overhead parallel threads and uniform access times on-chip. However, compiler optimizations to cluster (coarsen) threads are still needed for very fine-grained threads. }, author = {Naishlos,D. and Nuzman,J. and Tseng,C. W and Vishkin, Uzi} } @article {16161, title = {Facilitating data exploration with query previews: A study of user performance and preference}, journal = {Behaviour \& Information Technology}, volume = {19}, year = {2000}, month = {2000///}, pages = {393 - 403}, abstract = {Networked and local data exploration systems that use command languages, menus, or form fill-in interfaces rarely give users an indication of the distribution of data. This often leads users to waste time, posing queries that have zero-hit or mega-hit results. Query previews are a novel visual approach for browsing databases. Query previews supply users with data distribution information for selected attributes of the database, and give continuous feedback about the size of the result set as the query is being formed. Subsequent refinements might be necessary to narrow the search. As there is a risk that query previews are an additional step, leading to a more complex and slow search process, a within-subjects empirical study was ran with 12 subjects who used interfaces with and without query previews and with minimized network delays. Even with 12 subjects and minimized network delays statistically significant differences were found, showing that query previews could speed up performance 1.6 to 2.1 times and lead to higher user satisfaction.Networked and local data exploration systems that use command languages, menus, or form fill-in interfaces rarely give users an indication of the distribution of data. This often leads users to waste time, posing queries that have zero-hit or mega-hit results. Query previews are a novel visual approach for browsing databases. Query previews supply users with data distribution information for selected attributes of the database, and give continuous feedback about the size of the result set as the query is being formed. Subsequent refinements might be necessary to narrow the search. As there is a risk that query previews are an additional step, leading to a more complex and slow search process, a within-subjects empirical study was ran with 12 subjects who used interfaces with and without query previews and with minimized network delays. Even with 12 subjects and minimized network delays statistically significant differences were found, showing that query previews could speed up performance 1.6 to 2.1 times and lead to higher user satisfaction. }, isbn = {0144-929X}, doi = {10.1080/014492900750052651}, url = {http://www.tandfonline.com/doi/abs/10.1080/014492900750052651}, author = {Tanin,Egemen and Lotem,Amnon and Haddadin,Ihab and Shneiderman, Ben and Plaisant, Catherine and Slaughter,Laura} } @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.} } @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 {15942, title = {Meta-reasoning for intelligent dialog repair}, year = {2000}, month = {2000///}, institution = {Technical report, University of Maryland}, abstract = {Under consideration for other conferences (specify)? We present a logical approach and implmentation of a real-time rational agent for dialogue management, which includes an ability to represent, reason about, and repair (both implicitly and explicitly) incoherence in dialogue. We exemplify a target problem of negative feedback in action directive subdialogues, with an ability to make reference resolution sensitive to dialogue context and like intentions. The resulting system is able to behave more sensibly in several situations than earlier dialogue management systems in these same conditions. Meta-reasoning for intelligent dialog repair We present a logical approach and implmentation of a real-time rational agent for dialogue management, which includes an ability to represent, reason about, and repair (both implicitly and explicitly) incoherence in dialogue. We exemplify a target problem of negative feedback in action directive subdialogues, with an ability to make reference resolution sensitive to dialogue context and like intentions. The resulting system is able to behave more sensibly in several situations than earlier dialogue management systems in these same conditions.}, author = {Purang,K. and Traum,D. and Purushothaman,D. and Chong,W. and Okamato,Y. and Perlis, Don} } @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 {13011, title = {Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences}, journal = {J Mol Evol}, volume = {50}, year = {2000}, month = {2000/06//}, pages = {532 - 540}, abstract = {Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala.}, author = {Garc{\'\i}a-Varela,M and P{\'e}rez-Ponce de Le{\'o}n,G. and de la Torre,P and Cummings, Michael P. and Sarma,SS and Laclette,J. P} } @article {14652, title = {A Review of Current Routing Protocols for Ad Hoc}, journal = {IEEE Personal Communications}, volume = {29}, year = {2000}, month = {2000///}, pages = {156 - 71}, author = {Royer,E.M. and Toh,C.K. and Hicks, Michael W. and Kakkar,P. and Moore,J. T and Hicks, Michael W. and Moore,J. T and Alexander,D. S and Gunter,C. A and Nettles,S. and others} } @conference {18947, title = {Telicity as a cue to temporal and discourse structure in Chinese-English machine translation}, series = {NAACL-ANLP-Interlinguas {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {34 - 41}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Machine translation between any two languages requires the generation of information that is implicit in the source language. In translating from Chinese to English, tense and other temporal information must be inferred from other grammatical and lexical cues. Moreover, Chinese multiple-clause sentences may contain inter-clausal relations (temporal or otherwise) that must be explicit in English (e.g., by means of a discourse marker). Perfective and imperfective grammatical aspect markers can provide cues to temporal structure, but such information is not present in every sentence. We report on a project to use the lexical aspect features of (a)telicity reflected in the Lexical Conceptual Structure of the input text to suggest tense and discourse structure in the English translation of a Chinese newspaper corpus.}, doi = {10.3115/1117554.1117559}, url = {http://dx.doi.org/10.3115/1117554.1117559}, author = {Olsen,Mari and Traum,David and Van Ess-Dykema,Carol and Weinberg, Amy and Dolan,Ron} } @conference {17080, title = {Developing the next generation of Earth science data systems: the Global Land Cover Facility}, booktitle = {Geoscience and Remote Sensing Symposium, 1999. IGARSS {\textquoteright}99 Proceedings. IEEE 1999 International}, volume = {1}, year = {1999}, month = {1999///}, pages = {616-618 vol.1 - 616-618 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {A recent initiative by NASA has resulted in the formation of a federation of Earth science data partners. These Earth Science Information Partners (ESIPs) have been tasked with creating novel Earth science data products and services as well as distributing new and existing data sets to the Earth science community and the general public. The University of Maryland established its ESIP activities with the creation of the Global Land Cover Facility (GLCF). This joint effort of the Institute for Advanced Computer Studies (UMIACS) and the Department of Geography has developed an operational data archiving and distribution system aimed at advancing current land cover research efforts. The success of the GLCF is tied closely to assessing user needs as well. As the timely delivery of data products to the research community. This paper discusses the development and implementation of a web-based interface that allows users to query the authors{\textquoteright} data holdings and perform user requested processing tasks on demand. The GLCF takes advantage of a scaleable, high performance computing architecture for the manipulation of very large remote sensing data sets and the rapid spatial indexing of multiple format data types. The user interface has been developed with the cooperation of the Human-Computer Interaction Laboratory (HCIL) and demonstrates advances in spatial and temporal querying tools as well as the ability to overlay multiple raster and vector data sets. Their work provides one perspective concerning how critical earth science data may be handled in the near future by a coalition of distributed data centers}, keywords = {Computer architecture, data archiving, data distribution system, Data systems, Distributed computing, Earth science data products, Earth science data system, ESIP, geographic information system, geographic information systems, Geography, geophysical measurement technique, geophysical signal processing, geophysical techniques, Geoscience, GIS, GLCF, Global Land Cover Facility, High performance computing, Indexing, information service, Information services, Institute for Advanced Computer Studies, land cover, NASA, next generation, PACS, Remote sensing, terrain mapping, UMIACS, University of Maryland, User interfaces, web-based interface}, isbn = {0-7803-5207-6}, doi = {10.1109/IGARSS.1999.773583}, author = {Lindsay,F.E. and Townshend,J.R.G. and JaJa, Joseph F. and Humphries,J. and Plaisant, Catherine and Shneiderman, Ben} } @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.} } @article {16172, title = {The end of zero-hit queries: query previews for NASA{\textquoteright}s Global Change Master Directory}, journal = {International Journal on Digital Libraries}, volume = {2}, year = {1999}, month = {1999///}, pages = {79 - 90}, abstract = {The Human-Computer Interaction Laboratory (HCIL) of the University of Maryland and NASA have collaborated over three years to refine and apply user interface research concepts developed at HCIL in order to improve the usability of NASA data services. The research focused on dynamic query user interfaces, visualization, and overview + preview designs. An operational prototype, using query previews, was implemented with NASA{\textquoteright}s Global Change Master Directory (GCMD), a directory service for earth science datasets. Users can see the histogram of the data distribution over several attributes and choose among attribute values. A result bar shows the cardinality of the result set, thereby preventing users from submitting queries that would have zero hits. Our experience confirmed the importance of metadata accuracy and completeness. The query preview interfaces make visible the problems or gaps in the metadata that are undetectable with classic form fill-in interfaces. This could be seen as a problem, but we think that it will have a long-term beneficial effect on the quality of the metadata as data providers will be compelled to produce more complete and accurate metadata. The adaptation of the research prototype to the NASA data required revised data structures and algorithms.}, isbn = {1432-5012}, url = {http://dx.doi.org/10.1007/s007990050039}, author = {Greene,Stephan and Tanin,Egemen and Plaisant, Catherine and Shneiderman, Ben and Olsen,Lola and Major,Gene and Johns,Steve} } @article {16971, title = {An Exploratory Study of Video Browsing, User Interface Designs and Research Methodologies: Effectiveness in Information Seeking Tasks}, journal = {PROCEEDINGS OF THE ANNUAL MEETING-AMERICAN SOCIETY FOR INFORMATION SCIENCE}, volume = {36}, year = {1999}, month = {1999///}, pages = {681 - 692}, abstract = {The purpose of this exploratory study is to develop research methods to compare the effectiveness of two video browsing interface designs, or surrogates one static (storyboard) and one dynamic (slide show) on two distinct information seeking tasks (gist determination and object recognition). Although video data is multimodal, potentially consisting of images, speech, sound, and text, the surrogates tested depend on image data only and use key frames or stills extracted from source video. A test system was developed to determine the effects of different key frame displays on user performance in specified information seeking tasks. The independent variables were interface display and task type. The dependent variables were task accuracy and subjective satisfaction. Covariates included spatial visual ability and time-to-completion. The study used a repeated block factorial 2x2 design; each of 20 participants interacted with all four interface-task combinations. No statistically significant results for task accuracy were found. Statistically significant differences were found, however, for user satisfaction with the display types: users assessed the static display to be "easier" to use than the dynamic display for both task types, even though there were no performance differences. This methodological approach provides a useful way to learn about the relationship between surrogate types and user tasks during video browsing.}, author = {Tse,T. and Vegh,S. and Shneiderman, Ben and Marchionini,G.} } @conference {15923, title = {Fkpurang, darsana, traum, cfa, perlisg@ cs. umd. edu}, booktitle = {In Proceedings of the IJCAI{\textquoteright}99 Workshop on Practical Reasoning and Rationality}, year = {1999}, month = {1999///}, author = {Edu,C. U and Purang,K. and Purushothaman,D. and Traum,D. and Andersen,C. and Perlis, Don} } @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.} } @conference {15984, title = {Mixed initiative dialogue and intelligence via active logic}, booktitle = {proceedings of the AAAI99 Workshop on Mixed-Initiative Intelligence}, year = {1999}, month = {1999///}, pages = {60 - 67}, author = {Andersen,C. and Traum,D. and Purang,K. and Purushothaman,D. and Perlis, Don} } @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} } @conference {16023, title = {Practical reasoning and plan execution with active logic}, booktitle = {Proceedings of the IJCAI-99 Workshop on Practical Reasoning and Rationality}, year = {1999}, month = {1999///}, pages = {30 - 38}, author = {Purang,K. and Purushothaman,D. and Traum,D. and Andersen,C. and Perlis, Don} } @conference {17443, title = {Trust me, I{\textquoteright}m accountable: trust and accountability online}, booktitle = {CHI {\textquoteright}99 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {79 - 80}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We live in an increasingly wired world. According to Robert Putnam, people are spending less time in persistent personal face to face interactions and more time in pursuits such as watching TV and using the Internet. At the same time, independently measured "social capital" -- the extent to which we trust and work for a common good -- is declining. In this panel, we explore: the impacts of electronic media on trust and accountability; whether and how electronic media can be designed and used to increase deserved trust and accountability; the relationship between protecting privacy and increasing the efficacy of communication; and how people{\textquoteright}s tendency to treat computers as social actors impacts these issues. In brief, how can modern technology enhance humanity{\textquoteright}s humanity?}, keywords = {accountability, anonymity, Communication, computers and society, ethics, Internet, media effects, privacy, Reciprocity, repute, social actors, social capital, social impacts, trust, value-sensitive design, wired world, WWW}, isbn = {1-58113-158-5}, doi = {10.1145/632716.632766}, url = {http://doi.acm.org/10.1145/632716.632766}, author = {Friedman,Batya and Thomas,John C. and Grudin,Jonathan and Nass,Clifford and Nissenbaum,Helen and Schlager,Mark and Shneiderman, Ben} } @conference {18754, title = {3D spatial layouts using a-teams}, year = {1998}, month = {1998///}, abstract = {Spatial layout is the problem of arranging a set of componentsin an enclosure such that a set of objectives and constraints is sat- isfied. The constraints may include non-interference of objects, accessibility requirements and connection cost limits. Spatial lay- out problems are found primarily in the domains of electrical en- gineering and mechanical engineering in the design of integrated circuits and mechanical or electromechanical artifacts. Traditional approaches include ad-hoc (or specialized) heuristics, Genetic Al- gorithms and Simulated Annealing. The A-Teams approach pro- vides a way of synergistically combining these approaches in a modular agent based fashion. A-Teams are also open to the addi- tion of new agents. Modifications in the task requirements trans- late to modifications in the agent mix. In this paper we describe how modular A-Team based optimization can be used to solve 3 dimensional spatial layout problems. }, url = {http://www-2.cs.cmu.edu/afs/cs.cmu.edu/user/cjp/www/pubs/DETC98.pdf}, author = {Sachdev,S. and Paredis,C. J. J. and Gupta,S.K. and Talukdar,S. N.} } @article {17005, title = {Buttons vs. menus: An exploratory study of pull-down menu selection as compared to button bars}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {Button bars are a relatively new interaction method intended to speedup application use as compared to pull-down menus. This exploratory study compares three command selection methods: pull-down menus, button bars, and user choice of pull-down menus or button bars. Effectiveness was measured in two ways: speed of selection and error rate. 15 participants performed 15 word processor related tasks. Results show that in frequently used functions, such as character attribute selection (bold, italic, u nderline, etc.), button bars are faster. There were no statistically significant differences in error rates between the three interaction methods. (Also cross-referenced as CAR-TR-764) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/428}, author = {Ellis,Jason and Tran,Chi and Ryoo,Jake and Shneiderman, Ben} } @inbook {13763, title = {Enhancing Automatic Acquisition of Thematic Structure in a Large-Scale Lexicon for Mandarin Chinese}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {41 - 50}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes a refinement to our procedure for porting lexical conceptual structure (LCS) into new languages. Specifically we describe a two-step process for creating candidate thematic grids for Mandarin Chinese verbs, using the English verb heading the VP in the subde_nitions to separate senses, and roughly parsing the verb complement structure to match thematic structure templates. We accomplished a substantial reduction in manual effort, without substantive loss. The procedure is part of a larger process of creating a usable lexicon for interlingual machine translation from a large on-line resource with both too much and too little information.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_4}, author = {Olsen,Mari and Dorr, Bonnie J and Thomas,Scott}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @article {16446, title = {Equal Time for Data on the Internet with WebSemantics}, journal = {Advances in Database Technology{\textemdash}EDBT{\textquoteright}98}, year = {1998}, month = {1998///}, pages = {87 - 87}, author = {Raschid,G. A.M.L and Tomasic,A.} } @article {16178, title = {Facilitating Network Data Exploration with Query Previews: A Study of User Performance and Preference}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {Current network data exploration systems which use command languages (e.g.SQL) or form fill-in interfaces fail to give users an indication of the distribution of data items. This leads many users to waste time posing queries which have zero-hit or mega-hit result sets. Query previewing is a novel visual approach for browsing huge networked information warehouses. 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. Our within-subjects empirical comparison studied 12 subjects using a form fill-in interface with and without query previews. We found statistically significant differences showing that query previews sped up performance 1.6 to 2.1 times and led to higher subjective satisfaction. (Also cross-referenced as UMIACS-98-14) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/488}, author = {Tanin,Egemen and Lotem,Amnon and Haddadin,Ihab and Shneiderman, Ben and Plaisant, Catherine and Slaughter,Laura} } @conference {18728, title = {Integrated design and rapid manufacturing over the Internet}, year = {1998}, month = {1998///}, abstract = {An Internet-based infrastructure is being developed inorder to provide designers with access to multiple layered- manufacturing services. The design domain being addressed is that of small mechanisms or electro-mechanical assemblies that would be used in robots or other mechatronic devices. The approach presented relies on the formalization of the data exchange interface between designers and manufacturers. The primary operatives in this system are Design Clients, Manufacturing Services and Process Brokers. The Design Client allows designers to submit completed designs for algorithmic decomposition, or alternately, to compose a design from primitives and library components that have been primed with some process-related information. During this early phase, the Manufacturing Service consists of a highly automated machine that can be used to build ceramic parts, and the associated software components for design decomposition, process planning and machine control. In later phases, multiple service providers will be made accessible. The Process Broker implements a number of supporting services including process selection and optimal part orientation. Future broker services will include manufacturability analysis, directory services and accreditation etc. Currently, this interface is being built and evaluated internally at Stanford and CMU. It will be made available for use by other selected universities in the near future. }, url = {http://cdr.stanford.edu/interface/publications/DETC98CIE-5519.pdf}, author = {Rajagopalan,S. and Pinilla,J. M. and Losleben,P. and Tian,Q. and Gupta,S.K.} } @article {14988, title = {Models and high-performance algorithms for global BRDF retrieval}, journal = {Computational Science Engineering, IEEE}, volume = {5}, year = {1998}, month = {1998/12//oct}, pages = {16 - 29}, abstract = {The authors describe three models for retrieving information related to the scattering of light on the Earth{\textquoteright}s surface. Using these models, they{\textquoteright}ve developed algorithms for the IBM SP2 that efficiently retrieve this information}, keywords = {algorithms;, BRDF, Earth, geomorphology;, geophysical, global, high-performance, IBM, information, light, machines;, models;, Parallel, processing;, reflectivity;, retrieval, retrieval;, scattering;, signal, SP2;, surface;}, isbn = {1070-9924}, doi = {10.1109/99.735892}, author = {Zengyan Zhang and Kalluri, SNV and JaJa, Joseph F. and Liang,Shunlin and Townshend,J.R.G.} } @inbook {13718, title = {A Thematic Hierarchy for Efficient Generation from Lexical-Conceptual Structure}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {333 - 343}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes an implemented algorithm for syntactic realization of a target-language sentence from an interlingual representation called Lexical Conceptual Structure (LCS). We provide a mapping between LCS thematic roles and Abstract Meaning Representation (AMR) relations; these relations serve as input to an off-the-shelf generator (Nitrogen). There are two contributions of this work: (1) the development of a thematic hierarchy that provides ordering information for realization of arguments in their surface positions; (2) the provision of a diagnostic tool for detecting inconsistencies in an existing online LCS-based lexicon that allows us to enhance principles for thematic-role assignment.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_30}, author = {Dorr, Bonnie J and Habash,Nizar and Traum,David}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @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} } @article {16175, title = {Understanding Transportation Management Systems Performance with a Simulation-Based Learning Environment}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/12/05/}, abstract = {We have developed a simulation-based learning environment to provide systemdesigners and operators with an appreciation of the impact of incidents on traffic delay. We used an application framework developed at the University of Maryland for constructing simulation-based learning environments called SimPLE (Simulated Processes in a Learning Environment). Environments developed with SimPLE use dynamic simulations and visualizations to represent realistic time-dependent behavior and are coupled with guidance material and other software aids that facilitate learning. The simulation allows learners to close freeway lanes and divert traffic to an arterial road. Users can see the effect of the detour on freeway and arterial delay. Users can then adjust signal timing interactively on a time space diagram and watch the effect of their adjustment on green band changes and on arterial delays and total delays. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/500}, author = {Plaisant, Catherine and Tarnoff,Phil and Saraf,Aditya and Rose,Anne} } @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} } @inbook {17027, title = {Comprehension and object recognition capabilities for presentations of simultaneous video key frame surrogates}, booktitle = {Research and Advanced Technology for Digital LibrariesResearch and Advanced Technology for Digital Libraries}, series = {Lecture Notes in Computer Science}, volume = {1324}, year = {1997}, month = {1997///}, pages = {41 - 54}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The demand for more efficient browsing of video data is expected to increase as greater access to this type of data becomes available. This experiment looked at one technique for displaying video data using key frame surrogates that are presented as a ldquoslide showrdquo. Subjects viewed key frames for between one and four video clips simultaneously. Following this presentation, the subjects performed object recognition and gist comprehension tasks in order to determine human thresholds for divided attention between these multiple displays. It was our belief that subject performance would degrade as the number of slide shows shown simultaneously increased. For object recognition and gist comprehension tasks, a decrease in performance between the one slide show display and the two, three or four slide show displays was found. In the case of two or three video presentations, performance is about the same, and there remains adequate object recognition abilities and comprehension of the video clips. Performance drops off to unacceptable levels when four slide shows are displayed at once.}, isbn = {978-3-540-63554-3}, url = {http://dx.doi.org/10.1007/BFb0026720}, author = {Slaughters,Laura and Shneiderman, Ben and Marchionini,Gary}, editor = {Peters,Carol and Thanos,Costantino} } @conference {17545, title = {A constant-factor approximation algorithm for packet routing, and balancing local vs. global criteria}, booktitle = {Proceedings of the twenty-ninth annual ACM symposium on Theory of computing}, series = {STOC {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {636 - 643}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {Approximation algorithms, covering integer programs, discrete ham-sandwich theorems, Linear programming, packet routing, randomized algorithms, Randomized rounding, rounding theorems}, isbn = {0-89791-888-6}, doi = {10.1145/258533.258658}, url = {http://doi.acm.org/10.1145/258533.258658}, author = {Srinivasan, Aravind and Teo,Chung-Piaw} } @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 {16297, title = {An experiment to assess the cost-benefits of code inspections in large scale software development}, journal = {IEEE Transactions on Software Engineering}, volume = {23}, year = {1997}, month = {1997/06//}, pages = {329 - 346}, abstract = {We conducted a long term experiment to compare the costs and benefits of several different software inspection methods. These methods were applied by professional developers to a commercial software product they were creating. Because the laboratory for this experiment was a live development effort, we took special care to minimize cost and risk to the project, while maximizing our ability to gather useful data. The article has several goals: (1) to describe the experiment{\textquoteright}s design and show how we used simulation techniques to optimize it; (2) to present our results and discuss their implications for both software practitioners and researchers; and (3) to discuss several new questions raised by our findings. For each inspection, we randomly assigned three independent variables: (1) the number of reviewers on each inspection team (1, 2, or 4); (2) the number of teams inspecting the code unit (1 or 2); and (3) the requirement that defects be repaired between the first and second team{\textquoteright}s inspections. The reviewers for each inspection were randomly selected without replacement from a pool of 11 experienced software developers. The dependent variables for each inspection included inspection interval (elapsed time), total effort, and the defect detection rate. Our results showed that these treatments did not significantly influence the defect detection effectiveness, but that certain combinations of changes dramatically increased the inspection interval}, keywords = {Analysis of variance, code inspection cost benefits, code unit, commercial software product, Computer Society, cost-benefit analysis, Costs, defect detection effectiveness, defect detection rate, Design optimization, experienced software developers, experiment design, independent variables, Inspection, inspection interval, inspection team, Laboratories, large scale software development, Large-scale systems, live development effort, long term experiment, professional aspects, professional developers, Programming, reviewers, simulation techniques, software cost estimation, software inspection methods, software practitioners, Software quality, Switches}, isbn = {0098-5589}, doi = {10.1109/32.601071}, author = {Porter, Adam and Siy,H. P and Toman,C. A and Votta,L. G.} } @article {15608, title = {Parallelizing and algorithm for visibility on polyhedral terrain}, journal = {International Journal of Computational Geometry and Applications}, volume = {7}, year = {1997}, month = {1997///}, pages = {75 - 84}, abstract = {The best known output-sensitive sequential algorithm for computing the viewshedon a polyhedral terrain from a given viewpoint was proposed by Katz, Overmars, and Sharir 10, and achieves time complexity O((k + n(n)) logn) where n and k are the input and output sizes respectively, and () is the inverse Ackermann{\textquoteright}s function. In this paper, we present a parallel algorithm that is based on the work mentioned above, and achieves O(log2 n) time complexity, with work complexity O((k +n(n)) logn) in a CREW PRAM model. This improves on previous parallel complexity while maintaining work e ciency with respect to the best sequential complexity known. }, author = {Teng,Y. A and Mount, Dave and Puppo,E. and Davis, Larry S.} } @article {13878, title = {Toward Compact Monotonically Compositional Interlingua Using Lexical Aspect}, year = {1997}, month = {1997/12//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We describe a theoretical investigation into the semantic space described by our interlingua (IL), which currently has 191 main verb classes divided into 434 subclasses. represented by 237 distinct Lexical Conceptual Structures (LCSs). Using the model of aspect in Olsen (1994b, 1997a) monotonic aspectual composition we have identified 71 aspectually basic subclasses that are associated with one or more of 68 aspectually non-basic classes via some lexical ("type-shifting") rule (Bresnan 1982, Pinker 1984, Levin and Rappaport Hovav 1995). This allows us to refine the IL and address certain computational and theoretical issues at the same time. From a linguistic viewpoint, the expected benefits include a refinement of the aspectual model in (Olsen :1994b, 1997a) (which provides necessary but not sufficient conditions for aspectual composition), and a refinement of the verb classifications in (Levin 1993); we also expect our approach to eventually produce a systematic definition (in terms of LCSs and compositional operations) of the precise meaning components responsible for Levin{\textquoteright}s classification. Computationally, the lexicon is made more compact.}, keywords = {*LEXICOGRAPHY, *SEMANTICS, COMPOSITION(PROPERTY), linguistics, MODELS, STRUCTURES, THEORY, Vocabulary}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458248}, author = {Dorr, Bonnie J and Olsen,Mari B and Thomas,Scott C} } @article {14967, title = {Fast algorithms for removing atmospheric effects from satellite images}, journal = {Computational Science Engineering, IEEE}, volume = {3}, year = {1996}, month = {1996///summer}, pages = {66 - 77}, abstract = {The varied features of the earth{\textquoteright}s surface each reflect sunlight and other wavelengths of solar radiation in a highly specific way. This principle provides the foundation for the science of satellite based remote sensing. A vexing problem confronting remote sensing researchers, however, is that the reflected radiation observed from remote locations is significantly contaminated by atmospheric particles. These aerosols and molecules scatter and absorb the solar photons reflected by the surface in such a way that only part of the surface radiation can be detected by a sensor. The article discusses the removal of atmospheric effects due to scattering and absorption, ie., atmospheric correction. Atmospheric correction algorithms basically consist of two major steps. First, the optical characteristics of the atmosphere are estimated. Various quantities related to the atmospheric correction can then be computed by radiative transfer algorithms, given the atmospheric optical properties. Second, the remotely sensed imagery is corrected by inversion procedures that derive the surface reflectance. We focus on the second step, describing our work on improving the computational efficiency of the existing atmospheric correction algorithms. We discuss a known atmospheric correction algorithm and then introduce a substantially more efficient version which we have devised. We have also developed a parallel implementation of our algorithm}, keywords = {algorithms;reflectivity;remote, Atmospheric, based, computing;image, correction;atmospheric, effects;atmospheric, efficiency;inversion, enhancement;parallel, imagery;satellite, images;solar, implementation;reflected, particles;computational, photons;surface, procedures;parallel, radiation;atmospheric, radiation;remote, reflectance;atmospheric, remote, research;remotely, sensed, sensing, sensing;, sensing;satellite, techniques;geophysics}, isbn = {1070-9924}, doi = {10.1109/99.503316}, author = {Fallah-Adl,H. and JaJa, Joseph F. and Liang, S. and Townshend,J. and Kaufman,Y.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 {11922, title = {MARUTI at ARDEC.}, year = {1996}, month = {1996/07/11/}, institution = {University of Maryland, College Park}, abstract = {This is the final report of the effort undertaken at the University of Maryland, sponsored by DARPA under the DSSA (Domain Specific Software Architectures) program. The activities reported here required an active cooperation and collaboration of the US Army ARDEC (Automation and Robotics Laboratory) and the University of Maryland (Computer Science Department). The principal investigators have been developing a hard real time operating system, MARUTI, at the University of Maryland. The goal of this effort was to demonstrate the applicability and usefulness of this operating system for exercising PID control at high frequency on the ATB1000 testbed which has been used to simulate a gun turret. A MARUTI based PID controller which operates at 200 HZ and 400 HZ was successfully implemented to demonstrate this feasibility.}, keywords = {*OPERATING SYSTEMS(COMPUTERS), Computer architecture, COMPUTER PROGRAMMING AND SOFTWARE, CONTROL, Cooperation, DSSA(DOMAIN SPECIFIC SOFTWARE ARCHITECTURE), GUN TURRETS., HIGH FREQUENCY, Laboratories, REAL TIME, ROBOTICS, TEST BEDS}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA315086}, author = {Agrawala, Ashok K. and Tripathi,Satish K} } @conference {16474, title = {Scaling heterogeneous databases and the design of DISCO}, booktitle = {ICDCS}, year = {1996}, month = {1996///}, pages = {449 - 449}, author = {Tomasic,A. and Raschid, Louiqa and Valduriez,P.} } @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} } @article {15404, title = {Simulation of the logic switching characteristics of hot-carrier-degraded ultra-thin SOI CMOS inverters}, journal = {Solid-State Electronics}, volume = {39}, year = {1996}, month = {1996/11//}, pages = {1669 - 1674}, abstract = {The switching characteristics of ultra-thin SOI CMOS inverters with hot-carrier-induced degradations are examined by using device simulations. The simulator employs a robust fixed-point iteration method to avoid conventional matrix solutions. Potential-dependent interface traps and oxide trapped charges are used to model the degradations. The effects of front and back channel degradations in an nMOS device of a CMOS inverter are investigated in steady-state and transient regimes. The nonlinear variation of interface charges cannot be simulated by using a single nMOS device alone since the transition of the inverter is also determined by the pMOS transistor. It is found that the stagnant holes generated by impact ionization have a much greater effect on the rate of the pull-down transient than that of interface charges.}, isbn = {0038-1101}, doi = {10.1016/0038-1101(96)00073-1}, url = {http://www.sciencedirect.com/science/article/pii/0038110196000731}, author = {Tai,Gwo-Chung and Korman,Can E. and Mayergoyz, Issak D} } @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 {18378, title = {Complexity measure evaluation and selection}, journal = {Software Engineering, IEEE Transactions on}, volume = {21}, year = {1995}, month = {1995/08//}, pages = {641 - 650}, abstract = {A formal model of program complexity developed earlier by the authors is used to derive evaluation criteria for program complexity measures. This is then used to determine which measures are appropriate within a particular application domain. A set of rules for determining feasible measures for a particular application domain are given, and an evaluation model for choosing among alternative feasible measures is presented. This model is used to select measures from the classification trees produced by the empirically guided software development environment of R.W. Selby and A.A. Porter, and early experiments show it to be an effective process}, keywords = {alternative, complexity, criteria;evaluation, development, domain;classification, environment;evaluation, evaluation;empirically, evaluation;software, feasible, guided, measure, measures;application, measures;program, measures;software, metrics;software, model;feasible, performance, quality;software, selection;, software, trees;complexity}, isbn = {0098-5589}, doi = {10.1109/32.403788}, author = {Tian,J. and Zelkowitz, Marvin V} } @conference {14955, title = {Efficient Algorithms for Atmospheric Correction of Remotely Sensed Data}, booktitle = {Supercomputing, 1995. Proceedings of the IEEE/ACM SC95 Conference}, year = {1995}, month = {1995///}, pages = {12 - 12}, abstract = {Remotely sensed imagery has been used for developing and validating various studies regarding land cover dynamics. However, the large amounts of imagery collected by the satellites are largely contaminated by the effects of atmospheric particles. The objective of atmospheric correction is to retrieve the surface reflectance from remotely sensed imagery by removing the atmospheric effects. We introduce a number of computational techniques that lead to a substantial speedup of an atmospheric correction algorithm based on using look-up tables. Excluding I/O time, the previous known implementation processes one pixel at a time and requires about 2.63 seconds per pixel on a SPARC-10 machine, while our implementation is based on processing the whole image and takes about 4-20 microseconds per pixel on the same machine. We also develop a parallel version of our algorithm that is scalable in terms of both computation and I/O. Experimental results obtained show that a Thematic Mapper (TM) image (36 MB per band, 5 bands need to be corrected) can be handled in less than 4.3 minutes on a 32-node CM-5 machine, including I/O time.}, keywords = {Atmospheric, AVHRR;, computing;, correction;, high, I/O;, Parallel, performance, processing;, remote, scalable, sensing;, TM;}, doi = {10.1109/SUPERC.1995.242453}, author = {Fallah-Adl,H. and JaJa, Joseph F. and Liang,Shunlin and Kaufman,Y.J. and Townshend,J.} } @conference {14981, title = {Land cover dynamics investigation using parallel computers}, booktitle = {Geoscience and Remote Sensing Symposium, 1995. IGARSS {\textquoteright}95. {\textquoteright}Quantitative Remote Sensing for Science and Applications{\textquoteright}, International}, volume = {1}, year = {1995}, month = {1995//10/14}, pages = {332 -334 vol.1 - 332 -334 vol.1}, abstract = {A comprehensive and highly interdisciplinary research program is being carried out to investigate global land cover dynamics in heterogeneous parallel computing environments. Some of the problems are addressed including atmospheric correction, mixture modeling, image classifications by Markovian random fields and by segmentation, global image/map databases, object oriented parallel programming and parallel/IO. During the initial two years project, significant progress has been made in all of these areas}, keywords = {; geographic information system; geophysical measurement technique; geophysics computing; image classification; image map database; image segmentation; land cover dynamics; land surface; mixture modeling; object oriented programming; optical imaging; para, GIS; IR imaging; Markovian random fields; atmospheric correction}, doi = {10.1109/IGARSS.1995.520273}, author = {Liang, S. and Davis, Larry S. and Townshend,J. and Chellapa, Rama and DeFries, R. and Dubayah, R. and Goward,S. and JaJa, Joseph F. and Krishnamachar, S. and Roussopoulos, Nick and Saltz, J. and Samet, Hanan and Shock,T. and Srinivasan, M.} } @conference {16620, title = {A large-scale neural model linking local neuronal dynamics to positron emission tomography (PET) regional cerebral blood ffow (rCBF) data}, booktitle = {Soc Neurosci Abstr}, volume = {21}, year = {1995}, month = {1995///}, pages = {1988 - 1988}, author = {Tagamets,M. A and Horwitz,B. and Reggia, James A.} } @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 {17481, title = {Using Treemaps to Visualize the Analytic Hierarchy Process}, journal = {Information Systems ResearchInformation Systems Research}, volume = {6}, year = {1995}, month = {1995/12/01/}, pages = {357 - 375}, abstract = {Treemaps, a visualization method for large hierarchical data spaces, are used to augment the capabilities of the Analytic Hierarchy Process (AHP) for decision-making. Two direct manipulation tools, presented metaphorically as a {\textquotedblleft}pump{\textquotedblright} and a {\textquotedblleft}hook,{\textquotedblright} were developed and applied to the treemap to support AHP sensitivity analysis. Users can change the importance of criteria dynamically on the two-dimensional treemap and immediately see the impact on the outcome of the decision. This fluid process dramatically speeds up exploration and provides a better understanding of the relative impact of the component criteria. A usability study with six subjects using a prototype AHP application showed that treemap representation was acceptable from a visualization and data operation standpoint.}, keywords = {AHP, analytic hierarchy process, decision support, treemap, User interfaces, Visualization}, isbn = {1047-7047, 1526-5536}, doi = {10.1287/isre.6.4.357}, url = {http://isr.journal.informs.org/content/6/4/357}, author = {Asahi,Toshiyuki and Turo,David and Shneiderman, Ben} } @conference {17486, title = {Visual decision-making: using treemaps for the analytic hierarchy process}, booktitle = {Conference companion on Human factors in computing systems}, series = {CHI {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {405 - 406}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-755-3}, doi = {10.1145/223355.223747}, url = {http://doi.acm.org/10.1145/223355.223747}, author = {Asahi,Toshiyuki and Turo,David and Shneiderman, Ben} } @conference {17876, title = {High performance computing for land cover dynamics}, booktitle = {Pattern Recognition, 1994. Vol. 3-Conference C: Signal Processing, Proceedings of the 12th IAPR International Conference on}, year = {1994}, month = {1994///}, pages = {234 - 238}, author = {Parulekar,R. and Davis, Larry S. and Chellapa, Rama and Saltz, J. and Sussman, Alan and Townshend,J.} } @article {16623, title = {High-specificity neurological localization using a connectionist model}, journal = {Artificial Intelligence in Medicine}, volume = {6}, year = {1994}, month = {1994///}, pages = {521 - 532}, author = {Tuhrim,S. and Reggia, James A. and Peng,Y.} } @article {18401, title = {Measuring prime program complexity}, journal = {Information Sciences}, volume = {77}, year = {1994}, month = {1994/03//}, pages = {325 - 350}, abstract = {This paper uses the prime program decomposition of a program as the basis for a measure that closely correlates with our intuitive notion of program complexity. This measure is based upon the information theory ideas of randomness and entropy such that results about structured programming, data abstractions, and other programming paradigms can be stated in quantitative terms, and empirical means can be used to validate the assumptions used to develop the model. As a graph-based model, it can be applied to several graphical examples as extensions not otherwise available to source-code based models. This paper introduces the measure, derives several properties for it, and gives some simple examples to demonstrate that the measure is a plausible approximation of our notions concerning structured programming.}, isbn = {0020-0255}, doi = {10.1016/0020-0255(94)90007-8}, url = {http://www.sciencedirect.com/science/article/pii/0020025594900078}, author = {Zelkowitz, Marvin V and Tian,Jianhui} } @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} } @article {15374, title = {A parallel-in-time method for the transient simulation of SOI devices with drain current overshoots}, journal = {Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on}, volume = {13}, year = {1994}, month = {1994/08//}, pages = {1035 - 1044}, abstract = {This paper presents a new parallel-in-time algorithm for the two dimensional transient simulation of SOI devices. With this approach, simulation in both space and time domains is performed in parallel As a result, the CPU time is reduced significantly from the conventional serial-in-time method. This new approach fully exploits the inherent parallelism of the finite difference formulation of the basic semiconductor device equations and the massively parallel architecture of SIMD computers. The space domain computations are inherently parallel due to the nature of our technique of solving the finite-difference equations. Time domain parallelism is achieved by shifting the potentials from previous time points to subsequent points one-step forward along the time axis with each Gummel iteration. This algorithm employs a fixed-point iteration technique, therefore a direct solution of matrix equations is avoided. The algorithm is especially suitable for the transient simulation of SOI devices that exhibit transient drain current overshoot. Numerical experiments show that the new parallel-in-time method is up to eight times faster than the conventional serial-in-time method in SOI transient simulations. The program is coded in CM Fortran for the Connection Machine}, keywords = {2D, algorithms;semiconductor, analysis;transient, architecture;parallel-in-time, boundaries;silicon;time-domain, computations;time, computers;SOI, computing;finite, current, device, devices;drain, devices;parallel, difference, dimensional, domain, effect, engineering, equations;fixed-point, equations;space, field, Fortran;CPU, gate, iteration, iteration;SIMD, Machine;Gummel, method;semiconductor, methods;insulated, methods;metal-insulator-semiconductor, models;semiconductor-insulator, overshoots;finite-difference, Parallel, parallelism;transient, response;, simulation;CM, simulation;digital, simulation;electronic, simulation;two, technique;massively, time;Connection, transistors;iterative}, isbn = {0278-0070}, doi = {10.1109/43.298039}, author = {Tai,G.-C. and Korman,C.E. and Mayergoyz, Issak D} } @article {15405, title = {Simulation of the transient characteristics of partially- and fully-depleted SOI MOSFETs}, journal = {Solid-State Electronics}, volume = {37}, year = {1994}, month = {1994/07//}, pages = {1387 - 1394}, abstract = {We present a numerical technique which employs a local-in-time initial guess for the transient simulation of SOI MOSFETs. Specifically, the goal of this work is to compute the transient drain current which exhibits overshoot. A critical factor in such computations is the choice of the initial guess at each time point after the gate ramp. Our numerical simulations have shown that the use of the previous time point solution as an initial guess in the Gummel iterations fails to predict the decay in the drain current from its maximum overshoot value. This difficulty is circumvented when the steady-state solution is used as a local-in-time initial guess. We use the diagonally implicit Runge-Kutta method for the time domain discretization. A fixed-point iteration technique is employed for the space domain iterations. To demonstrate the usefulness of the local-in-time method, numerical results of the transient drain current for various device parameters, such as the silicon film doping, silicon film thickness and back-gate bias are presented.}, isbn = {0038-1101}, doi = {10.1016/0038-1101(94)90197-X}, url = {http://www.sciencedirect.com/science/article/pii/003811019490197X}, author = {Tai,Gwo-Chung and Korman,Can E. and Mayergoyz, Issak D} } @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} } @article {15210, title = {Approximation Algorithms for Graph Augmentation}, journal = {Journal of Algorithms}, volume = {14}, year = {1993}, month = {1993/03//}, pages = {214 - 225}, abstract = {The problem of increasing both edge and vertex connectivity of a graph at an optimal cost is studied. Since the general problem is NP-hard, we focus on efficient approximation schemes that come within a constant factor from the optima]. Previous algorithms either do not take edge costs into consideration, or they run slower than our algorithm. Our algorithm takes as input an undirected graph G0 = (V, E0) on n vertices, that is not necessarily connected, and a set Feasible of m weighted edges on V, and outputs a subset Aug of edges which when added to G0 make it two-connected. The weight of Aug, when G0 is initially connected, is no more than twice the weight of the least weight subset of edges of Feasible that increases the connectivity to two. The running time of our algorithm is O(m + n log n). As a consequence of our results, we can find an approximation to the least-weight two-connected spanning subgraph of a two-connected weighted graph.}, isbn = {0196-6774}, doi = {10.1006/jagm.1993.1010}, url = {http://www.sciencedirect.com/science/article/pii/S0196677483710102}, author = {Khuller, Samir and Thurimella,R.} } @article {16608, title = {A connectionist approach to diagnostic problem solving using causal networks}, journal = {Information sciences}, volume = {70}, year = {1993}, month = {1993///}, pages = {27 - 48}, author = {Reggia, James A. and Peng,Y. and Tuhrim,S.} } @conference {11926, title = {Multiple Resource Allocation for Multiprocessor Distributed Real-Time Systems}, booktitle = {In Workshop on Parallel and Distributed Real-Time Systems (PDRTS), IEEE IPPS{\textquoteright}93}, year = {1993}, month = {1993///}, abstract = {this report are those of the author(s) and should not be interpreted as representing the official policies, either expressed or implied, of the Defense Advanced Research Projects Agency, ONR, the U.S. Government or Honeywell. Computer facilities were provided in part by NSF grant CCR-8811954. Workshop on Parallel and Dist Real-Time Syst, IEEE IPPS{\textquoteright}93 April 1993 in the queue and tries to schedule it. If the task is successfully scheduled, it is removed from the queue and executed. Otherwise, the task is unlocked so that other processors may examine it in the same fashion. This scheme is convenient for a shared memory architecture, but becomes too expensive and cumbersome when such facility is not available in hardware (for example, in distributed systems). The goal of this paper is twofold: first, to study the problem of allocating multiple resources to a single task; and second, to provide a heuristic allocation policy for selecting a resource among multiple instances of identical resources. We consider a distributed system in which each site is a uniform memory access (UMA) multiprocessor, but the scheme is easily extensible to non-UMA models. For the first problem, a three-tiered resource allocation scheme is proposed. A hierarchy of the resources is defined to reduce the probability of allocation failure as the allocation progresses. To reduce the complexity of multiple resource allocation, we group the resources into schedulable sets of resources. Since the objective in real-time systems is to meet deadlines, this approach is acceptable so long as it meets a justifiable minimum level of resource utilization. It is shown that our approach allows modularity, flexibility, and potential concurrency in scheduling. Another contribution of this paper is in explicitly ide...}, author = {Mosse,Daniel and Noh,Sam H and Trinh,Bao and Agrawala, Ashok K.} } @article {18369, title = {An application of decision theory for the evaluation of software prototypes}, journal = {Journal of Systems and Software}, volume = {19}, year = {1992}, month = {1992///}, pages = {27 - 39}, author = {C{\'a}rdenas,S. R and Tian,J. and Zelkowitz, Marvin V} } @article {18360, title = {A formal program complexity model and its application}, journal = {Journal of Systems and Software}, volume = {17}, year = {1992}, month = {1992/03//}, pages = {253 - 266}, abstract = {This article takes an axiomatic approach to defining program complexity using complexity rankings and measures. A complexity ranking is an abstract, qualitative comparison between programs that is approximated by a complexity measure on each program. A set of axioms are stated and a classification scheme is presented with properties of each class. This is extended a series of properties developed by Weyuker. The formal model has many applications, including evaluating and classifying existing complexity measures and serving as criteria for complexity measure selection.}, isbn = {0164-1212}, doi = {10.1016/0164-1212(92)90114-Y}, url = {http://www.sciencedirect.com/science/article/pii/016412129290114Y}, author = {Tian,Jianhui and Zelkowitz, Marvin V} } @conference {18373, title = {An improved classification tree analysis of high cost modules based upon an axiomatic definition of complexity}, booktitle = {Software Reliability Engineering, 1992. Proceedings., Third International Symposium on}, year = {1992}, month = {1992/10//}, pages = {164 - 172}, abstract = {Identification of high cost modules has been viewed as one mechanism to improve overall system reliability, since such modules tend to produce more than their fair share of problems. A decision tree model has previously been used to identify such modules. In this paper, a previously developed axiomatic model of program complexity is merged with the previously developed decision tree process for an improvement in the ability to identify such modules. This improvement has been tested using data from the NASA Software Engineering Laboratory}, keywords = {(mathematics);, analysis;, axiomatic, classification, classification;, complexity;, computational, cost, decision, definition;, high, metrics;, model;, modules;, overall, program, reliability;, software, subroutines;, system, tree, TREES}, doi = {10.1109/ISSRE.1992.285848}, author = {Tian,Jianhui and Porter, Adam and Zelkowitz, Marvin V} } @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 {16534, title = {An experimental study of criteria for hypothesis plausibility}, journal = {Journal of Experimental \& Theoretical Artificial Intelligence}, volume = {3}, year = {1991}, month = {1991///}, pages = {129 - 144}, author = {Tuhrim,S. and Reggia, James A. and Goodall,S.} } @article {11950, title = {On the visual mathematics of tracking}, journal = {Image and vision computing}, volume = {9}, year = {1991}, month = {1991///}, pages = {235 - 251}, author = {Aloimonos, J. and Tsakiris, D. P} } @article {14791, title = {IPS-2: the second generation of a parallel program measurement system}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {1}, year = {1990}, month = {1990/04//}, pages = {206 - 217}, abstract = {IPS, a performance measurement system for parallel and distributed programs, is currently running on its second implementation. IPS{\textquoteright}s model of parallel programs uses knowledge about the semantics of a program{\textquoteright}s structure to provide two important features. First, IPS provides a large amount of performance data about the execution of a parallel program, and this information is organized so that access to it is easy and intuitive. Secondly, IPS provides performance analysis techniques that help to guide the programmer automatically to the location of program bottlenecks. The first implementation of IPS was a testbed for the basic design concepts, providing experience with a hierarchical program and measurement model, interactive program analysis, and automatic guidance techniques. It was built on the Charlotte distributed operating system. The second implementation, IPS-2, extends the basic system with new instrumentation techniques, an interactive and graphical user interface, and new automatic guidance analysis techniques. This implementation runs on 4.3BSD UNIX systems, on the VAX, DECstation, Sun 4, and Sequent Symmetry multiprocessor}, keywords = {4.3BSD UNIX systems, automatic guidance techniques, Automatic testing, Charlotte distributed operating system, CPA, DECstation, design concepts, distributed programs, graphical user interface, Graphical user interfaces, Instruments, interactive program analysis, IPS-2, measurement, message systems, network operating systems, Operating systems, parallel program measurement system, parallel programming, parallel programs, Performance analysis, performance analysis techniques, performance evaluation, performance measurement system, Power system modeling, program bottlenecks, program diagnostics, Programming profession, semantics, Sequent Symmetry multiprocessor, shared-memory systems, software tools, Springs, Sun, Sun 4, Unix, VAX}, isbn = {1045-9219}, doi = {10.1109/71.80132}, author = {Miller, B. P and Clark, M. and Hollingsworth, Jeffrey K and Kierstead, S. and Lim,S. -S and Torzewski, T.} } @conference {11998, title = {TRACKING IN A COMPLEX VISUAL ENVIRONMENT}, booktitle = {Computer Vision-ECCV 90: First European Conference on Computer Vision. Antibes, France, April 23-27, 1990. Proceedings}, volume = {1}, year = {1990}, month = {1990///}, pages = {249 - 249}, author = {Tsakiris,J. Y.A.D.P} } @article {16585, title = {A data flow implementation of a competition-based connectionist model* 1}, journal = {Journal of Parallel and Distributed Computing}, volume = {6}, year = {1989}, month = {1989///}, pages = {704 - 714}, author = {Tagamets,M. A and Reggia, James A.} } @article {16521, title = {Generating plausible diagnostic hypotheses with self-processing causal networks}, journal = {Journal of Experimental \& Theoretical Artificial Intelligence}, volume = {1}, year = {1989}, month = {1989///}, pages = {91 - 112}, author = {Wald,J. and Farach,M. and Tagamets,M. and Reggia, James A.} } @conference {16382, title = {Incremental computation via function caching}, booktitle = {Proceedings of the 16th ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, year = {1989}, month = {1989///}, pages = {315 - 328}, author = {Pugh, William and Teitelbaum,T.} } @article {16527, title = {Expert system development: letting the domain specialist directly author knowledge bases}, journal = {Expert systems: the user interface}, year = {1988}, month = {1988///}, pages = {37 - 56}, author = {Tuhrim,S. and Reggia, James A. and Floor,M.} } @article {16370, title = {ALEX-an Alexical Programming Language}, volume = {TR87-835}, year = {1987}, month = {1987///}, institution = {Cornell University}, abstract = {ALEX is an experimental language for high-level parallel programming. It is a testbed for exploring various non-traditional ways of expressing algorithmic ideas, making extensive use of high-resolution color graphics. The language itself is not a programming language in the traditional sense, since there is no lexical syntax. This paper discusses the basic design of the ALEX user interface.}, url = {http://hdl.handle.net/1813/6675}, author = {Kozen,D. and Teitelbaum,T. and Chen,W. Z and Field,J. H and Pugh, William and Vander Zanden,B. T} } @article {18119, title = {An efficient parallel biconnectivity algorithm}, journal = {SIAM Journal on Computing}, volume = {14}, year = {1985}, month = {1985///}, pages = {862 - 862}, author = {Tarjan,R. E and Vishkin, Uzi} } @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.} } @article {17410, title = {The effect of scope delimiters on program comprehension}, journal = {Software: Practice and Experience}, volume = {13}, year = {1983}, month = {1983/09/01/}, pages = {817 - 824}, abstract = {Scope delimiters, such as BEGIN-END or DO-END, are used in many programming languages, but they can lengthen and clutter a program listing. This paper provides experimental evidence that ENDIF or ENDWHILE statement terminators make for easier to comprehend programs than BEGIN-END pairs surrounding compound statements.}, keywords = {Programming language design, Scope delimiters, Software psychology}, isbn = {1097-024X}, doi = {10.1002/spe.4380130908}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.4380130908/abstract}, author = {Sykes,Floyd and Tillman,Raymond T and Shneiderman, Ben} } @article {16959, title = {An architecture for automatic relational database sytem conversion}, journal = {ACM Trans. Database Syst.}, volume = {7}, year = {1982}, month = {1982/06//}, pages = {235 - 257}, abstract = {Changes in requirements for database systems necessitate schema restructuring, database translation, and application or query program conversion. An alternative to the lengthy manual revision process is proposed by offering a set of 15 transformations keyed to the relational model of data and the relational algebra. Motivations, examples, and detailed descriptions are provided.}, keywords = {automatic conversion, Database systems, relational model, transformations}, isbn = {0362-5915}, doi = {10.1145/319702.319724}, url = {http://doi.acm.org/10.1145/319702.319724}, author = {Shneiderman, Ben and Thomas,Glenn} } @conference {16981, title = {Automatic database system conversion: schema revision, data translation, and source-to-source program transformation}, booktitle = {Proceedings of the June 7-10, 1982, national computer conference}, series = {AFIPS {\textquoteright}82}, year = {1982}, month = {1982///}, pages = {579 - 587}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Changing data requirements present database administrators with a difficult problem: the revision of the schema, the translation of the stored database, and the conversion of the numerous application programs. This paper describes an automatic database system conversion facility which provides one approach for coping with this problem. The Pure Definition Language and the Pure Manipulation Language have been designed to facilitate the conversions specified in the Pure Transformation Language. Two conversions and their effect on retrievals are demonstrated.}, isbn = {0-88283-035-X}, doi = {10.1145/1500774.1500849}, url = {http://doi.acm.org/10.1145/1500774.1500849}, author = {Shneiderman, Ben and Thomas,Glenn} } @article {16980, title = {Automatic database system conversion: A transformation language approach to sub-schema implementation}, journal = {IEEE Computer Software and Applications Conference}, year = {1980}, month = {1980///}, pages = {80 - 88}, author = {Thomas,G. and Shneiderman, Ben} } @conference {17318, title = {Path expressions for complex queries and automatic database program conversion}, booktitle = {Proceedings of the sixth international conference on Very Large Data Bases - Volume 6}, series = {VLDB {\textquoteright}80}, year = {1980}, month = {1980///}, pages = {33 - 44}, publisher = {VLDB Endowment}, organization = {VLDB Endowment}, abstract = {Our efforts to develop an automatic database system conversion facility yielded a powerful, yet simple query language which was designed for ease of conversion. The path expression of this query language is a convenient and appealing notation for describing complex traversals with multiple boolean qualifications. This paper describes the path expression, shows how automatic conversions can be done, introduces the boolean functions as part of the basic path expression, offers four extensions (path macros, implied path, path replacement, and path optimization), and discusses some implementation issues.}, keywords = {data definition language, data manipulation language, Database conversion, Database systems, path expressions, program conversion, query languages, transformation language}, url = {http://dl.acm.org/citation.cfm?id=1286887.1286891}, author = {Shneiderman, Ben and Thomas,Glenn} } @conference {17051, title = {Database Program Conversion: A Framework For Research}, booktitle = {Fifth International Conference on Very Large Data Bases, 1979}, year = {1979}, month = {1979/10/03/5}, pages = {299 - 312}, publisher = {IEEE}, organization = {IEEE}, keywords = {Application software, Costs, Data conversion, Data structures, Databases, Delay, Prototypes, Technology planning, US Government, Writing}, doi = {10.1109/VLDB.1979.718145}, author = {Taylor,R. W and Fry,J. P and Shneiderman, Ben and Smith,D. C.P and Su,S. Y.W} } @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.} }