@article {19693, title = {Tree-based Label Dependency Topic Models}, journal = {cs.umd.edu}, year = {Submitted}, abstract = {Abstract Multi-labeled corpora, where each document is tagged with a set of labels, are ubiquitous. When the number of unique labels in the dataset is large, there are naturally some dependencies among the labels. In this paper, we propose TREELAD{\textemdash}a ...}, url = {http://www.cs.umd.edu/~vietan/2013_l2h.pdf}, author = {Nguyen, V A and Jordan Boyd-Graber and Chang, J and Resnik, P} } @article {20548, title = {Rapid, quantitative therapeutic screening for Alzheimer{\textquoteright}s enzymes enabled by optimal signal transduction with transistors}, journal = {The Analyst}, volume = {145}, year = {2020}, month = {Feb-04-2021}, pages = {2925 - 2936}, issn = {0003-2654}, doi = {10.1039/C9AN01804B}, url = {http://xlink.rsc.org/?DOI=C9AN01804Bhttp://pubs.rsc.org/en/content/articlepdf/2020/AN/C9AN01804Bhttp://pubs.rsc.org/en/content/articlepdf/2020/AN/C9AN01804B}, author = {Le, Son T. and Morris, Michelle A. and Cardone, Antonio and Guros, Nicholas B. and Klauda, Jeffery B. and Sperling, Brent A. and Richter, Curt A. and Pant, Harish C. and Balijepalli, Arvind} } @article {20449, title = {Quantum Capacitance-Limited MoS2 Biosensors Enable Remote Label-Free Enzyme Measurements}, journal = {Nanoscale}, year = {2019}, month = {Jan-01-2019}, issn = {2040-3364}, doi = {10.1039/C9NR03171E}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2019/NR/C9NR03171Ehttp://pubs.rsc.org/en/content/articlepdf/2019/NR/C9NR03171E}, author = {Le, Son T and Guros, Nicholas B and Bruce, Robert C and Cardone, Antonio and Amin, Niranjana D and Zhang, Siyuan and Klauda, Jeffery and Pant, Harish C and Richter, Curt A and Balijepalli, Arvind} } @article {20289, title = {Environmental and hydroclimatic factors influencing Vibrio populations in the estuarine zone of the Bengal delta}, journal = {Environmental Monitoring and Assessment}, year = {2018}, month = {Jan-10-2018}, abstract = {The objective of this study was to determine environmental parameters driving Vibrio populations in the estuarine zone of the Bengal delta. Spatio-temporal data were collected at river estuary, mangrove, beach, pond, and canal sites. Effects of salinity, tidal amplitude, and a cyclone and tsunami were included in the study. Vibrio population shifts were found to be correlated with tide-driven salinity and suspended particulate matter (SPM). Increased abundance of Vibrio spp. in surface water was observed after a cyclone, attributed to re-suspension of benthic particulate organic carbon (POC), and increased availability of chitin and dissolved organic carbon (DOC). Approximately a two log10 increase in the (p < 0.05) number of Vibrio spp. was observed in < 20 μm particulates, compared with microphytoplankton (20{\textendash}60 μm) and zooplankton > 60 μm fractions. Benthic and suspended sediment comprised a major reservoir of Vibrio spp. Results of microcosm experiments showed enhanced growth of vibrios was related to concentration of organic matter in SPM. It is concluded that SPM, POC, chitin, and salinity significantly influence abundance and distribution of vibrios in the Bengal delta estuarine zone. Keywords Vibrio Salinity Cyclone Tide Chitin Sediment dynamics }, issn = {0167-6369}, doi = {10.1007/s10661-018-6925-7}, url = {https://link.springer.com/article/10.1007\%2Fs10661-018-6925-7}, author = {Neogi, Sucharit and Rubin, Lara and Alam, Munirul and Harder, Jens and Yamasaki, Shinji and Rita R Colwell} } @article {20283, title = {A Metagenomic Approach to Evaluating Surface Water Quality in Haiti}, journal = {International Journal of Environmental Research and Public Health}, volume = {1542}, year = {2018}, month = {Jan-10-2018}, pages = {2211}, abstract = {The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30309013}, author = {Roy, Monika and Arnaud, Jean and Jasmin, Paul and Hamner, Steve and Hasan, Nur and Rita R Colwell and Ford, Timothy} } @article {20320, title = {Application of a paper based device containing a new culture medium to detect Vibrio cholerae in water samples collected in Haiti}, journal = {Journal of Microbiological Methods}, volume = {133}, year = {2017}, month = {Jan-02-2017}, pages = {23 - 31}, issn = {01677012}, doi = {10.1016/j.mimet.2016.12.014}, url = {https://www.sciencedirect.com/science/article/pii/S0167701216303578?via\%3Dihub}, author = {Briquaire, Romain and Rita R Colwell and Boncy, Jacques and Rossignol, Emmanuel and Dardy, Aline and Pandini, Isabelle and Villeval, Fran{\c c}ois and Machuron, Jean-Louis and Huq, Anwar and Rashed, Shah and Vandevelde, Thierry and Rozand, Christine} } @article {20314, title = {Beyond cost-effectiveness: Using systems analysis for infectious disease preparedness}, journal = {Vaccine}, volume = {35}, year = {2017}, month = {Jan-01-2017}, pages = {A46 - A49}, abstract = {Until the recent outbreaks, Ebola vaccines ranked low in decision makers{\textquoteright} priority lists based on cost-effectiveness analysis and (or) corporate profitability. Despite a relatively small number of Ebola-related cases and deaths (compared to other causes), Ebola vaccines suddenly leapt to highest priority among international health agencies and vaccine developers. Clearly, earlier cost-effectiveness analyses badly missed some factors affecting real world decisions. Multi-criteria systems analysis can improve evaluation and prioritization of vaccine development and also of many other health policy and investment decisions. Neither cost-effectiveness nor cost-benefit analysis can capture important aspects of problems such as Ebola or the emerging threat of Zika, especially issues of inequality and disparity{\textemdash}issues that dominate the planning of many global health and economic organizations. Cost-benefit analysis requires assumptions about the specific value of life{\textemdash}an idea objectionable to many analysts and policy makers. Additionally, standard cost-effectiveness calculations cannot generally capture effects on people uninfected with Ebola for example, but nevertheless affected through such factors as contagion, herd immunity, and fear of dread disease, reduction of travel and commerce, and even the hope of disease eradication. Using SMART Vaccines, we demonstrate how systems analysis can visibly include important {\textquotedblleft}other factors{\textquotedblright} and more usefully guide decision making and beneficially alter priority setting processes.}, issn = {0264410X}, doi = {10.1016/j.vaccine.2016.08.090}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0264410X16309501}, author = {Phelps, Charles and Madhavan, Guruprasad and Rappuoli, Rino and Rita R Colwell and Fineberg, Harvey} } @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 {20322, title = {Hydroclimatic sustainability assessment of changing climate on cholera in the Ganges-Brahmaputra basin}, journal = {Advances in Water Resources}, volume = {108}, year = {2017}, month = {Jan-10-2017}, pages = {332 - 344}, abstract = {The association of cholera and climate has been extensively documented. However, determining the effects of changing climate on the occurrence of disease remains a challenge. Bimodal peaks of cholera in Bengal Delta are hypothesized to be linked to asymmetric flow of the Ganges and Brahmaputra rivers. Spring cholera is related to intrusion of bacteria-laden coastal seawater during low flow seasons, while autumn cholera results from cross-contamination of water resources when high flows in the rivers cause massive inundation. Coarse resolution of General Circulation Model (GCM) output (usually at 100 {\textendash} 300 km)cannot be used to evaluate variability at the local scale(10{\textendash}20 km),hence the goal of this study was to develop a framework that could be used to understand impacts of climate change on occurrence of cholera. Instead of a traditional approach of downscaling precipitation, streamflow of the two rivers was directly linked to GCM outputs, achieving reasonable accuracy (R2 = 0.89 for the Ganges and R2 = 0.91 for the Brahmaputra)using machine learning algorithms (Support Vector Regression-Particle Swarm Optimization). Copula methods were used to determine probabilistic risks of cholera under several discharge conditions. Key results, using model outputs from ECHAM5, GFDL, andHadCM3for A1B and A2 scenarios, suggest that the combined low flow of the two rivers may increase in the future, with high flows increasing for first half of this century, decreasing thereafter. Spring and autumn cholera, assuming societal conditions remain constant e.g., at the current rate, may decrease. However significant shifts were noted in the magnitude of river discharge suggesting that cholera dynamics of the delta may well demonstrate an uncertain predictable pattern of occurrence over the next century.}, issn = {03091708}, doi = {10.1016/j.advwatres.2016.11.018}, url = {https://linkinghub.elsevier.com/retrieve/pii/S030917081630728X}, author = {Nasr-Azadani, Fariborz and Khan, Rakibul and Rahimikollu, Javad and Unnikrishnan, Avinash and Akanda, Ali and Alam, Munirul and Huq, Anwar and Jutla, Antarpreet and Rita R Colwell} } @article {20317, title = {Vibrio cholerae O1 with Reduced Susceptibility to Ciprofloxacin and Azithromycin Isolated from a Rural Coastal Area of Bangladesh}, journal = {Frontiers in Microbiology}, year = {2017}, month = {Sep-02-2018}, abstract = {Cholera outbreaks occur each year in the remote coastal areas of Bangladesh and epidemiological surveillance and routine monitoring of cholera in these areas is challenging. In this study, a total of 97 Vibrio cholerae O1 isolates from Mathbaria, Bangladesh, collected during 2010 and 2014 were analyzed for phenotypic and genotypic traits, including antimicrobial susceptibility. Of the 97 isolates, 95 possessed CTX-phage mediated genes, ctxA, ace, and zot, and two lacked the cholera toxin gene, ctxA. Also both CTX+ and CTX- V. cholerae O1 isolated in this study carried rtxC, tcpAET, and hlyA. The classical cholera toxin gene, ctxB1, was detected in 87 isolates, while eight had ctxB7. Of 95 CTX+ V. cholerae O1, 90 contained rstRET and 5 had rstRCL. All isolates, except two, contained SXT related integrase intSXT. Resistance to penicillin, streptomycin, nalidixic acid, sulfamethoxazole-trimethoprim, erythromycin, and tetracycline varied between the years of study period. Most importantly, 93\% of the V. cholerae O1 were multidrug resistant. Six different resistance profiles were observed, with resistance to streptomycin, nalidixic acid, tetracycline, and sulfamethoxazole-trimethoprim predominant every year. Ciprofloxacin and azithromycin MIC were 0.003{\textendash}0.75 and 0.19{\textendash}2.00 μg/ml, respectively, indicating reduced susceptibility to these antibiotics. Sixteen of the V. cholerae O1 isolates showed higher MIC for azithromycin (>=0.5 μg/ml) and were further examined for 10 macrolide resistance genes, erm(A), erm(B), erm(C), ere(A), ere(B), mph(A), mph(B), mph(D), mef(A), and msr(A) with none testing positive for the macrolide resistance genes.}, doi = {10.3389/fmicb.2017.00252}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.00252}, author = {Rashed, Shah M. and Hasan, Nur A. and Alam, Munirul and Sadique, Abdus and Sultana, Marzia and Hoq, Md. Mozammel and Sack, R. Bradley and Rita R Colwell and Huq, Anwar} } @article {20309, title = {The microbiomes of blowflies and houseflies as bacterial transmission reservoirs}, journal = {Scientific Reports}, year = {2017}, month = {Jan-12-2017}, abstract = {Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.}, doi = {10.1038/s41598-017-16353-x}, url = {http://www.nature.com/articles/s41598-017-16353-x}, author = {Junqueira, AC and Ratan, Aakrosh and Acerbi, Enzo and Drautz-Moses, Daniela I. and Premkrishnan, BNV and Costea, PI and Linz, Bodo and Purbojati, Rikky W. and Paulo, Daniel F. and Gaultier, Nicolas E. and Subramanian, Poorani and Hasan, Nur A. and Rita R Colwell and Bork, Peer and Azeredo-Espin, Ana Maria L. and Bryant, Donald A. and Schuster, Stephan C.} } @article {20328, title = {Are natural reservoirs important for cholera surveillance? The case of an outbreak in a Brazilian estuary}, journal = {Letters in Applied Microbiology}, year = {2016}, month = {Jan-09-2016}, pages = {183 - 188}, abstract = {Paranagu{\'a} Bay is one of the largest estuarine systems on the Southern Brazilian coast. The only recorded cholera outbreak in this region since the early 20th century occurred in 1999 and resulted in 467 cases and at least three reported deaths in a population of approx. 150 000 people. This short communication reports historical, unpublished data related to that outbreak. Water, zooplankton and bivalve samples were collected and evaluated using direct fluorescence assay to determine whether Vibrio cholerae serogroups O1 and O139 were present in the estuarine system at that time. Most of the water (83\%) and zooplankton samples (75\%) were positive for V. cholerae O1, while V. cholerae O139 was not detected. Shellfish (Mytella sp.) were also positive for V. cholerae O1. These results indicate that the estuary, including biological vectors such as copepods and bivalves, comprise an important reservoir of V. cholerae O1 and a probable waterborne pathway for the disease, in addition to contamination with untreated sewage. }, doi = {10.1111/lam.12614}, url = {https://onlinelibrary.wiley.com/doi/10.1111/lam.12614}, author = {Martinelli Filho, J.E. and Lopes, R.M. and Rivera, I.N.G. and Rita R Colwell} } @article {20329, title = {Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic}, journal = {Proceedings of the National Academy of Sciences}, year = {2016}, month = {Nov-08-2017}, pages = {E5062 - E5071}, abstract = {Climate change is having a dramatic impact on marine animal and plant communities but little is known of its influence on marine prokaryotes, which represent the largest living biomass in the world oceans and play a fundamental role in maintaining life on our planet. In this study, for the first time to our knowledge, experimental evidence is provided on the link between multidecadal climatic variability in the temperate North Atlantic and the presence and spread of an important group of marine prokaryotes, the vibrios, which are responsible for several infections in both humans and animals. Using archived formalin-preserved plankton samples collected by the Continuous Plankton Recorder survey over the past half-century (1958{\textendash}2011), we assessed retrospectively the relative abundance of vibrios, including human pathogens, in nine areas of the North Atlantic and North Sea and showed correlation with climate and plankton changes. Generalized additive models revealed that long-term increase in Vibrio abundance is promoted by increasing sea surface temperatures (up to \~{}1.5 {\textdegree}C over the past 54 y) and is positively correlated with the Northern Hemisphere Temperature (NHT) and Atlantic Multidecadal Oscillation (AMO) climatic indices (P < 0.001). Such increases are associated with an unprecedented occurrence of environmentally acquired Vibrio infections in the human population of Northern Europe and the Atlantic coast of the United States in recent years.}, issn = {0027-8424}, doi = {10.1073/pnas.1609157113}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1609157113}, author = {Vezzulli, Luigi and Grande, Chiara and Reid, Philip C. and {\'e}laou{\"e}t, Pierre and Edwards, Martin and {\"o}fle, Manfred G. and Brettar, Ingrid and Rita R Colwell and Pruzzo, Carla} } @article {20332, title = {Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1}, journal = {FEMS Microbiology Letters}, volume = {36389}, year = {2016}, month = {Nov-06-2017}, pages = {fnw116}, abstract = {Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10-6) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.}, doi = {10.1093/femsle/fnw116}, url = {https://academic.oup.com/femsle/article-lookup/doi/10.1093/femsle/fnw116}, author = {Rashid, Mahamud-ur and Almeida, Mathieu and Azman, Andrew S. and Lindsay, Brianna R. and Sack, David A. and Rita R Colwell and Huq, Anwar and Morris, J. Glenn and Alam, Munirul and Stine, O. Colin}, editor = {Winstanley, Craig} } @article {20325, title = {Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak}, journal = {BMC Microbiology}, year = {2016}, month = {Jan-12-2016}, doi = {10.1186/s12866-016-0894-1}, url = {http://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0894-1}, author = {Ottesen, Andrea and Ramachandran, Padmini and Reed, Elizabeth and White, James R. and Hasan, Nur and Subramanian, Poorani and Ryan, Gina and Jarvis, Karen and Grim, Christopher and Daquiqan, Ninalynn and Hanes, Darcy and Allard, Marc and Rita R Colwell and Brown, Eric and Chen, Yi} } @article {20331, title = {In Plain View: A Transparent Systems Approach for Enhancing Health Policy Decisions}, year = {2016}, month = {07/2016}, url = {https://www.nae.edu/19582/Bridge/155266/155393.aspx}, author = {Guru Madhavan and Charles E. Phelps and Rita R Colwell and Rino Rappuoli and Harvey V. Fineberg} } @article {20330, title = {IncA/C Conjugative Plasmids Mobilize a New Family of Multidrug Resistance Islands in Clinical Vibrio cholerae Non-O1/Non-O139 Isolates from Haiti}, journal = {mBio}, year = {2016}, month = {Jul-09-2016}, abstract = {Mobile genetic elements play a pivotal role in the adaptation of bacterial populations, allowing them to rapidly cope with hostile conditions, including the presence of antimicrobial compounds. IncA/C conjugative plasmids (ACPs) are efficient vehicles for dissemination of multidrug resistance genes in a broad range of pathogenic species of Enterobacteriaceae. ACPs have sporadically been reported in Vibrio cholerae, the infectious agent of the diarrheal disease cholera. The regulatory network that controls ACP mobility ultimately depends on the transcriptional activation of multiple ACP-borne operons by the master activator AcaCD. Beyond ACP conjugation, AcaCD has also recently been shown to activate the expression of genes located in the Salmonella genomic island 1 (SGI1). Here, we describe MGIVchHai6, a novel and unrelated mobilizable genomic island (MGI) integrated into the 3' end of trmE in chromosome I of V. cholerae HC-36A1, a non-O1/non-O139 multidrug-resistant clinical isolate recovered from Haiti in 2010. MGIVchHai6 contains a mercury resistance transposon and an integron In104-like multidrug resistance element similar to the one of SGI1. We show that MGIVchHai6 excises from the chromosome in an AcaCD-dependent manner and is mobilized by ACPs. Acquisition of MGIVchHai6 confers resistance to β-lactams, sulfamethoxazole, tetracycline, chloramphenicol, trimethoprim, and streptomycin/spectinomycin. In silico analyses revealed that MGIVchHai6-like elements are carried by several environmental and clinical V. cholerae strains recovered from the Indian subcontinent, as well as from North and South America, including all non-O1/non-O139 clinical isolates from Haiti.}, doi = {10.1128/mBio.00509-16}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00509-16}, author = {Carraro, Nicolas and Rivard, Nicolas and Ceccarelli, Daniela and Rita R Colwell and Burrus, Vincent} } @article {20321, title = {Modeling Sustainability: Population, Inequality, Consumption, and Bidirectional Coupling of the Earth and Human Systems}, journal = {National Science Review}, year = {2016}, month = {Nov-12-2016}, pages = {nww081}, abstract = {Over the last two centuries, the impact of the Human System has grown dramatically, becoming strongly dominant within the Earth System in many different ways. Consumption, inequality, and population have increased extremely fast, especially since about 1950, threatening to overwhelm the many critical functions and ecosystems of the Earth System. Changes in the Earth System, in turn, have important feedback effects on the Human System, with costly and potentially serious consequences. However, current models do not incorporate these critical feedbacks. We argue that in order to understand the dynamics of either system, Earth System Models must be coupled with Human System Models through bidirectional couplings representing the positive, negative, and delayed feedbacks that exist in the real systems. In particular, key Human System variables, such as demographics, inequality, economic growth, and migration, are not coupled with the Earth System but are instead driven by exogenous estimates, such as United Nations population projections. This makes current models likely to miss important feedbacks in the real Earth{\textendash}Human system, especially those that may result in unexpected or counterintuitive outcomes, and thus requiring different policy interventions from current models. The importance and imminence of sustainability challenges, the dominant role of the Human System in the Earth System, and the essential roles the Earth System plays for the Human System, all call for collaboration of natural scientists, social scientists, and engineers in multidisciplinary research and modeling to develop coupled Earth{\textendash}Human system models for devising effective science-based policies and measures to benefit current and future generations.}, issn = {2095-5138}, doi = {10.1093/nsr/nww081}, url = {https://academic.oup.com/nsr/article-lookup/doi/10.1093/nsr/nww081}, author = {Motesharrei, Safa and Rivas, Jorge and Kalnay, Eugenia and Asrar, Ghassem R. and Busalacchi, Antonio J. and Cahalan, Robert F. and Cane, Mark A. and Rita R Colwell and Feng, Kuishuang and Franklin, Rachel S. and Hubacek, Klaus and Miralles-Wilhelm, Fernando and Miyoshi, Takemasa and Ruth, Matthias and Sagdeev, Roald and Shirmohammadi, Adel and Shukla, Jagadish and Srebric, Jelena and Yakovenko, Victor M. and Zeng, Ning} } @article {20335, title = {Phylogenetic Diversity of Vibrio cholerae Associated with Endemic Cholera in Mexico from 1991 to 2008}, journal = {mBio}, volume = {7}, year = {2016}, month = {Apr-05-2016}, abstract = {An outbreak of cholera occurred in 1991 in Mexico, where it had not been reported for more than a century and is now endemic. Vibrio cholerae O1 prototype El Tor and classical strains coexist with altered El Tor strains (1991 to 1997). Nontoxigenic (CTX-) V. cholerae El Tor dominated toxigenic (CTX+) strains (2001 to 2003), but V. cholerae CTX+ variant El Tor was isolated during 2004 to 2008, outcompeting CTX- V. cholerae. Genomes of six Mexican V. cholerae O1 strains isolated during 1991 to 2008 were sequenced and compared with both contemporary and archived strains of V. cholerae. Three were CTX+ El Tor, two were CTX- El Tor, and the remaining strain was a CTX+ classical isolate. Whole-genome sequence analysis showed the six isolates belonged to five distinct phylogenetic clades. One CTX- isolate is ancestral to the 6th and 7th pandemic CTX+ V. cholerae isolates. The other CTX- isolate joined with CTX- non-O1/O139 isolates from Haiti and seroconverted O1 isolates from Brazil and Amazonia. One CTX+ isolate was phylogenetically placed with the sixth pandemic classical clade and the V. cholerae O395 classical reference strain. Two CTX+ El Tor isolates possessing intact Vibrio seventh pandemic island II (VSP-II) are related to hybrid El Tor isolates from Mozambique and Bangladesh. The third CTX+ El Tor isolate contained West African-South American (WASA) recombination in VSP-II and showed relatedness to isolates from Peru and Brazil. Except for one isolate, all Mexican isolates lack SXT/R391 integrative conjugative elements (ICEs) and sensitivity to selected antibiotics, with one isolate resistant to streptomycin. No isolates were related to contemporary isolates from Asia, Africa, or Haiti, indicating phylogenetic diversity.}, doi = {10.1128/mBio.02160-15}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.02160-15}, author = {Choi, Seon Y and Rashed, Shah M. and Hasan, Nur A. and Alam, Munirul and Islam, Tarequl and Sadique, Abdus and Johura, Fatema-Tuz and Eppinger, Mark and Ravel, Jacques and Huq, Anwar and Cravioto, Alejandro and Rita R Colwell} } @article {20333, title = {Strategic Planning in Population Health and Public Health Practice: A Call to Action for Higher Education}, journal = {The Milbank Quarterly}, volume = {94906033}, year = {2016}, month = {Jan-03-2016}, pages = {109 - 125}, abstract = {POLICY POINTS: Scarce resources, especially in population health and public health practice, underlie the importance of strategic planning. Public health agencies{\textquoteright} current planning and priority setting efforts are often narrow, at times opaque, and focused on single metrics such as cost-effectiveness. As demonstrated by SMART Vaccines, a decision support software system developed by the Institute of Medicine and the National Academy of Engineering, new approaches to strategic planning allow the formal incorporation of multiple stakeholder views and multicriteria decision making that surpass even those sophisticated cost-effectiveness analyses widely recommended and used for public health planning. Institutions of higher education can and should respond by building on modern strategic planning tools as they teach their students how to improve population health and public health practice. CONTEXT: Strategic planning in population health and public health practice often uses single indicators of success or, when using multiple indicators, provides no mechanism for coherently combining the assessments. Cost-effectiveness analysis, the most complex strategic planning tool commonly applied in public health, uses only a single metric to evaluate programmatic choices, even though other factors often influence actual decisions. METHODS: Our work employed a multicriteria systems analysis approach--specifically, multiattribute utility theory--to assist in strategic planning and priority setting in a particular area of health care (vaccines), thereby moving beyond the traditional cost-effectiveness analysis approach. FINDINGS: (1) Multicriteria systems analysis provides more flexibility, transparency, and clarity in decision support for public health issues compared with cost-effectiveness analysis. (2) More sophisticated systems-level analyses will become increasingly important to public health as disease burdens increase and the resources to deal with them become scarcer. CONCLUSIONS: The teaching of strategic planning in public health must be expanded in order to fill a void in the profession{\textquoteright}s planning capabilities. Public health training should actively incorporate model building, promote the interactive use of software tools, and explore planning approaches that transcend restrictive assumptions of cost-effectiveness analysis. The Strategic Multi-Attribute Ranking Tool for Vaccines (SMART Vaccines), which was recently developed by the Institute of Medicine and the National Academy of Engineering to help prioritize new vaccine development, is a working example of systems analysis as a basis for decision support.}, doi = {10.1111/1468-0009.12182}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941964/}, author = {Phelps, Charles and Madhavan, Guruprasad and Rappuoli, Rino and LEVIN, SCOTT and Shortlife, Edward and Rita R Colwell} } @article {20349, title = {Concordance and discordance of sequence survey methods for molecular epidemiology}, journal = {PeerJ}, year = {2015}, month = {Jan-01-2015}, pages = {e761}, abstract = {The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.}, doi = {10.7717/peerj.761}, url = {https://peerj.com/articles/761}, author = {Castro-Nallar, Eduardo and Hasan, Nur A. and Cebula, Thomas A. and Rita R Colwell and Robison, Richard A. and Johnson, W. Evan and Crandall, Keith A.} } @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 {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 {20345, title = {Molecular tools in understanding the evolution of Vibrio cholerae}, journal = {Frontiers in Microbiology}, year = {2015}, month = {Jun-10-2015}, abstract = {Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.}, doi = {10.3389/fmicb.2015.01040}, url = {http://journal.frontiersin.org/Article/10.3389/fmicb.2015.01040/abstract}, author = {Rahaman, Md. Habibur and Islam, Tarequl and Rita R Colwell and Alam, Munirul} } @article {20351, title = {Non-O1/Non-O139 Vibrio cholerae Carrying Multiple Virulence Factors and V. cholerae O1 in the Chesapeake Bay, Maryland}, journal = {Applied and Environmental Microbiology}, year = {2015}, month = {Mar-03-2016}, pages = {1909 - 1918}, abstract = {Non-O1/non-O139 Vibrio cholerae inhabits estuarine and coastal waters globally, but its clinical significance has not been sufficiently investigated, despite the fact that it has been associated with septicemia and gastroenteritis. The emergence of virulent non-O1/non-O139 V. cholerae is consistent with the recognition of new pathogenic variants worldwide. Oyster, sediment, and water samples were collected during a vibrio surveillance program carried out from 2009 to 2012 in the Chesapeake Bay, Maryland. V. cholerae O1 was detected by a direct fluorescent-antibody (DFA) assay but was not successfully cultured, whereas 395 isolates of non-O1/non-O139 V. cholerae were confirmed by multiplex PCR and serology. Only a few of the non-O1/non-O139 V. cholerae isolates were resistant to ampicillin and/or penicillin. Most of the isolates were sensitive to all antibiotics tested, and 77 to 90\% carried the El Tor variant hemolysin gene hlyA ET, the actin cross-linking repeats in toxin gene rtxA, the hemagglutinin protease gene hap, and the type 6 secretion system. About 19 to 21\% of the isolates carried the neuraminidase-encoding gene nanH and/or the heat-stable toxin (NAG-ST), and only 5\% contained a type 3 secretion system. None of the non-O1/non-O139 V. cholerae isolates contained Vibrio pathogenicity island-associated genes. However, ctxA, ace, or zot was present in nine isolates. Fifty-five different genotypes showed up to 12 virulence factors, independent of the source of isolation, and represent the first report of both antibiotic susceptibility and virulence associated with non-O1/non-O139 V. cholerae from the Chesapeake Bay. Since these results confirm the presence of potentially pathogenic non-O1/non-O139 V. cholerae, monitoring for total V. cholerae, regardless of serotype, should be done within the context of public health.}, issn = {0099-2240}, doi = {10.1128/AEM.03540-14}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.03540-14}, author = {Ceccarelli, Daniela and Chen, Arlene and Hasan, Nur A. and Rashed, Shah M. and Huq, Anwar and Rita R Colwell}, editor = {Elkins, C. A.} } @article {20338, title = {Nontoxigenic Vibrio cholerae Non-O1/O139 Isolate from a Case of Human Gastroenteritis in the U.S. Gulf Coast}, journal = {Journal of Clinical Microbiology}, year = {2015}, month = {Jun-01-2016}, pages = {9 - 14}, abstract = {An occurrence of Vibrio cholerae non-O1/O139 gastroenteritis in the U.S. Gulf Coast is reported here. Genomic analysis revealed that the isolate lacked known virulence factors associated with the clinical outcome of a V. cholerae infection but did contain putative genomic islands and other accessory virulence factors. Many of these factors are widespread among environmental strains of V. cholerae, suggesting that there might be additional virulence factors in non-O1/O139 V. cholerae yet to be determined. Phylogenetic analysis revealed that the isolate belonged to a phyletic lineage of environmental V. cholerae isolates associated with sporadic cases of gastroenteritis in the Western Hemisphere, suggesting a need to monitor non-O1/O139 V. cholerae in the interest of public health.}, issn = {0095-1137}, doi = {10.1128/JCM.02187-14}, url = {http://jcm.asm.org/lookup/doi/10.1128/JCM.02187-14}, author = {Hasan, Nur A. and Rezayat, Talayeh and Blatz, Peter J. and Choi, Seon Young and Griffitt, Kimberly J. and Rashed, Shah M. and Huq, Anwar and Conger, Nicholas G. and Rita R Colwell and Grimes, D. Jay}, editor = {Munson, E.} } @article {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 {20334, title = {Occurrence in Mexico, 1998{\textendash}2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage}, journal = {Proceedings of the National Academy of Sciences}, volume = {111}, year = {2014}, month = {Aug-07-2014}, pages = {9917 - 9922}, issn = {0027-8424}, doi = {10.1073/pnas.1323408111}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1323408111}, author = {Alam, Munirul and Rashed, Shah M and Mannan, Shahnewaj Bin and Islam, Tarequl and Lizarraga-Partida, Marcial L. and Delgado, Gabriela and Morales-Espinosa, Rosario and Mendez, Jose Luis and Navarro, Armando and Watanabe, Haruo and Ohnishi, Makoto and Hasan, Nur A. and Huq, Anwar and Sack, R. Bradley and Rita R Colwell and Cravioto, Alejandro} } @article {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} } @inbook {19629, title = {Adaptive and Concurrent Secure Computation from New Adaptive, Non-malleable Commitments}, booktitle = {Advances in Cryptology - ASIACRYPT 2013}, series = {Lecture Notes in Computer Science}, year = {2013}, month = {2013/01/01/}, pages = {316 - 336}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a unified approach for obtaining general secure computation that achieves adaptive-Universally Composable (UC)-security. Using our approach we essentially obtain all previous results on adaptive concurrent secure computation, both in relaxed models (e.g., quasi-polynomial time simulation), as well as trusted setup models (e.g., the CRS model, the imperfect CRS model). This provides conceptual simplicity and insight into what is required for adaptive and concurrent security, as well as yielding improvements to set-up assumptions and/or computational assumptions in known models. Additionally, we provide the first constructions of concurrent secure computation protocols that are adaptively secure in the timing model, and the non-uniform simulation model. As a corollary we also obtain the first adaptively secure multiparty computation protocol in the plain model that is secure under bounded-concurrency. Conceptually, our approach can be viewed as an adaptive analogue to the recent work of Lin, Pass and Venkitasubramaniam [STOC {\textquoteleft}09], who considered only non-adaptive adversaries. Their main insight was that the non-malleability requirement could be decoupled from the simulation requirement to achieve UC-security. A main conceptual contribution of this work is, quite surprisingly, that it is still the case even when considering adaptive security. A key element in our construction is a commitment scheme that satisfies a strong definition of non-malleability. Our new primitive of concurrent equivocal non-malleable commitments, intuitively, guarantees that even when a man-in-the-middle adversary observes concurrent equivocal commitments and decommitments, the binding property of the commitments continues to hold for commitments made by the adversary. This definition is stronger than previous ones, and may be of independent interest. Previous constructions that satisfy our definition have been constructed in setup models, but either require existence of stronger encryption schemes such as CCA-secure encryption or require independent {\textquotedblleft}trapdoors{\textquotedblright} provided by the setup for every pair of parties to ensure non-malleability. A main technical contribution of this work is to provide a construction that eliminates these requirements and requires only a single trapdoor.}, keywords = {Algorithm Analysis and Problem Complexity, Applications of Mathematics, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-642-42032-0, 978-3-642-42033-7}, url = {http://link.springer.com/chapter/10.1007/978-3-642-42033-7_17}, author = {Dana Dachman-Soled and Malkin, Tal and Raykova, Mariana and Venkitasubramaniam, Muthuramakrishnan}, editor = {Sako, Kazue and Sarkar, Palash} } @book {20379, title = {Current Topics in Microbiology and Immunology One Health: The Human-Animal-Environment Interfaces in Emerging Infectious Diseases The Human Environment Interface: Applying Ecosystem Concepts to Health}, volume = {365}, year = {2013}, pages = {83 - 100}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, address = {Berlin, Heidelberg}, isbn = {978-3-642-36888-2}, issn = {0070-217X}, doi = {10.1007/978-3-642-36889-9}, url = {http://link.springer.com/10.1007/978-3-642-36889-9}, author = {Preston, Nicholas D. and Daszak, Peter and Rita R Colwell}, editor = {Mackenzie, John S. and Jeggo, Martyn and Daszak, Peter and Richt, Juergen A.} } @article {20378, title = {Detection of Vibrio cholerae in environmental waters including drinking water reservoirs of Azerbaijan}, journal = {Environmental Microbiology Reports}, year = {2013}, month = {Jan-02-2013}, pages = {30 - 38}, doi = {10.1111/j.1758-2229.2012.00369.x }, url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2012.00369.x}, author = {Rashid, Ahmadov and Haley, Bradd J. and Rajabov, Mukhtar and Ahmadova, Sevinj and Gurbanov, Shair and Rita R Colwell and Huq, Anwar} } @article {19687, title = {Lexical and Hierarchical Topic Regression}, year = {2013}, month = {2013/00/01}, pages = {1106 - 1114}, abstract = {Abstract Inspired by a two-level theory that unifies agenda setting and ideological framing, we propose supervised hierarchical latent Dirichlet allocation (SHLDA) which jointly captures documents{\textquoteright} multi-level topic structure and their polar response variables. Our ...}, url = {http://papers.nips.cc/paper/5163-lexical-and-hierarchical-topic-regression}, author = {Nguyen, Viet-An and Jordan Boyd-Graber and Resnik, Philip} } @article {19686, title = {Modeling topic control to detect influence in conversations using nonparametric topic models}, journal = {Machine Learning}, year = {2013}, month = {2013/00/01}, pages = {1 - 41}, publisher = {Springer US}, abstract = {Abstract Identifying influential speakers in multi-party conversations has been the focus of research in communication, sociology, and psychology for decades. It has been long acknowledged qualitatively that controlling the topic of a conversation is a sign of ...}, doi = {10.1007/s10994-013-5417-9/fulltext.html}, url = {http://link.springer.com/article/10.1007/s10994-013-5417-9/fulltext.html}, author = {Nguyen, Viet-An and Jordan Boyd-Graber and Resnik, Philip and Cai, Deborah A and Midberry, Jennifer E and Wang, Yuanxin} } @article {19702, title = {Personal informatics in the wild: hacking habits for health \& happiness}, journal = {CHI {\textquoteright}13 Extended Abstracts on Human Factors in Computing Systems}, year = {2013}, month = {2013/00/27}, pages = {3179 - 3182}, publisher = {SIGCHI, ACM Special Interest Group on Computer-Human InteractionACM}, address = {New York, New York, USA}, abstract = {Abstract Personal informatics is a class of systems that help people collect personal information to improve self-knowledge. Improving self-knowledge can foster self-insight and promote positive behaviors, such as healthy living and energy conservation. The ...}, isbn = {9781450319522}, doi = {10.1145/2468356.2479641}, url = {http://dl.acm.org/citation.cfm?doid=2468356.2479641}, author = {Li, Ian and Jon Froehlich and Larsen, Jakob E and Grevet, Catherine and Ramirez, Ernesto} } @article {19716, title = {TIGRFAMs and Genome Properties in 2013.}, journal = {Nucleic Acids Res}, volume = {41}, year = {2013}, month = {2013 Jan}, pages = {D387-95}, abstract = {

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

}, keywords = {Databases, Protein, Genome, Archaeal, Genome, Bacterial, Genomics, Internet, Markov chains, Molecular Sequence Annotation, Proteins, sequence alignment}, issn = {1362-4962}, doi = {10.1093/nar/gks1234}, author = {Haft, Daniel H and Jeremy D Selengut and Richter, Roland A and Harkins, Derek and Basu, Malay K and Beck, Erin} } @article {13505, title = {Automatic Authentication of Banknotes}, journal = {IEEE Transactions on Information Forensics \& Security}, year = {2012}, month = {2012///}, abstract = {In this paper, we address the problem of the automatic authentication of paper currency. Indian banknotes are used to show how a system can be developed for discriminating counterfeit notes from genuine notes. Image processing and pattern recognition techniques are designed to carefully analyze embedded security features. Experiments conducted on forensic samples show that a high precision low cost machine can be developed to address this problem. The analysis of current security features{\textquoteright} ability to protect against counterfeiting also suggest topics that should be considered in designing future currency notes.}, author = {Roy,Ankush and Halder,Biswaiit and Garain,Utpal and David Doermann} } @article {12980, title = {BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics}, journal = {Systematic BiologySyst Biol}, volume = {61}, year = {2012}, month = {2012/01/01/}, pages = {170 - 173}, abstract = {Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.}, keywords = {Bayesian phylogenetics, gpu, maximum likelihood, parallel computing}, isbn = {1063-5157, 1076-836X}, doi = {10.1093/sysbio/syr100}, url = {http://sysbio.oxfordjournals.org/content/61/1/170}, author = {Ayres,Daniel L and Darling,Aaron and Zwickl,Derrick J and Beerli,Peter and Holder,Mark T and Lewis,Paul O and Huelsenbeck,John P and Ronquist,Fredrik and Swofford,David L and Cummings, Michael P. and Rambaut,Andrew and Suchard,Marc A} } @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} } @conference {19218, title = {The design and evaluation of prototype eco-feedback displays for fixture-level water usage data}, year = {2012}, month = {2012}, pages = {2367 - 2376}, publisher = {ACM}, organization = {ACM}, isbn = {145031015X}, author = {Jon Froehlich and Findlater,L. and Ostergren, M. and Ramanathan, S. and Peterson,J. and Wragg, I. and Larson,E. and Fu, F. and Bai, M. and Patel,S.} } @conference {14906, title = {Dynamic changes in motivation in collaborative citizen-science projects}, booktitle = {Proceedings of the ACM 2012 conference on Computer Supported Cooperative Work}, series = {CSCW {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {217 - 226}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online citizen science projects engage volunteers in collecting, analyzing, and curating scientific data. Existing projects have demonstrated the value of using volunteers to collect data, but few projects have reached the full collaborative potential of scientists and volunteers. Understanding the shared and unique motivations of these two groups can help designers establish the technical and social infrastructures needed to promote effective partnerships. We present findings from a study of the motivational factors affecting participation in ecological citizen science projects. We show that volunteers are motivated by a complex framework of factors that dynamically change throughout their cycle of work on scientific projects; this motivational framework is strongly affected by personal interests as well as external factors such as attribution and acknowledgment. Identifying the pivotal points of motivational shift and addressing them in the design of citizen-science systems will facilitate improved collaboration between scientists and volunteers.}, keywords = {citizen science, Collaboration, crowdsourcing, ecology, motivation, scientists, volunteers}, isbn = {978-1-4503-1086-4}, doi = {10.1145/2145204.2145238}, url = {http://doi.acm.org/10.1145/2145204.2145238}, author = {Rotman,Dana and Preece,Jenny and Hammock,Jen and Procita,Kezee and Hansen,Derek and Parr,Cynthia and Lewis,Darcy and Jacobs, David W.} } @conference {19599, title = {Dynamic Searchable Symmetric Encryption}, booktitle = {CCS {\textquoteright}12 Proceedings of the 2012 ACM Conference on Computer and Communications Security }, series = {CCS {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {965 - 976}, publisher = {ACM}, organization = {ACM}, abstract = {Searchable symmetric encryption (SSE) allows a client to encrypt its data in such a way that this data can still be searched. The most immediate application of SSE is to cloud storage, where it enables a client to securely outsource its data to an untrusted cloud provider without sacrificing the ability to search over it. SSE has been the focus of active research and a multitude of schemes that achieve various levels of security and efficiency have been proposed. Any practical SSE scheme, however, should (at a minimum) satisfy the following properties: sublinear search time, security against adaptive chosen-keyword attacks, compact indexes and the ability to add and delete files efficiently. Unfortunately, none of the previously-known SSE constructions achieve all these properties at the same time. This severely limits the practical value of SSE and decreases its chance of deployment in real-world cloud storage systems. To address this, we propose the first SSE scheme to satisfy all the properties outlined above. Our construction extends the inverted index approach (Curtmola et al., CCS 2006) in several non-trivial ways and introduces new techniques for the design of SSE. In addition, we implement our scheme and conduct a performance evaluation, showing that our approach is highly efficient and ready for deployment.}, keywords = {Cloud computing, cloud storage, searchable symmetric encryption}, isbn = {978-1-4503-1651-4}, url = {http://doi.acm.org/10.1145/2382196.2382298}, author = {Kamara, Seny and Charalampos Papamanthou and Roeder, Tom} } @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 {20374, title = {Genetic characteristics of drug-resistant Vibrio cholerae O1 causing endemic cholera in Dhaka, 2006-2011}, journal = {Journal of Medical Microbiology}, year = {2012}, month = {Jan-12-2012}, pages = {1736 - 1745}, abstract = {Vibrio cholerae O1 biotype El Tor (ET), causing the seventh cholera pandemic, was recently replaced in Bangladesh by an altered ET possessing ctxB of the Classical (CL) biotype, which caused the first six cholera pandemics. In the present study, V. cholerae O1 strains associated with endemic cholera in Dhaka between 2006 and 2011 were analysed for major phenotypic and genetic characteristics. Of 54 representative V. cholerae isolates tested, all were phenotypically ET and showed uniform resistance to trimethoprim/sulfamethoxazole (SXT) and furazolidone (FR). Resistance to tetracycline (TE) and erythromycin (E) showed temporal fluctuation, varying from year to year, while all isolates were susceptible to gentamicin (CN) and ciprofloxacin (CIP). Year-wise data revealed erythromycin resistance to be 33.3 \% in 2006 and 11 \% in 2011, while tetracycline resistance accounted for 33, 78, 0, 100 and 27 \% in 2006, 2007, 2008, 2009 and 2010, respectively; interestingly, all isolates tested were sensitive to TE in 2011, as observed in 2008. All V. cholerae isolates tested possessed genetic elements such as SXT, ctxAB, tcpA ET, rstR ET and rtxC; none had IntlI (Integron I). Double mismatch amplification mutation assay (DMAMA)-PCR followed by DNA sequencing and analysis of the ctxB gene revealed a point mutation at position 58 (C{\textrightarrow}A), which has resulted in an amino acid substitution from histidine (H) to asparagine (N) at position 20 (genotype 7) since 2008. Although the multi-resistant strains having tetracycline resistance showed minor genetic divergence, V. choleraestrains were clonal, as determined by a PFGE (NotI)-based dendrogram. This study shows 2008{\textendash}2010 to be the time of transition from ctxB genotype 1 to genotype 7 in V. cholerae ET causing endemic cholera in Dhaka, Bangladesh.}, issn = {0022-2615}, doi = {10.1099/jmm.0.049635-0}, url = {http://jmm.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.049635-0}, author = {Rashed, S. M. and Mannan, S. B. and Johura, F.-T. and Islam, M. T. and Sadique, A. and Watanabe, H. and Sack, R. B. and Huq, A. and Rita R Colwell and Cravioto, A. and Alam, M.} } @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 {19718, title = {Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.}, journal = {ISME J}, volume = {6}, year = {2012}, month = {2012 Jun}, pages = {1186-99}, abstract = {

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.

}, keywords = {Computational Biology, Gammaproteobacteria, Genome, Bacterial, Genomic Library, metagenomics, Oceans and Seas, Phylogeny, plankton, Rhodopsin, RNA, Ribosomal, 16S, Seawater}, issn = {1751-7370}, doi = {10.1038/ismej.2011.189}, author = {Dupont, Chris L and Rusch, Douglas B and Yooseph, Shibu and Lombardo, Mary-Jane and Richter, R Alexander and Valas, Ruben and Novotny, Mark and Yee-Greenbaum, Joyclyn and Jeremy D Selengut and Haft, Dan H and Halpern, Aaron L and Lasken, Roger S and Nealson, Kenneth and Friedman, Robert and Venter, J Craig} } @article {12419, title = {Grammatical structures for word-level sentiment detection}, journal = {North American Association of Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {Existing work in fine-grained sentiment anal- ysis focuses on sentences and phrases but ig- nores the contribution of individual words and their grammatical connections. This is because of a lack of both (1) annotated data at the word level and (2) algorithms that can leverage syn- tactic information in a principled way. We ad- dress the first need by annotating articles from the information technology business press via crowdsourcing to provide training and testing data. To address the second need, we propose a suffix-tree data structure to represent syntac- tic relationships between opinion targets and words in a sentence that are opinion-bearing. We show that a factor graph derived from this data structure acquires these relationships with a small number of word-level features. We demonstrate that our supervised model per- forms better than baselines that ignore syntac- tic features and constraints.}, author = {Jordan Boyd-Graber and Sayeed,Asad B. and Rusk,Bryan and Weinberg, Amy} } @article {19315, title = {A Hybrid System for Error Detection in Electronic Dictionaries}, number = {CASL-1308-2}, year = {2012}, abstract = {A progress report on CASL{\textquoteright}s research on error detection in electronic dictionaries, including a hybrid system, application and evaluation on a second dictionary and a graphical user interface. }, author = {Zajic, David and David Doermann and Bloodgood,Michael and Rodrigues,Paul and Ye,Peng and Zotkina,Elena} } @article {19129, title = {Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli}, journal = {Infection and immunity}, volume = {80}, year = {2012}, month = {2012}, pages = {2791 - 2801}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea, mainly in developing countries. Although there are 25 different ETEC adhesins described in strains affecting humans, between 15\% and 50\% of the clinical isolates from different geographical regions are negative for these adhesins, suggesting that additional unidentified adhesion determinants might be present. Here, we report the discovery of Coli Surface Antigen 23 (CS23), a novel adhesin expressed by an ETEC serogroup O4 strain (ETEC 1766a), which was negative for the previously known ETEC adhesins, albeit it has the ability to adhere to Caco-2 cells. CS23 is encoded by an 8.8-kb locus which contains 9 open reading frames (ORFs), 7 of them sharing significant identity with genes required for assembly of K88-related fimbriae. This gene locus, named aal (adhesion-associated locus), is required for the adhesion ability of ETEC 1766a and was able to confer this adhesive phenotype to a nonadherent E. coli HB101 strain. The CS23 major structural subunit, AalE, shares limited identity with known pilin proteins, and it is more closely related to the CS13 pilin protein CshE, carried by human ETEC strains. Our data indicate that CS23 is a new member of the diverse adhesin repertoire used by ETEC strains.}, author = {Del Canto, F. and Botkin, D.J. and Valenzuela, P. and Popov, V. and Ruiz-Perez, F. and Nataro, J.P. and Levine, M.M. and Stine, O.C. and Pop, Mihai and Torres, A.G. and others} } @article {19721, title = {InterPro in 2011: new developments in the family and domain prediction database.}, journal = {Nucleic Acids Res}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D306-12}, abstract = {

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

}, keywords = {Databases, Protein, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, software, Terminology as Topic, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkr948}, author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F and Rivoire, Catherine and Sangrador-Vegas, Amaia and Jeremy D Selengut and Sigrist, Christian J A and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D and Wu, Cathy H and Yeats, Corin and Yong, Siew-Yit} } @article {12854, title = {Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico}, journal = {Journal of Clinical Microbiology}, year = {2012}, month = {04/2012}, abstract = {Vibrio cholerae O1 Classical (CL) biotype caused the 5th and 6th, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the 7th pandemic in Asia in the 1970{\textquoteright}s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia, and it had never been reported from Latin America, V. cholerae CL and ET biotypes, including hybrid ET were found associated with endemic cholera in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from endemic cholera in Mexico, between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits, and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and bio-typing data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim/sulfamethoxazole, furazolidone, ampicillin, and gentamycin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all the CL biotype strains, although the Mexican strains differed with the Bangladeshi strains in 1-2 DNA bands. The difference may be subtle, but consistent, as confirmed by the sub-clustering patterns in the PFGE-based dendrogram, and can serve as regional signature, suggesting pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from that of Asia.}, isbn = {0095-1137, 1098-660X}, doi = {10.1128/JCM.00189-12}, url = {http://jcm.asm.org/content/early/2012/04/12/JCM.00189-12}, author = {Alam,Munirul and Islam,M. Tarequl and Rashed,Shah Manzur and Johura,Fatema-Tuz and Bhuiyan,Nurul A. and Delgado,Gabriela and Morales,Rosario and Mendez,Jose Luis and Navarro,Armando and Watanabe,Haruo and Hasan,Nur-A. and Rita R Colwell and Cravioto,Alejandro} } @article {20381, title = {Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios}, journal = {The ISME Journal}, volume = {6111114882511}, year = {2012}, month = {Jan-01-2012}, pages = {21 - 30}, abstract = {The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45\% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.}, issn = {1751-7362}, doi = {10.1038/ismej.2011.89}, url = {http://www.nature.com/articles/ismej201189}, author = {Vezzulli, Luigi and Brettar, Ingrid and Pezzati, Elisabetta and Reid, Philip C and Rita R Colwell and H{\"o}fle, Manfred G and Pruzzo, Carla} } @conference {19170, title = {Making Recommendations in a Microblog to Improve the Impact of a Focal User}, booktitle = {6th ACM Conference on Recommender Systems (RecSys)}, year = {2012}, abstract = {We present a microblog recommendation system that can help monitor users, track conversations, and potentially improve diffusion impact. Given a Twitter network of active users and their followers, and historical activity of tweets, retweets and mentions, we build upon a prediction tool to predict the Top K users who will retweet or mention a focal user, in the future [10]. We develop personalized recommendations for each focal user. We identify characteristics of focal users such as the size of the follower network, or the level of sentiment averaged over all tweets; both have an impact on the quality of personalized recommendations. We use (high) betweenness centrality as a proxy of attractive users to target when making recommendations. Our recommendations successfully identify a greater fraction of users with higher betweenness centrality, in comparison to the overall distribution of betweenness centrality of the ground truth users for some focal user. }, author = {Wu,Shanchan and Gong, Leanna and Rand, William and Raschid, Louiqa} } @article {19275, title = {Mapping Parameterized Cyclo-static Dataflow Graphs onto Configurable Hardware}, journal = {Journal of Signal Processing Systems}, volume = {66}, year = {2012}, month = {2012}, pages = {285 - 301}, abstract = {In recent years, parameterized dataflow has evolved as a useful framework for modeling synchronous and cyclo-static graphs in which arbitrary parameters can be changed dynamically. Parameterized dataflow has proven to have significant expressive power for managing dynamics of DSP applications in important ways. However, efficient hardware synthesis techniques for parameterized dataflow representations are lacking. This paper addresses this void; specifically, the paper investigates efficient field programmable gate array (FPGA)-based implementation of parameterized cyclo-static dataflow (PCSDF) graphs. We develop a scheduling technique for throughput-constrained minimization of dataflow buffering requirements when mapping PCSDF representations of DSP applications onto FPGAs. The proposed scheduling technique is integrated with an existing formal schedule model, called the generalized schedule tree, to reduce schedule cost. To demonstrate our new, hardware-oriented PCSDF scheduling technique, we have designed a real-time base station emulator prototype based on a subset of long-term evolution (LTE), which is a key cellular standard.}, keywords = {4G communication systems, Circuits and Systems, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow modeling, Electrical Engineering, FPGA implementation, Image Processing and Computer Vision, Parameterized dataflow, pattern recognition, scheduling, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-011-0599-5}, author = {Kee, Hojin and Chung-Ching Shen and Bhattacharyya, Shuvra S. and Wong, Ian and Yong Rao and Kornerup, Jacob} } @article {19168, title = {Media, Aggregators and the Link Economy: Strategic Hyperlink Formation in Content Networks}, journal = {Management Science}, year = {2012}, abstract = {A key property of the World Wide Web is the possibility for firms to place virtually costless links to third-party content as a substitute or complement to their own content. This ability to hyperlink has enabled new types of players, such as search engines and content aggregators, to successfully enter content ecosystems, attracting traffic and revenues by hosting links to the content of others. This, in turn, has sparked a heated controversy between content producers and aggregators regarding the legitimacy and social costs/benefits of uninhibited free linking. This work is the first to model the implications of interrelated and strategic hyper-linking and content investments. Our results provide a nuanced view of the much-touted {\textquotedblleft}link economy,{\textquotedblright} highlighting both the beneficial consequences and the drawbacks of free hyperlinks for content producers and consumers. We show that content sites can reduce competition and improve profits by forming links to each other; in such networks one site makes high investments in content and other sites link to it. Interestingly, competitive dynamics often preclude the formation of link networks, even in settings where they would improve everyone{\textquoteright}s profits. Furthermore, such networks improve economic efficiency only when all members have similar abilities to produce content; otherwise the less capable nodes can free-ride on the content of the more capable nodes, reducing profits for the capable nodes as well as the average content quality available to consumers. Within these networks, aggregators have both positive and negative effects. By making it easier for consumers to access good quality content they increase the appeal of the entire content ecosystem relative to the alternatives. To the extent that this increases the total traffic flowing into the content ecosystem, aggregators can help increase the profits of the highest quality content sites. At the same time, however, the market entry of aggregators takes away some of the revenue that would otherwise go to content sites. Finally, by placing links to only a subset of available content, aggregators further increase competitive pressure on content sites. Interestingly, this can increase the likelihood that such sites will then attempt to alleviate the competitive pressure by forming link networks. }, author = {Dellarocas, Chris and Katona,Zsolt and Rand, William} } @conference {19318, title = {A Random Forest System Combination Approach for Error Detection in Digital Dictionaries}, booktitle = {Innovative hybrid approaches to the processing of textual data, EACL 2012 Workshop}, year = {2012}, month = {04/2012}, pages = {78-86}, abstract = {When digitizing a print bilingual dictionary, whether via optical character recognition or manual entry, it is inevitable that errors are introduced into the electronic version that is created. We investigate automating the process of detecting errors in an XML representation of a digitized print dictionary using a hybrid approach that combines rule-based, feature-based, and language model-based methods. We investigate combining methods and show that using random forests is a promising approach. We find that in isolation, unsupervised methods rival the performance of supervised methods. Random forests typically require training data so we investigate how we can apply random forests to combine individual base methods that are themselves unsupervised without requiring large amounts of training data. Experiments reveal empirically that a relatively small amount of data is sufficient and can potentially be further reduced through specific selection criteria. }, author = {Bloodgood,Michael and Ye,Peng and Rodrigues,Paul and Zajic, David and David Doermann} } @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 {20385, title = {Role of GbpA protein, an important virulence-related colonization factor, for Vibrio cholerae{\textquoteright}s survival in the aquatic environment}, journal = {Environmental Microbiology Reports}, year = {2012}, month = {Jan-08-2012}, pages = {439 - 445}, abstract = {Vibrio cholerae N-acetyl glucosamine-binding protein A (GbpA) is a chitin binding protein and a virulence factor involved in the colonization of human intestine. We investigated the distribution and genetic variations of gbpA in 488 V. cholerae strains of environmental and clinical origin, belonging to different serogroups and biotypes. We found that the gene is consistently present and highly conserved including an environmental V. cholerae-related strain of ancestral origin. The gene was also consistently expressed in a number of representative V. cholerae strains cultured in laboratory aquatic microcosms under conditions simulating those found in temperate marine environments. Functional analysis carried out on V. cholerae O1 El Tor N16961 showed that GbpA is not involved in adhesion to inorganic surfaces but promotes interaction with environmental biotic substrates (plankton and bivalve hepatopancreas cells) representing known marine reservoir or host for the bacterium. It is suggested that the ability of GbpA to colonize human intestinal cells most probably originated from its primary function in the aquatic environment.}, doi = {10.1111/j.1758-2229.2012.00356.x}, url = {http://doi.wiley.com/10.1111/j.1758-2229.2012.00356.x}, author = {Stauder, Monica and Huq, Anwar and Pezzati, Elisabetta and Grim, Christopher J. and Ramoino, Paola and Pane, Luigi and Rita R Colwell and Pruzzo, Carla and Vezzulli, Luigi} } @article {18712, title = {Rpn1 and Rpn2 coordinate ubiquitin processing factors at the proteasome}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, year = {2012}, month = {2012/02/08/}, abstract = {Substrates tagged with (poly)ubiquitin for degradation can be targeted directly to the 26S proteasome where they are proteolysed. Independently, ubiquitin-conjugates may also be delivered by bivalent shuttles. The majority of shuttles attach to the proteasome through a ubiquitin-like domain (UBL) while anchoring cargo at a C-terminal polyubiquitin-binding domain(s). We found that two shuttles of this class, Rad23 and Dsk2, dock at two different receptors embedded within a single subunit of the 19S proteasome regulatory particle (RP), Rpn1. Their association/dissociation constants and affinities for Rpn1 are similar. In contrast, another UBL-containing protein, the deubiquitinase Ubp6, is also anchored by Rpn1, yet dissociates slower, thus behaving as a sometimes proteasome subunit distinct from transiently-associated shuttles. Two neighboring subunits, Rpn10 and Rpn13, show a marked preference for polyubiquitin over UBLs. Rpn10 attaches to the central solenoid portion of Rpn1 although this association is stabilized by the presence of a third subunit, Rpn2. Rpn13 binds directly to the C-terminal portion of Rpn2. These intrinsic polyubiquitin receptors may compete with substrate shuttles for their polyubiquitin-conjugates, thereby aiding release of the emptied shuttles. By binding multiple ubiquitin-processing factors simultaneously, Rpn1 is uniquely suited to coordinate substrate recruitment, deubiquitination, and movement towards the catalytic core. The broad range of affinities for ubiquitin, ubiquitin-like, and non-ubiquitin signals by adjacent yet non-overlapping sites all within the Base illustrates a hub of activity that coordinates the intricate relay of substrates within the proteasome, and consequently influences substrate residency time and commitment to degradation.}, keywords = {deubiquitination, Proteasome, solenoid, Surface plasmon resonance (SPR), ubiquitin, Ubiquitin-dependent protease}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.M111.316323}, url = {http://www.jbc.org/content/early/2012/02/08/jbc.M111.316323}, author = {Rosenzweig,Rina and Bronner,Vered and Zhang,Daoning and Fushman, David and Glickman,Michael H.} } @article {15182, title = {Secure multi-party computation of boolean circuits with applications to privacy in on-line marketplaces}, journal = {Topics in Cryptology{\textendash}CT-RSA 2012}, year = {2012}, month = {2012///}, pages = {416 - 432}, abstract = {Protocols for generic secure multi-party computation (MPC) generally come in two forms: they either represent the function being computed as a boolean circuit, or as an arithmetic circuit over a large field. Either type of protocol can be used for any function, but the choice of which protocol to use can have a significant impact on efficiency. The magnitude of the effect, however, has never been quantified.With this in mind, we implement the MPC protocol of Goldreich, Micali, and Wigderson [13], which uses a boolean representation and is secure against a semi-honest adversary corrupting any number of parties. We then consider applications of secure MPC in on-line marketplaces, where customers select resources advertised by providers and it is desired to ensure privacy to the extent possible. Problems here are more naturally formulated in terms of boolean circuits, and we study the performance of our MPC implementation relative to existing ones that use an arithmetic-circuit representation. Our protocol easily handles tens of customers/providers and thousands of resources, and outperforms existing implementations including FairplayMP [3], VIFF [11], and SEPIA [7]. }, doi = {10.1007/978-3-642-27954-6_26}, author = {Choi,S. and Hwang,K.W. and Katz, Jonathan and Malkin,T. and Rubenstein,D.} } @article {12421, title = {SITS: A Hierarchical Nonparametric Model using Speaker Identity for Topic Segmentation in Multiparty Conversations}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {One of the key tasks for analyzing conversa- tional data is segmenting it into coherent topic segments. However, most models of topic segmentation ignore the social aspect of con- versations, focusing only on the words used. We introduce a hierarchical Bayesian nonpara- metric model, Speaker Identity for Topic Seg- mentation (SITS), that discovers (1) the top- ics used in a conversation, (2) how these top- ics are shared across conversations, (3) when these topics shift, and (4) a person-specific tendency to introduce new topics. We eval- uate against current unsupervised segmenta- tion models to show that including person- specific information improves segmentation performance on meeting corpora and on po- litical debates. Moreover, we provide evidence that SITS captures an individual{\textquoteright}s tendency to introduce new topics in political contexts, via analysis of the 2008 US presidential debates and the television program Crossfire.}, author = {Nguyen,Viet-An and Jordan Boyd-Graber and Resnik, Philip} } @article {12420, title = {Topic Models for Dynamic Translation Model Adaptation}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {We propose an approach that biases machine translation systems toward relevant transla- tions based on topic-specific contexts, where topics are induced in an unsupervised way using topic models; this can be thought of as inducing subcorpora for adaptation with- out any human annotation. We use these topic distributions to compute topic-dependent lex- ical weighting probabilities and directly in- corporate them into our translation model as features. Conditioning lexical probabilities on the topic biases translations toward topic- relevant output, resulting in significant im- provements of up to 1 BLEU and 3 TER on Chinese to English translation over a strong baseline.}, author = {Vladimir Eidelman and Jordan Boyd-Graber and Resnik, Philip} } @conference {19169, title = {When Does Simulated Data Match Real Data? Comparing Model Calibration Functions using Genetic Algorithms}, booktitle = {World Congress on Social Simulation (WCSS), Taipei, Taiwan}, year = {2012}, abstract = {Agent-based models can be manipulated to replicate real- world datasets, but choosing the best set of parameters to achieve this result can be difficult. To validate a model, the real-world dataset is often divided into a training and test set. The training set is used to calibrate the parameters and the test set is used to determine if the calibrated model represents the real-world data. The difference between the real-world data and the simulated data is determined using an error measure. When using an evolutionary computation technique to choose the parameters, this error measure becomes the fitness function, and choosing the appropriate measure becomes even more crucial for a successful calibration process. We survey the effect of five different error measures in the context of a toy problem and a real world problem (simulating on-line news consumption). We use each error measure in turn to calibrate on the training dataset, and then examine the results of all five error measures on both the training and testing datasets. For the toy problem, one measure was the Pareto-dominant choice for calibration, but no error measure dominated all the others for the real-world problem. }, author = {Stonedahl,Forrest and Rand, William} } @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 {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 {13071, title = {Action recognition using Partial Least Squares and Support Vector Machines}, booktitle = {Image Processing (ICIP), 2011 18th IEEE International Conference on}, year = {2011}, month = {2011/09//}, pages = {533 - 536}, abstract = {We introduce an action recognition approach based on Partial Least Squares (PLS) and Support Vector Machines (SVM). We extract very high dimensional feature vectors representing spatio-temporal properties of actions and use multiple PLS regressors to find relevant features that distinguish amongst action classes. Finally, we use a multi-class SVM to learn and classify those relevant features. We applied our approach to INRIA{\textquoteright}s IXMAS dataset. Experimental results show that our method is superior to other methods applied to the IXMAS dataset.}, keywords = {analysis;support, approach;multiclass, approximations;regression, dataset;action, dimensional, extraction;feature, extraction;image, feature, high, INRIA, IXMAS, least, machines;, machines;very, partial, properties;support, recognition, recognition;least, regressors;spatiotemporal, squares, SVM;multiple, vector, vectors}, doi = {10.1109/ICIP.2011.6116399}, author = {Ramadan,S. and Davis, Larry S.} } @conference {16042, title = {Active progress bars: facilitating the switch to temporary activities}, 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 = {1963 - 1968}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we seek to find a better way of effective task management when a progress bar interrupts user{\textquoteright}s primary activity. We propose to augment progress bars with user controlled functionalities facilitating the switch to temporary activities. We detail a taxonomy of waiting period contexts and possible temporary tasks, then report on 5 participatory design, and a follow-up survey of 96 respondents. Finally we describe an early prototype of active progress bars, and report on initial use.}, keywords = {Frustration, participatory design, progress bars, task switching}, isbn = {978-1-4503-0268-5}, doi = {10.1145/1979742.1979883}, url = {http://doi.acm.org/10.1145/1979742.1979883}, author = {Hurter,Christophe and Girouard,Audrey and Riche,Nathalie and Plaisant, Catherine} } @article {16400, title = {Agent-based modeling in marketing: Guidelines for rigor}, journal = {International Journal of Research in Marketing}, volume = {28}, year = {2011}, month = {2011/09//}, pages = {181 - 193}, abstract = {Agent-based modeling can illuminate how complex marketing phenomena emerge from simple decision rules. Marketing phenomena that are too complex for conventional analytical or empirical approaches can often be modeled using this approach. Agent-based modeling investigates aggregate phenomena by simulating the behavior of individual {\textquotedblleft}agents,{\textquotedblright} such as consumers or organizations. Some useful examples of agent-based modeling have been published in marketing journals, but widespread acceptance of the agent-based modeling method and publication of this method in the highest-level marketing journals have been slowed by the lack of widely accepted standards of how to do agent-based modeling rigorously. We address this need by proposing guidelines for rigorous agent-based modeling. We demonstrate these guidelines, and the value of agent-based modeling for marketing research, through the use of an example. We use an agent-based modeling approach to replicate the Bass model of the diffusion of innovations, illustrating the use of the proposed guidelines to ensure the rigor of the analysis. We also show how extensions of the Bass model that would be difficult to carry out using traditional marketing research techniques are possible to implement using a rigorous agent-based approach.}, isbn = {0167-8116}, doi = {10.1016/j.ijresmar.2011.04.002}, url = {http://www.sciencedirect.com/science/article/pii/S0167811611000504}, author = {Rand, William and Rust,Roland T.} } @article {18547, title = {Architecting for innovation}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011///}, pages = {24 - 36}, abstract = {We argue that the biggest problem with the current Internet architecture is not a particular functional deficiency, but its inability to accommodate innovation. To address this problem we propose a minimal architectural "framework" in which comprehensive architectures can reside. The proposed Framework for Internet Innovation (FII) --- which is derived from the simple observation that network interfaces should be extensible and abstract --- allows for a diversity of architectures to coexist, communicate, and evolve. We demonstrate FII{\textquoteright}s ability to accommodate diversity and evolution with a detailed examination of how information flows through the architecture and with a skeleton implementation of the relevant interfaces.}, keywords = {diversity, Evolution, innovation, internet architecture}, isbn = {0146-4833}, doi = {10.1145/2002250.2002256}, url = {http://doi.acm.org/10.1145/2002250.2002256}, author = {Koponen,Teemu and Shenker,Scott and Balakrishnan,Hari and Feamster, Nick and Ganichev,Igor and Ghodsi,Ali and Godfrey,P. Brighten and McKeown,Nick and Parulkar,Guru and Raghavan,Barath and Rexford,Jennifer and Arianfar,Somaya and Kuptsov,Dmitriy} } @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 {16247, title = {Bacillus Anthracis Comparative Genome Analysis in Support of the Amerithrax Investigation}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {108}, year = {2011}, month = {2011/03/22/}, pages = {5027 - 5032}, abstract = {Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on microbial genotyping schemes based on a small portion of a genome sequence. Amerithrax, the investigation into the anthrax letter attacks, applied high-resolution whole-genome sequencing and comparative genomics to identify key genetic features of the letters{\textquoteright} Bacillus anthracis Ames strain. During systematic microbiological analysis of the spore material from the letters, we identified a number of morphological variants based on phenotypic characteristics and the ability to sporulate. The genomes of these morphological variants were sequenced and compared with that of the B. anthracis Ames ancestor, the progenitor of all B. anthracis Ames strains. Through comparative genomics, we identified four distinct loci with verifiable genetic mutations. Three of the four mutations could be directly linked to sporulation pathways in B. anthracis and more specifically to the regulation of the phosphorylation state of Spo0F, a key regulatory protein in the initiation of the sporulation cascade, thus linking phenotype to genotype. None of these variant genotypes were identified in single-colony environmental B. anthracis Ames isolates associated with the investigation. These genotypes were identified only in B. anthracis morphotypes isolated from the letters, indicating that the variants were not prevalent in the environment, not even the environments associated with the investigation. This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.1016657108}, url = {http://www.pnas.org/content/108/12/5027}, author = {Rasko,David A and Worsham,Patricia L and Abshire,Terry G and Stanley,Scott T and Bannan,Jason D and Wilson,Mark R and Langham,Richard J and Decker,R. Scott and Jiang,Lingxia and Read,Timothy D. and Phillippy,Adam M and Salzberg,Steven L. and Pop, Mihai and Van Ert,Matthew N and Kenefic,Leo J and Keim,Paul S and Fraser-Liggett,Claire M and Ravel,Jacques} } @conference {12398, title = {Believe Me{\textemdash}We Can Do This! Annotating Persuasive Acts in Blog Text}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, author = {Anand,P. and King,J. and Jordan Boyd-Graber and Wagner,E. and Martell,C. and Oard, Douglas and Resnik, Philip} } @article {12984, title = {Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?}, journal = {Systematic BiologySyst Biol}, volume = {60}, year = {2011}, month = {2011/12/01/}, pages = {782 - 796}, abstract = {This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45\% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78{\textendash}85\% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A {\textquotedblleft}more-genes-only{\textquotedblright} data set (41 taxa{\texttimes}26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.}, keywords = {Ditrysia, gene sampling, Hexapoda, Lepidoptera, missing data, molecular phylogenetics, nuclear genes, taxon sampling}, isbn = {1063-5157, 1076-836X}, doi = {10.1093/sysbio/syr079}, url = {http://sysbio.oxfordjournals.org/content/60/6/782}, author = {Cho,Soowon and Zwick,Andreas and Regier,Jerome C and Mitter,Charles and Cummings, Michael P. and Yao,Jianxiu and Du,Zaile and Zhao,Hong and Kawahara,Akito Y and Weller,Susan and Davis,Donald R and Baixeras,Joaquin and Brown,John W and Parr,Cynthia} } @inbook {19628, title = {A Canonical Form for Testing Boolean Function Properties}, booktitle = {Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques}, series = {Lecture Notes in Computer Science}, year = {2011}, month = {2011/01/01/}, pages = {460 - 471}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {In a well-known result Goldreich and Trevisan (2003) showed that every testable graph property has a {\textquotedblleft}canonical{\textquotedblright} tester in which a set of vertices is selected at random and the edges queried are the complete graph over the selected vertices. We define a similar-in-spirit canonical form for Boolean function testing algorithms, and show that under some mild conditions property testers for Boolean functions can be transformed into this canonical form. Our first main result shows, roughly speaking, that every {\textquotedblleft}nice{\textquotedblright} family of Boolean functions that has low noise sensitivity and is testable by an {\textquotedblleft}independent tester,{\textquotedblright} has a canonical testing algorithm. Our second main result is similar but holds instead for families of Boolean functions that are closed under ID-negative minors. Taken together, these two results cover almost all of the constant-query Boolean function testing algorithms that we know of in the literature, and show that all of these testing algorithms can be automatically converted into a canonical form.}, keywords = {Algorithm Analysis and Problem Complexity, Boolean functions, Computation by Abstract Devices, Computer Communication Networks, Computer Graphics, Data structures, Discrete Mathematics in Computer Science, property testing}, isbn = {978-3-642-22934-3, 978-3-642-22935-0}, url = {http://link.springer.com/chapter/10.1007/978-3-642-22935-0_39}, author = {Dana Dachman-Soled and Servedio, Rocco A.}, editor = {Goldberg, Leslie Ann and Jansen, Klaus and Ravi, R. and Rolim, Jos{\'e} D. P.} } @article {12869, title = {Clonal transmission, dual peak, and off-season cholera in Bangladesh}, journal = {Infection Ecology \& Epidemiology}, volume = {1}, year = {2011}, month = {08/2011}, abstract = {Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March{\textendash}May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March{\textendash}May and September{\textendash}November) pattern in the city of Dhaka that is bordered by a heavily polluted freshwater river system and flood embankment. In August 2007, extreme flooding was accompanied by an unusually severe diarrhea outbreak in Dhaka that resulted in a record high illness. This study was aimed to understand the unusual outbreak and if it was related to the circulation of a new V. cholerae clone. Nineteen V. cholerae isolated during the peak of the 2007 outbreak were subjected to extensive phenotypic and molecular analyses, including multi-locus genetic screening by polymerase chain reaction (PCR), sequence-typing of the ctxB gene, and pulsed-field gel electrophoresis (PFGE). Factors associated with the unusual incidence of cholera were determined and analysis of the disease severity was done. Overall, microbiological and molecular data confirmed that the hypervirulent V. cholerae was O1 biotype El Tor (ET) that possessed cholera toxin (CT) of the classical biotype. The PFGE (NotI) and dendrogram clustering confirmed that the strains were clonal and related to the pre-2007 variant ET from Dhaka and Matlab and resembled one of two distinct clones of the variant ET confirmed to be present in the estuarine ecosystem of Bangladesh. Results of the analyses of both diarrheal case data for three consecutive years (2006{\textendash}2008) and regional hydroclimatology over three decades (1980{\textendash}2009) clearly indicate that the pattern of cholera occurring in Dhaka, and not seen at other endemic sites, was associated with flood waters transmitting the infectious clone circulating via the fecal-oral route during and between the dual seasonal cholera peaks in Dhaka. Circular river systems and flood embankment likely facilitate transmission of infectious V. cholerae throughout the year that leads to both sudden and off-season outbreaks in the densely populated urban ecosystem of Dhaka. Clonal recycling of hybrid El Tor with increasing virulence in a changing climate and in a region with a growing urban population represents a serious public health concern for Bangladesh.}, doi = {10.3402/iee.v1i0.7273}, author = {Alam,M. and Islam,A. and Bhuiyan,N. A. and Rahim,N. and Hossain,A. and Khan,G. Y. and Ahmed,D. and Watanabe,H. and Izumiya,H. and Faruque,A. S. G. and Rita R Colwell} } @conference {16407, title = {Comparing Social Tags to Microblogs}, booktitle = {Privacy, security, risk and trust (passat), 2011 IEEE third international conference on and 2011 IEEE third international conference on social computing (socialcom)}, year = {2011}, month = {2011/10//}, pages = {1380 - 1383}, abstract = {As Internet usage and e-commerce grow, online social media serve as popular outlets for consumers to express sentiments about products. On Amazon, users can tag an album with a keyword, while tweets on Twitter represent a more natural conversation. The differing natures of these media make them difficult to compare. This project collects and analyzes social media data for newly released music albums and develops new methods of comparing a product{\textquoteright}s social tags to its microblogging data. It explores information retrieval and rank correlation measures as similarity measures, as well as term frequency-inverse document frequency (tf-idf) processing. We conclude that with sufficient Twitter activity about an album, social tags do represent the most frequent conversations occurring on Twitter. These results imply that managers can collect and analyze tags and use them as a proxy for most common consumer feedback from microblogging, which is more difficult to collect.}, keywords = {(online);, album;online, commerce;information, correlation, document, frequency-inverse, frequency;electronic, Internet, measure;social, measures;similarity, media;rank, networking, retrieval;microblog;music, retrieval;music;social, social, tags;term, usage;Twitter;e-commerce;information}, doi = {10.1109/PASSAT/SocialCom.2011.52}, author = {Lai,V. and Rajashekar,C. and Rand, William} } @conference {13531, title = {Correcting Errors in Digital Lexicographic Resources Using a Dictionary Manipulation Language}, booktitle = {Electronic lexicography in the 21st century: new applications for new users (eLEX2011)}, year = {2011}, month = {2011///}, pages = {297 - 301}, abstract = {We describe a paradigm for combining manual and automatic error correction of noisy structured lexicographic data. Modifications to the structure and underlying text of the lexicographic data are expressed in a simple, interpreted programming language. Dictionary Manipulation Language (DML) commands identify nodes by unique identifiers, and manipulations are performed using simple commands such as create, move, set text, etc. Corrected lexicons are produced by applying sequences of DML commands to the source version of the lexicon. DML commands can be written manually to repair one-off errors or generated automatically to correct recurring problems. We discuss advantages of the paradigm for the task of editing digital bilingual dictionaries.}, author = {Zajic, David and Maxwell,Michael and David Doermann and Rodrigues,Paul and Bloodgood,Michael} } @conference {13535, title = {Detecting Structural Irregularity in Electronic Dictionaries Using Language Modeling}, booktitle = {Electronic lexicography in the 21st century: new applications for new users (eLEX2011)}, year = {2011}, month = {2011///}, pages = {227 - 232}, abstract = {Dictionaries are often developed using Extensible Markup Language (XML)-based standards. Very often, these standards allow many high-level repeating elements to represent lexical entries, and utilize descendants of these repeating elements to represent the structure within each lexical entry, in the form of an XML tree. In many cases, dictionaries are published that have errors and inconsistencies that would be too expensive to find manually. This paper discusses a method for dictionary writers to audit structural regularity across entries in a dictionary, quickly, by using statistical language modelling. The approach learns the patterns of XML nodes that could occur within an XML tree, and then calculates the probability of each XML tree in the dictionary against these patterns to look for entries that diverge from the norm.}, author = {Rodrigues,Paul and Zajic, David and Bloodgood,Michael and Ye,Peng and David Doermann} } @conference {14393, title = {Differential adaptive diffusion: Understanding diversity and learning whom to trust in viral marketing}, booktitle = {Fifth International AAAI Conference on Weblogs and Social Media}, year = {2011}, month = {2011///}, abstract = {Viral marketing mechanisms use the existing social network between customers to spread information about products and encourage product adoption. Existing viral marketing models focus on the dynamics of the diffusion process, however they typically: (a) only consider a single product campaign and (b) fail to model the evolution of the social network, as the trust between individuals changes over time, during the course of multiple campaigns. In this work, we propose an adaptive vi- ral marketing model which captures: (1) multiple different product campaigns, (2) the diversity in customer preferences among different product categories, and (3) changing con- fidence in peers{\textquoteright} recommendations over time. By applying our model to a real-world network extracted from the Digg social news website, we provide insights into the effects of network dynamics on the different products{\textquoteright} adoption. Our experiments show that our proposed model outperforms ear- lier non-adaptive diffusion models in predicting future prod- uct adoptions. We also show how this model can be used to explore new viral marketing strategies that are more success- ful than classic strategies which ignore the dynamic nature of social networks.}, author = {Sharara,H. and Rand, William and Getoor, Lise} } @article {19656, title = {Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization}, journal = {Nature Medicine}, volume = {17}, year = {2011}, month = {2011/09//}, pages = {1101 - 1108}, abstract = {Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin{\textendash}dependent epithelial traits and Sec23a-mediated tumor cell secretome.View full text }, isbn = {1078-8956}, url = {http://www.nature.com/nm/journal/v17/n9/abs/nm.2401.html}, author = {Korpal, Manav and Ell, Brian J. and Buffa, Francesca M. and Ibrahim, Toni and Blanco, Mario A. and Celi{\`a}-Terrassa, Toni and Mercatali, Laura and Zia Khan and Goodarzi, Hani and Hua, Yuling and Wei, Yong and Hu, Guohong and Garcia, Benjamin A. and Ragoussis, Jiannis and Amadori, Dino and Harris, Adrian L. and Kang, Yibin} } @article {14317, title = {Disaggregated End-Use Energy Sensing for the Smart Grid}, journal = {IEEE Pervasive Computing}, volume = {10}, year = {2011}, month = {2011/03//Jan}, pages = {28 - 39}, abstract = {This article surveys existing and emerging disaggregation techniques for energy-consumption data and highlights signal features that might be used to sense disaggregated data in an easily installed and cost-effective manner.}, keywords = {Calibration, disaggregated end-use energy sensing, Disaggregated energy sensing, disaggregation data techniques, Electricity, Energy consumption, Energy efficiency, energy-consumption data, Gas, Home appliances, Sensors, Smart grid, Smart grids, smart power grids, Sustainability, Water}, isbn = {1536-1268}, doi = {10.1109/MPRV.2010.74}, author = {Jon Froehlich and Larson,E. and Gupta,S. and Cohn,G. and Reynolds,M. and Patel,S.} } @inbook {12455, title = {Distributed Sensing and Processing for Multi-Camera Networks}, booktitle = {Distributed Video Sensor NetworksDistributed Video Sensor Networks}, year = {2011}, month = {2011///}, pages = {85 - 101}, publisher = {Springer London}, organization = {Springer London}, abstract = {Sensor networks with large numbers of cameras are becoming increasingly prevalent in a wide range of applications, including video conferencing, motion capture, surveillance, and clinical diagnostics. In this chapter, we identify some of the fundamental challenges in designing such systems: robust statistical inference, computationally efficiency, and opportunistic and parsimonious sensing. We show that the geometric constraints induced by the imaging process are extremely useful for identifying and designing optimal estimators for object detection and tracking tasks. We also derive pipelined and parallelized implementations of popular tools used for statistical inference in non-linear systems, of which multi-camera systems are examples. Finally, we highlight the use of the emerging theory of compressive sensing in reducing the amount of data sensed and communicated by a camera network.}, isbn = {978-0-85729-127-1}, url = {http://dx.doi.org/10.1007/978-0-85729-127-1_6}, author = {Sankaranarayanan,Aswin C. and Chellapa, Rama and Baraniuk,Richard G.}, editor = {Bhanu,Bir and Ravishankar,Chinya V. and Roy-Chowdhury,Amit K. and Aghajan,Hamid and Terzopoulos,Demetri} } @article {16495, title = {A Dual Framework and Algorithms for Targeted Online Data Delivery}, journal = {IEEE Transactions on Knowledge and Data Engineering}, volume = {23}, year = {2011}, month = {2011///}, pages = {5 - 21}, abstract = {A variety of emerging online data delivery applications challenge existing techniques for data delivery to human users, applications, or middleware that are accessing data from multiple autonomous servers. In this paper, we develop a framework for formalizing and comparing pull-based solutions and present dual optimization approaches. The first approach, most commonly used nowadays, maximizes user utility under the strict setting of meeting a priori constraints on the usage of system resources. We present an alternative and more flexible approach that maximizes user utility by satisfying all users. It does this while minimizing the usage of system resources. We discuss the benefits of this latter approach and develop an adaptive monitoring solution Satisfy User Profiles (SUPs). Through formal analysis, we identify sufficient optimality conditions for SUP. Using real (RSS feeds) and synthetic traces, we empirically analyze the behavior of SUP under varying conditions. Our experiments show that we can achieve a high degree of satisfaction of user utility when the estimations of SUP closely estimate the real event stream, and has the potential to save a significant amount of system resources. We further show that SUP can exploit feedback to improve user utility with only a moderate increase in resource utilization.}, keywords = {client/server multitier systems, distributed databases, online data delivery., online information services}, isbn = {1041-4347}, doi = {http://doi.ieeecomputersociety.org/10.1109/TKDE.2010.15}, author = {Roitman,Haggai and Gal,Avigdor and Raschid, Louiqa} } @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 {16431, title = {Estimating Functional Agent-Based Models: An Application to Bid Shading in Online Markets Format}, journal = {Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2011)}, year = {2011}, month = {2011///}, abstract = {Bid shading is a common strategy in online auctions to avoid the "winner{\textquoteright}s curse". While almost all bidders shade their bids, at least to some degree, it is impossible to infer the degree and volume of shaded bids directly from observed bidding data. In fact, most bidding data only allows us to observe the resulting price process, i.e. whether prices increase fast (due to little shading) or whether they slow down (when all bidders shade their bids). In this work, we propose an agent-based model that simulates bidders with different bidding strategies and their interaction with one another. We calibrate that model (and hence estimate properties about the propensity and degree of shaded bids) by matching the emerging simulated price process with that of the observed auction data using genetic algorithms. From a statistical point of view, this is challenging because we match functional draws from simulated and real price processes. We propose several competing fitness functions and explore how the choice alters the resulting ABM calibration. We apply our model to the context of eBay auctions for digital cameras and show that a balanced fitness function yields the best results.}, keywords = {Agent-based modeling, business, Calibration, Genetic algorithms, internet auctions, simulation}, url = {http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1846639}, author = {Guo,Wei and Jank,Wolfgang and Rand, William} } @article {19272, title = {Exploiting Statically Schedulable Regions in Dataflow Programs}, journal = {Journal of Signal Processing Systems}, volume = {63}, year = {2011}, month = {2011}, pages = {129 - 142}, abstract = {Dataflow descriptions have been used in a wide range of Digital Signal Processing (DSP) applications, such as multi-media processing, and wireless communications. Among various forms of dataflow modeling, Synchronous Dataflow (SDF) is geared towards static scheduling of computational modules, which improves system performance and predictability. However, many DSP applications do not fully conform to the restrictions of SDF modeling. More general dataflow models, such as CAL (Eker and Janneck 2003), have been developed to describe dynamically-structured DSP applications. Such generalized models can express dynamically changing functionality, but lose the powerful static scheduling capabilities provided by SDF. This paper focuses on the detection of SDF-like regions in dynamic dataflow descriptions{\textemdash}in particular, in the generalized specification framework of CAL. This is an important step for applying static scheduling techniques within a dynamic dataflow framework. Our techniques combine the advantages of different dataflow languages and tools, including CAL (Eker and Janneck 2003), DIF (Hsu et al. 2005) and CAL2C (Roquier et al. 2008). In addition to detecting SDF-like regions, we apply existing SDF scheduling techniques to exploit the static properties of these regions within enclosing dynamic dataflow models. Furthermore, we propose an optimized approach for mapping SDF-like regions onto parallel processing platforms such as multi-core processors.}, keywords = {Cal, Circuits and Systems, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow, DIF, Electrical Engineering, Image Processing and Computer Vision, multicore processors, pattern recognition, Quasi-static scheduling, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-009-0445-1}, author = {Gu, Ruirui and Janneck, J{\"o}rn W. and Raulet, Micka{\"e}l and Bhattacharyya, Shuvra S.} } @conference {13068, title = {Face verification using large feature sets and one shot similarity}, booktitle = {Biometrics (IJCB), 2011 International Joint Conference on}, year = {2011}, month = {2011/10//}, pages = {1 - 8}, abstract = {We present a method for face verification that combines Partial Least Squares (PLS) and the One-Shot similarity model[28]. First, a large feature set combining shape, texture and color information is used to describe a face. Then PLS is applied to reduce the dimensionality of the feature set with multi-channel feature weighting. This provides a discriminative facial descriptor. PLS regression is used to compute the similarity score of an image pair by One-Shot learning. Given two feature vector representing face images, the One-Shot algorithm learns discriminative models exclusively for the vectors being compared. A small set of unlabeled images, not containing images belonging to the people being compared, is used as a reference (negative) set. The approach is evaluated on the Labeled Face in the Wild (LFW) benchmark and shows very comparable results to the state-of-the-art methods (achieving 86.12\% classification accuracy) while maintaining simplicity and good generalization ability.}, keywords = {analysis;set, approximations;regression, descriptor;labeled, Face, feature, in, information;face, information;texture, least, LFW;PLS;PLS, recognition;least, regression;color, sets;one, shot, similarity;partial, squares, squares;shape, the, theory;, verification;facial, wild;large}, doi = {10.1109/IJCB.2011.6117498}, author = {Guo,Huimin and Robson Schwartz,W. and Davis, Larry S.} } @article {12454, title = {A Fast Bilinear Structure from Motion Algorithm Using a Video Sequence and Inertial Sensors}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {33}, year = {2011}, month = {2011/01//}, pages = {186 - 193}, abstract = {In this paper, we study the benefits of the availability of a specific form of additional information-the vertical direction (gravity) and the height of the camera, both of which can be conveniently measured using inertial sensors and a monocular video sequence for 3D urban modeling. We show that in the presence of this information, the SfM equations can be rewritten in a bilinear form. This allows us to derive a fast, robust, and scalable SfM algorithm for large scale applications. The SfM algorithm developed in this paper is experimentally demonstrated to have favorable properties compared to the sparse bundle adjustment algorithm. We provide experimental evidence indicating that the proposed algorithm converges in many cases to solutions with lower error than state-of-art implementations of bundle adjustment. We also demonstrate that for the case of large reconstruction problems, the proposed algorithm takes lesser time to reach its solution compared to bundle adjustment. We also present SfM results using our algorithm on the Google StreetView research data set.}, keywords = {3D urban modeling, algorithms, Artificial intelligence, CAMERAS, computer vision., Convergence, fast bilinear structure, Google StreetView research data set, Image Interpretation, Computer-Assisted, Image reconstruction, Image sensors, Image sequences, Imaging, Three-Dimensional, inertial sensors, Information Storage and Retrieval, Linear systems, minimization, MOTION, motion algorithm, Motion estimation, multiple view geometry, Pattern Recognition, Automated, Sensors, SfM equations, sparse bundle adjustment algorithm, structure from motion, Three dimensional displays, vertical direction, Video Recording, video sequence, video signal processing}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2010.163}, author = {Ramachandran, M. and Veeraraghavan,A. and Chellapa, Rama} } @conference {17175, title = {From slacktivism to activism: participatory culture in the age of social media}, 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 = {819 - 822}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Social networking sites (e.g. Facebook), microblogging services (e.g. Twitter), and content-sharing sites (e.g. YouTube and Flickr) have introduced the opportunity for wide-scale, online social participation. Visibility of national and international priorities such as public health, political unrest, disaster relief, and climate change has increased, yet we know little about the benefits - and possible costs - of engaging in social activism via social media. These powerful social issues introduce a need for scientific research into technology mediated social participation. What are the actual, tangible benefits of "greening" Twitter profile pictures in support of the Iranian elections? Does cartooning a Facebook profile picture really raise awareness of child abuse? Are there unintended negative effects through low-risk, low-cost technology-mediated participation? And, is there a difference - in both outcome and engagement level - between different types of online social activism? This SIG will investigate technology mediated social participation through a critical lens, discussing both the potential positive and negative outcomes of such participation. Approaches to designing for increased participation, evaluating effects of participation, and next steps in scientific research directions will be discussed.}, keywords = {activism, change, design, participation, slacktivism, social media}, isbn = {978-1-4503-0268-5}, doi = {10.1145/1979742.1979543}, url = {http://doi.acm.org/10.1145/1979742.1979543}, author = {Rotman,Dana and Vieweg,Sarah and Yardi,Sarita and Chi,Ed and Preece,Jenny and Shneiderman, Ben and Pirolli,Peter and Glaisyer,Tom} } @article {16433, title = {Future link prediction in the blogosphere for recommendation}, journal = {Proceedings of the International Conference on Weblogs and Social Media (ICWSM)}, year = {2011}, month = {2011///}, abstract = {The phenomenal growth in both scale and importance of so-cial media such as blogs, micro-blogs and user-generated content, has created a need for tools that monitor information diffusion and make recommendations within these platforms. An essential element of social media, particularly blogs, is the hyperlink graph that connects various pieces of content. There are two types of links within the blogosphere; one from blog post to blog post, and another from blog post to blog channel (an event stream of blog posts). These links can be viewed as a proxy for the flow of information between blog channels and to reflect influence. Given this assumption about links, the ability to predict future links can facilitate the monitoring of information diffusion, making recommen- dations, and word-of-mouth (WOM) marketing. We propose different methods for link predictions and we evaluate these methods on an extensive blog dataset. }, author = {Wu,S. and Raschid, Louiqa and Rand, William} } @conference {17181, title = {Group-in-a-Box Layout for Multi-faceted Analysis of Communities}, 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 = {354 - 361}, publisher = {IEEE}, organization = {IEEE}, abstract = {Communities in social networks emerge from interactions among individuals and can be analyzed through a combination of clustering and graph layout algorithms. These approaches result in 2D or 3D visualizations of clustered graphs, with groups of vertices representing individuals that form a community. However, in many instances the vertices have attributes that divide individuals into distinct categories such as gender, profession, geographic location, and similar. It is often important to investigate what categories of individuals comprise each community and vice-versa, how the community structures associate the individuals from the same category. Currently, there are no effective methods for analyzing both the community structure and the category-based partitions of social graphs. We propose Group-In-a-Box (GIB), a meta-layout for clustered graphs that enables multi-faceted analysis of networks. It uses the tree map space filling technique to display each graph cluster or category group within its own box, sized according to the number of vertices therein. GIB optimizes visualization of the network sub-graphs, providing a semantic substrate for category-based and cluster-based partitions of social graphs. We illustrate the application of GIB to multi-faceted analysis of real social networks and discuss desirable properties of GIB using synthetic datasets.}, keywords = {Algorithm design and analysis, category based social graph partitions, clustered graphs, clustering, Clustering algorithms, Communities, data visualisation, force-directed, gender, geographic location, graph layout algorithms, graph theory, group-in-a-box, group-in-a-box layout, Image edge detection, Layout, meta-layout, multifaceted community analysis, network subgraph visualization, network visualization, pattern clustering, profession, semantic substrates, Social network services, social networking (online), social networks, treemap space filling technique, Visualization}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.139}, author = {Rodrigues,E.M. and Milic-Frayling,N. and Smith,M. and Shneiderman, Ben and Hansen,D.} } @article {12866, title = {The Importance of Chitin in the Marine Environment}, journal = {Marine Biotechnology}, year = {2011}, month = {2011///}, pages = {1 - 8}, abstract = {Chitin is the most abundant renewable polymer in the oceans and is an important source of carbon and nitrogen for marine organisms. The process of chitin degradation is a key step in the cycling of nutrients in the oceans and chitinolytic bacteria play a significant role in this process. These bacteria are autochthonous to both marine and freshwater ecosystems and produce chitinases that degrade chitin, an insoluble polysaccharide, to a biologically useful form. In this brief review, a description of the structure of chitin and diversity of chitinolytic bacteria in the oceans is provided, in the context of the significance of chitin degradation for marine life.}, doi = {10.1007/s10126-011-9388-1}, author = {Souza,C. P. and Almeida,B. C. and Rita R Colwell and Rivera,I. N. G.} } @article {16043, title = {Improved Identification and Visualization of Emergency Department Patient Visits}, journal = {Annals of Emergency Medicine}, volume = {58}, year = {2011}, month = {2011///}, pages = {S309 - S309}, author = {Hettinger,AZ and Rackoff,A. and Wongsuphasawat,K. and Cheng,H. and Fairbanks,RJ and Plaisant, Catherine and Smith,M. S} } @article {13003, title = {Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae)}, journal = {BMC Evol Biol}, volume = {11:182}, year = {2011}, month = {2011///}, author = {Kawahara,A. Y and Ohshima,I and Kawakita,A and Regier,J. C and Mitter,C and Cummings, Michael P. and Davis,DR and Wagner,DL and De Prinis,J and Lopez-Vaamonde,C} } @article {13004, title = {Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera)}, journal = {Systematic Entomology}, volume = {36}, year = {2011}, month = {2011/01/01/}, pages = {31 - 43}, abstract = {This study has as its primary aim the robust resolution of higher-level relationships within the lepidopteran superfamily Bombycoidea. Our study builds on an earlier analysis of five genes (\~{}6.6 kbp) sequenced for 50 taxa from Bombycoidea and its sister group Lasiocampidae, plus representatives of other macrolepidoteran superfamilies. The earlier study failed to yield strong support for the monophyly of and basal splits within Bombycoidea, among others. Therefore, in an effort to increase support specifically for higher-level nodes, we generated 11.7 kbp of additional data from 20 genes for 24 of 50 bombycoid and lasiocampid taxa. The data from the genes are all derived from protein-coding nuclear genes previously used to resolve other lepidopteran relationships. With these additional data, all but a few higher-level nodes are strongly supported. Given our decision to minimize project costs by augmenting genes for only 24 of the 50 taxa, we explored whether the resulting pattern of missing data in the combined-gene matrix introduced a nonphylogenetic bias, a possibility reported by others. This was achieved by comparing node support values (i.e. nonparametric bootstrap values) based on likelihood and parsimony analyses of three datasets that differ in their number of taxa and level of missing data: 50 taxa/5 genes (dataset A), 50 taxa/25 genes (dataset B) and 24 taxa/25 genes (dataset C). Whereas datasets B and C provided similar results for common nodes, both frequently yielded higher node support relative to dataset A, arguing that: (i) more data yield increased node support and (ii) partial gene augmentation does not introduce an obvious nonphylogenetic bias. A comparison of single-gene bootstrap analyses identified four nodes for which one or two of the 25 genes provided modest to strong support for a grouping not recovered by the combined-gene result. As a summary proposal, two of these four groupings (one each within Bombycoidea and Lasiocampidae) were deemed sufficiently problematic to regard them as unresolved trichotomies. Since the alternative groupings were always highly localized on the tree, we did not judge a combined-gene analysis to present a problem outside those regions. Based on our robustly resolved results, we have revised the classification of Bombycoidea: the family Bombycidae is restricted to its nominate subfamily, and its tribe Epiini is elevated to subfamily rank (Epiinae stat.rev.), whereas the bombycid subfamily Phiditiinae is reinstated as a separate family (Phiditiidae stat.rev.). The bombycid subfamilies Oberthueriinae Kuznetzov \& Stekolnikov, 1985, syn.nov. and Prismostictinae Forbes, 1955, syn.nov., and the family Mirinidae Kozlov, 1985, syn.nov. are established as subjective junior synonyms of Endromidae Boisduval, 1828. The family Anthelidae (Lasiocampoidea) is reincluded in the superfamily Bombycoidea.}, isbn = {1365-3113}, doi = {10.1111/j.1365-3113.2010.00543.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3113.2010.00543.x/abstract;jsessionid=B5B1F8BF73034A4C41427FB1FBD7383F.d02t04}, author = {Zwick,Andreas and Regier,Jerome C and Mitter,Charles and Cummings, Michael P.} } @article {12865, title = {Vibrio Cholerae O1 Detection in Estuarine and Coastal Zooplankton}, journal = {Journal of Plankton Research}, volume = {33}, year = {2011}, month = {01/2011}, pages = {51 - 62}, abstract = {Vibrio cholerae is an autochthonous marine bacterium, and its association with diverse planktonic crustaceans has been extensively investigated; however, the presence of V. cholerae on individuals of most phyla of planktonic animals is still incompletely understood. The objective of this study was to analyze the distribution of V. cholerae serogroup O1 associated with specific zooplankton taxa in an estuary and the adjacent continental shelf of the southeastern Brazilian coast. The occurrence of the bacterium was assessed in zooplankton samples, specifically on the most abundant taxa, using direct fluorescence assay (DFA) and direct viable count{\textendash}direct fluorescence assay (DVC{\textendash}DFA) methods. Vibrio cholerae O1 was detected in 88\% of samples collected from the Santos-Bertioga estuary and in 67\% of samples from the shelf. The salinity of the estuarine water ranged from 21.8 to 34.6, significantly lower than the shelf water which was 32.1{\textendash}36.1. Salinity was the only environmental variable measured that displayed a significant correlation with the presence of V. cholerae (P< 0.05). Vibrio cholerae O1 was detected in chaetognaths, pluteus larvae of echinoderms and planktonic fish eggs (Engraulidae), all new sites for this bacterium.}, keywords = {DFA, estuary, plankton, Southwest Atlantic}, isbn = {0142-7873, 1464-3774}, doi = {10.1093/plankt/fbq093}, url = {http://plankt.oxfordjournals.org/content/33/1/51}, author = {Martinelli Filho,Jos{\'e} E. and Lopes,Rubens M. and Rivera,Irma N. G. and Rita R Colwell} } @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 {19035, title = {Link prediction by de-anonymization: How We Won the Kaggle Social Network Challenge}, year = {2011}, month = {2011}, pages = {1825 - 1834}, abstract = {This paper describes the winning entry to the IJCNN 2011 Social Network Challenge run by Kaggle.com. The goal of the contest was to promote research on real-world link prediction, and the dataset was a graph obtained by crawling the popular Flickr social photo sharing website, with user identities scrubbed. By de-anonymizing much of the competition test set using our own Flickr crawl, we were able to effectively game the competition. Our attack represents a new application of de-anonymization to gaming machine learning contests, suggesting changes in how future competitions should be run. We introduce a new simulated annealing-based weighted graph matching algorithm for the seeding step of de-anonymization. We also show how to combine de-anonymization with link prediction-the latter is required to achieve good performance on the portion of the test set not de-anonymized-for example by training the predictor on the de-anonymized portion of the test set, and combining probabilistic predictions from de-anonymization and link prediction.}, keywords = {deanonymization, Flickr social photo sharing Website, graph theory, IJCNN 2011 social network challenge, Kaggle social network challenge, learning (artificial intelligence), machine learning, realworld link prediction, Simulated annealing, simulated annealing-based weighted graph matching algorithm, social networking (online)}, author = {Narayanan, A. and Elaine Shi and Rubinstein, B.I.P.} } @article {12864, title = {Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios}, journal = {The ISME Journal}, volume = {6}, year = {2011}, month = {2011/07/14/}, pages = {21 - 30}, abstract = {The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45\% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases.}, keywords = {ecophysiology, ecosystems, environmental biotechnology, geomicrobiology, ISME J, microbe interactions, microbial communities, microbial ecology, microbial engineering, microbial epidemiology, microbial genomics, microorganisms}, isbn = {1751-7362}, doi = {10.1038/ismej.2011.89}, url = {http://www.nature.com/ismej/journal/v6/n1/full/ismej201189a.html?WT.ec_id=ISMEJ-201201}, author = {Vezzulli,Luigi and Brettar,Ingrid and Pezzati,Elisabetta and Reid,Philip C. and Rita R Colwell and H{\"o}fle,Manfred G. and Pruzzo,Carla} } @article {12859, title = {Metagenomic 16S rDNA Targeted PCR-DGGE in Determining Bacterial Diversity in Aquatic Ecosystem}, journal = {Bangladesh Journal of Microbiology}, volume = {27}, year = {2011}, month = {2011/12/13/}, abstract = {Bacterial numbers in surface water samples, collected randomly from six different water bodies, were estimated by acridine orange direct counting (AODC) and conventional culture-based heterotrophic plate counting (HPC). Bacterial genomic DNA was prepared from water samples by employing methods used for stool samples, including the population dynamics, were determined by primer extension of the 16S rDNA (V6/V8 region) using polymerase chain reaction (PCR), followed by denaturing gradient gel electrophoresis (DGGE), a metagenomic tool that is capable of separating unrelated DNAs based on the differences in their sequences and GC contents. The bacterial numbers in water samples ranged from 103 {\textendash} 106 CFU/ mL for HPC and 104 {\textendash} 107 cells/ mL for AODC, showing that a great majority of bacteria prevail as uncultivable which do not respond to culture methods that are used widely for tracking bacterial pathogens. The acridine orange-stained bacteria varied in sizes and shapes, and appeared either as planktonic (solitary) cells or as clusters of biofilms, showing the presence of diverse community under the epifluorescence microscope. The DGGE of the ca. 457 bp amplicons, as confirmed by agarose gel electrophoresis, produced bands that ranged in intensities and numbers from 18 to 31, with each band possibly indicating the presence of one or more closely related bacterial species. The enrichment of pathogenic bacteria in the aquatic ecosystem is known to precede the seasonal diarrhoeal outbreaks; therefore, bacterial community dynamics determined by Metagenomic 16S PCR-DGGE during pre-epidemic enrichment appears promising in predicting the upcoming diarrheal outbreaks.}, isbn = {1011-9981}, doi = {10.3329/bjm.v27i2.9171}, url = {http://www.banglajol.info/bd/index.php/BJM/article/view/9171}, author = {Hasan,Nur A. and Chowdhury,W Bari and Rahim,Niaz and Sultana,Marzia and Shabnam,S Antara and Mai,Volker and Ali,Afsar and Morris,Glen J and Sack,R. Bradley and Huq,Anwar and Rita R Colwell and Endtz,Hubert Ph and Cravioto,Alejandro and Alam,Munirul} } @conference {17299, title = {Motivation for Participation in Online Neighborhood Watch Communities: An Empirical Study Involving Invitation Letters}, 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 = {760 - 765}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a three-part experiment designed to investigate the motivations of users of a community safety and neighborhood watch social networking website. The experiment centers around an intervention into the invitation system that current users employ to invite nonmembers to join the site, and involves several versions of an invitation email which differ by expressing one of four possible motivations for using such a site. The research presented investigates how potential users{\textquoteright} choice of whether or not to join the site is affected by the use case presented by the invitation. It also includes an investigation of the motivations of current users of the site, as reported in an online survey. The experiment yielded no significant difference in responses to the emails. Overall, invitations that included a specific motivation slightly outperformed those which did not, but not to a statistically significant degree. We conclude that although users have specific motivations for using the site, as reported in the survey, attempting to increase response rates to invitation emails by suggesting use cases of the site is surprisingly unlikely to be successful.}, keywords = {Art, Communities, community safety, Electronic mail, Interviews, invitation email, invitations, motivation, neighborhood watch, Online communities, online neighborhood watch communities, online survey, participation, Safety, Security, social media, Social network services, social networking (online), social networking Website}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.108}, author = {Violi,N. and Shneiderman, Ben and Hanson,A. and Rey,P. J} } @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.} } @article {16489, title = {New models and algorithms for throughput maximization in broadcast scheduling}, journal = {Approximation and Online Algorithms}, year = {2011}, month = {2011///}, pages = {71 - 82}, author = {Chekuri,C. and Gal,A. and Im,S. and Khuller, Samir and Li,J. and McCutchen,R. and Moseley,B. and Raschid, Louiqa} } @conference {14902, title = {Odd Leaf Out: Improving Visual Recognition with Games}, booktitle = {Privacy, security, risk and trust (passat), 2011 ieee third international conference on and 2011 ieee third international conference on social computing (socialcom)}, year = {2011}, month = {2011/10//}, pages = {87 - 94}, abstract = {A growing number of projects are solving complex computational and scientific tasks by soliciting human feedback through games. Many games with a purpose focus on generating textual tags for images. In contrast, we introduce a new game, Odd Leaf Out, which provides players with an enjoyable and educational game that serves the purpose of identifying misclassification errors in a large database of labeled leaf images. The game uses a novel mechanism to solicit useful information from players{\textquoteright} incorrect answers. A study of 165 players showed that game data can be used to identify mislabeled leaves much more quickly than would have been possible using a computer vision algorithm alone. Domain novices and experts were equally good at identifying mislabeled images, although domain experts enjoyed the game more. We discuss the successes and challenges of this new game, which can be applied to other domains with labeled image datasets.}, keywords = {algorithm;educational, classification;object, computational, computing;botany;computer, datasets;misclassification, errors;scientific, feedback;labeled, game;human, games;computer, games;image, image, leaf, Odd, Out;complex, recognition;, recognition;biology, tags;visual, tasks;computer, tasks;textual, VISION}, doi = {10.1109/PASSAT/SocialCom.2011.225}, author = {Hansen,D. L and Jacobs, David W. and Lewis,D. and Biswas,A. and Preece,J. and Rotman,D. and Stevens,E.} } @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 {19271, title = {Overview of the MPEG Reconfigurable Video Coding Framework}, journal = {Journal of Signal Processing Systems}, volume = {63}, year = {2011}, month = {2011}, pages = {251 - 263}, abstract = {Video coding technology in the last 20 years has evolved producing a variety of different and complex algorithms and coding standards. So far the specification of such standards, and of the algorithms that build them, has been done case by case providing monolithic textual and reference software specifications in different forms and programming languages. However, very little attention has been given to provide a specification formalism that explicitly presents common components between standards, and the incremental modifications of such monolithic standards. The MPEG Reconfigurable Video Coding (RVC) framework is a new ISO standard currently under its final stage of standardization, aiming at providing video codec specifications at the level of library components instead of monolithic algorithms. The new concept is to be able to specify a decoder of an existing standard or a completely new configuration that may better satisfy application-specific constraints by selecting standard components from a library of standard coding algorithms. The possibility of dynamic configuration and reconfiguration of codecs also requires new methodologies and new tools for describing the new bitstream syntaxes and the parsers of such new codecs. The RVC framework is based on the usage of a new actor/ dataflow oriented language called CAL for the specification of the standard library and instantiation of the RVC decoder model. This language has been specifically designed for modeling complex signal processing systems. CAL dataflow models expose the intrinsic concurrency of the algorithms by employing the notions of actor programming and dataflow. The paper gives an overview of the concepts and technologies building the standard RVC framework and the non standard tools supporting the RVC model from the instantiation and simulation of the CAL model to software and/or hardware code synthesis.}, keywords = {CAL actor language, Circuits and Systems, Code synthesis, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow programming, Electrical Engineering, Image Processing and Computer Vision, pattern recognition, Reconfigurable Video Coding, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-009-0399-3}, author = {Bhattacharyya, Shuvra S. and Eker, Johan and Janneck, J{\"o}rn W. and Lucarz, Christophe and Mattavelli, Marco and Raulet, Micka{\"e}l} } @conference {12449, title = {P2C2: Programmable pixel compressive camera for high speed imaging}, booktitle = {2011 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2011}, month = {2011/06/20/25}, pages = {329 - 336}, publisher = {IEEE}, organization = {IEEE}, abstract = {We describe an imaging architecture for compressive video sensing termed programmable pixel compressive camera (P2C2). P2C2 allows us to capture fast phenomena at frame rates higher than the camera sensor. In P2C2, each pixel has an independent shutter that is modulated at a rate higher than the camera frame-rate. The observed intensity at a pixel is an integration of the incoming light modulated by its specific shutter. We propose a reconstruction algorithm that uses the data from P2C2 along with additional priors about videos to perform temporal super-resolution. We model the spatial redundancy of videos using sparse representations and the temporal redundancy using brightness constancy constraints inferred via optical flow. We show that by modeling such spatio-temporal redundancies in a video volume, one can faithfully recover the underlying high-speed video frames from the observed low speed coded video. The imaging architecture and the reconstruction algorithm allows us to achieve temporal super-resolution without loss in spatial resolution. We implement a prototype of P2C2 using an LCOS modulator and recover several videos at 200 fps using a 25 fps camera.}, keywords = {Brightness, brightness constancy constraint, camera sensor, CAMERAS, compressive video sensing, high speed imaging, high-speed video frames, Image sequences, imaging, imaging architecture, independent shutter, Liquid crystal on silicon, low speed coded video, Modulation, optical flow, P2C2, programmable pixel compressive camera, reconstruction algorithm, sparse representation, Spatial resolution, spatio-temporal redundancies, temporal redundancy, temporal super-resolution, video coding}, isbn = {978-1-4577-0394-2}, doi = {10.1109/CVPR.2011.5995542}, author = {Reddy, D. and Veeraraghavan,A. and Chellapa, Rama} } @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 {16435, title = {Predicting author blog channels with high value future posts for monitoring}, journal = {Proceedings of the Twenty-Fifth Conference on Artificial Intelligence (AAAI)}, year = {2011}, month = {2011///}, abstract = {The phenomenal growth of social media, both in scale andimportance, has created a unique opportunity to track infor- mation diffusion and the spread of influence, but can also make efficient tracking difficult. Given data streams rep- resenting blog posts on multiple blog channels and a focal query post on some topic of interest, our objective is to pre- dict which of those channels are most likely to contain a fu- ture post that is relevant, or similar, to the focal query post. We denote this task as the future author prediction problem (FAPP). This problem has applications in information diffu- sion for brand monitoring and blog channel personalization and recommendation. We develop prediction methods in- spired by (na{\i}ve) information retrieval approaches that use historical posts in the blog channel for prediction. We also train a ranking support vector machine (SVM) to solve the problem. We evaluate our methods on an extensive social media dataset; despite the difficulty of the task, all methods perform reasonably well. Results show that ranking SVM prediction can exploit blog channel and diffusion characteris- tics to improve prediction accuracy. Moreover, it is surpris- ingly good for prediction in emerging topics and identifying inconsistent authors. }, author = {Wu,S. and Elsayed,T. and Rand, William and Raschid, Louiqa} } @conference {19019, title = {Privacy-preserving aggregation of time-series data}, volume = {17}, year = {2011}, month = {2011}, abstract = {We consider how an untrusted data aggregator canlearn desired statistics over multiple participants{\textquoteright} data, without compromising each individual{\textquoteright}s privacy. We propose a construction that allows a group of partici- pants to periodically upload encrypted values to a data aggregator, such that the aggregator is able to compute the sum of all participants{\textquoteright} values in every time period, but is unable to learn anything else. We achieve strong privacy guarantees using two main techniques. First, we show how to utilize applied cryptographic techniques to allow the aggregator to decrypt the sum from multiple ciphertexts encrypted under different user keys. Second, we describe a distributed data randomization procedure that guarantees the differential privacy of the outcome statistic, even when a subset of participants might be compromised. }, url = {http://www.eecs.berkeley.edu/~elaines/docs/ndss2011.pdf}, author = {Elaine Shi and Chan, T. and Rieffel, E. and Chow, R. and Song,D.} } @conference {16428, title = {Recommendations in social media for brand monitoring}, booktitle = {Proceedings of the fifth ACM conference on Recommender systems}, series = {RecSys {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {345 - 348}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a recommendation system for social media that draws upon monitoring and prediction methods. We use historical posts on some focal topic or historical links to a focal blog channel to recommend a set of authors to follow. Such a system would be useful for brand managers interested in monitoring conversations about their products. Our recommendations are based on a prediction system that trains a ranking Support Vector Machine (RSVM) using multiple features including the content of a post, similarity between posts, links between posts and/or blog channels, and links to external websites. We solve two problems, Future Author Prediction (FAP) and Future Link Prediction (FLP), and apply the prediction outcome to make recommendations. Using an extensive experimental evaluation on a blog dataset, we demonstrate the quality and value of our recommendations.}, keywords = {blog, brand monitoring, recommendation, social media}, isbn = {978-1-4503-0683-6}, doi = {10.1145/2043932.2043999}, url = {http://doi.acm.org/10.1145/2043932.2043999}, author = {Wu,Shanchan and Rand, William and Raschid, Louiqa} } @article {16033, title = {Research Directions in Data Wrangling: Visualizations and Transformations for Usable and Credible Data}, journal = {Information VisualizationInformation Visualization}, volume = {10}, year = {2011}, month = {2011/10/01/}, pages = {271 - 288}, abstract = {In spite of advances in technologies for working with data, analysts still spend an inordinate amount of time diagnosing data quality issues and manipulating data into a usable form. This process of {\textquoteleft}data wrangling{\textquoteright} often constitutes the most tedious and time-consuming aspect of analysis. Though data cleaning and integration arelongstanding issues in the database community, relatively little research has explored how interactive visualization can advance the state of the art. In this article, we review the challenges and opportunities associated with addressing data quality issues. We argue that analysts might more effectively wrangle data through new interactive systems that integrate data verification, transformation, and visualization. We identify a number of outstanding research questions, including how appropriate visual encodings can facilitate apprehension of missing data, discrepant values, and uncertainty; how interactive visualizations might facilitate data transform specification; and how recorded provenance and social interaction might enable wider reuse, verification, and modification of data transformations.}, keywords = {data cleaning, data quality, data transformation, Uncertainty, Visualization}, isbn = {1473-8716, 1473-8724}, doi = {10.1177/1473871611415994}, url = {http://ivi.sagepub.com/content/10/4/271}, author = {Kandel,Sean and Heer,Jeffrey and Plaisant, Catherine and Kennedy,Jessie and Van Ham,Frank and Riche,Nathalie Henry and Weaver,Chris and Lee,Bongshin and Brodbeck,Dominique and Buono,Paolo} } @article {15190, title = {Secure computation with sublinear amortized work}, year = {2011}, month = {2011///}, institution = {Cryptology ePrint Archive, Report 2011/482}, abstract = {Traditional approaches to secure computation begin by representing the function f beingcomputed as a circuit. For any function f that depends on each of its inputs, this implies a protocol with complexity at least linear in the input size. In fact, linear running time is inherent for secure computation of non-trivial functions, since each party must {\textquotedblleft}touch{\textquotedblright} every bit of their input lest information about other party{\textquoteright}s input be leaked. This seems to rule out many interesting applications of secure computation in scenarios where at least one of the inputs is huge and sublinear-time algorithms can be utilized in the insecure setting; private database search is a prime example. We present an approach to secure two-party computation that yields sublinear-time proto- cols, in an amortized sense, for functions that can be computed in sublinear time on a random access machine (RAM). Furthermore, a party whose input is {\textquotedblleft}small{\textquotedblright} is required to maintain only small state. We provide a generic protocol that achieves the claimed complexity, based on any oblivious RAM and any protocol for secure two-party computation. We then present an optimized version of this protocol, where generic secure two-party computation is used only for evaluating a small number of simple operations. }, author = {Gordon,D. and Katz, Jonathan and Kolesnikov,V. and Malkin,T. and Raykova,M. and Vahlis,Y.} } @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 {16674, title = {Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language}, journal = {Arxiv preprint arXiv:1105.5444}, year = {2011}, month = {2011///}, author = {Resnik, Philip} } @article {18535, title = {SilverLine: Data and Network Isolation for Cloud Services}, journal = {2nd USENIX Workshop on Hot Topics in Cloud Computing}, year = {2011}, month = {2011///}, abstract = {Although cloud computing service providers offer op-portunities for improving the administration, reliability, and maintenance of hosted services, they also concen- trate network resources and data in a small number of cloud service providers. The concentration of data and resources also entails various associated risks, including sharing the underlying infrastructure with unknown (and untrusted) tenants and relying on the availability and se- curity of the underlying infrastructure itself. These se- curity risks represent some of the most significant bar- riers to the adoption of cloud-based services. To begin tackling these risks, a cloud hosting infrastructure should provide strong guarantees for resource and data isolation. This paper examines data and network isolation prob- lems with today{\textquoteright}s cloud hosting infrastructures and pro- poses SilverLine, a collection of techniques to improve data and network isolation for a cloud tenants{\textquoteright} service. }, author = {Mundada,Y. and Ramachandran,A. and Feamster, Nick} } @conference {18599, title = {Spam or ham?: characterizing and detecting fraudulent "not spam" reports in web mail systems}, booktitle = {Proceedings of the 8th Annual Collaboration, Electronic messaging, Anti-Abuse and Spam Conference}, series = {CEAS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {210 - 219}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Web mail providers rely on users to "vote" to quickly and col-laboratively identify spam messages. Unfortunately, spammers have begun to use bots to control large collections of compromised Web mail accounts not just to send spam, but also to vote "not spam" on incoming spam emails in an attempt to thwart collaborative filtering. We call this practice a vote gaming attack. This attack confuses spam filters, since it causes spam messages to be mislabeled as legitimate; thus, spammer IP addresses can continue sending spam for longer. In this paper, we introduce the vote gaming attack and study the extent of these attacks in practice, using four months of email voting data from a large Web mail provider. We develop a model for vote gaming attacks, explain why existing detection mechanisms cannot detect them, and develop a new, scalable clustering-based detection method that identifies compromised accounts that engage in vote-gaming attacks. Our method detected 1.1 million potentially compromised accounts with only a 0.17\% false positive rate, which is nearly 10 times more effective than existing clustering methods used to detect bots that send spam from compromised Web mail accounts.}, isbn = {978-1-4503-0788-8}, doi = {10.1145/2030376.2030401}, url = {http://doi.acm.org/10.1145/2030376.2030401}, author = {Ramachandran,Anirudh and Dasgupta,Anirban and Feamster, Nick and Weinberger,Kilian} } @article {19118, title = {Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral}, journal = {Electronic Journal of Biotechnology}, volume = {14}, year = {2011}, month = {2011}, pages = {8 - 9}, author = {Lopez, J.V. and Ledger, A. and Santiago-V{\'a}zquez, L.Z. and Pop, Mihai and Sommer, D.D. and Ranzer, L.K. and Feldman, R.A. and Russell, G.K.} } @article {18543, title = {A survey of virtual LAN usage in campus networks}, journal = {Communications Magazine, IEEE}, volume = {49}, year = {2011}, month = {2011/07//}, pages = {98 - 103}, abstract = {VLANs are widely used in today{\textquoteright}s enterprise networks to improve Ethernet scalability and support network policies. However, manuals and textbooks offer very little information about how VLANs are actually used in practice. Through discussions with network administrators and analysis of configuration data, we describe how three university campuses and one academic department use VLANs to achieve a variety of goals. We argue that VLANs are ill-suited to some of these goals (e.g., VLANs are often used to realize access control policies, but constrain the types of policies that can be expressed). Furthermore, the use of VLANs leads to significant complexity in the configuration of network devices.}, keywords = {academic department, campus network, educational computing, Educational institutions, Ethernet scalability, Local area networks, network policy support, university campus, virtual LAN usage, VLAN}, isbn = {0163-6804}, doi = {10.1109/MCOM.2011.5936161}, author = {Yu,Minlan and Rexford,J. and Sun,Xin and Rao,Sanjay and Feamster, Nick} } @article {17439, title = {TreeCovery: Coordinated dual treemap visualization for exploring the Recovery Act}, journal = {Government Information Quarterly}, year = {2011}, month = {2011///}, abstract = {The American Recovery and Reinvestment Act dedicated $787 billion to stimulate the U.S. economy and mandated the release of the data describing the exact distribution of that money. The dataset is a large and complex one; one of its distinguishing features is its bi-hierarchical structure, arising from the distribution of money through agencies to specific projects and the natural aggregation of awards based on location. To offer a comprehensive overview of the data, a visualization must incorporate both these hierarchies. We present TreeCovery, a tool that accomplishes this through the use of two coordinated treemaps. The tool includes a number of innovative features, including coordinated zooming and filtering and a proportional highlighting technique across the two trees. TreeCovery was designed to facilitate data exploration, and initial user studies suggest that it will be helpful in insight generation. RATB (Recovery Accountability and Transparency Board) has tested TreeCovery and is considering including the concept in their visual analytics.}, keywords = {Recovery Act, user interface, Visual analytic}, isbn = {0740-624X}, doi = {10.1016/j.giq.2011.07.004}, url = {http://www.sciencedirect.com/science/article/pii/S0740624X11001055}, author = {Rios-Berrios,Miguel and Sharma,Puneet and Lee,Tak Yeon and Schwartz,Rachel and Shneiderman, Ben} } @conference {16417, title = {When does simulated data match real data?}, booktitle = {Proceedings of the 13th annual conference companion on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {231 - 232}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Agent-based models can replicate real-world patterns, but finding parameters that achieve the best match can be difficult. To validate a model, a real-world dataset is often divided into a training set (to calibrate the parameters) and a test set (to validate the calibrated model). The difference between the training and test data and the simulated data is determined using an error measure. In the context of evolutionary computation techniques, the error measure also serves as a fitness function, and thus affects evolutionary search dynamics. We survey the effect of five different error measures on both a toy problem and a real world problem of matching a model to empirical online news consumption behavior. We use each error measure separately for calibration on the training dataset, and then examine the results of all five error measures on both the training and testing datasets. We show that certain error measures sometimes serve as better fitness functions than others, and in fact using one error measure may result in better calibration (on a different measure) than using the different measure directly. For the toy problem, the Pearson{\textquoteright}s correlation measure dominated all other measures, but no single error measure was Pareto dominant for the real world problem.}, keywords = {Agent-based modeling, business, Calibration, Genetic algorithms, information search, network analysis}, isbn = {978-1-4503-0690-4}, doi = {10.1145/2001858.2001988}, url = {http://doi.acm.org/10.1145/2001858.2001988}, author = {Stonedahl,Forrest and Anderson,David and Rand, William} } @article {17748, title = {Annotated RDF}, journal = {ACM Trans. Comput. Logic}, volume = {11}, year = {2010}, month = {2010/01//}, pages = {10:1{\textendash}10:41 - 10:1{\textendash}10:41}, abstract = {Real-world use of RDF requires the ability to transparently represent and explain metadata associated with RDF triples. For example, when RDF triples are extracted automatically by information extraction programs, there is a need to represent where the triples came from, what their temporal validity is, and how certain we are that the triple is correct. Today, there is no theoretically clean and practically scalable mechanism that spans these different needs - reification is the only solution propose to date, and its implementations have been ugly. In this paper, we present Annotated RDF (or aRDF for short) in which RDF triples are annotated by members of a partially ordered set (with bottom element) that can be selected in any way desired by the user. We present a formal declarative semantics (model theory) for annotated RDF and develop algorithms to check consistency of aRDF theories and to answer queries to aRDF theories. We show that annotated RDF supports users who need to think about the uncertainty, temporal aspects, and provenance of the RDF triples in an RDF database. We develop a prototype aRDF implementation and show that our algorithms work efficiently even on real world data sets containing over 10 million triples.}, keywords = {annotated RDF, Query processing, view maintenance}, isbn = {1529-3785}, doi = {10.1145/1656242.1656245}, url = {http://doi.acm.org/10.1145/1656242.1656245}, author = {Udrea,Octavian and Recupero,Diego Reforgiato and V.S. Subrahmanian} } @article {12474, title = {Applications of a Simple Characterization of Human Gait in Surveillance}, journal = {Systems, Man, and Cybernetics, Part B: Cybernetics, IEEE Transactions on}, volume = {40}, year = {2010}, month = {2010/08//}, pages = {1009 - 1020}, abstract = {Applications of a simple spatiotemporal characterization of human gait in the surveillance domain are presented. The approach is based on decomposing a video sequence into x-t slices, which generate periodic patterns referred to as double helical signatures (DHSs). The features of DHS are given as follows: 1) they naturally encode the appearance and kinematics of human motion and reveal geometric symmetries and 2) they are effective and efficient for recovering gait parameters and detecting simple events. We present an iterative local curve embedding algorithm to extract the DHS from video sequences. Two applications are then considered. First, the DHS is used for simultaneous segmentation and labeling of body parts in cluttered scenes. Experimental results showed that the algorithm is robust to size, viewing angles, camera motion, and severe occlusion. Then, the DHS is used to classify load-carrying conditions. By examining various symmetries in DHS, activities such as carrying, holding, and walking with objects that are attached to legs are detected. Our approach possesses several advantages: a compact representation that can be computed in real time is used; furthermore, it does not depend on silhouettes or landmark tracking, which are sensitive to errors in background subtraction stage.}, keywords = {algorithms, Artificial intelligence, Automated;Photography;Reproducibility of Results;Sensitivity and Specificity;Video Recording;, Biometry, Computer-Assisted;Pattern Recognition, double helical signatures, Gait, gait analysis, human gait, human motion kinematics, HUMANS, Image Enhancement, Image Interpretation, Image motion analysis, iterative local curve embedding algorithm, Object detection, simple spatiotemporal characterization, video sequence, Video surveillance}, isbn = {1083-4419}, doi = {10.1109/TSMCB.2010.2044173}, author = {Yang Ran and Qinfen Zheng and Chellapa, Rama and Strat, T.M.} } @conference {19284, title = {Automated generation of an efficient MPEG-4 Reconfigurable Video Coding decoder implementation}, booktitle = {2010 Conference on Design and Architectures for Signal and Image Processing (DASIP)}, year = {2010}, month = {2010}, pages = {265 - 272}, abstract = {This paper proposes an automatic design flow from user-friendly design to efficient implementation of video processing systems. This design flow starts with the use of coarse-grain dataflow representations based on the CAL language, which is a complete language for dataflow programming of embedded systems. Our approach integrates previously developed techniques for detecting synchronous dataflow (SDF) regions within larger CAL networks, and exploiting the static structure of such regions using analysis tools in The Dataflow interchange format Package (TDP). Using a new XML format that we have developed to exchange dataflow information between different dataflow tools, we explore systematic implementation of signal processing systems using CAL, SDF-like region detection, TDP-based static scheduling, and CAL-to-C (CAL2C) translation. Our approach, which is a novel integration of three complementary dataflow tools - the CAL parser, TDP, and CAL2C - is demonstrated on an MPEG Reconfigurable Video Coding (RVC) decoder.}, keywords = {automated generation, automatic design flow, CAL language, CAL networks, CAL-to-C translation, CAL2C translation, coarse-grain dataflow representations, Computational modeling, data flow computing, dataflow information, Dataflow programming, decoding, Digital signal processing, Libraries, MPEG-4 reconfigurable video coding decoder implementation, parallel languages, SDF detection, synchronous dataflow detection, TDP, TDP-based static scheduling, The Dataflow interchange format Package, Transform coding, user-friendly design, video coding, video processing systems, XML, XML format}, author = {Gu, Ruirui and Piat, J. and Raulet, M. and Janneck, J.W. and Bhattacharyya, Shuvra S.} } @article {16459, title = {BioNav: An Ontology-Based Framework to Discover Semantic Links in the Cloud of Linked Data}, journal = {The Semantic Web: Research and Applications}, year = {2010}, month = {2010///}, pages = {441 - 445}, author = {Vidal,M. E and Raschid, Louiqa and M{\'a}rquez,N. and Rivera,J. and Ruckhaus,E.} } @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} } @conference {16500, title = {Challenges in personalized authority flow based ranking of social media}, booktitle = {Proceedings of the 19th ACM international conference on Information and knowledge management}, year = {2010}, month = {2010///}, pages = {1409 - 1412}, author = {Sayyadi,H. and Edmonds,J. and Hristidis,V. and Raschid, Louiqa} } @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 {15261, title = {Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs}, journal = {Research in Computational Molecular Biology}, year = {2010}, month = {2010///}, pages = {456 - 472}, abstract = {In this paper, we focus on finding complex annotation patterns representing novel and interesting hypotheses from gene annotation data. We define a generalization of the densest subgraph problem by adding an additional distance restriction (defined by a separate metric) to the nodes of the subgraph. We show that while this generalization makes the problem NP-hard for arbitrary metrics, when the metric comes from the distance metric of a tree, or an interval graph, the problem can be solved optimally in polynomial time. We also show that the densest subgraph problem with a specified subset of vertices that have to be included in the solution can be solved optimally in polynomial time. In addition, we consider other extensions when not just one solution needs to be found, but we wish to list all subgraphs of almost maximum density as well. We apply this method to a dataset of genes and their annotations obtained from The Arabidopsis Information Resource (TAIR). A user evaluation confirms that the patterns found in the distance restricted densest subgraph for a dataset of photomorphogenesis genes are indeed validated in the literature; a control dataset validates that these are not random patterns. Interestingly, the complex annotation patterns potentially lead to new and as yet unknown hypotheses. We perform experiments to determine the properties of the dense subgraphs, as we vary parameters, including the number of genes and the distance.}, doi = {10.1007/978-3-642-12683-3_30}, author = {Saha,B. and Hoch,A. and Khuller, Samir and Raschid, Louiqa and Zhang,X. N} } @article {14545, title = {Deploying sensor networks with guaranteed fault tolerance}, journal = {IEEE/ACM Transactions on Networking (TON)}, volume = {18}, year = {2010}, month = {2010///}, pages = {216 - 228}, author = {Bredin,J. L and Demaine,E. D and Hajiaghayi, Mohammad T. and Rus,D.} } @conference {16685, title = {Error driven paraphrase annotation using Mechanical Turk}, booktitle = {Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon{\textquoteright}s Mechanical Turk}, year = {2010}, month = {2010///}, pages = {217 - 221}, author = {Buzek,O. and Resnik, Philip and Bederson, Benjamin B.} } @article {18903, title = {Evolution of state-dependent risk preferences}, journal = {ACM Transactions on Intelligent Systems and Technology (TIST)}, volume = {1}, year = {2010}, month = {2010/10//}, pages = {6:1{\textendash}6:21 - 6:1{\textendash}6:21}, abstract = {Researchers have invested much effort in constructing models of the state-dependent (sometimes risk-averse and sometimes risk-prone) nature of human decision making. An important open question is how state-dependent risk behavior can arise and remain prominent in populations. We believe that one part of the answer is the interplay between risk-taking and sequentiality of choices in populations subject to evolutionary population dynamics. To support this hypothesis, we provide simulation and analytical results for evolutionary lottery games, including results on evolutionary stability. We consider a parameterized class of imitation dynamics in which the parameter 0 <= α <= 1 yields the replicator dynamic with α = 1 and the imitate-the-better dynamic with α = 0. Our results demonstrate that for every population dynamic in this class except for the replicator dynamic, the interplay between risk-taking and sequentiality of choices allows state-dependent risk behavior to have an evolutionary advantage over expected-value maximization.}, keywords = {decision theory, Evolutionary games, Population Dynamics, risk}, isbn = {2157-6904}, doi = {10.1145/1858948.1858954}, url = {http://doi.acm.org/10.1145/1858948.1858954}, author = {Roos,Patrick and Carr,J. Ryan and Nau, Dana S.} } @inbook {12995, title = {Evolutionary framework for Lepidoptera model systems}, booktitle = {Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera}, year = {2010}, month = {2010///}, pages = {1 - 24}, publisher = {Taylor \& Francis}, organization = {Taylor \& Francis}, address = {Boca Raton}, abstract = {{\textquotedblleft}Model systems{\textquotedblright} are specific organisms upon which detailed studies have been conducted examining a fundamental biological question. If the studies are robust, their results can be extrapolated among an array of organisms that possess features in common with the subject organism. The true power of model systems lies in the ability to extrapolate these details across larger groups of organisms. In order to generalize these results, comparative studies are essential and require that model systems be placed into their evolutionary or phylogenetic context. This chapter examines model systems in the insect order Lepidoptera from the perspective of several different superfamilies. Historically, many species of Lepidoptera have been essential in the development of invaluable model systems in the fields of development biology, genetics, molecular biology, physiology, co-evolution, population dynamics, and ecology.}, author = {Roe,A. and Weller,S. and Baixeras,J. and Brown,J. W and Cummings, Michael P. and Davis,DR and Horak,M and Kawahara,A. Y and Mitter,C and Parr,C.S. and Regier,J. C and Rubinoff,D and Simonsen,TJ and Wahlberg,N and Zwick,A.}, editor = {Goldsmith,M and Marec,F} } @conference {16416, title = {Evolving viral marketing strategies}, booktitle = {Proceedings of the 12th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1195 - 1202}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {One method of viral marketing involves seeding certain consumers within a population to encourage faster adoption of the product throughout the entire population. However, determining how many and which consumers within a particular social network should be seeded to maximize adoption is challenging. We define a strategy space for consumer seeding by weighting a combination of network characteristics such as average path length, clustering coefficient, and degree. We measure strategy effectiveness by simulating adoption on a Bass-like agent-based model, with five different social network structures: four classic theoretical models (random, lattice, small-world, and preferential attachment) and one empirical (extracted from Twitter friendship data). To discover good seeding strategies, we have developed a new tool, called BehaviorSearch, which uses genetic algorithms to search through the parameter-space of agent-based models. This evolutionary search also provides insight into the interaction between strategies and network structure. Our results show that one simple strategy (ranking by node degree) is near-optimal for the four theoretical networks, but that a more nuanced strategy performs significantly better on the empirical Twitter-based network. We also find a correlation between the optimal seeding budget for a network, and the inequality of the degree distribution.}, keywords = {Agent-based modeling, business, diffusion, Genetic algorithms, simulation, social networks, viral marketing}, isbn = {978-1-4503-0072-8}, doi = {10.1145/1830483.1830701}, url = {http://doi.acm.org/10.1145/1830483.1830701}, author = {Stonedahl,Forrest and Rand, William and Wilensky,Uri} } @article {14869, title = {Face Verification Across Age Progression Using Discriminative Methods}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {5}, year = {2010}, month = {2010/03//}, pages = {82 - 91}, abstract = {Face verification in the presence of age progression is an important problem that has not been widely addressed. In this paper, we study the problem by designing and evaluating discriminative approaches. These directly tackle verification tasks without explicit age modeling, which is a hard problem by itself. First, we find that the gradient orientation, after discarding magnitude information, provides a simple but effective representation for this problem. This representation is further improved when hierarchical information is used, which results in the use of the gradient orientation pyramid (GOP). When combined with a support vector machine GOP demonstrates excellent performance in all our experiments, in comparison with seven different approaches including two commercial systems. Our experiments are conducted on the FGnet dataset and two large passport datasets, one of them being the largest ever reported for recognition tasks. Second, taking advantage of these datasets, we empirically study how age gaps and related issues (including image quality, spectacles, and facial hair) affect recognition algorithms. We found surprisingly that the added difficulty of verification produced by age gaps becomes saturated after the gap is larger than four years, for gaps of up to ten years. In addition, we find that image quality and eyewear present more of a challenge than facial hair.}, keywords = {algorithms;support, databases;, dataset;age, FGnet, hair;gradient, information;image, information;recognition, machine;face, machines;visual, methods;eyewear;face, methods;support, orientation, orientation;gradient, progression;commercial, pyramid;hierarchical, quality;magnitude, recognition;gradient, systems;discriminative, vector, verification;facial}, isbn = {1556-6013}, doi = {10.1109/TIFS.2009.2038751}, author = {Ling,Haibin and Soatto,S. and Ramanathan,N. and Jacobs, David W.} } @article {13961, title = {Fast Computation of Kernel Estimators}, journal = {Journal of Computational and Graphical Statistics}, volume = {19}, year = {2010}, month = {2010///}, pages = {205 - 220}, abstract = {The computational complexity of evaluating the kernel density estimate (or its derivatives) at m evaluation points given n sample points scales quadratically as O(nm)?making it prohibitively expensive for large datasets. While approximate methods like binning could speed up the computation, they lack a precise control over the accuracy of the approximation. There is no straightforward way of choosing the binning parameters a priori in order to achieve a desired approximation error. We propose a novel computationally efficient ε-exact approximation algorithm for the univariate Gaussian kernel-based density derivative estimation that reduces the computational complexity from O(nm) to linear O(n+m). The user can specify a desired accuracy ε. The algorithm guarantees that the actual error between the approximation and the original kernel estimate will always be less than ε. We also apply our proposed fast algorithm to speed up automatic bandwidth selection procedures. We compare our method to the best available binning methods in terms of the speed and the accuracy. Our experimental results show that the proposed method is almost twice as fast as the best binning methods and is around five orders of magnitude more accurate. The software for the proposed method is available online.}, isbn = {1061-8600}, doi = {10.1198/jcgs.2010.09046}, url = {http://www.tandfonline.com/doi/abs/10.1198/jcgs.2010.09046}, author = {Raykar,Vikas C. and Duraiswami, Ramani and Zhao,Linda H.} } @article {16265, title = {Finishing genomes with limited resources: lessons from an ensemble of microbial genomes}, journal = {BMC Genomics}, volume = {11}, year = {2010}, month = {2010/04/16/}, pages = {242 - 242}, abstract = {While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-11-242}, url = {http://www.biomedcentral.com/1471-2164/11/242}, author = {Nagarajan,Niranjan and Cook,Christopher and Di Bonaventura,Maria Pia and Ge,Hong and Richards,Allen and Bishop-Lilly,Kimberly A and DeSalle,Robert and Read,Timothy D. and Pop, Mihai} } @conference {19297, title = {FPGA-based design and implementation of the 3GPP-LTE physical layer using parameterized synchronous dataflow techniques}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010}, pages = {1510 - 1513}, abstract = {Synchronous dataflow (SDF) is an ubiquitous dataflow model of computation that has been studied extensively for efficient simulation and software synthesis of DSP applications. In recent years, parameterized SDF (PSDF) has evolved as a useful framework for modeling SDF graphs in which arbitrary parameters can be changed dynamically. However, the potential to enable efficient hardware synthesis has been treated relatively sparsely in the literature for SDF and even more so for the newer, more general PSDF model. This paper investigates efficient FPGA-based design and implementation of the physical layer for 3GPP-Long Term Evolution (LTE), a next generation cellular standard. To capture the SDF behavior of the functional core of LTE along with higher level dynamics in the standard, we use a novel PSDF-based FPGA architecture framework. We implement our PSDF-based, LTE design framework using National Instrument{\textquoteright}s LabVIEW FPGA, a recently-introduced commercial platform for reconfigurable hardware implementation. We show that our framework can effectively model the dynamics of the LTE protocol, while also providing a synthesis framework for efficient FPGA implementation.}, keywords = {3G mobile communication, 3GPP-long term evolution, 3GPP-LTE physical layer, 4G communication systems, Computational modeling, data flow analysis, data flow graphs, Dataflow modeling, Digital signal processing, DSP applications, Field programmable gate arrays, FPGA architecture framework, FPGA implementation, FPGA-based design, Hardware, hardware synthesis, Instruments, LabVIEW FPGA, Logic Design, LTE, next generation cellular standard, parameterized synchronous data flow technique, Pervasive computing, Physical layer, Physics computing, Production, PSDF graph, reconfigurable hardware implementation, Runtime, software synthesis, Ubiquitous Computing, ubiquitous data flow model}, author = {Kee, Hojin and Bhattacharyya, Shuvra S. and Wong, I. and Yong Rao} } @article {14584, title = {Genetic and Physiological Activation of Osmosensitive Gene Expression Mimics Transcriptional Signatures of Pathogen Infection in C. elegans}, journal = {PLoS ONEPLoS ONE}, volume = {5}, year = {2010}, month = {2010/02/02/}, pages = {e9010 - e9010}, abstract = {The soil-dwelling nematode C. elegans is a powerful system for comparative molecular analyses of environmental stress response mechanisms. Infection of worms with bacterial and fungal pathogens causes the activation of well-characterized innate immune transcriptional programs in pathogen-exposed hypodermal and intestinal tissues. However, the pathophysiological events that drive such transcriptional responses are not understood. Here, we show that infection-activated transcriptional responses are, in large part, recapitulated by either physiological or genetic activation of the osmotic stress response. Microarray profiling of wild type worms exposed to non-lethal hypertonicity identified a suite of genes that were also regulated by infection. Expression profiles of five different osmotic stress resistant (osr) mutants under isotonic conditions reiterated the wild type transcriptional response to osmotic stress and also showed substantial similarity to infection-induced gene expression under isotonic conditions. Computational, transgenic, and functional approaches revealed that two GATA transcription factors previously implicated in infection-induced transcriptional responses, elt-2 and elt-3, are also essential for coordinated tissue-specific activation of osmosensitive gene expression and promote survival under osmotically stressful conditions. Together, our data suggest infection and osmotic adaptation share previously unappreciated transcriptional similarities which might be controlled via regulation of tissue-specific GATA transcription factors.}, doi = {10.1371/journal.pone.0009010}, url = {http://dx.doi.org/10.1371/journal.pone.0009010}, author = {Rohlfing,Anne-Katrin and Miteva,Yana and Hannenhalli, Sridhar and Lamitina,Todd} } @conference {12403, title = {Holistic sentiment analysis across languages: multilingual supervised latent Dirichlet allocation}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, series = {EMNLP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {45 - 55}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {In this paper, we develop multilingual supervised latent Dirichlet allocation (MlSLDA), a probabilistic generative model that allows insights gleaned from one language{\textquoteright}s data to inform how the model captures properties of other languages. MlSLDA accomplishes this by jointly modeling two aspects of text: how multilingual concepts are clustered into thematically coherent topics and how topics associated with text connect to an observed regression variable (such as ratings on a sentiment scale). Concepts are represented in a general hierarchical framework that is flexible enough to express semantic ontologies, dictionaries, clustering constraints, and, as a special, degenerate case, conventional topic models. Both the topics and the regression are discovered via posterior inference from corpora. We show MlSLDA can build topics that are consistent across languages, discover sensible bilingual lexical correspondences, and leverage multilingual corpora to better predict sentiment.}, url = {http://dl.acm.org/citation.cfm?id=1870658.1870663}, author = {Jordan Boyd-Graber and Resnik, Philip} } @inbook {16274, title = {Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets}, booktitle = {Bioinformatics Research and Applications}, series = {Lecture Notes in Computer Science}, volume = {6053}, year = {2010}, month = {2010///}, pages = {101 - 112}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge. We show that MetaPath outperforms other common approaches when evaluated on simulated datasets. We also demonstrate the power of our methods in analyzing two, publicly available, metagenomic datasets: a comparison of the gut microbiome of obese and lean twins; and a comparison of the gut microbiome of infant and adult subjects. We demonstrate that the subpathways identified by our method provide valuable insights into the biological activities of the microbiome.}, isbn = {978-3-642-13077-9}, url = {http://dx.doi.org/10.1007/978-3-642-13078-6_12}, author = {Liu,Bo and Pop, Mihai}, editor = {Borodovsky,Mark and Gogarten,Johann and Przytycka,Teresa and Rajasekaran,Sanguthevar} } @conference {16692, title = {Improving translation via targeted paraphrasing}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, year = {2010}, month = {2010///}, pages = {127 - 137}, author = {Resnik, Philip and Buzek,O. and Hu,C. and Kronrod,Y. and Quinn,A. and Bederson, Benjamin B.} } @article {16052, title = {Interactive information visualization for exploring and querying electronic health records: A systematic review}, year = {2010}, month = {2010///}, institution = {Human-Computer Interaction Lab, University of Maryland}, abstract = {To overcome the complexity and scale of making medical decisions based on electronic health records (EHRs) a variety of visual methods have been proposed. This paper surveys twelve state-of-the-art information visualization systems described in the scientific literature and compares them based on a set of carefully selected criteria. It aims to systematically examine the systems{\textquoteright} strengths and weaknesses to inform future information visualization designs.We select twelve state-of-the-art information visualization systems from information visualization, medical information systems and human-computer interaction conferences and journals. We compare the systems using the following criteria: (1) data types covered, (2) multivariate analysis support, (3) number of patients records used (one or many), and (4) user intents addressed. The review describes the twelve systems in detail and evaluates the systems using the aforementioned criteria. We discuss how the systems differ in their features and highlight how these differences are related to their design and affect the user intent model. Examples of findings include: (1) most systems handle numerical or categorical data but not both, (2) most systems are specifically designed for looking at a single patient or multiple patients but not both, (3) most systems utilize horizontal time lines to represent time, (4) only systems that handle multiple patient records have good support for Filter, and (5) some specific user intents (e.g. the Encode and Connect intents) are rarely addressed. Based on our review results, we believe that effective information visualization can facilitate analysis of patient records, and we encourage the information visualization community to study the application of their systems and conduct more in depth evaluations. We identify potential future research topics in interactive support for data abstraction and medical tasks that involve looking at a single or multiple records. Finally, we propose to create a repository for data and tasks so benchmarks can be established for both academic and commercial patient record visualization systems. }, author = {Rind,A. and Wang,T. D and Aigner,W. and Miksh,S. and Wongsuphasawat,K. and Plaisant, Catherine and Shneiderman, Ben} } @article {13798, title = {Interlingual Annotation of Parallel Text Corpora: A New Framework for Annotation and Evaluation}, journal = {Natural Language Engineering}, volume = {16}, year = {2010}, month = {2010///}, pages = {197 - 243}, abstract = {This paper focuses on an important step in the creation of a system of meaning representation and the development of semantically annotated parallel corpora, for use in applications such as machine translation, question answering, text summarization, and information retrieval. The work described below constitutes the first effort of any kind to annotate multiple translations of foreign-language texts with interlingual content. Three levels of representation are introduced: deep syntactic dependencies (IL0), intermediate semantic representations (IL1), and a normalized representation that unifies conversives, nonliteral language, and paraphrase (IL2). The resulting annotated, multilingually induced, parallel corpora will be useful as an empirical basis for a wide range of research, including the development and evaluation of interlingual NLP systems and paraphrase-extraction systems as well as a host of other research and development efforts in theoretical and applied linguistics, foreign language pedagogy, translation studies, and other related disciplines.}, doi = {10.1017/S1351324910000070}, author = {Dorr, Bonnie J and Passonneau,Rebecca J. and Farwell,David and Green,Rebecca and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Levin,Lori and Miller,Keith J. and Mitamura,Teruko and Rambow,Owen and Siddharthan,Advaith} } @article {12144, title = {Linking Software Development and Business Strategy Through Measurement}, journal = {Computer}, volume = {43}, year = {2010}, month = {2010/04//}, pages = {57 - 65}, abstract = {The GQM+Strategies approach extends the goal/question/metric paradigm for measuring the success or failure of goals and strategies, adding enterprise-wide support for determining action on the basis of measurement results. An organization can thus integrate its measurement program across all levels.}, keywords = {approach;business, aspects;software, development;organisational, engineering;, GQM+Strategies, program;software, strategy;enterprise, support;measurement, wide}, isbn = {0018-9162}, doi = {10.1109/MC.2010.108}, author = {Basili, Victor R. and Lindvall,M. and Regardie,M. and Seaman,C. and Heidrich,J. and Munch,J. and Rombach,D. and Trendowicz,A.} } @conference {19290, title = {Loop transformations for interface-based hierarchies IN SDF graphs}, booktitle = {2010 21st IEEE International Conference on Application-specific Systems Architectures and Processors (ASAP)}, year = {2010}, month = {2010}, pages = {341 - 344}, abstract = {Data-flow has proven to be an attractive computation model for programming digital signal processing (DSP) applications. A restricted version of data-flow, termed synchronous data-flow (SDF), offers strong compile-time predictability properties, but has limited expressive power. A new type of hierarchy (Interface-based SDF) has been proposed allowing more expressivity while maintaining its predictability. One of the main problems with this hierarchical SDF model is the lack of trade-off between parallelism and network clustering. This paper presents a systematic method for applying an important class of loop transformation techniques in the context of interface-based SDF semantics. The resulting approach provides novel capabilities for integrating parallelism extraction properties of the targeted loop transformations with the useful modeling, analysis, and code reuse properties provided by SDF.}, keywords = {Application software, code generation, Computer architecture, Computer interfaces, Data-Flow programming, Digital signal processing, Loop parallelization, PARALLEL PROCESSING, Power engineering computing, Power system modeling, Processor scheduling, Programming profession, scheduling, SDF graph, system recovery}, author = {Piat, J. and Bhattacharyya, Shuvra S. and Raulet, M.} } @conference {12405, title = {Measuring transitivity using untrained annotators}, booktitle = {Proceedings of the NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon{\textquoteright}s Mechanical Turk}, series = {CSLDAMT {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {188 - 194}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Hopper and Thompson (1980) defined a multi-axis theory of transitivity that goes beyond simple syntactic transitivity and captures how much "action" takes place in a sentence. Detecting these features requires a deep understanding of lexical semantics and real-world pragmatics. We propose two general approaches for creating a corpus of sentences labeled with respect to the Hopper-Thompson transitivity schema using Amazon Mechanical Turk. Both approaches assume no existing resources and incorporate all necessary annotation into a single system; this is done to allow for future generalization to other languages. The first task attempts to use language-neutral videos to elicit human-composed sentences with specified transitivity attributes. The second task uses an iterative process to first label the actors and objects in sentences and then annotate the sentences{\textquoteright} transitivity. We examine the success of these techniques and perform a preliminary classification of the transitivity of held-out data.}, url = {http://dl.acm.org/citation.cfm?id=1866696.1866726}, author = {Madnani,Nitin and Jordan Boyd-Graber and Resnik, Philip} } @conference {12407, title = {Modeling perspective using adaptor grammars}, booktitle = {Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing}, series = {EMNLP {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {284 - 292}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Strong indications of perspective can often come from collocations of arbitrary length; for example, someone writing get the government out of my X is typically expressing a conservative rather than progressive viewpoint. However, going beyond unigram or bigram features in perspective classification gives rise to problems of data sparsity. We address this problem using nonparametric Bayesian modeling, specifically adaptor grammars (Johnson et al., 2006). We demonstrate that an adaptive na{\"\i}ve Bayes model captures multiword lexical usages associated with perspective, and establishes a new state-of-the-art for perspective classification results using the Bitter Lemons corpus, a collection of essays about mid-east issues from Israeli and Palestinian points of view.}, url = {http://dl.acm.org/citation.cfm?id=1870658.1870686}, author = {Hardisty,Eric A. and Jordan Boyd-Graber and Resnik, Philip} } @inbook {15770, title = {Modelling Type 1a Supernova Light Curves}, booktitle = {Exponential Data Fitting and Its ApplicationsExponential Data Fitting and Its Applications}, year = {2010}, month = {2010///}, pages = {169 - 186}, publisher = {Bentham Science Publishers Ltd.}, organization = {Bentham Science Publishers Ltd.}, url = {http://www.bentham.org/ebooks/9781608050482/http://www.bentham.org/ebooks/9781608050482/}, author = {Rust,Bert W. and O{\textquoteright}Leary, Dianne P. and Mullen,Katharine M.}, editor = {Pereyra,V. and Scherer,G.} } @inbook {15597, title = {New Approaches to Robust, Point-Based Image Registration}, booktitle = {Image Registration for Remote SensingImage Registration for Remote Sensing}, year = {2010}, month = {2010///}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, abstract = {We consider various algorithmic solutions to image registration based on thealignment of a set of feature points. We present a number of enhancements to a branch-and-bound algorithm introduced by Mount, Netanyahu, and Le Moigne (Pattern Recognition, Vol. 32, 1999, pp. 17{\textendash}38), which presented a registration algorithm based on the partial Hausdorff distance. Our enhance- ments include a new distance measure, the discrete Gaussian mismatch, and a number of improvements and extensions to the above search algorithm. Both distance measures are robust to the presence of outliers, that is, data points from either set that do not match any point of the other set. We present experimental studies, which show that the new distance measure considered can provide significant improvements over the partial Hausdorff distance in instances where the number of outliers is not known in advance. These experiments also show that our other algorithmic improvements can offer tangible improvements. We demonstrate the algorithm{\textquoteright}s efficacy by considering images involving different sensors and different spectral bands, both in a traditional framework and in a multiresolution framework. }, isbn = {9780521516112}, author = {Mount, Dave and Netanyahu,N. S and Ratanasanya,S.}, editor = {LeMoigne,Jacqueline and Netanyahu,Nathan S. and Eastman,Roger D.} } @article {16053, title = {New forms of Human-Computer Interaction for Visualizing Information}, journal = {Information Visualization}, year = {2010}, month = {2010///}, abstract = {The Graphical User Interface (GUI) {\textendash} although developed in research laboratories in the late 1970s {\textendash} is still the dominant interaction paradigm in Information Visualization. We propose a new interaction paradigm called Blended Interaction. It combines ideas of Embodied Cognition, Multimodal Interaction, Reality-Based Interaction \& Ubiquitous Computing. This is intended to stress that a single increase in the reality aspect of the interaction cannot go far enough. The particular challenge {\textendash} and from the user{\textquoteright}s standpoint, the key advantage {\textendash} lies in a meaningful marriage between the tested real-world options and the digital world. As a minimum this marriage must exist on the levels of the interaction, communication, of the way we solve problems with conventional tools (workflows), and of the design of the space or the architecture of buildings and places. The digital world often offers entirely new possibilities and takes the form of interactive devices of various shapes but also of intelligent everyday objects (e.g. the {\textquoteright}Internet of things{\textquoteright}). In our view, interaction concepts can indeed offer a new quality of interaction, but only when the design of the interaction includes all these domains at the same time and with equal weighting. We test the suitability of our ideas of Blended Interaction concepts by using specific application examples that are being worked on as part of current research projects. Our experiences show that this new interaction paradigm has also great potential for interacting with visualization. For example, we have developed multi-touch scatter plots \& facet maps for tangible user interfaces supporting the searching \& browsing in Digital Libraries. We have embedded different visualizations into a Zoomable Object-oriented Information Landscape (ZOIL), which supports our vision of using visualizations on different displays of different size at the same time. We have developed specific kind of search tokens that supports collaborative search activities. For example, we try to address the following research questions: * How can future interactive InfoVis tools look like, especially in the light of the idea Blended Interaction? * How can future interactive InfoVis tools benefit from Multi-Displays \& Multimodal environments used by Multiple Users? * What are the specific design requirements for multi-touch visualizations? * How can we support the collaborative use visualization tools?}, author = {Reiterer,H. and Kerren,A. and Plaisant, Catherine and Stasko,J.T.} } @article {12224, title = {Overlay Networking and Resiliency}, journal = {Guide to Reliable Internet Services and Applications}, year = {2010}, month = {2010///}, pages = {221 - 251}, author = {Bhattacharjee, Bobby and Rabinovich,M.} } @article {16600, title = {Parsimonious rule generation for a nature-inspired approach to self-assembly}, journal = {ACM Transactions on Autonomous and Adaptive Systems (TAAS)}, volume = {5}, year = {2010}, month = {2010///}, pages = {1 - 24}, author = {Grushin,A. and Reggia, James A.} } @article {16391, title = {The problem with zoning: nonlinear effects of interactions between location preferences and externalities on land use and utility}, journal = {Environment and Planning B: Planning and Design}, volume = {37}, year = {2010}, month = {2010///}, pages = {408 - 428}, author = {Zellner,M.L. and Riolo,R.L. and Rand, William and Brown,D.G. and Page,S.E. and Fernandez,L.E.} } @conference {15918, title = {Sectored Random Projections for Cancelable Iris Biometrics}, booktitle = {2010 IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP)}, year = {2010}, month = {2010/03//}, pages = {1838 - 1841}, publisher = {IEEE}, organization = {IEEE}, abstract = {Privacy and security are essential requirements in practical biometric systems. In order to prevent the theft of biometric patterns, it is desired to modify them through revocable and non invertible transformations called Cancelable Biometrics. In this paper, we propose an efficient algorithm for generating a Cancelable Iris Biometric based on Sectored Random Projections. Our algorithm can generate a new pattern if the existing one is stolen, retain the original recognition performance and prevent extraction of useful information from the transformed patterns. Our method also addresses some of the drawbacks of existing techniques and is robust to degradations due to eyelids and eyelashes.}, keywords = {biometric pattern, Biometrics, Cancelable Biometrics, cancelable iris biometrics, data mining, data privacy, Degradation, Eyelashes, Eyelids, Iris, iris recognition, pattern recognition, privacy, random processes, Random Projections, Robustness, sectored random projection, Secure Biometrics, Security, security of data}, isbn = {978-1-4244-4295-9}, doi = {10.1109/ICASSP.2010.5495383}, author = {Pillai,J.K. and Patel, Vishal M. and Chellapa, Rama and Ratha,N. K} } @article {12501, title = {Secure and robust iris recognition using random projections and sparse representations}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, year = {2010}, month = {2010///}, pages = {1 - 1}, author = {Pillai, J. and Patel, Vishal M. and Chellapa, Rama and Ratha, N.} } @article {15152, title = {Secure network coding over the integers}, journal = {Public Key Cryptography{\textendash}PKC 2010}, year = {2010}, month = {2010///}, pages = {142 - 160}, abstract = {Network coding offers the potential to increase throughput and improve robustness without any centralized control. Unfortunately, network coding is highly susceptible to {\textquotedblleft}pollution attacks{\textquotedblright} in which malicious nodes modify packets improperly so as to prevent message recovery at the recipient(s); such attacks cannot be prevented using standard end-to-end cryptographic authentication because network coding mandates that intermediate nodes modify data packets in transit.Specialized {\textquotedblleft}network coding signatures{\textquotedblright} addressing this problem have been developed in recent years using homomorphic hashing and homomorphic signatures. We contribute to this area in several ways: {\textbullet} We show the first homomorphic signature scheme based on the RSA assumption (in the random oracle model). {\textbullet} We give a homomorphic hashing scheme that is more efficient than existing schemes, and which leads to network coding signatures based on the hardness of factoring (in the standard model). {\textbullet} We describe variants of existing schemes that reduce the communication overhead for moderate-size networks, and improve computational efficiency (in some cases quite dramatically {\textendash} e.g., we achieve a 20-fold speedup in signature generation at intermediate nodes). Underlying our techniques is a modified approach to random linear network coding where instead of working in a vector space over a field, we work in a module over the integers (with small coefficients). }, doi = {10.1007/978-3-642-13013-7_9}, author = {Gennaro,R. and Katz, Jonathan and Krawczyk,H. and Rabin,T.} } @article {16592, title = {Self-assembly of neural networks viewed as swarm intelligence}, journal = {Swarm Intelligence}, volume = {4}, year = {2010}, month = {2010///}, pages = {1 - 36}, author = {Martin,C. E and Reggia, James A.} } @article {16397, title = {THE SHAKY LADDER HYPERPLANE-DEFINED FUNCTIONS AND CLASSIC DYNAMIC PROBLEMS}, journal = {International Journal of Computational Intelligence and Applications}, volume = {09}, year = {2010}, month = {2010///}, pages = {33 - 33}, abstract = {To improve the understanding of the GA in dynamic environments we explore a set of test problems, the shaky ladder hyper-defined functions (sl-hdf), and extend these functions to create versions that are equivalent to many classical dynamic problems. We do this by constraining the space of all sl-hdfs to create representations of these classical functions. We have examined three classical problems, and compared sl-hdf versions of these problems with their standard representations. These results show that the sl-hdfs are representative of a larger class of problems, and can represent a larger class of test suite. Previous results on sl-hdf showed that GA performance is best in the Defined Cliffs variant of the sl-hdf. We build upon these results to improve GA performance in several classes of real world dynamic problems by modifying the problem representation. These results lend insight into dynamic problems where the GA will perform well.}, isbn = {1469-0268}, doi = {10.1142/S1469026810002756}, url = {http://www.worldscinet.com/ijcia/09/0901/S1469026810002756.html}, author = {Alharbi,Abir and Rand, William} } @article {19725, title = {Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {52}, abstract = {

BACKGROUND: Comparative genomics methods such as phylogenetic profiling can mine powerful inferences from inherently noisy biological data sets. We introduce Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL), a method that applies the Partial Phylogenetic Profiling (PPP) approach locally within a protein sequence to discover short sequence signatures associated with functional sites. The approach is based on the basic scoring mechanism employed by PPP, namely the use of binomial distribution statistics to optimize sequence similarity cutoffs during searches of partitioned training sets.

RESULTS: Here we illustrate and validate the ability of the SIMBAL method to find functionally relevant short sequence signatures by application to two well-characterized protein families. In the first example, we partitioned a family of ABC permeases using a metabolic background property (urea utilization). Thus, the TRUE set for this family comprised members whose genome of origin encoded a urea utilization system. By moving a sliding window across the sequence of a permease, and searching each subsequence in turn against the full set of partitioned proteins, the method found which local sequence signatures best correlated with the urea utilization trait. Mapping of SIMBAL "hot spots" onto crystal structures of homologous permeases reveals that the significant sites are gating determinants on the cytosolic face rather than, say, docking sites for the substrate-binding protein on the extracellular face. In the second example, we partitioned a protein methyltransferase family using gene proximity as a criterion. In this case, the TRUE set comprised those methyltransferases encoded near the gene for the substrate RF-1. SIMBAL identifies sequence regions that map onto the substrate-binding interface while ignoring regions involved in the methyltransferase reaction mechanism in general. Neither method for training set construction requires any prior experimental characterization.

CONCLUSIONS: SIMBAL shows that, in functionally divergent protein families, selected short sequences often significantly outperform their full-length parent sequence for making functional predictions by sequence similarity, suggesting avenues for improved functional classifiers. When combined with structural data, SIMBAL affords the ability to localize and model functional sites.

}, keywords = {algorithms, Amino Acid Sequence, Gene Expression Profiling, Molecular Sequence Data, Phylogeny, Proteins, Sequence Analysis, Protein, Structure-Activity Relationship}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-52}, author = {Jeremy D Selengut and Rusch, Douglas B and Haft, Daniel H} } @conference {18864, title = {Strategy generation in multi-agent imperfect-information pursuit games}, series = {AAMAS {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {947 - 954}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {We describe a formalism and algorithms for game-tree search in partially-observable Euclidean space, and implementation and tests in a scenario where a multi-agent team, called tracking agents, pursues a target agent that wants to evade the tracking agents. Our contributions include--- {\textbullet} A formalism that combines geometric elements (agents{\textquoteright} locations and trajectories and observable regions, and obstacles that restrict mobility and observability) with game-theoretic elements (information sets, utility functions, and strategies). {\textbullet} A recursive formula for information-set minimax values based on our formalism, and a implementation of the formula in a game-tree search algorithm. {\textbullet} A heuristic evaluation function for use at the leaf nodes of the game-tree search. It works by doing a quick lookahead search of its own, in a relaxed version of the problem. {\textbullet} Experimental results in 500 randomly generated trials. With the strategies generated by our heuristic, the tracking agents were more than twice as likely to know the target agent{\textquoteright}s location at the end of the game than with the strategies generated by heuristics that compute estimates of the target{\textquoteright}s possible locations.}, keywords = {game tree search, multi-agent planning, visibility-based pursuit-evasion games}, isbn = {978-0-9826571-1-9}, url = {http://dl.acm.org/citation.cfm?id=1838206.1838333}, author = {Raboin,Eric and Nau, Dana S. and Kuter,Ugur and Gupta, Satyandra K. and Svec,Petr} } @article {13869, title = {System and method for analysis of an opinion expressed in documents with regard to a particular topic}, volume = {11/808,278}, year = {2010}, month = {2010//01/28}, abstract = {System and method for analysis of an opinion expressed in documents on a particular topic computes opinion strength on a continuous numeric scale, or qualitatively. A variety of opinion scoring techniques are plugged in to score opinion expressing words and sentences in documents. These scores are aggregated to measure the opinion intensity of documents. Multilingual opinion analysis is supported by capability to concurrently identify and visualize the opinion intensity expressed in documents in multiple languages. A multi-dimensional representation of the measured opinion intensity is generated which is agreeable with multi-lingual domain.}, url = {http://www.google.com/patents?id=j9fLAAAAEBAJ}, author = {V.S. Subrahmanian and Picariello,Antonio and Dorr, Bonnie J and Reforgiato,Diego Recupero and Cesarano,Carmine and Sagoff,Amelia} } @conference {16504, title = {On trade-offs in event delivery systems}, booktitle = {Proceedings of the Fourth ACM International Conference on Distributed Event-Based Systems}, year = {2010}, month = {2010///}, pages = {116 - 127}, author = {Roitman,H. and Gal,A. and Raschid, Louiqa} } @article {16048, title = {Understanding Interactive Legends: a Comparative Evaluation with Standard Widgets}, journal = {Computer Graphics Forum}, volume = {29}, year = {2010}, month = {2010/06/01/}, pages = {1193 - 1202}, abstract = {Interactive information visualization systems rely on widgets to allow users to interact with the data and modify the representation. We define interactive legends as a class of controls combining the visual representation of static legends and interaction mechanisms of widgets. As interactive legends start to appear in popular websites, we categorize their designs for common data types and evaluate their effectiveness compare to standard widgets. Results suggest that 1) interactive legends can lead to faster perception of the mapping between data values and visual encodings and 2) interaction time is affected differently depending on the data type. Additionally, our study indicates superiority both in terms of perception and interaction of ordinal controls over numerical ones. Numerical techniques are mostly used in today{\textquoteright}s systems. By providing solutions to allowing users to modify ranges interactively, we believe that interactive legends make it possible to increase the use of ordinal techniques for visual exploration.}, keywords = {H.5 [Information Interfaces and Presentation]: Miscellaneous{\textemdash}}, isbn = {1467-8659}, doi = {10.1111/j.1467-8659.2009.01678.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8659.2009.01678.x/abstract;jsessionid=F01A4A94A1103DF771F7EEF705FCF66F.d02t03}, author = {Riche,Nathalie Henry and Lee,Bongshin and Plaisant, Catherine} } @conference {14306, title = {Using symbolic evaluation to understand behavior in configurable software systems}, booktitle = {Software Engineering, 2010 ACM/IEEE 32nd International Conference on}, volume = {1}, year = {2010}, month = {2010///}, pages = {445 - 454}, author = {Reisner,E. and Song,C. and Ma,K.K. and Foster, Jeffrey S. and Porter, Adam} } @article {13030, title = {Validating the systematic position of {\i}t Plationus Segers, Murugan \& Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase}, journal = {Hydrobiologia}, volume = {644}, year = {2010}, month = {2010/05//}, pages = {361 - 370}, abstract = {Members of the family Brachionidae are free-living organisms that range in size from 170 to 250 microns. They comprise part of the zooplankton in freshwater and marine systems worldwide. Morphologically, members of the family are characterized by a single piece loricated body without furrows, grooves, sulci or dorsal head shields, and a malleate trophi. Differences in these structures have been traditionally used to recognize 217 species that are classified into seven genera. However, the validity of the species, Plationus patulus, P. patulus macracanthus P. polyacanthus, and P. felicitas have been confused because they were alternatively assigned in Brachionus or Platyias, when considering only morphological and ecological characters. Based on scanning electron microscope (SEM) images of the trophi, these taxa were assigned in a new genus, Plationus. In this study, we examined the systematic position of P. patulus and P. patulus macracanthus using DNA sequences of two genes: the cytochrome oxidase subunit 1 (cox1) and domains D2 and D3 of the large subunit of the nuclear ribosomal RNA (LSU). In addition, the cox1 and LSU sequences representing five genera of Brachionidae (Anuraeopsis, Brachionus, Keratella, Plationus, and Platyias) plus four species of three families from the order Ploima were used as the outgroup. The maximum likelihood (ML) analyses were conducted for each individual gene as well as for the combined (cox1 + LSU) data set. The ML tree from the combined data set yielded the family Brachionidae as a monophyletic group with weak bootstrap support (< 50\%). Five main clades in this tree had high (> 85\%) bootstrap support. The first clade was composed of three populations of P. patulus + P. patulus macracanthus. The second clade was composed of a single species of Platyias. The third clade was composed of six species of Brachionus. The fourth clade included a single species of the genus Anuraeopsis, and the fifth clade was composed of three species of the genus Keratella. The genetic divergence between Plationus and Platyias ranged from 18.4 to 19.2\% for cox1, and from 4.5 to 4.9\% for LSU, and between Brachionus and Plationus, it ranged from 16.9 to 23.1\% (cox1), and from 7.3 to 9.1\% (LSU). Morphological evidence, the amount of genetic divergence, the systematic position of Plationus within the family Brachionidae, and the position of Plationus as a sister group of Brachionus and Platyias support the validity of Plationus patulus and P. patulus macracanthus into the genus Plationus.}, keywords = {Cox1;, likelihood;, LSU;, maximum, Phylogeny, Plationus;}, doi = {DOI 10.1007/s10750-010-0203-1}, author = {Reyna-Fabian,ME and Laclette,J. P and Cummings, Michael P. and Garc{\'\i}a-Varela,M} } @conference {19463, title = {Who{\textquoteright}s Hogging the Bandwidth: The Consequences of Revealing the Invisible in the Home}, booktitle = {SIGCHI {\textquoteright}10}, series = {CHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {659 - 668}, publisher = {ACM}, organization = {ACM}, abstract = {As more technologies enter the home, householders are burdened with the task of digital housekeeping-managing and sharing digital resources like bandwidth. In response to this, we created and evaluated a domestic tool for bandwidth management called Home Watcher. Our field trial showed that when resource contention amongst different household members is made visible, people{\textquoteright}s understanding of bandwidth changes and household politics are revealed. In this paper, we describe the consequences of showing real time resource usage in a home, and how this varies depending on the social make up of the household.}, keywords = {bandwidth monitoring, home broadband, home networks}, isbn = {978-1-60558-929-9}, url = {http://doi.acm.org/10.1145/1753326.1753423}, author = {Marshini Chetty and Banks, Richard and Harper, Richard and Regan, Tim and Sellen, Abigail and Gkantsidis, Christos and Karagiannis, Thomas and Key, Peter} } @conference {18613, title = {Wide-area route control for distributed services}, booktitle = {Proceedings of the 2010 USENIX conference on USENIX annual technical conference}, series = {USENIXATC{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {2 - 2}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Many distributed services would benefit from control over the flow of traffic to and from their users, to offer better performance and higher reliability at a reasonable cost. Unfortunately, although today{\textquoteright}s cloud-computing platforms offer elastic computing and bandwidth resources, they do not give services control over wide-area routing. We propose replacing the data center{\textquoteright}s border router with a Transit Portal (TP) that gives each service the illusion of direct connectivity to upstream ISPs, without requiring each service to deploy hardware, acquire IP address space, or negotiate contracts with ISPs. Our TP prototype supports many layer-two connectivity mechanisms, amortizes memory and message overhead over multiple services, and protects the rest of the Internet from misconfigured and malicious applications. Our implementation extends and synthesizes open-source software components such as the Linux kernel and the Quagga routing daemon. We also implement a management plane based on the GENI control framework and couple this with our four-site TP deployment and Amazon EC2 facilities. Experiments with an anycast DNS application demonstrate the benefits the TP offers to distributed services.}, url = {http://dl.acm.org/citation.cfm?id=1855840.1855842}, author = {Valancius,Vytautas and Feamster, Nick and Rexford,Jennifer and Nakao,Akihiro} } @article {12533, title = {Age progression in human faces: A survey}, journal = {Journal of Visual Languages and Computing}, volume = {15}, year = {2009}, month = {2009///}, pages = {3349 - 3361}, abstract = {Facial aging, a new dimension that has recently beenadded to the problem of face recognition, poses interesting theo- retical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community, has recently found enhanced interest in the computer vision community. How do humans perceive age ? What constitutes an age-invariant signature that can be derived from faces ? How compactly can the facial growth event be described ? How does facial aging impact recognition performance ? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification etc. and offer insights into future research on this topic. }, author = {Ramanathan,N. and Chellapa, Rama and Biswas,S.} } @conference {16470, title = {ApproxRank: Estimating Rank for a Subgraph}, booktitle = {IEEE 25th International Conference on Data Engineering, 2009. ICDE {\textquoteright}09}, year = {2009}, month = {2009/04/29/March}, pages = {54 - 65}, publisher = {IEEE}, organization = {IEEE}, abstract = {Customized semantic query answering, personalized search, focused crawlers and localized search engines frequently focus on ranking the pages contained within a subgraph of the global Web graph. The challenge for these applications is to compute PageRank-style scores efficiently on the subgraph, i.e., the ranking must reflect the global link structure of the Web graph but it must do so without paying the high overhead associated with a global computation. We propose a framework of an exact solution and an approximate solution for computing ranking on a subgraph. The IdealRank algorithm is an exact solution with the assumption that the scores of external pages are known. We prove that the IdealRank scores for pages in the subgraph converge. Since the PageRank-style scores of external pages may not typically be available, we propose the ApproxRank algorithm to estimate scores for the subgraph. Both IdealRank and ApproxRank represent the set of external pages with an external node L1 and extend the subgraph with links to L1. They also modify the PageRank-style transition matrix with respect to L1. We analyze the L1 distance between IdealRank scores and ApproxRank scores of the subgraph and show that it is within a constant factor of the L1 distance of the external pages (e.g., the true PageRank scores and uniform scores assumed by ApproxRank). We compare ApproxRank and a stochastic complementation approach (SC), a current best solution for this problem, on different types of subgraphs. ApproxRank has similar or superior performance to SC and typically improves on the runtime performance of SC by an order of magnitude or better. We demonstrate that ApproxRank provides a good approximation to PageRank for a variety of subgraphs.}, keywords = {Application software, ApproxRank, Computer applications, Crawlers, customized semantic query answering, Data engineering, Educational institutions, Explosions, focused crawlers, global Web graph, graph theory, IdealRank algorithm, Internet, localized search engines, PageRank-style, personalized search, Query processing, Runtime, Search engines, Stochastic processes, Web pages}, isbn = {978-1-4244-3422-0}, doi = {10.1109/ICDE.2009.108}, author = {Yao Wu and Raschid, Louiqa} } @article {12518, title = {Computational methods for modeling facial aging: A survey}, journal = {Journal of Visual Languages \& Computing}, volume = {20}, year = {2009}, month = {2009/06//}, pages = {131 - 144}, abstract = {Facial aging, a new dimension that has recently been added to the problem of face recognition, poses interesting theoretical and practical challenges to the research community. The problem which originally generated interest in the psychophysics and human perception community has recently found enhanced interest in the computer vision community. How do humans perceive age? What constitutes an age-invariant signature that can be derived from faces? How compactly can the facial growth event be described? How does facial aging impact recognition performance? In this paper, we give a thorough analysis on the problem of facial aging and further provide a complete account of the many interesting studies that have been performed on this topic from different fields. We offer a comparative analysis of various approaches that have been proposed for problems such as age estimation, appearance prediction, face verification, etc. and offer insights into future research on this topic.}, keywords = {age estimation, Age progression, Craniofacial growth, face recognition}, isbn = {1045-926X}, doi = {10.1016/j.jvlc.2009.01.011}, url = {http://www.sciencedirect.com/science/article/pii/S1045926X09000032}, author = {Ramanathan,Narayanan and Chellapa, Rama and Biswas,Soma} } @article {16739, title = {Conceptual modeling: past, present and the continuum of the future}, journal = {Conceptual Modeling: Foundations and Applications}, year = {2009}, month = {2009///}, pages = {139 - 152}, author = {Roussopoulos, Nick and Karagiannis,D.} } @conference {13097, title = {Concurrent transition and shot detection in football videos using Fuzzy Logic}, booktitle = {Image Processing (ICIP), 2009 16th IEEE International Conference on}, year = {2009}, month = {2009/11//}, pages = {4341 - 4344}, abstract = {Shot detection is a fundamental step in video processing and analysis that should be achieved with high degree of accuracy. In this paper, we introduce a unified algorithm for shot detection in sports video using fuzzy logic as a powerful inference mechanism. Fuzzy logic overcomes the problems of hard cut thresholds and the need to large training data used in previous work. The proposed algorithm integrates many features like color histogram, edgeness, intensity variance, etc. Membership functions to represent different features and transitions between shots have been developed to detect different shot boundary and transition types. We address the detection of cut, fade, dissolve, and wipe shot transitions. The results show that our algorithm achieves high degree of accuracy.}, keywords = {analysis;inference, boundary;shot, Color, colour, detection;sports, functions;shot, histogram;concurrent, logic;image, logic;inference, mechanism;intensity, mechanisms;sport;video, processing;, processing;videonanalysis;fuzzy, signal, transition;edgeness;football, variance;membership, video;video, videos;fuzzy}, doi = {10.1109/ICIP.2009.5413648}, author = {Refaey,M.A. and Elsayed,K.M. and Hanafy,S.M. and Davis, Larry S.} } @conference {15269, title = {A cooperative combinatorial Particle Swarm Optimization algorithm for side-chain packing}, booktitle = {IEEE Swarm Intelligence Symposium, 2009. SIS {\textquoteright}09}, year = {2009}, month = {2009/04/30/March}, pages = {22 - 29}, publisher = {IEEE}, organization = {IEEE}, abstract = {Particle Swarm Optimization (PSO) is a well-known, competitive technique for numerical optimization with real-parameter representation. This paper introduces CCPSO, a new Cooperative Particle Swarm Optimization algorithm for combinatorial problems. The cooperative strategy is achieved by splitting the candidate solution vector into components, where each component is optimized by a particle. Particles move throughout a continuous space, their movements based on the influences exerted by static particles that then get feedback based on the fitness of the candidate solution. Here, the application of this technique to side-chain packing (a proteomics optimization problem) is investigated. To verify the efficiency of the proposed CCPSO algorithm, we test our algorithm on three side-chain packing problems and compare our results with the provably optimal result. Computational results show that the proposed algorithm is very competitive, obtaining a conformation with an energy value within 1\% of the provably optimal solution in many proteins.}, keywords = {Algorithm design and analysis, Amino acids, combinatorial mathematics, cooperative combinatorial particle swarm optimization algorithm, Design optimization, Encoding, Feedback, numerical optimization, Optimization methods, particle swarm optimisation, Particle swarm optimization, Partitioning algorithms, Proteins, proteomics, proteomics optimization, Robustness, side-chain packing}, isbn = {978-1-4244-2762-8}, doi = {10.1109/SIS.2009.4937840}, author = {Lapizco-Encinas,G. and Kingsford, Carl and Reggia, James A.} } @conference {12230, title = {CPM: Adaptive Video-on-Demand with Cooperative Peer Assists and Multicast}, booktitle = {INFOCOM 2009, IEEE}, year = {2009}, month = {2009/04//}, pages = {91 - 99}, abstract = {We present CPM, a unified approach that exploits server multicast, assisted by peer downloads, to provide efficient video-on-demand (VoD) in a service provider environment. We describe our architecture and show how CPM is designed to dynamically adapt to a wide range of situations including highly different peer-upload bandwidths, content popularity, user request arrival patterns, video library size, and subscriber population. We demonstrate the effectiveness of CPM using simulations (based on an actual implementation codebase) across the range of situations described above and show that CPM does significantly better than traditional unicast, different forms of multicast, as well as peer-to-peer schemes. Along with synthetic parameters, we augment our experiments using data from a deployed VoD service to evaluate the performance of CPM.}, keywords = {assists;multicast;peer-to-peer, communication;peer-to-peer, computing;video, CPM;cooperative, demand;, on, parameters;video-on-demand;multicast, peer, schemes;synthetic}, doi = {10.1109/INFCOM.2009.5061910}, author = {Gopalakrishnan,V. and Bhattacharjee, Bobby and Ramakrishnan,K.K. and Jana,R. and Srivastava,D.} } @conference {17037, title = {Creativity challenges and opportunities in social computing}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {3283 - 3286}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {There is a convergence in recent theories of creativity that go beyond characteristics and cognitive processes of individuals to recognize the importance of the social construction of creativity. In parallel, there has been a rise in social computing supporting the collaborative construction of knowledge. The panel will discuss the challenges and opportunities from the confluence of these two developments by bringing together the contrasting and controversial perspective of the individual panel members. It will synthesize from different perspectives an analytic framework to understand these new developments, and how to promote rigorous research methods and how to identify the unique challenges in developing evaluation and assessment methods for creativity research.}, keywords = {creativity, social computing}, isbn = {978-1-60558-247-4}, doi = {10.1145/1520340.1520470}, url = {http://doi.acm.org/10.1145/1520340.1520470}, author = {Fischer,Gerhard and Jennings,Pamela and Maher,Mary Lou and Resnick,Mitchel and Shneiderman, Ben} } @article {16401, title = {Design guidelines for agent based model visualization}, journal = {Journal of Artificial Societies and Social Simulation}, volume = {12}, year = {2009}, month = {2009///}, pages = {1 - 1}, abstract = {In the field of agent-based modeling (ABM), visualizations play an important role in identifying, communicating and understanding important behavior of the modeled phenomenon. However, many modelers tend to create ineffective visualizations of Agent Based Models (ABM) due to lack of experience with visual design. This paper provides ABM visualization design guidelines in order to improve visual design with ABM toolkits. These guidelines will assist the modeler in creating clear and understandable ABM visualizations. We begin by introducing a non-hierarchical categorization of ABM visualizations. This categorization serves as a starting point in the creation of an ABM visualization. We go on to present well-known design techniques in the context of ABM visualization. These techniques are based on Gestalt psychology, semiology of graphics, and scientific visualization. They improve the visualization design by facilitating specific tasks, and providing a common language to critique visualizations through the use of visual variables. Subsequently, we discuss the application of these design techniques to simplify, emphasize and explain an ABM visualization. Finally, we illustrate these guidelines using a simple redesign of a NetLogo ABM visualization. These guidelines can be used to inform the development of design tools that assist users in the creation of ABM visualizations.}, author = {Kornhauser,D. and Wilensky,U. and Rand, William} } @article {12532, title = {Detecting humans carrying objects}, journal = {SPIE Newsroom}, year = {2009}, month = {2009///}, abstract = {Decomposing an image sequence into slices that generate twisted patterns sufficiently characterizes human gait and a particular class of activities.}, isbn = {18182259}, doi = {10.1117/2.1200902.1511}, url = {https://spie.org/x33692.xml?ArticleID=x33692}, author = {Yang Ran and Qinfen Zheng and Chellapa, Rama} } @article {12891, title = {Determination of relationships among non-toxigenic Vibrio cholerae O1 biotype El Tor strains from housekeeping gene sequences and ribotype patterns}, journal = {Research in Microbiology}, volume = {160}, year = {2009}, month = {2009/01//}, pages = {57 - 62}, abstract = {Sequencing of three housekeeping genes, mdh, dnaE and recA, and ribotyping for seven non-toxigenic Vibrio cholerae O1 strains isolated from different geographic sources indicate a phylogenetic relationship among the strains. Results of MLST and ribotyping indicate a clear difference between three toxigenic strains (N16961, O395, and 569B) and three non-toxigenic strains from India (GS1, GS2, and GW87) and one Guam strain (X392), the latter of which were similar in both MLST and ribotyping, while two other non-toxigenic strains from the USA and India (2740-80 and OR69) appeared to be more closely related to toxigenic strains than to non-toxigenic strains, although this was not supported by ribotyping. These results provide clues to the emergence of toxigenic strains from a non-toxigenic progenitor by acquisition of virulence gene clusters. Results of split decomposition analysis suggest that widespread recombination occurs among the three housekeeping genes and that recombination plays an important role in the emergence of toxigenic strains of V. cholerae O1.}, keywords = {Housekeeping genes, Ribotyping, sequencing, Vibrio cholerae}, isbn = {0923-2508}, doi = {10.1016/j.resmic.2008.10.008}, url = {http://www.sciencedirect.com/science/article/pii/S0923250808001794}, author = {Mohapatra,Saswat S. and Ramachandran,Dhanya and Mantri,Chinmay K. and Rita R Colwell and Singh,Durg V.} } @article {16642, title = {A distributed learning algorithm for particle systems}, journal = {Integrated Computer-Aided Engineering}, volume = {16}, year = {2009}, month = {2009///}, pages = {1 - 20}, author = {Rodr{\'\i}guez,A. and Reggia, James A.} } @article {17095, title = {Do you know the way to SNA?: A process model for analyzing and visualizing social media data}, journal = {University of Maryland Tech Report: HCIL-2009-17}, year = {2009}, month = {2009///}, abstract = {Traces of activity left by social media users can shed lighton individual behavior, social relationships, and community efficacy. Tools and processes to analyze social traces are essential for enabling practitioners to study and nurture meaningful and sustainable social interaction. Yet such tools and processes remain in their infancy. We conducted a study of 15 graduate students who were learning to apply Social Network Analysis (SNA) to data from online communities. Based on close observations of their emergent practices, we derived the Network Analysis and Visualization (NAV) process model and identified stages where intervention from peers, experts, and an SNA tool were most useful. We show how the NAV model informs the design of SNA tools and services, education practices, and support for social media practitioners. }, author = {Hansen,D. L and Rotman,D. and Bonsignore,E. and Milic-Frayling,N. and Rodrigues,E.M. and Smith,M. and Shneiderman, Ben} } @inbook {19635, title = {Efficient Robust Private Set Intersection}, booktitle = {Applied Cryptography and Network Security}, series = {Lecture Notes in Computer Science}, year = {2009}, month = {2009/01/01/}, pages = {125 - 142}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Computing Set Intersection privately and efficiently between two mutually mistrusting parties is an important basic procedure in the area of private data mining. Assuring robustness, namely, coping with potentially arbitrarily misbehaving (i.e., malicious) parties, while retaining protocol efficiency (rather than employing costly generic techniques) is an open problem. In this work the first solution to this problem is presented.}, keywords = {Coding and Information Theory, Computer Communication Networks, Cryptographic protocols, Data Encryption, Data Structures, Cryptology and Information Theory, Information Systems Applications (incl.Internet), Privacy Preserving Data Mining, Secure Two-party Computation, Set Intersection, Systems and Data Security}, isbn = {978-3-642-01956-2, 978-3-642-01957-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-01957-9_8}, author = {Dana Dachman-Soled and Malkin, Tal and Raykova, Mariana and Yung, Moti}, editor = {Abdalla, Michel and Pointcheval, David and Fouque, Pierre-Alain and Vergnaud, Damien} } @article {16404, title = {The emergence of zoning policy games in exurban jurisdictions: Informing collective action theory}, journal = {Land Use Policy}, volume = {26}, year = {2009}, month = {2009/04//}, pages = {356 - 367}, abstract = {Theoretical urban policy literature predicts the likelihood of free riding in the management of common goods such as forested open space; such outcome is often characterized as a Prisoner{\textquoteright}s Dilemma game. Numerous cases exist in which neighboring jurisdictions cooperate to maintain public goods, challenging the expected results, yet theoretical explanations of these cases have not been fully developed. In this paper, we use an agent-based model to explore how underlying micro-behaviors affect the payoffs obtained by two neighboring municipalities in a hypothetical exurban area. Payoffs are measured in terms of regional forested space and of local tax revenue at the end of the agent-based simulations; the municipalities affect these payoffs through their choice of residential zoning policies and the spillover effect between the neighboring jurisdictions. Zoning restrictions influence the conversion of farmland into residential subdivisions of different types, and consequently the location of heterogeneous residential households in the region. Developers and residents respond to the changing landscape characteristics, thus establishing a feedback between early and future land-use patterns. The structure of the simulated payoffs is analyzed using standard game theory. Our analysis shows that a variety of games, in addition to Prisoner{\textquoteright}s Dilemma, can emerge between the neighboring jurisdictions. Other games encourage coordination or subsidization, offering some explanations for the unexpected observations. The game realized in any given context depends on the initial characteristics of the landscape, the value given to the objectives each township seeks to maximize, and the income distribution of the population.}, keywords = {Agent-based modeling, game theory, Land-use policy, Local government cooperation, Scale interaction}, isbn = {0264-8377}, doi = {10.1016/j.landusepol.2008.04.004}, url = {http://www.sciencedirect.com/science/article/pii/S0264837708000604}, author = {Zellner,Moira L. and Page,Scott E. and Rand, William and Brown,Daniel G. and Robinson,Derek T. and Nassauer,Joan and Low,Bobbi} } @conference {12517, title = {Enforcing integrability by error correction using l1-minimization}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {2350 - 2357}, abstract = {Surface reconstruction from gradient fields is an important final step in several applications involving gradient manipulations and estimation. Typically, the resulting gradient field is non-integrable due to linear/non-linear gradient manipulations, or due to presence of noise/outliers in gradient estimation. In this paper, we analyze integrability as error correction, inspired from recent work in compressed sensing, particulary lscr0 - lscr1 equivalence. We propose to obtain the surface by finding the gradient field which best fits the corrupted gradient field in lscr1 sense. We present an exhaustive analysis of the properties of lscr1 solution for gradient field integration using linear algebra and graph analogy. We consider three cases: (a) noise, but no outliers (b) no-noise but outliers and (c) presence of both noise and outliers in the given gradient field. We show that lscr1 solution performs as well as least squares in the absence of outliers. While previous lscr0 - lscr1 equivalence work has focused on the number of errors (outliers), we show that the location of errors is equally important for gradient field integration. We characterize the lscr1 solution both in terms of location and number of outliers, and outline scenarios where lscr1 solution is equivalent to lscr0 solution. We also show that when lscr1 solution is not able to remove outliers, the property of local error confinement holds: i.e., the errors do not propagate to the entire surface as in least squares. We compare with previous techniques and show that lscr1 solution performs well across all scenarios without the need for any tunable parameter adjustments.}, keywords = {-, algebra;lscr0, algebra;minimisation;, analogy;integrability;least, compressed, correction;gradient, equivalence;lscr1-minimization;noise-outlier;surface, estimation;gradient, field, integration;gradient, lscr1, manipulation;graph, methods;graph, reconstruction;error, reconstruction;linear, sensing;error, squares;linear, theory;image}, doi = {10.1109/CVPR.2009.5206603}, author = {Reddy, D. and Agrawal,A. and Chellapa, Rama} } @conference {16691, title = {Estimating semantic distance using soft semantic constraints in knowledge-source-corpus hybrid models}, booktitle = {Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 2-Volume 2}, year = {2009}, month = {2009///}, pages = {775 - 783}, author = {Marton,Y. and Mohammad,S. and Resnik, Philip} } @conference {17168, title = {First Steps to Netviz Nirvana: Evaluating Social Network Analysis with NodeXL}, booktitle = {International Conference on Computational Science and Engineering, 2009. CSE {\textquoteright}09}, volume = {4}, year = {2009}, month = {2009/08/29/31}, pages = {332 - 339}, publisher = {IEEE}, organization = {IEEE}, abstract = {Social Network Analysis (SNA) has evolved as a popular, standard method for modeling meaningful, often hidden structural relationships in communities. Existing SNA tools often involve extensive pre-processing or intensive programming skills that can challenge practitioners and students alike. NodeXL, an open-source template for Microsoft Excel, integrates a library of common network metrics and graph layout algorithms within the familiar spreadsheet format, offering a potentially low-barrier-to-entry framework for teaching and learning SNA. We present the preliminary findings of 2 user studies of 21 graduate students who engaged in SNA using NodeXL. The majority of students, while information professionals, had little technical background or experience with SNA techniques. Six of the participants had more technical backgrounds and were chosen specifically for their experience with graph drawing and information visualization. Our primary objectives were (1) to evaluate NodeXL as an SNA tool for a broad base of users and (2) to explore methods for teaching SNA. Our complementary dual case-study format demonstrates the usability of NodeXL for a diverse set of users, and significantly, the power of a tightly integrated metrics/visualization tool to spark insight and facilitate sense-making for students of SNA.}, keywords = {Computer science, computer science education, data visualisation, Data visualization, Educational institutions, graph drawing, graph layout algorithm, Information services, Information Visualization, Internet, Libraries, Microsoft Excel open-source template, MILC, multi-dimensional in-depth long-term case studies, Netviz Nirvana, NodeXL, Open source software, Programming profession, SNA, social network analysis, Social network services, social networking (online), spreadsheet programs, structural relationship, teaching, visual analytics, visualization tool, Web sites}, isbn = {978-1-4244-5334-4}, doi = {10.1109/CSE.2009.120}, author = {Bonsignore,E. M and Dunne,C. and Rotman,D. and Smith,M. and Capone,T. and Hansen,D. L and Shneiderman, Ben} } @conference {16485, title = {Flexible and efficient querying and ranking on hyperlinked data sources}, booktitle = {Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology}, year = {2009}, month = {2009///}, pages = {553 - 564}, author = {Varadarajan,R. and Hristidis,V. and Raschid, Louiqa and Vidal,M. E and Ib{\'a}\ nez,L. and Rodr{\'\i}guez-Drumond,H.} } @article {12178, title = {From New Zealand to Mongolia: Co-designing and deploying a digital library for the world{\textquoteright}s children}, journal = {Special issue of Children, Youth and Environments: Children in Technological Environments: Interaction, Development, and Design}, year = {2009}, month = {2009///}, author = {Druin, Allison and Bederson, Benjamin B. and Rose,A. and Weeks,A.} } @article {14614, title = {Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo}, journal = {DiabetesDiabetes}, volume = {58}, year = {2009}, month = {2009/10/01/}, pages = {2211 - 2219}, abstract = {OBJECTIVE Adipose inflammation plays a central role in obesity-related metabolic and cardiovascular complications. However, few human adipose-secreted proteins are known to mediate these processes. We hypothesized that microarray mRNA profiling of human adipose during evoked inflammation could identify novel adipocytokines.RESEARCH DESIGN AND METHODS Healthy human volunteers (n = 14) were treated with intravenous endotoxin (3 ng/kg lipopolysaccharide [LPS]) and underwent subcutaneous adipose biopsies before and after LPS. On Affymetrix U133Plus 2.0 arrays, adipose mRNAs modulated >1.5-fold (with P < 0.00001) were selected. SignalP 3.0 and SecretomeP 2.0 identified genes predicted to encode secreted proteins. Of these, 86 candidates were chosen for validation in adipose from an independent human endotoxemia protocol (N = 7, with 0.6 ng/kg LPS) and for exploration of cellular origin in primary human adipocytes and macrophages in vitro. RESULTS Microarray identified 776 adipose genes modulated by LPS; 298 were predicted to be secreted. Of detectable prioritized genes, 82 of 85 (96\% [95\% CI 90{\textendash}99]) were upregulated (fold changes >1.0) during the lower-dose (LPS 0.6 ng/kg) validation study and 51 of 85 (59\% [49{\textendash}70]) were induced greater than 1.5-fold. Treatment of primary adipocytes with LPS and macrophage polarization to M1 proinflammatory phenotype increased expression by 1.5-fold for 58 and 73\% of detectable genes, respectively. CONCLUSIONS We demonstrate that evoked inflammation of human adipose in vivo modulated expression of multiple genes likely secreted by adipocytes and monocytes. These included established adipocytokines and chemokines implicated in recruitment and activation of lymphocytes, adhesion molecules, antioxidants, and several novel genes with unknown function. Such candidates may represent biomarkers and therapeutic targets for obesity-related complications. }, isbn = {0012-1797, 1939-327X}, doi = {10.2337/db09-0256}, url = {http://diabetes.diabetesjournals.org/content/58/10/2211}, author = {Shah,Rachana and Lu,Yun and Hinkle,Christine C and McGillicuddy,Fiona C and Kim,Roy and Hannenhalli, Sridhar and Cappola,Thomas P. and Heffron,Sean and Wang,XingMei and Mehta,Nehal N and Putt,Mary and Reilly,Muredach P} } @article {13780, title = {Generating surveys of scientific paradigms}, journal = {Proceedings of HLT-NAACL}, year = {2009}, month = {2009///}, abstract = {The number of research publications in var-ious disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of tech- nical material. In this paper we present the first steps in producing an automatically gen- erated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization tech- niques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the frame- work of multi-document survey creation, cita- tion texts can play a crucial role. }, author = {Mohammad,S. and Dorr, Bonnie J and Egan,M. and Hassan,A. and Muthukrishan,P. and Qazvinian,V. and Radev,D. and Zajic, David} } @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} } @conference {12509, title = {How would you look as you age ?}, booktitle = {Image Processing (ICIP), 2009 16th IEEE International Conference on}, year = {2009}, month = {2009/11//}, pages = {53 - 56}, abstract = {Facial appearances change with increase in age. While generic growth patterns that are characteristic of different age groups can be identified, facial growth is also observed to be influenced by individual-specific attributes such as one{\textquoteright}s gender, ethnicity, life-style etc. In this paper, we propose a facial growth model that comprises of transformation models for facial shape and texture. We collected empirical data pertaining to facial growth from a database of age-separated face images of adults and used the same in developing the aforementioned transformation models. The proposed model finds applications in predicting one{\textquoteright}s appearance across ages and in performing face verification across ages.}, keywords = {age-separated, appearances;facial, database;face, Face, growth, image, model;face, model;facial, models;facial, recognition;image, SHAPE, TEXTURE, texture;, transformation, verification;facial}, doi = {10.1109/ICIP.2009.5413998}, author = {Ramanathan,N. and Chellapa, Rama} } @conference {16679, title = {Improved statistical machine translation using monolingually-derived paraphrases}, booktitle = {Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1-Volume 1}, year = {2009}, month = {2009///}, pages = {381 - 390}, author = {Marton,Y. and Callison-Burch,C. and Resnik, Philip} } @conference {16604, title = {Improving rule extraction from neural networks by modifying hidden layer representations}, booktitle = {Neural Networks, 2009. IJCNN 2009. International Joint Conference on}, year = {2009}, month = {2009///}, pages = {1316 - 1321}, author = {Huynh,T. Q and Reggia, James A.} } @article {13040, title = {The infinite hierarchical factor regression model}, journal = {Arxiv preprint arXiv:0908.0570}, year = {2009}, month = {2009///}, author = {Rai,P. and Daum{\'e}, Hal} } @conference {15491, title = {An Initial Characterization of Industrial Graphical User Interface Systems}, booktitle = {Software Testing Verification and Validation, 2009. ICST {\textquoteright}09. International Conference on}, year = {2009}, month = {2009/04//}, pages = {11 - 20}, abstract = {To date we have developed and applied numerous model-based GUI testing techniques; however, we are unable to provide definitive improvement schemes to real-world GUI test planners, as our data was derived from open source applications, small compared to industrial systems. This paper presents a study of three industrial GUI-based software systems developed at ABB, including data on classified defects detected during late-phase testing and customer usage, test suites, and source code change metrics. The results show that (1) 50\% of the defects found through the GUI are categorized as data access and handling, control flow and sequencing, correctness, and processing defects, (2) system crashes exposed defects 12-19\% of the time, and (3) GUI and non-GUI components are constructed differently, in terms of source code metrics.}, keywords = {Graphical user interfaces, GUI-based software systems, industrial graphical user interface systems, model-based GUI testing techniques, program testing, software metrics, source code change metrics}, doi = {10.1109/ICST.2009.11}, author = {Brooks,P.A. and Robinson,B.P. and Memon, Atif M.} } @article {19460, title = {The Ins and Outs of Home Networking: The Case for Useful and Usable Domestic Networking}, journal = {ACM Trans. Comput.-Hum. Interact.}, volume = {16}, year = {2009}, month = {2009/06//}, pages = {8:1 - 8:28}, abstract = {Householders are increasingly adopting home networking as a solution to the demands created by the presence of multiple computers, devices, and the desire to access the Internet. However, current network solutions are derived from the world of work (and initially the military) and provide poor support for the needs of the home. We present the key findings to emerge from empirical studies of home networks in the UK and US. The studies reveal two key kinds of work that effective home networking relies upon: one, the technical work of setting up and maintaining the home network, and the other, the collaborative and socially organized work of the home which the network is embedded in and supports. The two are thoroughly intertwined and rely upon one another for their realization, yet neither is adequately supported by current networking technologies and applications. Explication of the {\textquotedblleft}work to make the home network work{\textquotedblright} opens up the design space for the continued integration of the home network in domestic life and elaboration of future support. Key issues for development include the development of networking facilities that do not require advanced networking knowledge, that are flexible and support the local social order of the home and the evolution of its routines, and which ultimately make the home network visible and accountable to household members.}, keywords = {home networking, Human computer interaction}, isbn = {1073-0516}, url = {http://doi.acm.org/10.1145/1534903.1534905}, author = {Grinter, Rebecca E. and Edwards, W. Keith and Marshini Chetty and Poole, Erika S. and Sung, Ja-Young and Yang, Jeonghwa and Crabtree, Andy and Tolmie, Peter and Rodden, Tom and Greenhalgh, Chris and Benford, Steve} } @inbook {13797, title = {Interlingual annotation of multilingual text corpora and FrameNet}, booktitle = {Multilingual FrameNets in Computational LexicographyMultilingual FrameNets in Computational Lexicography}, volume = {200}, year = {2009}, month = {2009/07/14/}, pages = {287 - 318}, publisher = {Mouton de Gruyter}, organization = {Mouton de Gruyter}, address = {Berlin, New York}, isbn = {978-3-11-021296-9, 978-3-11-021297-6}, url = {http://www.degruyter.com/view/books/9783110212976/9783110212976.4.287/9783110212976.4.287.xml}, author = {Farwell,David and Dorr, Bonnie J and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Green,Rebecca and Levin,Lori and Miller,Keith and Mitamura,Teruko and Rambow,Owen and Reeder,Flo and Siddharthan,Advaith}, editor = {Bisang,Walter and Hock,Hans Henrich and Winter,Werner and Boas,Hans C.} } @article {12534, title = {Learning Facial Aging Models: A Face Recognition Perspective}, journal = {Biometrics: theory, methods, and applications}, volume = {9}, year = {2009}, month = {2009///}, pages = {271 - 271}, author = {Ramanathan,N. and Chellapa, Rama} } @conference {16683, title = {More than words: Syntactic packaging and implicit sentiment}, booktitle = {Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, year = {2009}, month = {2009///}, pages = {503 - 511}, author = {Greene,S. and Resnik, Philip} } @article {13058, title = {Multi-label prediction via sparse infinite CCA}, journal = {Advances in Neural Information Processing Systems}, volume = {22}, year = {2009}, month = {2009///}, pages = {1518 - 1526}, author = {Rai,P. and Daum{\'e}, Hal} } @article {13613, title = {Off-Line Loop Investigation for Handwriting Analysis}, journal = {IEEETransactions on Pattern Analysis and Machine Intelligence}, volume = {31}, year = {2009}, month = {2009/02//}, pages = {193 - 209}, author = {Steinherz,T. and David Doermann and Rivlin,E. and Intrator,N.} } @article {16606, title = {An oscillatory hebbian network model of short-term memory}, journal = {Neural computation}, volume = {21}, year = {2009}, month = {2009///}, pages = {741 - 761}, author = {Winder,R. K and Reggia, James A. and Weems,S. A and Bunting,M. F} } @article {16432, title = {Participatory simulation as a tool for agent-based simulation}, journal = {Proceedings of the International Conference on Agents and Artificial Intelligence (ICAART-09)}, year = {2009}, month = {2009///}, abstract = {Participatory simulation, as described by Wilensky \& Stroup (1999c), is a form of agent-based simulation inwhich multiple humans control or design individual agents in the simulation. For instance, in a participatory simulation of an ecosystem, fifty participants might each control the intake and output of one agent, such that the food web emerges from the interactions of the human-controlled agents. We argue that participatory simulation has been under-utilized outside of strictly educational contexts, and that it provides myriad benefits to designers of traditional agent-based simulations. These benefits include increased robustness of the model, increased comprehensibility of the findings, and simpler design of individual agent behaviors. To make this argument, we look to recent research such as that from crowdsourcing (von Ahn, 2005) and the reinforcement learning of autonomous agent behavior (Abbeel, 2008). }, author = {Berland,M. and Rand, William} } @inbook {19041, title = {Predicate Privacy in Encryption Systems}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, volume = {5444}, year = {2009}, month = {2009}, pages = {457 - 473}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Predicate encryption is a new encryption paradigm which gives a master secret key owner fine-grained control over access to encrypted data. The master secret key owner can generate secret key tokens corresponding to predicates. An encryption of data x can be evaluated using a secret token corresponding to a predicate f ; the user learns whether the data satisfies the predicate, i.e., whether f ( x ) = 1. Prior work on public-key predicate encryption has focused on the notion of data or plaintext privacy, the property that ciphertexts reveal no information about the encrypted data to an attacker other than what is inherently revealed by the tokens the attacker possesses. In this paper, we consider a new notion called predicate privacy , the property that tokens reveal no information about the encoded query predicate. Predicate privacy is inherently impossible to achieve in the public-key setting and has therefore received little attention in prior work. In this work, we consider predicate encryption in the symmetric-key setting and present a symmetric-key predicate encryption scheme which supports inner product queries. We prove that our scheme achieves both plaintext privacy and predicate privacy.}, keywords = {Computer science}, isbn = {978-3-642-00456-8}, url = {http://www.springerlink.com/content/1717x5445k4718rp/abstract/}, author = {Shen, Emily and Elaine Shi and Waters,Brent}, editor = {Reingold, Omer} } @article {18527, title = {Pushing Enterprise Security Down the Network Stack}, volume = {GT-CS-09-03}, year = {2009}, month = {2009///}, institution = {Georgia Institute of Technology}, abstract = {Network security is typically reactive: Networks provide connectivity and subsequently alter this connectivity according to various security policies, as implemented in middleboxes, or at higher layers. This approach gives rise to complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. In this paper, we propose a proactive approach to securing networks, whereby security-related actions (e.g., dropping or redirecting traffic) are embedded into the network fabric itself, leaving only a fixed set of actions to higher layers. We explore this approach in the context of network access control. Our design uses programmable switches to manipulate traffic at lower layers; these switches interact with policy and monitoring at higher layers. We apply our approach to Georgia Tech{\textquoteright}s network access control system, show how the new design can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.}, url = {http://hdl.handle.net/1853/30782}, author = {Clark,R. and Feamster, Nick and Nayak,A. and Reimers,A.} } @article {12515, title = {Rate-Invariant Recognition of Humans and Their Activities}, journal = {Image Processing, IEEE Transactions on}, volume = {18}, year = {2009}, month = {2009/06//}, pages = {1326 - 1339}, abstract = {Pattern recognition in video is a challenging task because of the multitude of spatio-temporal variations that occur in different videos capturing the exact same event. While traditional pattern-theoretic approaches account for the spatial changes that occur due to lighting and pose, very little has been done to address the effect of temporal rate changes in the executions of an event. In this paper, we provide a systematic model-based approach to learn the nature of such temporal variations (time warps) while simultaneously allowing for the spatial variations in the descriptors. We illustrate our approach for the problem of action recognition and provide experimental justification for the importance of accounting for rate variations in action recognition. The model is composed of a nominal activity trajectory and a function space capturing the probability distribution of activity-specific time warping transformations. We use the square-root parameterization of time warps to derive geodesics, distance measures, and probability distributions on the space of time warping functions. We then design a Bayesian algorithm which treats the execution rate function as a nuisance variable and integrates it out using Monte Carlo sampling, to generate estimates of class posteriors. This approach allows us to learn the space of time warps for each activity while simultaneously capturing other intra- and interclass variations. Next, we discuss a special case of this approach which assumes a uniform distribution on the space of time warping functions and show how computationally efficient inference algorithms may be derived for this special case. We discuss the relative advantages and disadvantages of both approaches and show their efficacy using experiments on gait-based person identification and activity recognition.}, keywords = {Automated;Video Recording;, Bayesian algorithm;Monte Carlo sampling;action recognition;activity-specific time warping transformations;computationally efficient inference algorithms;distance measures;execution rate function;function space;gait-based person identification;geodesics;no, Statistical;Monte Carlo Method;Movement;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2009.2017143}, author = {Veeraraghavan,A. and Srivastava, A. and Roy-Chowdhury, A.K. and Chellapa, Rama} } @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 {18598, title = {Resonance: dynamic access control for enterprise networks}, booktitle = {Proceedings of the 1st ACM workshop on Research on enterprise networking}, series = {WREN {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {11 - 18}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Enterprise network security is typically reactive, and it relies heavily on host security and middleboxes. This approach creates complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. We argue that imbuing the network layer with mechanisms for dynamic access control can remedy these ills. We propose Resonance, a system for securing enterprise networks, where the network elements themselves enforce dynamic access control policies based on both flow-level information and real-time alerts. Resonance uses programmable switches to manipulate traffic at lower layers; these switches take actions (e.g., dropping or redirecting traffic) to enforce high-level security policies based on input from both higherlevel security policies and distributed monitoring and inference systems. We describe the design of Resonance, apply it to Georgia Tech{\textquoteright}s network access control system, show how it can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.}, keywords = {Access control, enterprise networks, programmable networks}, isbn = {978-1-60558-443-0}, doi = {10.1145/1592681.1592684}, url = {http://doi.acm.org/10.1145/1592681.1592684}, author = {Nayak,Ankur Kumar and Reimers,Alex and Feamster, Nick and Clark,Russ} } @article {12884, title = {RNA Colony Blot Hybridization Method for Enumeration of Culturable Vibrio Cholerae and Vibrio Mimicus Bacteria}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/09/01/}, pages = {5439 - 5444}, abstract = {A species-specific RNA colony blot hybridization protocol was developed for enumeration of culturable Vibrio cholerae and Vibrio mimicus bacteria in environmental water samples. Bacterial colonies on selective or nonselective plates were lysed by sodium dodecyl sulfate, and the lysates were immobilized on nylon membranes. A fluorescently labeled oligonucleotide probe targeting a phylogenetic signature sequence of 16S rRNA of V. cholerae and V. mimicus was hybridized to rRNA molecules immobilized on the nylon colony lift blots. The protocol produced strong positive signals for all colonies of the 15 diverse V. cholerae-V. mimicus strains tested, indicating 100\% sensitivity of the probe for the targeted species. For visible colonies of 10 nontarget species, the specificity of the probe was calculated to be 90\% because of a weak positive signal produced by Grimontia (Vibrio) hollisae, a marine bacterium. When both the sensitivity and specificity of the assay were evaluated using lake water samples amended with a bioluminescent V. cholerae strain, no false-negative or false-positive results were found, indicating 100\% sensitivity and specificity for culturable bacterial populations in freshwater samples when G. hollisae was not present. When the protocol was applied to laboratory microcosms containing V. cholerae attached to live copepods, copepods were found to carry approximately 10,000 to 50,000 CFU of V. cholerae per copepod. The protocol was also used to analyze pond water samples collected in an area of cholera endemicity in Bangladesh over a 9-month period. Water samples collected from six ponds demonstrated a peak in abundance of total culturable V. cholerae bacteria 1 to 2 months prior to observed increases in pathogenic V. cholerae and in clinical cases recorded by the area health clinic. The method provides a highly specific and sensitive tool for monitoring the dynamics of V. cholerae in the environment. The RNA blot hybridization protocol can also be applied to detection of other gram-negative bacteria for taxon-specific enumeration.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.02007-08}, url = {http://aem.asm.org/content/75/17/5439}, author = {Grim,Christopher J. and Zo,Young-Gun and Hasan,Nur A. and Ali,Afsar and Chowdhury,Wasimul B. and Islam,Atiqul and Rashid,Mohammed H. and Alam,Munirul and Morris,J. Glenn and Huq,Anwar and Rita R Colwell} } @article {16525, title = {Running memory span: A comparison of behavioral capacity limits with those of an attractor neural network}, journal = {Cognitive Systems Research}, volume = {10}, year = {2009}, month = {2009/06//}, pages = {161 - 171}, abstract = {We studied a computational model of short term memory capacity that performs a simulated running memory span task using Hebbian learning and rapid decay of connection strengths to keep recent items active for later recall. This model demonstrates recall performance similar to humans performing the same task, with a capacity limit of approximately three items and a prominent recency effect. The model also shows that this capacity depends on decay to release the model from accumulating interference. Model findings are compared with data from two behavioral experiments that used varying task demands to tax memory capacity limits. Following additional theoretical predictions from the computational model, behavioral data support that when task demands require attention to be spread too thin to keep items available for later recall, capacity limits suffer. These findings are important both for understanding the mechanisms underlying short term memory capacity, and also to memory researchers interested in the role of attention in capacity limitations.}, keywords = {Attractor neural network, Computational model, Running span, Short term memory, Working memory capacity}, isbn = {1389-0417}, doi = {10.1016/j.cogsys.2008.09.001}, url = {http://www.sciencedirect.com/science/article/pii/S1389041708000569}, author = {Weems,Scott A. and Winder,Ransom K. and Bunting,Michael and Reggia, James A.} } @inbook {19645, title = {Simple, Black-Box Constructions of Adaptively Secure Protocols}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2009}, month = {2009/01/01/}, pages = {387 - 402}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a compiler for transforming an oblivious transfer (OT) protocol secure against an adaptive semi-honest adversary into one that is secure against an adaptive malicious adversary. Our compiler achieves security in the universal composability framework, assuming access to an ideal commitment functionality, and improves over previous work achieving the same security guarantee in two ways: it uses black-box access to the underlying protocol and achieves a constant multiplicative overhead in the round complexity. As a corollary, we obtain the first constructions of adaptively secure protocols in the stand-alone model using black-box access to a low-level primitive.}, keywords = {Algorithm Analysis and Problem Complexity, computers and society, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, Systems and Data Security}, isbn = {978-3-642-00456-8, 978-3-642-00457-5}, url = {http://link.springer.com/chapter/10.1007/978-3-642-00457-5_23}, author = {Choi, Seung Geol and Dana Dachman-Soled and Malkin, Tal and Wee, Hoeteck}, editor = {Reingold, Omer} } @conference {13048, title = {Streamed learning: one-pass SVMs}, booktitle = {Proceedings of the 21st international jont conference on Artifical intelligence}, year = {2009}, month = {2009///}, pages = {1211 - 1216}, author = {Rai,P. and Daum{\'e}, Hal and Venkatasubramanian,S.} } @article {18721, title = {Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13}, journal = {Molecular Cell}, volume = {35}, year = {2009}, month = {2009/08/14/}, pages = {280 - 290}, abstract = {SummaryDegradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of~one ubiquitin subunit (the {\textquotedblleft}proximal{\textquotedblright} one) is covalently bonded to G76 of the other (the {\textquotedblleft}distal{\textquotedblright} subunit). We demonstrate that S5a{\textquoteright}s UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains. }, keywords = {Proteins}, isbn = {1097-2765}, doi = {10.1016/j.molcel.2009.06.010}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509004018}, author = {Zhang,Naixia and Wang,Qinghua and Ehlinger,Aaron and Randles,Leah and Lary,Jeffrey W. and Kang,Yang and Haririnia,Aydin and Storaska,Andrew J. and Cole,James L. and Fushman, David and Walters,Kylie J.} } @article {12539, title = {Surface reconstruction from gradient fields via gradient transformations}, journal = {International Journal of Computer Vision}, year = {2009}, month = {2009///}, author = {Agrawal,A. and Raskar, R. and Chellapa, Rama} } @article {17397, title = {Temporal Summaries: Supporting Temporal Categorical Searching, Aggregation and Comparison}, journal = {IEEE Transactions on Visualization and Computer Graphics}, volume = {15}, year = {2009}, month = {2009/12//Nov}, pages = {1049 - 1056}, abstract = {When analyzing thousands of event histories, analysts often want to see the events as an aggregate to detect insights and generate new hypotheses about the data. An analysis tool must emphasize both the prevalence and the temporal ordering of these events. Additionally, the analysis tool must also support flexible comparisons to allow analysts to gather visual evidence. In a previous work, we introduced align, rank, and filter (ARF) to accentuate temporal ordering. In this paper, we present temporal summaries, an interactive visualization technique that highlights the prevalence of event occurrences. Temporal summaries dynamically aggregate events in multiple granularities (year, month, week, day, hour, etc.) for the purpose of spotting trends over time and comparing several groups of records. They provide affordances for analysts to perform temporal range filters. We demonstrate the applicability of this approach in two extensive case studies with analysts who applied temporal summaries to search, filter, and look for patterns in electronic health records and academic records.}, keywords = {Aggregates, Collaborative work, Computational Biology, Computer Graphics, Data analysis, data visualisation, Data visualization, Databases, Factual, Displays, Event detection, Filters, Heparin, History, Human computer interaction, Human-computer interaction, HUMANS, Information Visualization, Interaction design, interactive visualization technique, Medical Records Systems, Computerized, Pattern Recognition, Automated, Performance analysis, Springs, temporal categorical data visualization, temporal categorical searching, temporal ordering, temporal summaries, Thrombocytopenia, Time factors}, isbn = {1077-2626}, doi = {10.1109/TVCG.2009.187}, author = {Wang,T. D and Plaisant, Catherine and Shneiderman, Ben and Spring, Neil and Roseman,D. and Marchand,G. and Mukherjee,V. and Smith,M.} } @article {16056, title = {Temporal Summaries: Supporting Temporal Categorical Searching, Aggregation and Comparison}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {15}, year = {2009}, month = {2009/12//nov}, pages = {1049 - 1056}, abstract = {When analyzing thousands of event histories, analysts often want to see the events as an aggregate to detect insights and generate new hypotheses about the data. An analysis tool must emphasize both the prevalence and the temporal ordering of these events. Additionally, the analysis tool must also support flexible comparisons to allow analysts to gather visual evidence. In a previous work, we introduced align, rank, and filter (ARF) to accentuate temporal ordering. In this paper, we present temporal summaries, an interactive visualization technique that highlights the prevalence of event occurrences. Temporal summaries dynamically aggregate events in multiple granularities (year, month, week, day, hour, etc.) for the purpose of spotting trends over time and comparing several groups of records. They provide affordances for analysts to perform temporal range filters. We demonstrate the applicability of this approach in two extensive case studies with analysts who applied temporal summaries to search, filter, and look for patterns in electronic health records and academic records.}, keywords = {Automated;Thrombocytopenia;Time Factors;, Computerized;Pattern Recognition, Factual;Heparin;Humans;Medical Records Systems, interactive visualization technique;temporal categorical searching;temporal ordering;temporal summaries;data visualisation;human computer interaction;Computational Biology;Computer Graphics;Databases}, isbn = {1077-2626}, doi = {10.1109/TVCG.2009.187}, author = {Wang,T. D and Plaisant, Catherine and Shneiderman, Ben and Spring, Neil and Roseman,D. and Marchand,G. and Mukherjee,V. and Smith,M.} } @article {19726, title = {Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.}, journal = {Appl Environ Microbiol}, volume = {75}, year = {2009}, month = {2009 Apr}, pages = {2046-56}, abstract = {

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

}, keywords = {Anti-Bacterial Agents, bacteria, Biological Transport, Carbohydrate Metabolism, Cyanobacteria, DNA, Bacterial, Fungi, Genome, Bacterial, Macrolides, Molecular Sequence Data, Nitrogen, Phylogeny, Proteobacteria, Sequence Analysis, DNA, sequence homology, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.02294-08}, author = {Ward, Naomi L and Challacombe, Jean F and Janssen, Peter H and Henrissat, Bernard and Coutinho, Pedro M and Wu, Martin and Xie, Gary and Haft, Daniel H and Sait, Michelle and Badger, Jonathan and Barabote, Ravi D and Bradley, Brent and Brettin, Thomas S and Brinkac, Lauren M and Bruce, David and Creasy, Todd and Daugherty, Sean C and Davidsen, Tanja M and DeBoy, Robert T and Detter, J Chris and Dodson, Robert J and Durkin, A Scott and Ganapathy, Anuradha and Gwinn-Giglio, Michelle and Han, Cliff S and Khouri, Hoda and Kiss, Hajnalka and Kothari, Sagar P and Madupu, Ramana and Nelson, Karen E and Nelson, William C and Paulsen, Ian and Penn, Kevin and Ren, Qinghu and Rosovitz, M J and Jeremy D Selengut and Shrivastava, Susmita and Sullivan, Steven A and Tapia, Roxanne and Thompson, L Sue and Watkins, Kisha L and Yang, Qi and Yu, Chunhui and Zafar, Nikhat and Zhou, Liwei and Kuske, Cheryl R} } @article {18724, title = {Together, Rpn10 and Dsk2 Can Serve as a Polyubiquitin Chain-Length Sensor}, journal = {Molecular Cell}, volume = {36}, year = {2009}, month = {2009/12/24/}, pages = {1018 - 1033}, abstract = {SummaryAs a signal for substrate targeting, polyubiquitin meets various layers of receptors upstream to the 26S proteasome. We obtained structural information on two receptors, Rpn10 and Dsk2, alone and in complex with (poly)ubiquitin or with each other. A~hierarchy of affinities emerges with Dsk2 binding monoubiquitin tighter than Rpn10 does, whereas Rpn10 prefers the ubiquitin-like domain of Dsk2 to monoubiquitin, with increasing affinities for longer polyubiquitin chains. We demonstrated the formation of ternary complexes of both receptors simultaneously with (poly)ubiquitin and found that, depending on the ubiquitin chain length, the orientation of the resulting complex is entirely different, providing for alternate signals. Dynamic rearrangement provides a chain-length sensor, possibly explaining how accessibility of Dsk2 to the proteasome is limited unless it carries a properly tagged cargo. We propose a mechanism for a malleable ubiquitin signal that depends both on chain length and combination of receptors to produce tetraubiquitin as an efficient signal threshold. }, keywords = {Proteins, signaling}, isbn = {1097-2765}, doi = {10.1016/j.molcel.2009.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509008260}, author = {Zhang,Daoning and Chen,Tony and Ziv,Inbal and Rosenzweig,Rina and Matiuhin,Yulia and Bronner,Vered and Glickman,Michael H. and Fushman, David} } @conference {16677, title = {Topological ordering of function words in hierarchical phrase-based translation}, booktitle = {Proceedings of the Joint Conference of the 47th Annual Meeting of the ACL and the 4th International Joint Conference on Natural Language Processing of the AFNLP: Volume 1-Volume 1}, year = {2009}, month = {2009///}, pages = {324 - 332}, author = {Setiawan,H. and Kan,M.Y. and Li,H. and Resnik, Philip} } @article {13026, title = {Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study}, journal = {BMC Evol Biol}, volume = {9}, year = {2009}, month = {2009///}, pages = {280 - 280}, abstract = {BACKGROUND: In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98\% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS: Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION: Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.}, doi = {10.1186/1471-2148-9-280}, author = {Regier,J. C and Zwick,A. and Cummings, Michael P. and Kawahara,A. Y and Cho,S. and Weller,S. and Roe,A. and Baixeras,J. and Brown,J. W and Parr,C. and Davis,DR and Epstein,M and Hallwachs,W and Hausmann,A and Janzen,DH and Kitching,IJ and Solis,MA and Yen,S-H and Bazinet,A. L and Mitter,C} } @conference {16665, title = {The University of Maryland statistical machine translation system for the Fourth Workshop on Machine Translation}, booktitle = {Proceedings of the Fourth Workshop on Statistical Machine Translation}, year = {2009}, month = {2009///}, pages = {145 - 149}, author = {Dyer,C. and Setiawan,H. and Marton,Y. and Resnik, Philip} } @conference {16583, title = {An unsupervised learning method for representing simple sentences}, booktitle = {Neural Networks, 2009. IJCNN 2009. International Joint Conference on}, year = {2009}, month = {2009///}, pages = {2133 - 2140}, author = {Monner,D. and Reggia, James A.} } @conference {13888, title = {Using citations to generate surveys of scientific paradigms}, booktitle = {Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, series = {NAACL {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {584 - 592}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {The number of research publications in various disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of technical material. In this paper we present the first steps in producing an automatically generated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization techniques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the framework of multi-document survey creation, citation texts can play a crucial role.}, isbn = {978-1-932432-41-1}, url = {http://dl.acm.org/citation.cfm?id=1620754.1620839}, author = {Mohammad,Saif and Dorr, Bonnie J and Egan,Melissa and Hassan,Ahmed and Muthukrishan,Pradeep and Qazvinian,Vahed and Radev,Dragomir and Zajic, David} } @article {12885, title = {Using Satellite Images of Environmental Changes to Predict Infectious Disease Outbreaks}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {15}, year = {2009}, month = {2009/09//}, pages = {1341 - 1346}, abstract = {A strong global satellite imaging system is essential for predicting outbreaks., Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today{\textquoteright}s ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response.}, isbn = {1080-6040}, doi = {10.3201/eid/1509.081334}, author = {Ford,Timothy E. and Rita R Colwell and Rose,Joan B. and Morse,Stephen S. and Rogers,David J. and Yates,Terry L.} } @conference {12806, title = {Validating Automotive Control Software Using Instrumentation-Based Verification}, booktitle = {Automated Software Engineering, International Conference on}, year = {2009}, month = {2009///}, pages = {15 - 25}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper discusses the results of an application of a formally based verification technique, called Instrumentation-Based Verification (IBV), to a production automotive lighting controller. The goal of the study is to assess, from both a tools as well as a methodological perspective, the performance of IBV in an industrial setting. The insights obtained as a result of the project include a refinement of a previously developed architecture for requirements specifications; observations about changes to model-based design workflows; insights into the role of requirements during development; and the capability of automated verification to detect inconsistencies among requirements as well as between requirements and design models.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ASE.2009.98}, author = {Ray,Arnab and Morschhaeuser,Iris and Ackermann,Chris and Cleaveland, Rance and Shelton,Charles and Martin,Chris} } @article {17491, title = {Visual overviews for discovering key papers and influences across research fronts}, journal = {Journal of the American Society for Information Science and Technology}, volume = {60}, year = {2009}, month = {2009/11/01/}, pages = {2219 - 2228}, abstract = {Gaining a rapid overview of an emerging scientific topic, sometimes called research fronts, is an increasingly common task due to the growing amount of interdisciplinary collaboration. Visual overviews that show temporal patterns of paper publication and citation links among papers can help researchers and analysts to see the rate of growth of topics, identify key papers, and understand influences across subdisciplines. This article applies a novel network-visualization tool based on meaningful layouts of nodes to present research fronts and show citation links that indicate influences across research fronts. To demonstrate the value of two-dimensional layouts with multiple regions and user control of link visibility, we conducted a design-oriented, preliminary case study with 6 domain experts over a 4-month period. The main benefits were being able (a) to easily identify key papers and see the increasing number of papers within a research front, and (b) to quickly see the strength and direction of influence across related research fronts.}, isbn = {1532-2890}, doi = {10.1002/asi.21160}, url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.21160/abstract}, author = {Aris,Aleks and Shneiderman, Ben and Qazvinian,Vahed and Radev,Dragomir} } @conference {16503, title = {Web Monitoring 2.0: Crossing Streams to Satisfy Complex Data Needs}, booktitle = {IEEE 25th International Conference on Data Engineering, 2009. ICDE {\textquoteright}09}, year = {2009}, month = {2009/04/29/March}, pages = {1215 - 1218}, publisher = {IEEE}, organization = {IEEE}, abstract = {Web monitoring 2.0 supports the complex information needs of clients who probe multiple information sources and generate mashups by integrating across these volatile streams. A proxy that aims at satisfying multiple customized client profiles will face a scalability challenge in trying to maximize the number of clients served while at the same time fully satisfying complex client needs. In this paper, we introduce an abstraction of complex execution intervals, a combination of time intervals and information streams, to capture complex client needs. Given some budgetary constraints (e.g., bandwidth), we present offline algorithmic solutions for the problem of maximizing completeness of capturing complex profiles.}, keywords = {Bandwidth, complex client information need, Data Delivery, Data engineering, database management systems, Educational institutions, Internet, Mashups, mashups generation, Monitoring, multiple information source, offline algorithmic solution, Portals, PROBES, Profiles, Query processing, scalability, scheduling, volatile information stream, Web 2.0, Web Monitoring}, isbn = {978-1-4244-3422-0}, doi = {10.1109/ICDE.2009.204}, author = {Roitman,H. and Gal,A. and Raschid, Louiqa} } @conference {18926, title = {Within epsilon of optimal play in the cultaptation social learning game}, series = {AAMAS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1327 - 1328}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {Social learning, in which members of a society learn by observing the behavior of others, is an important foundation for human culture, and is observed in many other species as well. It seems natural to assume that social learning evolved due to the inherent superiority of copying others{\textquoteright} success rather than learning on one{\textquoteright}s own via trial-and-error innovation. However, there has also been substantial work questioning this intuition [3, 5, 1, 6, 4]. For example, blindly copying information from others is not useful if the information is wrong---or if it once was right but has since become outdated. Under what conditions does social learning outperform trial-and-error learning, and what kinds of social-learning strategies are likely to perform well?}, isbn = {978-0-9817381-7-8}, url = {http://dl.acm.org/citation.cfm?id=1558109.1558276}, author = {Carr,Ryan and Raboin,Eric and Parker,Austin and Nau, Dana S.} } @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.} } @article {12562, title = {Activity representation using 3D shape models}, journal = {J. Image Video Process.}, volume = {2008}, year = {2008}, month = {2008/01//}, pages = {5:1{\textendash}5:16 - 5:1{\textendash}5:16}, abstract = {We present a method for characterizing human activities using 3D deformable shape models. The motion trajectories of points extracted from objects involved in the activity are used to build models for each activity, and these models are used for classification and detection of unusual activities. The deformable models are learnt using the factorization theorem for nonrigid 3D models. We present a theory for characterizing the degree of deformation in the 3D models from a sequence of tracked observations. This degree, termed as deformation index (DI), is used as an input to the 3D model estimation process. We study the special case of ground plane activities in detail because of its importance in video surveillance applications. We present results of our activity modeling approach using videos of both high-resolution single individual activities and ground plane surveillance activities.}, isbn = {1687-5176}, doi = {10.1155/2008/347050}, url = {http://dx.doi.org/10.1155/2008/347050}, author = {Abdelkader,Mohamed F. and Roy-Chowdhury,Amit K. and Chellapa, Rama and Akdemir,Umut} } @article {18694, title = {Affinity Makes the Difference: Nonselective Interaction of the UBA Domain of Ubiquilin-1 with Monomeric Ubiquitin and Polyubiquitin Chains}, journal = {Journal of Molecular Biology}, volume = {377}, year = {2008}, month = {2008/03/14/}, pages = {162 - 180}, abstract = {Ubiquilin/PLIC proteins belong to the family of UBL{\textendash}UBA proteins implicated in the regulation of the ubiquitin-dependent proteasomal degradation of cellular proteins. A human presenilin-interacting protein, ubiquilin-1, has been suggested as potential therapeutic target for treating Huntington{\textquoteright}s disease. Ubiquilin{\textquoteright}s interactions with mono- and polyubiquitins are mediated by its UBA domain, which is one of the tightest ubiquitin binders among known ubiquitin-binding domains. Here we report the three-dimensional structure of the UBA domain of ubiquilin-1 (UQ1-UBA) free in solution and in complex with ubiquitin. UQ1-UBA forms a compact three-helix bundle structurally similar to other known UBAs, and binds to the hydrophobic patch on ubiquitin with a Kd of 20~μM. To gain structural insights into UQ1-UBA{\textquoteright}s interactions with polyubiquitin chains, we have mapped the binding interface between UQ1-UBA and Lys48- and Lys63-linked di-ubiquitins and characterized the strength of UQ1-UBA binding to these chains. Our NMR data show that UQ1-UBA interacts with the individual ubiquitin units in both chains in a mode similar to its interaction with mono-ubiquitin, although with an improved binding affinity for the chains. Our results indicate that, in contrast to UBA2 of hHR23A that has strong binding preference for Lys48-linked chains, UQ1-UBA shows little or no binding selectivity toward a particular chain linkage or between the two ubiquitin moieties in the same chain. The structural data obtained in this study provide insights into the possible structural reasons for the diversity of polyubiquitin chain recognition by UBA domains.}, keywords = {polyubiquitin, protein{\textendash}protein interaction, UBA domain, ubiquilin, ubiquitin}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2007.12.029}, url = {http://www.sciencedirect.com/science/article/pii/S0022283607016452}, author = {Zhang,Daoning and Raasi,Shahri and Fushman, David} } @article {13724, title = {Applying automatically generated semantic knowledge: A case study in machine translation}, journal = {NSF Symposium on Semantic Knowledge Discovery, Organization and Use}, year = {2008}, month = {2008///}, abstract = {In this paper, we discuss how we apply automatically generated semantic knowledge to benefit statisticalmachine translation (SMT). Currently, almost all statistical machine translation systems rely heavily on memorizing translations of phrases. Some systems attempt to go further and generalize these learned phrase translations into templates using empirically derived information about word alignments and a small amount of syntactic information, if at all. There are several issues in a SMT pipeline that could be addressed by the application of semantic knowledge, if such knowledge were easily available. One such issue, an important one, is that of reference sparsity. The fundamental problem that translation systems have to face is that there is no such thing as the correct translation for any sentence. In fact, any given source sentence can often be translated into the target language in many valid ways. Since there can be many {\textquotedblleft}correct answers,{\textquotedblright} almost all models employed by SMT systems require, in addition to a large bitext, a held-out development set comprised of multiple high-quality, human-authored reference translations in the target language in order to tune their parameters relative to a translation quality metric.1 There are several reasons that this requirement is not an easy one to satisfy. First, with a few exceptions{\textemdash}notably NIST{\textquoteright}s annual MT evaluations{\textemdash}most new MT research data sets are provided with only a single reference translation. Second, obtaining multiple reference translations in rapid development, low-density source language scenarios (e.g. (Oard, 2003)) is likely to be severely limited (or made entirely impractical) by limitations of time, cost, and ready availability of qualified translators. }, author = {Madnani,N. and Resnik, Philip and Dorr, Bonnie J and Schwartz,R.} } @article {13725, title = {Are multiple reference translations necessary? investigating the value of paraphrased reference translations in parameter optimization}, journal = {Proceedings of the Eighth Conference of the Association for Machine Translation in the Americas, October}, year = {2008}, month = {2008///}, abstract = {Most state-of-the-art statistical machine trans-lation systems use log-linear models, which are defined in terms of hypothesis features and weights for those features. It is standard to tune the feature weights in order to maxi- mize a translation quality metric, using held- out test sentences and their corresponding ref- erence translations. However, obtaining refer- ence translations is expensive. In our earlier work (Madnani et al., 2007), we introduced a new full-sentence paraphrase technique, based on English-to-English decoding with an MT system, and demonstrated that the resulting paraphrases can be used to cut the number of human reference translations needed in half. In this paper, we take the idea a step further, asking how far it is possible to get with just a single good reference translation for each item in the development set. Our analysis suggests that it is necessary to invest in four or more hu- man translations in order to significantly im- prove on a single translation augmented by monolingual paraphrases. }, author = {Madnani,N. and Resnik, Philip and Dorr, Bonnie J and Schwartz,R.} } @conference {18548, title = {Authenticated out-of-band communication over social links}, booktitle = {Proceedings of the first workshop on Online social networks}, series = {WOSN {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {61 - 66}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many existing host-based applications rely on their own authentication mechanisms and peer discovery services. Although social networking sites already provide mechanisms for users both to discover other users (e.g., by logging on to the social network Web site) and to communicate securely with each other (e.g., using instant messages within the social networking site), today{\textquoteright}s applications have no way to exploit the relationships and trust that are inherent in these networks. This paper proposes Authenticatr, a framework that allows applications to use the authentication and peer discovery mechanisms inherent in social networking sites to bootstrap their own authenticated communication channels. We describe motivating applications, detail the interface that Authenticatr exposes to applications, and discuss practical considerations and security threats.}, keywords = {Authentication, Security, social networks}, isbn = {978-1-60558-182-8}, doi = {10.1145/1397735.1397749}, url = {http://doi.acm.org/10.1145/1397735.1397749}, author = {Ramachandran,Anirudh V. and Feamster, Nick} } @article {16543, title = {Automated design of distributed control rules for the self-assembly of prespecified artificial structures}, journal = {Robotics and Autonomous Systems}, volume = {56}, year = {2008}, month = {2008/04/30/}, pages = {334 - 359}, abstract = {The self-assembly problem involves the design of agent-level control rules that will cause the agents to form some desired, target structure, subject to environmental constraints. This paper describes a fully automated rule generation procedure that allows structures to successfully self-assemble in a simulated environment with constrained, continuous motion. This environment implicitly imposes ordering constraints on the self-assembly process, where certain parts of the target structure must be assembled before others, and where it may be necessary to assemble (and subsequently disassemble) temporary structures such as staircases. A provably correct methodology is presented for computing a partial order on the self-assembly process, and for generating rules that enforce this order at runtime. The assembly and disassembly of structures is achieved by generating another set of rules, which are inspired by construction behavior among certain species of social insects. Computational experiments verify the effectiveness of the approach on a diverse set of target structures.}, keywords = {Collective problem solving, Coordination, Self-assembly, Stigmergy, Swarm intelligence}, isbn = {0921-8890}, doi = {10.1016/j.robot.2007.08.006}, url = {http://www.sciencedirect.com/science/article/pii/S092188900700111X}, author = {Grushin,Alexander and Reggia, James A.} } @article {13129, title = {Automatic online tuning for fast Gaussian summation}, journal = {Advances in Neural Information Processing Systems}, year = {2008}, month = {2008///}, abstract = {Many machine learning algorithms require the summation of Gaussian kernelfunctions, an expensive operation if implemented straightforwardly. Several meth- ods have been proposed to reduce the computational complexity of evaluating such sums, including tree and analysis based methods. These achieve varying speedups depending on the bandwidth, dimension, and prescribed error, making the choice between methods difficult for machine learning tasks. We provide an algorithm that combines tree methods with the Improved Fast Gauss Transform (IFGT). As originally proposed the IFGT suffers from two problems: (1) the Taylor series expansion does not perform well for very low bandwidths, and (2) parameter se- lection is not trivial and can drastically affect performance and ease of use. We address the first problem by employing a tree data structure, resulting in four eval- uation methods whose performance varies based on the distribution of sources and targets and input parameters such as desired accuracy and bandwidth. To solve the second problem, we present an online tuning approach that results in a black box method that automatically chooses the evaluation method and its parameters to yield the best performance for the input data, desired accuracy, and bandwidth. In addition, the new IFGT parameter selection approach allows for tighter error bounds. Our approach chooses the fastest method at negligible additional cost, and has superior performance in comparisons with previous approaches. }, author = {Morariu,V. and Srinivasan,B.V. and Raykar,V.C. and Duraiswami, Ramani and Davis, Larry S.} } @article {17757, title = {AVA: Adjective-Verb-Adverb Combinations for Sentiment Analysis}, journal = {Intelligent Systems, IEEE}, volume = {23}, year = {2008}, month = {2008/08//july}, pages = {43 - 50}, abstract = {Most research on determining the strength of subjective expressions in a sentence or document uses single, specific parts of speech such as adjectives, adverbs, or verbs. To date, almost no research covers the development of a single comprehensive framework in which we can analyze sentiment that takes all three into account. The authors propose the AVA (adjective verb adverb) framework for identifying opinions on any given topic. In AVA, a user can select any topic t of interest and any document d. AVA will return a score that d expresses topic t. The score is expressed on a $\#$x02013;1 (maximally negative) to +1 (maximally positive) scale.}, isbn = {1541-1672}, doi = {10.1109/MIS.2008.57}, author = {V.S. Subrahmanian and Reforgiato,Diego} } @article {16790, title = {Bandwidth-constrained queries in sensor networks}, journal = {The VLDB Journal}, volume = {17}, year = {2008}, month = {2008///}, pages = {443 - 467}, author = {Deligiannakis,A. and Kotidis,Y. and Roussopoulos, Nick} } @inbook {17569, title = {Budgeted Allocations in the Full-Information Setting}, booktitle = {Approximation, Randomization and Combinatorial Optimization. Algorithms and TechniquesApproximation, Randomization and Combinatorial Optimization. Algorithms and Techniques}, series = {Lecture Notes in Computer Science}, volume = {5171}, year = {2008}, month = {2008///}, pages = {247 - 253}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We build on the work of Andelman \& Mansour and Azar, Birnbaum, Karlin, Mathieu \& Thach Nguyen to show that the full-information (i.e., offline) budgeted-allocation problem can be approximated to within 4/3: we conduct a rounding of the natural LP relaxation, for which our algorithm matches the known lower-bound on the integrality gap.}, isbn = {978-3-540-85362-6}, url = {http://dx.doi.org/10.1007/978-3-540-85363-3_20}, author = {Srinivasan, Aravind}, editor = {Goel,Ashish and Jansen,Klaus and Rolim,Jos{\'e} and Rubinfeld,Ronitt} } @conference {16506, title = {Capturing Approximated Data Delivery Tradeoffs}, booktitle = {Data Engineering, 2008. ICDE 2008. IEEE 24th International Conference on}, year = {2008}, month = {2008/04//}, pages = {1471 - 1473}, abstract = {This paper presents a middleware data delivery setting with a proxy that is required to maximize the completeness of captured updates, specified in its clients{\textquoteright} profiles, while minimizing at the same time the delay in delivering the updates to clients. The two objectives may conflict when the monitoring budget is limited. Therefore, any solution should consider this tradeoff in satisfying both objectives. We term this problem the "proxy dilemma" and formalize it as a biobjective optimization problem. Such problem occurs in many contemporary applications, such as mobile and sensor networks, and poses scalability challenges in delivering up-to-date data from remote resources to meet client specifications. We present a Pareto set as a formal solution to the proxy dilemma. We discuss the complexity of generating a Pareto set for the proxy dilemma and suggest an approximation scheme to this problem.}, keywords = {approximation scheme, approximation theory, biobjective optimization problem, Middleware, middleware data delivery tradeoffs, mobile networks, Pareto optimisation, Pareto set, proxy dilemma problem, sensor networks}, doi = {10.1109/ICDE.2008.4497593}, author = {Roitman,H. and Gal,A. and Raschid, Louiqa} } @conference {12547, title = {Compressed sensing for multi-view tracking and 3-D voxel reconstruction}, booktitle = {Image Processing, 2008. ICIP 2008. 15th IEEE International Conference on}, year = {2008}, month = {2008/10//}, pages = {221 - 224}, abstract = {Compressed sensing (CS) suggests that a signal, sparse in some basis, can be recovered from a small number of random projections. In this paper, we apply the CS theory on sparse background-subtracted silhouettes and show the usefulness of such an approach in various multi-view estimation problems. The sparsity of the silhouette images corresponds to sparsity of object parameters (location, volume etc.) in the scene. We use random projections (compressed measurements) of the silhouette images for directly recovering object parameters in the scene coordinates. To keep the computational requirements of this recovery procedure reasonable, we tessellate the scene into a bunch of non-overlapping lines and perform estimation on each of these lines. Our method is scalable in the number of cameras and utilizes very few measurements for transmission among cameras. We illustrate the usefulness of our approach for multi-view tracking and 3-D voxel reconstruction problems.}, keywords = {3D, background-subtracted, coding;, Estimation, image, problems;multi-view, projections;silhouette, reconstruction;CS, reconstruction;video, sensing;multi-view, silhouettes;image, sparsity;sparse, theory;compressed, tracking;random, voxel}, doi = {10.1109/ICIP.2008.4711731}, author = {Reddy, D. and Sankaranarayanan,A. C and Cevher, V. and Chellapa, Rama} } @article {12569, title = {Compressive sensing for background subtraction}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {155 - 168}, abstract = {Compressive sensing (CS) is an emerging field that provides a framework for image recovery using sub-Nyquist sampling rates. The CS theory shows that a signal can be reconstructed from a small set of random projections, provided that the signal is sparse in some basis, e.g., wavelets. In this paper, we describe a method to directly recover background subtracted images using CS and discuss its applications in some communication constrained multi-camera computer vision problems. We show how to apply the CS theory to recover object silhouettes (binary background subtracted images) when the objects of interest occupy a small portion of the camera view, i.e., when they are sparse in the spatial domain. We cast the background subtraction as a sparse approximation problem and provide different solutions based on convex optimization and total variation. In our method, as opposed to learning the background, we learn and adapt a low dimensional compressed representation of it, which is sufficient to determine spatial innovations; object silhouettes are then estimated directly using the compressive samples without any auxiliary image reconstruction. We also discuss simultaneous appearance recovery of the objects using compressive measurements. In this case, we show that it may be necessary to reconstruct one auxiliary image. To demonstrate the performance of the proposed algorithm, we provide results on data captured using a compressive single-pixel camera. We also illustrate that our approach is suitable for image coding in communication constrained problems by using data captured by multiple conventional cameras to provide 2D tracking and 3D shape reconstruction results with compressive measurements.}, author = {Cevher, V. and Sankaranarayanan, A. and Duarte, M. and Reddy, D. and Baraniuk, R. and Chellapa, Rama} } @article {16687, title = {Cross-language parser adaptation between related languages}, journal = {NLP for Less Privileged Languages}, year = {2008}, month = {2008///}, pages = {35 - 35}, author = {Zeman,D. and Resnik, Philip} } @conference {16415, title = {CrossNet: a framework for crossover with network-based chromosomal representations}, booktitle = {Proceedings of the 10th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {1057 - 1064}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose a new class of crossover operators for genetic algorithms (CrossNet) which use a network-based (or graph-based) chromosomal representation. We designed CrossNet with the intent of providing a framework for creating crossover operators that take advantage of domain-specific knowledge for solving problems. Specifically, GA users supply a network which defines the epistatic relationships between genes in the genotype. CrossNet-based crossover uses this information with the goal of improving linkage. We performed two experiments that compared CrossNet-based crossover with one-point and uniform crossover. The first experiment involved the density classification problem for cellular automata (CA), and the second experiment involved fitting two randomly generated hyperplane-defined functions (hdf{\textquoteright}s). Both of these exploratory experiments support the hypothesis that CrossNet-based crossover can be useful, although performance improvements were modest. We discuss the results and remain hopeful about the successful application of CrossNet to other domains. We conjecture that future work with the CrossNet framework will provide a useful new perspective for investigating linkage and chromosomal representations.}, keywords = {crossover, Genetic algorithms, graphs, linkage, NETWORKS, recombination}, isbn = {978-1-60558-130-9}, doi = {10.1145/1389095.1389290}, url = {http://doi.acm.org/10.1145/1389095.1389290}, author = {Stonedahl,Forrest and Rand, William and Wilensky,Uri} } @article {12127, title = {CrossTalk: The Journal of Defense Software Engineering. Volume 21, Number 10, October 2008}, year = {2008}, month = {2008///}, institution = {DTIC Document}, author = {Basili, Victor R. and Dangle,K. and Esker,L. and Marotta,F. and Rus,I. and Brosgol,B. M and Jamin,S. and Arthur,J. D and Ravichandar,R. and Wisnosky,D. E} } @article {18511, title = {Detecting botnet membership with dnsbl counterintelligence}, journal = {Botnet Detection}, year = {2008}, month = {2008///}, pages = {131 - 142}, doi = {DOI: 10.1007/978-0-387-68768-1_7}, author = {Ramachandran,A. and Feamster, Nick and Dagon,D.} } @article {18518, title = {A Dynamic Reputation Service for Spotting Spammers}, volume = {GT-CS-08-09}, year = {2008}, month = {2008///}, institution = {School of Computer Science, Georgia Tech}, abstract = {This paper presents the design, implementation, evalu-ation, and initial deployment of SpamSpotter, the first open, large-scale, real-time reputation system for filtering spam. Existing blacklists (e.g., SpamHaus) have trouble keeping pace with spammers{\textquoteright} increasing ability to send spam from {\textquotedblleft}fresh{\textquotedblright} IP addresses, and filters based purely on content are easily evadable. In contrast, SpamSpotter dynamically classifies email senders in real time based on their global sending behavior, rather than based on ephemeral features such as an IP address or the content of the message. In implementing SpamSpotter, we address significant challenges involving both dynamism (i.e., de- termining when to {\textquotedblleft}retrain{\textquotedblright} our dynamic classification algorithms) and scale (i.e., maintaining fast, accurate per- formance in the face of tremendous email message vol- ume). We have evaluated the performance and accuracy of SpamSpotter using traces from a large email-hosting provider and a spam appliance vendor that receives 300 million messages a day. Our evaluation shows that SpamSpotter is scalable, fast, and accurate. SpamSpotter is also operational today: it will currently answer queries from existing spam filtering software (e.g., SpamAssas- sin) with only minor configuration changes. }, author = {Ramachandran,A. and Hao,S. and Khandelwal,H. and Feamster, Nick and Vempala,S.} } @conference {13984, title = {Efficient Kriging via Fast Matrix-Vector Products}, booktitle = {Aerospace Conference, 2008 IEEE}, year = {2008}, month = {2008/03//}, pages = {1 - 7}, abstract = {Interpolating scattered data points is a problem of wide ranging interest. Ordinary kriging is an optimal scattered data estimator, widely used in geosciences and remote sensing. A generalized version of this technique, called cokriging, can be used for image fusion of remotely sensed data. However, it is computationally very expensive for large data sets. We demonstrate the time efficiency and accuracy of approximating ordinary kriging through the use of fast matrix-vector products combined with iterative methods. We used methods based on the fast Multipole methods and nearest neighbor searching techniques for implementations of the fast matrix-vector products.}, keywords = {cokriging, data, data;scattered, efficiency;geophysical, estimator;remotely, fusion;, fusion;interpolation;iterative, matrix-vector, methods;image, methods;nearest, methods;remote, multipole, neighbor, points;time, products;fast, scattered, searching;optimal, sensed, sensing;sensor, technique;fast, techniques;iterative}, doi = {10.1109/AERO.2008.4526433}, author = {Memarsadeghi,N. and Raykar,V.C. and Duraiswami, Ramani and Mount, Dave} } @conference {15544, title = {Efficient Kriging via Fast Matrix-Vector Products}, booktitle = {Aerospace Conference, 2008 IEEE}, year = {2008}, month = {2008/03//}, pages = {1 - 7}, abstract = {Interpolating scattered data points is a problem of wide ranging interest. Ordinary kriging is an optimal scattered data estimator, widely used in geosciences and remote sensing. A generalized version of this technique, called cokriging, can be used for image fusion of remotely sensed data. However, it is computationally very expensive for large data sets. We demonstrate the time efficiency and accuracy of approximating ordinary kriging through the use of fast matrix-vector products combined with iterative methods. We used methods based on the fast Multipole methods and nearest neighbor searching techniques for implementations of the fast matrix-vector products.}, keywords = {cokriging technique, fast matrix-vector products, fast multipole methods, geophysical techniques, image fusion, Interpolation, iterative methods, nearest neighbor searching, optimal scattered data estimator, Remote sensing, remotely sensed data, scattered data points, sensor fusion, time efficiency}, doi = {10.1109/AERO.2008.4526433}, author = {Memarsadeghi,N. and Raykar,V.C. and Duraiswami, Ramani and Mount, Dave} } @conference {15585, title = {Enhancements in robust feature matching}, booktitle = {Electrical Engineering/Electronics, Computer, Telecommunications and Information Technology, 2008. ECTI-CON 2008. 5th International Conference on}, volume = {1}, year = {2008}, month = {2008/05//}, pages = {505 - 508}, abstract = {We present in this paper a number of new enhancements to a branch-and-bound algorithm given by Mount, Netanyahu, and Le Moigne [8] for feature matching. We introduce a new distance measure, which is more robust to the presence of outliers than the previously used measure, as well as a new variant of the search algorithm and a new search strategy. We also present experimental results, which show that these enhancements offer significant tangible improvements in performance.}, keywords = {branch-and-bound algorithm, distance measure, Image Enhancement, Image matching, robust feature matching, tree searching}, doi = {10.1109/ECTICON.2008.4600481}, author = {Ratanasanya,S. and Mount, Dave and Netanyahu,N. S and Achalakul,T.} } @article {12834, title = {Executable Specifications for Real-Time Distributed Systems}, journal = {Electronic Notes in Theoretical Computer Science}, volume = {203}, year = {2008}, month = {2008/06/05/}, pages = {3 - 17}, abstract = {One of the challenges in designing distributed, embedded systems is the paucity of formal, executable specification notations that provide support for both real-time and asynchronous communication. This paper describes a timed architecture design language (Timed Architecture Interaction Diagrams or TAID) that, by virtue of its formal, executable semantics, combines the benefits of synchronous specification notations with the advantages of traditional architecture description languages. In addition, TAID provides support for a variety of temporal inter-process communication (IPC) primitives as a native feature of the language, so that the encapsulated communication behavior (captured by real-time {\^a}{\texteuro}{\oe}buses{\^a}{\texteuro} in TAID) may be re-used across designs and serve as specifications for more detailed model implementations.}, keywords = {distributed systems, Formal Methods, real-time, Simulations, Software architecture}, isbn = {1571-0661}, doi = {10.1016/j.entcs.2008.05.007}, url = {http://www.sciencedirect.com/science/article/pii/S1571066108003216}, author = {Ray,Arnab and Cleaveland, Rance} } @article {18670, title = {Experiences with building an intrusion-tolerant group communication system}, journal = {Software: Practice and Experience}, volume = {38}, year = {2008}, month = {2008///}, pages = {639 - 666}, abstract = {There are many group communication systems (GCSs) that provide consistent group membership and reliable, ordered multicast properties in the presence of crash faults. However, relatively few GCS implementations are able to provide these properties in the presence of malicious faults resulting from intrusions. We describe the systematic transformation of a crash-tolerant GCS, namely C-Ensemble, into an intrusion-tolerant GCS, the ITUA GCS. To perform the transformation, we devised intrusion-tolerant versions of key group communication protocols. We then inserted implementations of the protocols into C-Ensemble and made significant changes to the rest of the C-Ensemble protocol stack to make the stack intrusion tolerant. We quantify the cost of providing intrusion-tolerant group communication in two ways. First, we quantify the implementation effort by presenting a detailed analysis of the amount of change required to the original C-Ensemble system. In doing so, we provide insight into the choice of building an intrusion-tolerant GCS from scratch versus building one by leveraging a crash-tolerant implementation. Second, we quantify the run-time performance cost of tolerating intrusions by presenting results from an experimental evaluation of the main intrusion-tolerant microprotocols. The results are analyzed to identify the parts that contribute the most overhead while providing intrusion tolerance during both normal operation and recovery from intrusions. Copyright {\textcopyright} 2007 John Wiley \& Sons, Ltd.}, keywords = {distributed protocols, experimental evaluation, Fault tolerance, Group communication, intrusion tolerance}, isbn = {1097-024X}, doi = {10.1002/spe.848}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.848/abstract}, author = {Ramasamy,HariGovind V. and Pandey,Prashant and Michel Cukier and Sanders,William H.} } @conference {16496, title = {Exploiting ontology structure and patterns of annotation to mine significant associations between pairs of controlled vocabulary terms}, booktitle = {Data Integration in the Life Sciences}, year = {2008}, month = {2008///}, pages = {44 - 60}, author = {Lee,W. J and Raschid, Louiqa and Sayyadi,H. and Srinivasan,P.} } @article {16396, title = {Exurbia from the bottom-up: Confronting empirical challenges to characterizing a complex system}, journal = {Geoforum}, volume = {39}, year = {2008}, month = {2008/03//}, pages = {805 - 818}, abstract = {We describe empirical results from a multi-disciplinary project that support modeling complex processes of land-use and land-cover change in exurban parts of Southeastern Michigan. Based on two different conceptual models, one describing the evolution of urban form as a consequence of residential preferences and the other describing land-cover changes in an exurban township as a consequence of residential preferences, local policies, and a diversity of development types, we describe a variety of empirical data collected to support the mechanisms that we encoded in computational agent-based models. We used multiple methods, including social surveys, remote sensing, and statistical analysis of spatial data, to collect data that could be used to validate the structure of our models, calibrate their specific parameters, and evaluate their output. The data were used to investigate this system in the context of several themes from complexity science, including have (a) macro-level patterns; (b) autonomous decision making entities (i.e., agents); (c) heterogeneity among those entities; (d) social and spatial interactions that operate across multiple scales and (e) nonlinear feedback mechanisms. The results point to the importance of collecting data on agents and their interactions when producing agent-based models, the general validity of our conceptual models, and some changes that we needed to make to these models following data analysis. The calibrated models have been and are being used to evaluate landscape dynamics and the effects of various policy interventions on urban land-cover patterns.}, keywords = {Ecological effects, Land-cover change, Land-use change, spatial modeling, Urban sprawl}, isbn = {0016-7185}, doi = {10.1016/j.geoforum.2007.02.010}, url = {http://www.sciencedirect.com/science/article/pii/S0016718507000371}, author = {Brown,Daniel G. and Robinson,Derek T. and An,Li and Nassauer,Joan I. and Zellner,Moira and Rand, William and Riolo,Rick and Page,Scott E. and Low,Bobbi and Wang,Zhifang} } @article {13977, title = {A Fast Algorithm for Learning a Ranking Function from Large-Scale Data Sets}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {30}, year = {2008}, month = {2008/07//}, pages = {1158 - 1170}, abstract = {We consider the problem of learning a ranking function that maximizes a generalization of the Wilcoxon-Mann-Whitney statistic on the training data. Relying on an e-accurate approximation for the error function, we reduce the computational complexity of each iteration of a conjugate gradient algorithm for learning ranking functions from O(m2) to O(m), where m is the number of training samples. Experiments on public benchmarks for ordinal regression and collaborative filtering indicate that the proposed algorithm is as accurate as the best available methods in terms of ranking accuracy, when the algorithms are trained on the same data. However, since it is several orders of magnitude faster than the current state-of-the-art approaches, it is able to leverage much larger training data sets.}, keywords = {Automated;, Factual;Information Storage and Retrieval;Likelihood Functions;Models, Statistical;Pattern Recognition, Wilcoxon-Mann-Whitney statistics;collaborative filtering;error function;gradient algorithm;large-scale data sets;learning ranking functions;ranking function;training data;computational complexity;error analysis;learning (artificial intelligence);regressio}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.70776}, author = {Raykar,V.C. and Duraiswami, Ramani and Krishnapuram,B.} } @conference {18567, title = {Fast monitoring of traffic subpopulations}, booktitle = {Proceedings of the 8th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {257 - 270}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network accounting, forensics, security, and performance monitoring applications often need to examine detailed traces from subsets of flows ("subpopulations"), where the application desires flexibility in specifying the subpopulation (e.g., to detect a portscan, the application must observe many packets between a source and a destination with one packet to each port). However, the dynamism and volume of network traffic on many high-speed links necessitates traffic sampling, which adversely affects subpopulation monitoring: because many subpopulations of interest to operators are low-volume flows, conventional sampling schemes (e.g., uniform random sampling) miss much of the subpopulation{\textquoteright}s traffic. Today{\textquoteright}s routers and network devices provide scant support for monitoring specific traffic subpopulations. This paper presents the design, implementation, and evaluation of FlexSample, a traffic monitoring engine that dynamically extracts traffic from subpopulations that operators define using conditions on packet header fields. FlexSample uses a fast, flexible counter array to provide rough estimates of packets{\textquoteright} membership in respective subpopulations. Based on these coarse estimates, FlexSample then makes per-packet sampling decisions to sample proportionately from each subpopulation (as specified by a network operator), subject to an overall sampling constraint. We apply FlexSample to extract subpopulations such as port scans and traffic to high-degree nodes and find that it is able to capture significantly more packets from these subpopulations than conventional approaches.}, keywords = {counters, flexsample, sampling, traffic statistics, traffic subpopulations}, isbn = {978-1-60558-334-1}, doi = {10.1145/1452520.1452551}, url = {http://doi.acm.org/10.1145/1452520.1452551}, author = {Ramachandran,Anirudh and Seetharaman,Srinivasan and Feamster, Nick and Vazirani,Vijay} } @article {16262, title = {Figaro: A Novel Statistical Method for Vector Sequence Removal}, journal = {Bioinformatics}, volume = {24}, year = {2008}, month = {2008/02/15/}, pages = {462 - 467}, abstract = {Motivation: Sequences produced by automated Sanger sequencing machines frequently contain fragments of the cloning vector on their ends. Software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experiment{\textemdash}information often omitted from public databases. Furthermore, the clipping coordinates themselves are missing or incorrectly reported. As an example, within the \~{}1.24 billion shotgun sequences deposited in the NCBI Trace Archive, as many as \~{}735 million (\~{}60\%) lack vector clipping information. Correct clipping information is essential to scientists attempting to validate, improve and even finish the increasingly large number of genomes released at a {\textquoteleft}draft{\textquoteright} quality level.Results: We present here Figaro, a novel software tool for identifying and removing the vector from raw sequence data without prior knowledge of the vector sequence. The vector sequence is automatically inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics. We show that Figaro achieves 99.98\% sensitivity when tested on \~{}1.5 million shotgun reads from Drosophila pseudoobscura. We further explore the impact of accurate vector trimming on the quality of whole-genome assemblies by re-assembling two bacterial genomes from shotgun sequences deposited in the Trace Archive. Designed as a module in large computational pipelines, Figaro is fast, lightweight and flexible. Availability: Figaro is released under an open-source license through the AMOS package (http://amos.sourceforge.net/Figaro). Contact: mpop@umiacs.umd.edu }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/btm632}, url = {http://bioinformatics.oxfordjournals.org/content/24/4/462}, author = {White,James Robert and Roberts,Michael and Yorke,James A. and Pop, Mihai} } @article {18517, title = {Fishing for Phishing from the Network Stream}, volume = {GT-CS-08-08}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {Phishing is an increasingly prevalent social-engineering attack that attempts identity theft using spoofed Web pages of legitimate organizations. Unfortunately, current phishing detection methods are neither complete nor responsive because they rely on user reports, and many also require clientside software. Anti-phishing techniques could be more effective if they (1) could detect phishing attacks automatically from the network traffic; (2) could operate without cooperation from end-users. This paper performs a preliminary study to determine the feasibility of detecting phishing attacks in real-time, from the network traffic stream itself. We develop a model to identify the stages where in-network phishing detection is feasible and the data sources that can be analyzed to provide relevant information at each stage. Based on this model, we develop and evaluate a detection method based on features that exist in the network traffic it- self and are correlated with confirmed phishing attacks.}, url = {http://hdl.handle.net/1853/25463}, author = {Ramachandran,A. and Feamster, Nick and Krishnamurthy,B. and Spatscheck,O. and Van der Merwe,J.} } @article {16717, title = {Generalizing Word Lattice Translation}, year = {2008}, month = {2008/02//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Word lattice decoding has proven useful in spoken language translation; we argue that it provides a compelling model for translation of text genres, as well. We extend lattice decoding to hierarchical phrase-based models, providing a unified treatment with phrase-based decoding by treating lattices as a case of weighted finite-state automata. In the process, we resolve a significant complication that lattice representations introduce in reordering models. Our experiments evaluating the approach demonstrate substantial gains for Chinese-English and Arabic-English translation.}, keywords = {*MACHINE TRANSLATION, *STATISTICAL MACHINE TRANSLATION, *WORD LATTICE TRANSLATION, grammars, HIERARCHICAL PHRASE-BASED MODELS, linguistics, MODELS, STATISTICAL PROCESSES}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA481994}, author = {Dyer,Christopher and Muresan,Smaranda and Resnik, Philip} } @conference {16421, title = {GoGoBot: group collaboration, multi-agent modeling, and robots}, booktitle = {Proceedings of the 7th international joint conference on Autonomous agents and multiagent systems: demo papers}, series = {AAMAS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {1715 - 1716}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {Multi-agent simulation is a powerful technique used to encode real-world simple rules in virtual agents and then simulate their interactions [1]. Participatory simulations are similar to multi-agent simulation except individuals play the role of virtual agents, sometimes in combination with these virtual agents [2]. Finally, the bifocal modeling framework has enabled the examination of agents embodied in physical entities using sensors and actuators [3]. All three of these technologies are concerned with the creation, manipulation, and development of agents in one form or another. Thus combining these three disparate systems in to one unified platform would be useful. Multi-agent simulation platforms, participatory simulations, and bifocal modeling have all been demonstrated separately in the past. However many extant systems are difficult if not impossible to integrate.}, keywords = {multi-agent simulation, participatory simulation, ROBOTICS}, url = {http://dl.acm.org/citation.cfm?id=1402744.1402780}, author = {Rand, William and Blikstein,Paulo and Wilensky,Uri} } @article {14970, title = {High Performance Computing Algorithms for Land Cover}, year = {2008}, month = {2008///}, institution = {CiteSeerX}, abstract = {Global and regional land cover studies require the ability to apply complex models on selected subsets of large amounts of multi-sensor and multi-temporal data sets that have been derived from raw instrument measurements using widely accepted pre-processing algorithms. The computational and storage requirements of most such studies far exceed what is possible on a single workstation environment. We have been pursuing a new approach that couples scalable and open distributed heterogeneous hardware with the development of high performance software for processing, indexing, and organizing remotely sensed data. Hierarchical data management tools are used to ingest raw data, create metadata, and organize the archived data so as to automatically achieve computational load balancing among the available nodes and minimize I/O overheads. We illustrate our approach with four specific examples. The first is the development of the first fast operational scheme for the atmospheric correction of Landsat TM scenes, while the second example focuses on image segmentation using a novel hierarchical connected components algorithm. Retrieval of global BRDF (Bidirectional Reflectance Distribution Function) in the red and near infrared wavelengths using four years (1983 to 1986) of Pathfinder AVHRR Land (PAL) data set is the focus of our third example. The fourth example is the development of a hierarchical data organization scheme that allows on-demand processing and retrieval of regional and global AVHRR data sets. Our results show that substantial improvements in computational times can be achieved by using the high performance computing technology.}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.58.4213}, author = {Dynamics Using Remote and Satya Kalluri and Bader,David A. and John Townshend and JaJa, Joseph F. and Zengyan Zhang and Fallah-adl,Hassan} } @article {18492, title = {Hosting virtual networks on commodity hardware}, volume = {GT-CS-07-10}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {This paper describes Trellis, a software platform for hostingmultiple virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topol- ogy, control protocols, and forwarding tables, which low- ers the barrier for deploying custom services on an isolated, reconfigurable, and programmable network, while amor- tizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed vir- tual networks. We describe the design and implementation, of Trellis, including kernel-level performance optimizations, and evaluate its supported packet-forwarding rates against other virtualization technologies. We are in the process of upgrading the VINI facility to use Trellis. We also plan to release Trellis as part of MyVINI, a standalone software dis- tribution that allows researchers and application developers to deploy their own virtual network hosting platforms. }, author = {Bhatia,S. and Motiwala,M. and Muhlbauer,W. and Valancius,V. and Bavier,A. and Feamster, Nick and Peterson,L. and Rexford,J.} } @article {13449, title = {LEARNING STRUCTURED BAYESIAN NETWORKS: COMBINING ABSTRACTION HIERARCHIES AND TREE-STRUCTURED CONDITIONAL PROBABILITY TABLES}, journal = {Computational Intelligence}, volume = {24}, year = {2008}, month = {2008/02/01/}, pages = {1 - 22}, abstract = {Context-specific independence representations, such as tree-structured conditional probability distributions, capture local independence relationships among the random variables in a Bayesian network (BN). Local independence relationships among the random variables can also be captured by using attribute-value hierarchies to find an appropriate abstraction level for the values used to describe the conditional probability distributions. Capturing this local structure is important because it reduces the number of parameters required to represent the distribution. This can lead to more robust parameter estimation and structure selection, more efficient inference algorithms, and more interpretable models. In this paper, we introduce Tree-Abstraction-Based Search (TABS), an approach for learning a data distribution by inducing the graph structure and parameters of a BN from training data. TABS combines tree structure and attribute-value hierarchies to compactly represent conditional probability tables. To construct the attribute-value hierarchies, we investigate two data-driven techniques: a global clustering method, which uses all of the training data to build the attribute-value hierarchies, and can be performed as a preprocessing step; and a local clustering method, which uses only the local network structure to learn attribute-value hierarchies. We present empirical results for three real-world domains, finding that (1) combining tree structure and attribute-value hierarchies improves the accuracy of generalization, while providing a significant reduction in the number of parameters in the learned networks, and (2) data-derived hierarchies perform as well or better than expert-provided hierarchies.}, keywords = {abstraction hierarchies, background knowledge, Bayesian networks, clustering, machine learning, MDL}, isbn = {1467-8640}, doi = {10.1111/j.1467-8640.2007.00320.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8640.2007.00320.x/abstract;jsessionid=1C2AC5C6C44B47B8A26E3D5FC3F8FE74.d01t04}, author = {desJardins, Marie and Rathod,Priyang and Getoor, Lise} } @conference {13118, title = {A Logic Framework for Sports Video Summarization Using Text-Based Semantic Annotation}, booktitle = {Semantic Media Adaptation and Personalization, 2008. SMAP {\textquoteright}08. Third International Workshop on}, year = {2008}, month = {2008/12//}, pages = {69 - 75}, abstract = {Detection of semantic events in sports videos is an essential step towards video summarization. A large volume of research has been conducted for automatic semantic event detection and summarization of sports videos. In this paper we present a novel sports video summarization framework using a combination of text, video and logic analysis. Parse trees are used to analyze structured and free-style text webcasting of sports games and extract the game{\^A}{\textquestiondown}s semantic events, such as goals and penalties in soccer games. Semantic events are then hierarchically arranged before being passed to a logic processing engine. The logic engine receives the summary preferences from the user and subsequently parses the event hierarchy to generate the game{\^A}{\textquestiondown}s summary according to the user{\^A}{\textquestiondown}s preferences. The proposed framework was applied to both soccer and basketball videos. We achieved an average accuracy of 98.6\% and 100\% on soccer and basketball videos, respectively.}, keywords = {(mathematics);video, analysis;trees, annotation;Internet;broadcasting;sport;text, AUTOMATIC, detection;logic, engine;parse, event, PROCESSING, processing;, semantic, signal, summarization;text, trees;sports, video, Webcasting;text-based}, doi = {10.1109/SMAP.2008.25}, author = {Refaey,M.A. and Abd-Almageed, Wael and Davis, Larry S.} } @inbook {12915, title = {The marine environment and human health: the cholera model}, booktitle = {Global Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease EmergenceGlobal Climate Change and Extreme Weather Events: Understanding the Contributions to Infectious Disease Emergence}, year = {2008}, month = {2008///}, publisher = {National Academies Press}, organization = {National Academies Press}, isbn = {9780309124027}, author = {Rita R Colwell}, editor = {Relman,David} } @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.} } @conference {12244, title = {Matchmaking and implementation issues for a P2P desktop grid}, booktitle = {Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on}, year = {2008}, month = {2008/04//}, pages = {1 - 5}, abstract = {We present some recent and ongoing work in our decentralized desktop computing grid project. Specifically, we discuss matching jobs with compute nodes in a peer-to-peer grid of heterogeneous platforms, and the implementation of our algorithms in a concrete system.}, keywords = {computing, computing;, computing;peer-to-peer, desktop, grid;decentralized, grid;grid, grid;peer-to-peer, P2P}, doi = {10.1109/IPDPS.2008.4536388}, author = {Marsh,M. and Kim,Jik-Soo and Nam,Beomseok and Jaehwan Lee and Ratanasanya,S. and Bhattacharjee, Bobby and Keleher,P. and Richardson,D. and Wellnitz,D.} } @article {12147, title = {Measures and Risk Indicators for Early Insight into Software Safety. Development of Fault-Tolerant Systems}, year = {2008}, month = {2008/10//}, institution = {ABERDEEN TEST CENTER MD}, abstract = {Software contributes an ever-increasing level of functionality and control in today{\textquoteright}s systems. This increased use of software can dramatically increase the complexity and time needed to evaluate the safety of a system. Although the actual system safety cannot be verified during its development, measures can reveal early insights into potential safety problems and risks. An approach for developing early software safety measures is presented in this article. The approach and the example software measures presented are based on experience working with the safety engineering group on a large Department of Defense program.}, keywords = {*SOFTWARE ENGINEERING, *SYSTEM SAFETY, COMPUTER PROGRAMMING AND SOFTWARE, fault tolerant computing, INDICATORS, measurement, REPRINTS, risk, SAFETY ENGINEERING}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA487120}, author = {Basili, Victor R. and Marotta,Frank and Dangle,Kathleen and Esker,Linda and Rus,Ioana} } @article {18584, title = {Method and System for Detecting and Responding to Attacking Networks}, volume = {11/538,212}, year = {2008}, month = {2008/01/31/}, abstract = {A system and method for detecting a first network of compromised computers in a second network of computers, comprising: collecting Domain Name System (DNS) data for the second network; examining the collected data relative to DNS data from known comprised and/or uncompromised computers in the second network; and determining the existence of the first network and/or the identity of compromised computers in the second network based on the examination.}, url = {http://www.google.com/patents?id=TYunAAAAEBAJ}, author = {Dagon,David and Feamster, Nick and Lee,Weake and Edmonds,Robert and Lipton,Richard and Ramachandran,Anirudh}, editor = {Damballa, Inc.} } @article {12851, title = {Model Based Design Verification: A Monitor Based Approach}, volume = {2008-01-0741}, year = {2008}, month = {2008/04//}, institution = {SAE International}, address = {Warrendale, PA}, abstract = {This paper assesses the utility of an automated functional verification methodology in the design of a body electronics application. The use of design models as detailed specifications for software is gaining steady acceptance in the automotive industry because of the advantages it offers in terms of rapid system prototyping and automatic code generation. This paper argues that such modeling effort can also be used to provide support for design verification, so that errors may be pinpointed before they find their way into code, when they become much harder and more expensive to isolate, diagnose and repair.}, url = {http://papers.sae.org/2008-01-0741}, author = {Ackermann,Chris and Ray,Arnab and Cleaveland, Rance and Heit,J{\"u}rgen and Martin,Christopher and Shelton,Charles} } @conference {12550, title = {Modeling shape and textural variations in aging faces}, booktitle = {Automatic Face Gesture Recognition, 2008. FG {\textquoteright}08. 8th IEEE International Conference on}, year = {2008}, month = {2008/09//}, pages = {1 - 8}, abstract = {We propose a two fold approach towards modeling facial aging in adults. Firstly, we develop a shape transformation model that is formulated as a physically-based parametric muscle model that captures the subtle deformations facial features undergo with age. The model implicitly accounts for the physical properties and geometric orientations of the individual facial muscles. Next, we develop an image gradient based texture transformation function that characterizes facial wrinkles and other skin artifacts often observed during different ages. Facial growth statistics (both in terms of shape and texture) play a crucial role in developing the aforementioned transformation models. From a database that comprises of pairs of age separated face images of many individuals, we extract age-based facial measurements across key fiducial features and further, study textural variations across ages. We present experimental results that illustrate the applications of the proposed facial aging model in tasks such as face recognition and facial appearance prediction across aging.}, keywords = {Aging, analysis;, faces;image, function;face, gradient;modeling, model;textural, recognition;image, shape;shape, texture;statistical, transformation, variations;texture}, doi = {10.1109/AFGR.2008.4813337}, author = {Ramanathan,N. and Chellapa, Rama} } @article {16385, title = {Multi-agent learning with a distributed genetic algorithm}, journal = {AAMAS 2008: ALAMAS + ALAg Workshop}, year = {2008}, month = {2008///}, abstract = {Lightweight agents distributed in space have the potential to solve many complex problems. In this paper, we examine a model where agents represent individuals in a genetic algorithm (GA) solving a shared problem. We examine two questions: (1) How does the network density of connections between agents a ffect the performance of the systems? (2) How does the interaction topology a affect the performance of the system? In our model, agents exist in either a random network topology with long-distance communication, or a location-based topology, where agents only communicate with near neighbors. We examine both fixed and dynamic networks. Within the context of our investigation, our initial results indicate that relatively low network density achievesthe same results as a panmictic, or fully connected, population. Additionally, we find that dynamic networks outperform fixed networks, and that random network topologies outperform proximity-based network topologies. We conclude by showing how this model can be useful not only for multi-agent learning, but also for genetic algorithms, agent-based simulation and models of diff usion of innovation. }, author = {Stonedahl,F. and Rand, William and Wilensky,U.} } @conference {12556, title = {Multi-biometric cohort analysis for biometric fusion}, booktitle = {Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on}, year = {2008}, month = {2008/04/31/4}, pages = {5224 - 5227}, abstract = {Biometric matching decisions have traditionally been made based solely on a score that represents the similarity of the query biometric to the enrolled biometric(s) of the claimed identity. Fusion schemes have been proposed to benefit from the availability of multiple biometric samples (e.g., multiple samples of the same fingerprint) or multiple different biometrics (e.g., face and fingerprint). These commonly adopted fusion approaches rarely make use of the large number of non-matching biometric samples available in the database in the form of other enrolled identities or training data. In this paper, we study the impact of combining this information with the existing fusion methodologies in a cohort analysis framework. Experimental results are provided to show the usefulness of such a cohort-based fusion of face and fingerprint biometrics.}, keywords = {(access, analysis;biometrics, biometric, biometrics;fingerprint, biometrics;multi-biometric, cohort, control);face, data;, decisions;face, fusion;biometric, identification;security, MATCHING, of, recognition;fingerprint}, doi = {10.1109/ICASSP.2008.4518837}, author = {Aggarwal,G. and Ratha,N. K and Bolle, R.M. and Chellapa, Rama} } @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.} } @conference {12548, title = {A Non-generative Approach for Face Recognition Across Aging}, booktitle = {Biometrics: Theory, Applications and Systems, 2008. BTAS 2008. 2nd IEEE International Conference on}, year = {2008}, month = {2008/10//undefin}, pages = {1 - 6}, abstract = {Human faces undergo a lot of change in appearance as they age. Though facial aging has been studied for decades, it is only recently that attempts have been made to address the problem from a computational point of view. Most of these early efforts follow a simulation approach in which matching is performed by synthesizing face images at the target age. Given the innumerable different ways in which a face can potentially age, the synthesized aged image may not be similar to the actual aged image. In this paper, we bypass the synthesis step and directly analyze the drifts of facial features with aging from a purely matching perspective. Our analysis is based on the observation that facial appearance changes in a coherent manner as people age. We provide measures to capture this coherency in feature drifts. Illustrations and experimental results show the efficacy of such an approach for matching faces across age progression.}, keywords = {appearance;nongenerative, approach;face, Face, image, matching;, recognition;facial, recognition;image, synthesis;face}, doi = {10.1109/BTAS.2008.4699331}, author = {Biswas,S. and Aggarwal,G. and Ramanathan,N. and Chellapa, Rama} } @article {18503, title = {Packets with provenance}, volume = {GT-CS-08-02}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {Traffic classification and distinction allows network operators to provision resources, enforce trust, control unwanted traffic, and traceback unwanted traffic to its source. Today{\textquoteright}s classification mechanisms rely primarily on IP addresses and port numbers; unfortunately, these fields are often too coarse and ephemeral, and moreover, they do not reflect traffic{\textquoteright}s provenance, associated trust, or relationship to other processes or hosts. This paper presents the design, analysis, user-space implementation, and evaluation of Pedigree, which consists of two components: a trusted tagger that resides on hosts and tags packets with information about their provenance (i.e., identity and history of potential input from hosts and resources for the process that generated them), and an arbiter, which decides what to do with the traffic that carries certain tags. Pedigree allows operators to write traffic classification policies with expressive semantics that reflect properties of the actual process that generated the traffic. Beyond offering new function and flexibility in traffic classification, Pedigree represents a new and interesting point in the design space between filtering and capabilities, and it allows network operators to leverage host-based trust models to decide treatment of network traffic.}, url = {http://hdl.handle.net/1853/25467}, author = {Ramachandran,A. and Bhandankar,K. and Tariq,M.B. and Feamster, Nick} } @conference {12173, title = {Readability of scanned books in digital libraries}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {705 - 714}, author = {Quinn,A.J. and Hu,C. and Arisaka,T. and Rose,A. and Bederson, Benjamin B.} } @article {16390, title = {Reciprocity between the cerebellum and the cerebral cortex: Nonlinear dynamics in microscopic modules for generating voluntary motor commands}, journal = {Complexity}, volume = {14}, year = {2008}, month = {2008/11/01/}, pages = {29 - 45}, abstract = {The cerebellum and basal ganglia are reciprocally connected with the cerebral cortex, forming many loops that function as distributed processing modules. Here we present a detailed model of one microscopic loop between the motor cortex and the cerebellum, and we show how small arrays of these microscopic loops (CB modules) can be used to generate biologically plausible motor commands for controlling movement. A fundamental feature of CB modules is the presence of positive feedback loops between the cerebellar nucleus and the motor cortex. We use nonlinear dynamics to model one microscopic loop and to investigate its bistable properties. Simulations demonstrate an ability to program a motor command well in advance of command generation and an ability to vary command duration. However, control of command intensity is minimal, which could interfere with the control of movement velocity. To assess these hypotheses, we use a minimal nonlinear model of the neuromuscular (NM) system that translates motor commands into actual movements. Simulations of the combined CB-NM modular model indicate that movement duration is readily controlled, whereas velocity is poorly controlled. We then explore how an array of eight CB-NM modules can be used to control the direction and endpoint of a planar movement. In actuality, thousands of such microscopic loops function together as an array of adjustable pattern generators for programming and regulating the composite motor commands that control limb movements. We discuss the biological plausibility and limitations of the model. We also discuss ways in which an agent-based representation can take advantage of the modularity in order to model this complex system. {\textcopyright} 2008 Wiley Periodicals, Inc. Complexity, 2008}, keywords = {agent-based modeling, cerebellum, equilibrium point control, motor command, motor cortex, Movement, neural network, nonlinear dynamics}, isbn = {1099-0526}, doi = {10.1002/cplx.20241}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cplx.20241/abstract}, author = {Wang,Jun and Dam,Gregory and Yildirim,Sule and Rand, William and Wilensky,Uri and Houk,James C.} } @article {15799, title = {Residual periodograms for choosing regularization parameters for ill-posed problems}, journal = {Inverse Problems}, volume = {24}, year = {2008}, month = {2008/06/01/}, pages = {034005 - 034005}, abstract = {Consider an ill-posed problem transformed if necessary so that the errors in the data are independent identically normally distributed with mean zero and variance 1. We survey regularization and parameter selection from a linear algebra and statistics viewpoint and compare the statistical distributions of regularized estimates of the solution and the residual. We discuss methods for choosing a regularization parameter in order to assure that the residual for the model is statistically plausible. Ideally, as proposed by Rust (1998 Tech. Rep. NISTIR 6131, 2000 Comput. Sci. Stat. 32 333{\textendash}47 ), the results of candidate parameter choices should be evaluated by plotting the resulting residual along with its periodogram and its cumulative periodogram, but sometimes an automated choice is needed. We evaluate a method for choosing the regularization parameter that makes the residuals as close as possible to white noise, using a diagnostic test based on the periodogram. We compare this method with standard techniques such as the discrepancy principle, the L-curve and generalized cross validation, showing that it performs better on two new test problems as well as a variety of standard problems.}, isbn = {0266-5611, 1361-6420}, doi = {10.1088/0266-5611/24/3/034005}, url = {http://iopscience.iop.org/0266-5611/24/3/034005}, author = {Rust,Bert W. and O{\textquoteright}Leary, Dianne P.} } @article {13016, title = {Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence}, journal = {Syst Biol}, volume = {57}, year = {2008}, month = {2008/12//}, pages = {920 - 938}, abstract = {This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations{\textendash}first codon positions encoding leucine and arginine, which were also compositionally heterogeneous{\textendash}yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned{\textendash}fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II.}, doi = {10.1080/10635150802570791}, author = {Regier,J. C and Shultz,J. W and Ganley,A. R.D and Hussey,A. and Shi,D. and Ball,B. and Zwick,A. and Stajich,J. E and Cummings, Michael P. and Martin,J. W and Cunningham,CW} } @conference {16458, title = {Satisfying Complex Data Needs using Pull-Based Online Monitoring of Volatile Data Sources}, booktitle = {Data Engineering, International Conference on}, year = {2008}, month = {2008///}, pages = {1465 - 1467}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Emerging applications on the Web require better management of volatile data in pull-based environments. In a pull based setting, data may be periodically removed from the server. Data may also become obsolete, no longer serving client needs. In both cases, we consider such data to be volatile. To model such constraints on data usability, and support complex user needs we define profiles to specify which data sources are to be monitored and when. Using a novel abstraction of execution intervals we model complex profiles that access simultaneously several servers to gain from the used data. Given some budgetary constraints (e.g., bandwidth), the paper formalizes the problem of maximizing completeness.}, isbn = {978-1-4244-1836-7}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDE.2008.4497591}, author = {Roitman,Haggai and Gal,Avigdor and Raschid, Louiqa} } @article {16282, title = {Scaffolding and Validation of Bacterial Genome Assemblies Using Optical Restriction Maps}, journal = {Bioinformatics}, volume = {24}, year = {2008}, month = {2008/05/15/}, pages = {1229 - 1235}, abstract = {Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of mate-pair information. In this article we propose methods to overcome such limitations by incorporating information from optical restriction maps.Results: We demonstrate the robustness of our methods to sequencing and assembly errors using extensive experiments on simulated datasets. We then present the results obtained by applying our algorithms to data generated from two bacterial genomes Yersinia aldovae and Yersinia kristensenii. The resulting assemblies contain a single scaffold covering a large fraction of the respective genomes, suggesting that the careful use of optical maps can provide a cost-effective framework for the assembly of genomes. Availability: The tools described here are available as an open-source package at ftp://ftp.cbcb.umd.edu/pub/software/soma Contact: mpop@umiacs.umd.edu }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/btn102}, url = {http://bioinformatics.oxfordjournals.org/content/24/10/1229}, author = {Nagarajan,Niranjan and Read,Timothy D. and Pop, Mihai} } @article {16443, title = {SCALABLE CATALOG INFRASTRUCTURE FOR MANAGING ACCESS COSTS AND SOURCE SELECTION IN WIDE AREA NETWORKS}, journal = {International Journal of Cooperative Information Systems}, volume = {17}, year = {2008}, month = {2008///}, pages = {77 - 109}, author = {Zadorozhny,V. and Raschid, Louiqa and Gal,A.} } @article {16070, title = {Searching Electronic Health Records for Temporal Patterns in Patient Histories: A Case Study with Microsoft Amalga}, journal = {AMIA Annual Symposium ProceedingsAMIA Annu Symp Proc}, volume = {2008}, year = {2008}, month = {2008///}, pages = {601 - 605}, abstract = {As electronic health records (EHR) become more widespread, they enable clinicians and researchers to pose complex queries that can benefit immediate patient care and deepen understanding of medical treatment and outcomes. However, current query tools make complex temporal queries difficult to pose, and physicians have to rely on computer professionals to specify the queries for them. This paper describes our efforts to develop a novel query tool implemented in a large operational system at the Washington Hospital Center (Microsoft Amalga, formerly known as Azyxxi). We describe our design of the interface to specify temporal patterns and the visual presentation of results, and report on a pilot user study looking for adverse reactions following radiology studies using contrast.}, isbn = {1942-597X}, author = {Plaisant, Catherine and Lam,Stanley and Shneiderman, Ben and Smith,Mark S. and Roseman,David and Marchand,Greg and Gillam,Michael and Feied,Craig and Handler,Jonathan and Rappaport,Hank} } @article {14853, title = {Searching the world{\textquoteright}s herbaria: A system for visual identification of plant species}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {116 - 129}, abstract = {We describe a working computer vision system that aids in the identification of plant species. A user photographs an isolated leaf on a blank background, and the system extracts the leaf shape and matches it to the shape of leaves of known species. In a few seconds, the system displays the top matching species, along with textual descriptions and additional images. This system is currently in use by botanists at the Smithsonian Institution National Museum of Natural History. The primary contributions of this paper are: a description of a working computer vision system and its user interface for an important new application area; the introduction of three new datasets containing thousands of single leaf images, each labeled by species and verified by botanists at the US National Herbarium; recognition results for two of the three leaf datasets; and descriptions throughout of practical lessons learned in constructing this system.}, doi = {10.1007/978-3-540-88693-8_9}, author = {Belhumeur,P. and Chen,D. and Feiner,S. and Jacobs, David W. and Kress,W. and Ling,H. and Lopez,I. and Ramamoorthi,R. and Sheorey,S. and White,S.} } @article {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 {14574, title = {Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure}, journal = {Circulation: Cardiovascular Genetics}, volume = {1}, year = {2008}, month = {2008/12/01/}, pages = {117 - 125}, abstract = {Background{\textemdash} We report the first comprehensive analysis of gene expression differences by sex and age in left ventricular samples from 102 patients with dilated cardiomyopathy.Methods and Results{\textemdash} Gene expression data (HG-U133A gene chip, Affymetrix) were analyzed from 30 females and 72 males from 3 separate centers. More than 1800 genes displayed sexual dimorphism in the heart (adjusted P value <0.05). A significant number of these genes were highly represented in gene ontology pathways involved in ion transport and G-protein-coupled receptor signaling. Localization of these genes revealed enrichment on both the sex chromosomes as well as chromosomes 3, 4, and 14. The second goal of this study was to determine the effect of age on gene expression. Within the female cohort, >140 genes were differentially expressed in the <55 years age group compared with the >55 years age group. These genes were highly represented in gene ontology pathways involved in DNA damage. In contrast, zero genes in the male cohort <55 years met statistical significance when compared with the >55 years age group.Conclusions{\textemdash} Gene expression in dilated cardiomyopathy displayed evidence of sexual dimorphism similar to other somatic tissues and age dimorphism within the female cohort.}, doi = {10.1161/CIRCGENETICS.108.802652}, url = {http://circgenetics.ahajournals.org/content/1/2/117.abstract}, author = {Fermin,David R. and Barac,Ana and Lee,Sangjin and Polster,Sean P. and Hannenhalli, Sridhar and Bergemann,Tracy L. and Grindle,Suzanne and Dyke,David B. and Pagani,Francis and Miller,Leslie W. and Tan,Sarah and dos Remedios,Cris and Cappola,Thomas P. and Margulies,Kenneth B. and Hall,Jennifer L.} } @article {16673, title = {Soft syntactic constraints for hierarchical phrased-based translation}, journal = {Proceedings of ACL-08: HLT}, year = {2008}, month = {2008///}, pages = {1003 - 1011}, author = {Marton,Y. and Resnik, Philip} } @conference {18608, title = {Trellis: a platform for building flexible, fast virtual networks on commodity hardware}, booktitle = {Proceedings of the 2008 ACM CoNEXT Conference}, series = {CoNEXT {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {72:1{\textendash}72:6 - 72:1{\textendash}72:6}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe Trellis, a platform for hosting virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topology, control protocols, and forwarding tables, while amortizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed virtual networks. We describe the design and implementation of Trellis and evaluate its packet-forwarding rates relative to other virtualization technologies and native kernel forwarding performance.}, isbn = {978-1-60558-210-8}, doi = {10.1145/1544012.1544084}, url = {http://doi.acm.org/10.1145/1544012.1544084}, author = {Bhatia,Sapan and Motiwala,Murtaza and Muhlbauer,Wolfgang and Mundada,Yogesh and Valancius,Vytautas and Bavier,Andy and Feamster, Nick and Peterson,Larry and Rexford,Jennifer} } @article {18609, title = {UFO: a resilient layered routing architecture}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {38}, year = {2008}, month = {2008/09//}, pages = {59 - 62}, abstract = {Conventional wisdom has held that routing protocols cannot achieve both scalability and high availability. Despite scaling relatively well, today{\textquoteright}s Internet routing system does not react quickly to changing network conditions (e.g., link failures or excessive congestion). Overlay networks, on the other hand, can respond quickly to changing network conditions, but their reliance on aggressive probing does not scale to large topologies. The paper presents a layered routing architecture called UFO (Underlay Fused with Overlays), which achieves the best of both worlds by having the "underlay" provide explicit notification about network conditions to help improve the efficiency and scalability of routing overlays.}, keywords = {network monitoring, overlay networks, routing architecture}, isbn = {0146-4833}, doi = {10.1145/1452335.1452344}, url = {http://doi.acm.org/10.1145/1452335.1452344}, author = {Zhu,Yaping and Bavier,Andy and Feamster, Nick and Rangarajan,Sampath and Rexford,Jennifer} } @article {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 {12566, title = {Video stabilization and mosaicing}, journal = {The Essential Guide to Video Processing,}, year = {2008}, month = {2008///}, pages = {109 - 138}, author = {Ramachandran, M. and Veeraraghavan,A. and Chellapa, Rama} } @conference {16765, title = {Virtual access points for vehicular networks}, booktitle = {Proceedings of the 1st international conference on MOBILe Wireless MiddleWARE, Operating Systems, and Applications}, year = {2008}, month = {2008///}, pages = {14 - 14}, author = {Frangiadakis,N. and C{\^a}mara,D. and Filali,F. and Loureiro,A. A.F and Roussopoulos, Nick} } @article {13352, title = {Adaptive query processing}, journal = {Foundations and Trends in Databases}, volume = {1}, year = {2007}, month = {2007/01//}, pages = {1 - 140}, abstract = {As the data management field has diversified to consider settings in which queries are increasingly complex, statistics are less available, or data is stored remotely, there has been an acknowledgment that the traditional optimize-then-execute paradigm is insufficient. This has led to a plethora of new techniques, generally placed under the common banner of adaptive query processing, that focus on using runtime feed-back to modify query processing in a way that provides better response time or more efficient CPU utilization.In this survey paper, we identify many of the common issues, themes, and approaches that pervade this work, and the settings in which each piece of work is most appropriate. Our goal with this paper is to be a "value-add" over the existing papers on the material, providing not only a brief overview of each technique, but also a basic framework for understanding the field of adaptive query processing in general. We focus primarily on intra-query adaptivity of long-running, but not full-fledged streaming, queries. We conclude with a discussion of open research problems that are of high importance. }, isbn = {1931-7883}, doi = {10.1561/1900000001}, url = {http://dx.doi.org/10.1561/1900000001}, author = {Deshpande, Amol and Ives,Zachary and Vijayshankar Raman} } @conference {13354, title = {Adaptive query processing: why, how, when, what next?}, booktitle = {Proceedings of the 33rd international conference on Very large data bases}, series = {VLDB {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1426 - 1427}, publisher = {VLDB Endowment}, organization = {VLDB Endowment}, abstract = {Adaptive query processing has been the subject of a great deal of recent work, particularly in emerging data management environments such as data integration and data streams. We provide an overview of the work in this area, identifying its common themes, laying out the space of query plans, and discussing open research problems. We discuss why adaptive query processing is needed, how it is being implemented, where it is most appropriately used, and finally, what next, i.e., open research problems.}, isbn = {978-1-59593-649-3}, url = {http://dl.acm.org/citation.cfm?id=1325851.1326033}, author = {Deshpande, Amol and Ives,Zachary and Vijayshankar Raman} } @article {18663, title = {Archetypal behavior in computer security}, journal = {Journal of Systems and Software}, volume = {80}, year = {2007}, month = {2007/10//}, pages = {1594 - 1606}, abstract = {The purpose of this study is to understand observed behavior and to diagnose and find solutions to issues encountered in organizational computer security using a systemic approach, namely system archetypes. In this paper we show the feasibility of archetypes application and the benefits of simulation. We developed a model and simulation of some aspects of security based on system dynamics principles. The system dynamics simulation model can be used in support of decision-making, training, and teaching regarding the mitigation of computer security risks. In this paper, we combine two archetypes and show the computer security relevance of such combinations. Presented are instances of the archetypes {\textquotedblleft}Escalation{\textquotedblright}, in which an organization must continuously increase its efforts to counter additional attacker effort; and {\textquotedblleft}Limits to Growth{\textquotedblright}, in which the gains from an organization{\textquoteright}s security efforts plateau or decline due to its limited capacity for security-related tasks. We describe a scenario where these archetypes (individually and combined) can help in diagnosis and understanding, and present simulation of {\textquotedblleft}what-if{\textquotedblright} scenarios suggesting how an organization might remedy these problems and maximize its gains from security efforts.}, keywords = {Attacks and countermeasures, Escalation, Limits to Growth, Organization computer security, System archetypes, System dynamics, System dynamics modeling and simulation}, isbn = {0164-1212}, doi = {10.1016/j.jss.2007.01.046}, url = {http://www.sciencedirect.com/science/article/pii/S0164121207000155}, author = {Rosenfeld,Shalom N. and Rus,Ioana and Michel Cukier} } @article {12916, title = {Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {73}, year = {2007}, month = {2007/12/15/}, pages = {7926 - 7933}, abstract = {The association of Vibrio cholerae with zooplankton has been suggested as an important factor in transmission of human epidemic cholera, and the ability to colonize zooplankton surfaces may play a role in the temporal variation and predominance of the two different serogroups (V. cholerae O1 El Tor and O139) in the aquatic environment. To date, interactions between specific serogroups and species of plankton remain poorly understood. Laboratory microcosm experiments were carried out to compare quantitatively the colonization of two copepod species, Acartia tonsa and Eurytemora affinis, by each of the epidemic serogroups. V. cholerae O1 consistently achieved higher abundances than V. cholerae O139 in colonizing adults of each copepod species as well as the multiple life stages of E. affinis. This difference in colonization may be significant in the general predominance of V. cholerae O1 in cholera epidemics in rural Bangladesh where water supplies are taken directly from the environment.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01238-07}, url = {http://aem.asm.org/content/73/24/7926}, author = {Rawlings,Tonya K. and Ruiz,Gregory M. and Rita R Colwell} } @article {12981, title = {Biased data reduce efficiency and effectiveness of conservation reserve networks}, journal = {Ecology Letters}, volume = {10}, year = {2007}, month = {2007/05/01/}, pages = {364 - 374}, abstract = {Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as {\textquoteleft}complete{\textquoteright}, we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1{\textendash}5\% of species, and resulted in reserve networks that were 9{\textendash}17\% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data.}, keywords = {Bias, biodiversity conservation, complementarity, efficiency, marxan, rarity, reserve networks, reserve selection algorithms, species detection}, isbn = {1461-0248}, doi = {10.1111/j.1461-0248.2007.01025.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2007.01025.x/abstract}, author = {Grand,Joanna and Cummings, Michael P. and Rebelo,Tony G and Ricketts,Taylor H and Neel,Maile C} } @conference {16448, title = {Bid based scheduler with backfilling for a multiprocessor system}, booktitle = {Proceedings of the ninth international conference on Electronic commerce}, year = {2007}, month = {2007///}, pages = {459 - 468}, author = {Yahav,I. and Raschid, Louiqa and Andrade,H.} } @conference {13146, title = {Bilattice-based Logical Reasoning for Human Detection}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {The capacity to robustly detect humans in video is a critical component of automated visual surveillance systems. This paper describes a bilattice based logical reasoning approach that exploits contextual information and knowledge about interactions between humans, and augments it with the output of different low level detectors for human detection. Detections from low level parts-based detectors are treated as logical facts and used to reason explicitly about the presence or absence of humans in the scene. Positive and negative information from different sources, as well as uncertainties from detections and logical rules, are integrated within the bilattice framework. This approach also generates proofs or justifications for each hypothesis it proposes. These justifications (or lack thereof) are further employed by the system to explain and validate, or reject potential hypotheses. This allows the system to explicitly reason about complex interactions between humans and handle occlusions. These proofs are also available to the end user as an explanation of why the system thinks a particular hypothesis is actually a human. We employ a boosted cascade of gradient histograms based detector to detect individual body parts. We have applied this framework to analyze the presence of humans in static images from different datasets.}, keywords = {automated, detection;parts-based, detectors;static, histograms;human, images;formal, interactions;gradient, logic;image, logical, mechanisms;surveillance;video, processing;, reasoning;complex, recognition;inference, signal, Surveillance, systems;bilattice-based, visual}, doi = {10.1109/CVPR.2007.383133}, author = {Shet,V. D and Neumann, J. and Ramesh,V. and Davis, Larry S.} } @article {16439, title = {BIPASS: BioInformatics Pipeline Alternative Splicing Services}, journal = {Nucleic Acids Research}, volume = {35}, year = {2007}, month = {2007///}, pages = {W292 - W292}, author = {Legendre,C. and Raschid, Louiqa and Snyder,B.} } @article {18497, title = {Bitstore: An incentive-compatible solution for blocked downloads in bittorrent}, journal = {Proc. Joint Workshop on The Economics of Networked Systems and Incentive-Based Computing (NetEcon)}, year = {2007}, month = {2007///}, abstract = {As many as 30\% of all files shared on public BitTorrentnetworks suffer from the lack of {\textquotedblleft}seeders{\textquotedblright} (peers that have complete copies of the file being shared); peers attempting to download such a file ({\textquotedblleft}leechers{\textquotedblright}) may have to wait indef- initely to obtain certain file chunks that are not distributed in the file{\textquoteright}s network of peers (the {\textquotedblleft}swarm{\textquotedblright}). We call this the Blocked Leecher Problem (BLP). To alleviate BLP, we propose BitStore, a larger, secure network of BitTorrent users (not necessarily all sharing the same content) where nodes offer their resources (such as disk space and bandwidth) for public use. Peers sharing any file can use the storage network to maintain replicas for each chunk of the file. Any leecher seeking chunks that are absent from in its own swarm can query the public network, locate the node storing the said chunks, and retrieve them. BitStore also provides robust incentives for nodes contributing re- sources: In return for storing and serving chunks, such nodes can negotiate micropayments using a second-price auction. Peers who receive these credits may later use them to re- trieve blocks they need from the storage network. This paper quantifies the BLP, presents an overview of the BitStore design, and discusses various challenges related to storage management and incentives. }, author = {Ramachandran,A. and Sarma,A.D. and Feamster, Nick} } @article {18507, title = {Building a Better Mousetrap}, volume = {GIT-CSS-07-01}, year = {2007}, month = {2007///}, institution = {Georgia Institute of Technology. College of Computing}, abstract = {Routers in the network core are unable to maintain detailed statistics for every packet; thus, traffic statistics are often based on packet sampling, which reduces accuracy. Because tracking large ("heavy-hitter") traffic flows is important both for pricing and for traffic engineering, much attention has focused on maintaining accurate statistics for such flows, often at the expense of small-volume flows. Eradicating these smaller flows makes it difficult to observe communication structure, which is sometimes more important than maintaining statistics about flow sizes. This paper presents FlexSample, a sampling framework that allows network operators to get the best of both worlds: For a fixed sampling budget, FlexSample can capture significantly more small-volume flows for only a small increase in relative error of large traffic flows. FlexSample uses a fast, lightweight counter array that provides a coarse estimate of the size ("class") of each traffic flow; a router then can sample at different rates according to the class of the traffic using any existing sampling strategy. Given a fixed sampling rate and a target fraction of sampled packets to allocate across traffic classes, FlexSample computes packet sampling rates for each class that achieve these allocations online. Through analysis and trace-based experiments, we find that FlexSample captures at least 50\% more mouse flows than strategies that do not perform class-dependent packet sampling. We also show how FlexSample can be used to capture unique flows for specific applications.}, url = {http://hdl.handle.net/1853/14350}, author = {Ramachandran,A. and Seetharaman,S. and Feamster, Nick and Vazirani,V.} } @conference {16746, title = {Caching in Mobile Environments: A New Analysis and the Mobile-Cache System}, booktitle = {IEEE 18th International Symposium on Personal, Indoor and Mobile Radio Communications, 2007. PIMRC 2007}, year = {2007}, month = {2007/09/03/7}, pages = {1 - 5}, publisher = {IEEE}, organization = {IEEE}, abstract = {In the near future, we will be surrounded by ubiquitous wireless networks and so information dissemination for mobile users is a key issue. Hybrid push-pull constitutes a very effective and scalable solution. Our contribution is twofold. First we provide a new analysis that takes into account the user mobility. We argue that in a highly mobile setting, analysis and optimization goals discussed in past papers become irrelevant, since the most important aspect of the system is not delay, but rather the ability to answer as many queries as possible. As we show, the optimal pull-push bandwidth ratio depends on the mobility patterns of the users. Second, we use our findings to build Mobile-Cache, a system that can efficiently answer multiple queries over a wireless environment.}, keywords = {Bandwidth, Broadcasting, cache storage, Cities and towns, FCC, hybrid push-pull solution, information dissemination, Intelligent networks, Land mobile radio, mobile communication, Mobile computing, mobile environment, mobile radio, mobile-cache system, multiple query answering, pull-push bandwidth ratio, Query processing, Road safety, road vehicles, ubiquitous wireless network, Vehicle safety}, isbn = {978-1-4244-1144-3}, doi = {10.1109/PIMRC.2007.4394076}, author = {Frangiadakis,N. and Roussopoulos, Nick} } @article {18897, title = {CARA: A Cultural-Reasoning Architecture}, journal = {IEEE Intelligent Systems}, volume = {22}, year = {2007}, month = {2007///}, pages = {12 - 16}, abstract = {The Cognitive Architecture for Reasoning about Adversaries supports methods to gather data about different cultural groups and learn the intensity of those groups{\textquoteright} opinions on various topics. It also lets users build and extract models of those groups{\textquoteright} behavior and continuously refine those models through shared multiperson learning experiences. Researchers have applied the architecture to develop cultural-reasoning applications for example, a game that teaches soldiers about cultural norms in an Afghan village.}, keywords = {cultural reasoning, opinion extraction, opponent modeling}, isbn = {1541-1672}, author = {V.S. Subrahmanian and Albanese,Massimiliano and Martinez,Mar?a Vanina and Nau, Dana S. and Reforgiato,Diego and Simari,Gerardo I. and Sliva,Amy and Udrea,Octavian and Wilkenfeld,Jonathan} } @article {16238, title = {Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus}, journal = {Journal of Biological Chemistry}, volume = {282}, year = {2007}, month = {2007/10/12/}, pages = {30051 - 30061}, abstract = {We report here the discovery and characterization of Ehp, a new secreted Staphylococcus aureus protein that potently inhibits the alternative complement activation pathway. Ehp was identified through a genomic scan as an uncharacterized secreted protein from S. aureus, and immunoblotting of conditioned S. aureus culture medium revealed that the Ehp protein was secreted at the highest levels during log-phase bacterial growth. The mature Ehp polypeptide is composed of 80 residues and is 44\% identical to the complement inhibitory domain of S. aureus Efb (extracellular fibrinogen-binding protein). We observed preferential binding by Ehp to native and hydrolyzed C3 relative to fully active C3b and found that Ehp formed a subnanomolar affinity complex with these various forms of C3 by binding to its thioester-containing C3d domain. Site-directed mutagenesis demonstrated that Arg75 and Asn82 are important in forming the Ehp{\textperiodcentered}C3d complex, but loss of these side chains did not completely disrupt Ehp/C3d binding. This suggested the presence of a second C3d-binding site in Ehp, which was mapped to the proximity of Ehp Asn63. Further molecular level details of the Ehp/C3d interaction were revealed by solving the 2.7-{\r A} crystal structure of an Ehp{\textperiodcentered}C3d complex in which the low affinity site had been mutationally inactivated. Ehp potently inhibited C3b deposition onto sensitized surfaces by the alternative complement activation pathway. This inhibition was directly related to Ehp/C3d binding and was more potent than that seen for Efb-C. An altered conformation in Ehp-bound C3 was detected by monoclonal antibody C3-9, which is specific for a neoantigen exposed in activated forms of C3. Our results suggest that increased inhibitory potency of Ehp relative to Efb-C is derived from the second C3-binding site in this new protein.}, doi = {10.1074/jbc.M704247200}, url = {http://www.jbc.org/content/282/41/30051.abstract}, author = {Hammel,Michal and Sfyroera,Georgia and Pyrpassopoulos,Serapion and Ricklin,Daniel and Ramyar,Kasra X. and Pop, Mihai and Jin,Zhongmin and Lambris,John D. and Geisbrecht,Brian V.} } @conference {16395, title = {Coevolution of Predators and Prey in a Spatial Model}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO)}, year = {2007}, month = {2007///}, address = {London, England}, author = {Ottino-Lofler,J. and Rand, William and Wilensky,U.} } @article {14103, title = {Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei}, journal = {Parasitology research}, volume = {100}, year = {2007}, month = {2007///}, pages = {887 - 892}, author = {Djikeng,A. and Raverdy,S. and Foster, Jeffrey S. and Bartholomeu,D. and Zhang,Y. and El-Sayed, Najib M. and Carlow,C.} } @article {13740, title = {Combining outputs from multiple machine translation systems}, journal = {Human Language Technologies 2007: The Conference of the North American Chapter of the Association for Computational Linguistics; Proceedings of the Main Conference}, year = {2007}, month = {2007///}, pages = {228 - 235}, abstract = {Currently there are several approaches tomachine translation (MT) based on differ- ent paradigms; e.g., phrasal, hierarchical and syntax-based. These three approaches yield similar translation accuracy despite using fairly different levels of linguistic knowledge. The availability of such a variety of systems has led to a growing interest toward finding better translations by combining outputs from multiple sys- tems. This paper describes three differ- ent approaches to MT system combina- tion. These combination methods oper- ate on sentence, phrase and word level exploiting information from N -best lists, system scores and target-to-source phrase alignments. The word-level combination provides the most robust gains but the best results on the development test sets (NIST MT05 and the newsgroup portion of GALE 2006 dry-run) were achieved by combining all three methods. }, author = {Rosti,A.V.I. and Ayan,N.F. and Xiang,B. and Matsoukas,S. and Schwartz,R. and Dorr, Bonnie J} } @conference {18879, title = {Conditionalization: Adapting forward-chaining planners to partially observable environments}, year = {2007}, month = {2007///}, abstract = {We provide a general way to take forward-chainingplanners for classical planning domains and condition- alize them, i.e., adapt them to generate policies for partially observable planning domains. For domain-configurable planners such as SHOP2, TLPlan, and TALplanner, our generalization tech- nique preserves the ability to use domain knowledge to achieve highly efficient planning. We demonstrate this experimentally in two problem domains. The experi- ments compare PKS and MBP (two existing planners for partially observable planning) and CondSHOP2, a version of the HTN planner SHOP2 created by apply- ing our conditionalization method. To our surprise, PKS and MBP could solve only the simplest problems in our test domains. In contrast, CondSHOP2 solved all of the test problems quite eas- ily. This suggests that the ability to use domain knowl- edge may be not just desirable but indeed essential for solving large problems in partially observable domains. }, url = {http://www.cs.umd.edu/~nau/papers/kuter2007conditionalization.pdf}, author = {Kuter,U. and Nau, Dana S. and Reisner,E. and Goldman,R.} } @conference {12252, title = {Creating a Robust Desktop Grid using Peer-to-Peer Services}, booktitle = {Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International}, year = {2007}, month = {2007/03//}, pages = {1 - 7}, abstract = {The goal of the work described in this paper is to design and build a scalable infrastructure for executing grid applications on a widely distributed set of resources. Such grid infrastructure must be decentralized, robust, highly available, and scalable, while efficiently mapping application instances to available resources in the system. However, current desktop grid computing platforms are typically based on a client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. Fortunately, these problems can be addressed through the capabilities promised by new techniques and approaches in peer-to-peer (P2P) systems. By employing P2P services, our system allows users to submit jobs to be run in the system and to run jobs submitted by other users on any resources available in the system, essentially allowing a group of users to form an ad-hoc set of shared resources. The initial target application areas for the desktop grid system are in astronomy and space science simulation and data analysis.}, keywords = {allocation;, architecture;load, balancing;peer-to-peer, client-server, computing;peer-to-peer, computing;resource, desktop, grid;scalable, infrastructure;client-server, system;robust, systems;grid}, doi = {10.1109/IPDPS.2007.370505}, author = {Kim,J.-S. and Nam,B. and Marsh,M. and Keleher,P. and Bhattacharjee, Bobby and Richardson,D. and Wellnitz,D. and Sussman, Alan} } @conference {16425, title = {The defined cliffs variant in dynamic environments: a case study using the shaky ladder hyperplane-defined functions}, booktitle = {Proceedings of the 9th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1158 - 1164}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The shaky ladder hyperplane-defined functions (sl-hdfs) are a test suite utilized for exploring the behavior of the genetic algorithm (GA) in dynamic environments. This test suite can generate arbitrary problems with similar levels of difficulty and it provides a platform for systematic controlled observations of the GA in dynamic environments. Previous work has found two factors that contribute to the GA{\textquoteright}s success on sl-hdfs: (1) short initial building blocks and (2) significantly changing the reward structure during fitness landscape changes. Therefore a test function that combines these two features should facilitate even better GA performance. This has led to the construction of a new sl-hdf variant, "Defined Cliffs," in which we combine short elementary building blocks with sharp transitions in the environment. We examine this variant with two different levels of dynamics, static and regularly changing, using four different metrics. The results show superior GA performance on the Defined Cliffs over all previous variants (Cliffs, Weight, and Smooth). Our observations and conclusions in this variant further the understanding of the GA in dynamic environments.}, keywords = {building blocks, dynamic environments, Genetic algorithms, shaky ladder hyperplane-defined functions}, isbn = {978-1-59593-697-4}, doi = {10.1145/1276958.1277186}, url = {http://doi.acm.org/10.1145/1276958.1277186}, author = {Alharbi,Abir and Rand, William and Riolo,Rick} } @article {18756, title = {Development of in-mold assembly process for realizing mesoscale revolute joints}, journal = {Transactions of North American Manufacturing Research Institution of SME}, volume = {35}, year = {2007}, month = {2007///}, abstract = {In-mold Assembly process at the mesoscalepresents several manufacturing challenges. Results reported in this paper demonstrate the technical feasibility of creating rigid body mesoscale revolute joints using In-Mold Assembly process. The following new results are reported in this paper. First, we describe a mold design with varying cavity shape to perform In-Mold Assembly. This mold design uses an accurate mold piece positioning method to avoid damage to delicate mesoscale parts during the cavity change step. Second, we describe a mold insert fabrication process for making mold inserts with the desired surface characteristics for mesoscale molding. Finally, we describe methods to limit the adhesion at the interfaces and hence create articulated revolute joint. Using the advances reported in this paper we have successfully molded a mesoscale revolute joint. To the best of our knowledge, this is the first demonstration of In-Mold Assembly process using a varying cavity shape mold to create a mesoscale revolute joint. }, url = {ftp://ftp.eng.umd.edu/:/home/glue/s/k/skgupta/pub/Publication/NAMRC07_Ananthanarayanan_draft.pdf}, author = {Ananthanarayanan,A. and Gupta,S.K. and Bruck,H. A. and Yu,Z. and Rajurkar,K. P.} } @inbook {19567, title = {Distribution-Free Testing Lower Bounds for Basic Boolean Functions}, booktitle = {Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {494 - 508}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {In the distribution-free property testing model, the distance between functions is measured with respect to an arbitrary and unknown probability distribution \mathcal{D} over the input domain. We consider distribution-free testing of several basic Boolean function classes over {0,1} n , namely monotone conjunctions, general conjunctions, decision lists, and linear threshold functions. We prove that for each of these function classes, Ω((n/logn)1/5) oracle calls are required for any distribution-free testing algorithm. Since each of these function classes is known to be distribution-free properly learnable (and hence testable) using Θ(n) oracle calls, our lower bounds are within a polynomial factor of the best possible.}, keywords = {Algorithm Analysis and Problem Complexity, Discrete Mathematics in Computer Science, Numeric Computing}, isbn = {978-3-540-74207-4, 978-3-540-74208-1}, url = {http://link.springer.com/chapter/10.1007/978-3-540-74208-1_36}, author = {Dana Dachman-Soled and Servedio, Rocco A.}, editor = {Charikar, Moses and Jansen, Klaus and Reingold, Omer and Rolim, Jos{\'e} D. P.} } @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} } @inbook {19491, title = {Ecotopia: An Ecological Framework for Change Management in Distributed Systems}, booktitle = {Architecting Dependable Systems IV}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {262 - 286}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Dynamic change management in an autonomic, service-oriented infrastructure is likely to disrupt the critical services delivered by the infrastructure. Furthermore, change management must accommodate complex real-world systems, where dependability and performance objectives are managed across multiple distributed service components and have specific criticality/value models. In this paper, we present Ecotopia, a framework for change management in complex service-oriented architectures (SOA) that is ecological in its intent: it schedules change operations with the goal of minimizing the service-delivery disruptions by accounting for their impact on the SOA environment. The change-planning functionality of Ecotopia is split between multiple objective-advisors and a system-level change-orchestrator component. The objective advisors assess the change-impact on service delivery by estimating the expected values of the Key Performance Indicators (KPIs), during and after change. The orchestrator uses the KPI estimations to assess the per-objective and overall business-value changes over a long time-horizon and to identify the scheduling plan that maximizes the overall business value. Ecotopia handles both external change requests, like software upgrades, and internal changes requests, like fault-recovery actions. We evaluate the Ecotopia framework using two realistic change-management scenarios in distributed enterprise systems.}, keywords = {Autonomic Computing, Dynamic Change Management, Fault-Tolerant Architecture, Operating systems, Performability, Service Orchestration, software engineering}, isbn = {978-3-540-74033-9, 978-3-540-74035-3}, url = {http://link.springer.com/chapter/10.1007/978-3-540-74035-3_12}, author = {Tudor Dumitras and Ro{\c s}u, Daniela and Dan, Asit and Narasimhan, Priya}, editor = {Lemos, Rog{\'e}rio de and Gacek, Cristina and Romanovsky, Alexander} } @article {12357, title = {Efficient simulation of critical synchronous dataflow graphs}, journal = {ACM Transactions on Design Automation of Electronic Systems (TODAES)}, volume = {12}, year = {2007}, month = {2007///}, pages = {1 - 28}, author = {Hsu,C. J and Ko,M. Y and Bhattacharyya, Shuvra S. and Ramasubbu,S. and Pino,J. L} } @article {16670, title = {Evaluating a cross-cultural children{\textquoteright}s online book community: Lessons learned for sociability, usability, and cultural exchange}, journal = {Interacting with Computers}, volume = {19}, year = {2007}, month = {2007/07//}, pages = {494 - 511}, abstract = {The use of computers for human-to-human communication among adults has been studied for many years, but using computer technology to enable children from all over the world to talk to each other has rarely been discussed by researchers. The goal of our research is to fill this gap and explore the design and evaluation of children{\textquoteright}s cross-language online communities via a case study of the International Children{\textquoteright}s Digital Library Communities (ICDLCommunities). This project supports the development of communities for children (ages 7{\textendash}11) that form around the International Digital Children{\textquoteright}s Library (ICDL) book collection. In this community the children can learn about each others{\textquoteright} cultures and make friends even if they do not speak the same language. They can also read and create stories and ask and answer questions about these. From this evaluation study we learned that: (i) children are very interested in their counterparts in other countries and a remarkable amount of communication takes place even when they do not share a common language; (ii) representing their identity online in many different forms is particularly important to children when communicating in an online community; (iii) children enjoy drawing but representing stories in a sequence of diagrams is challenging and needs support; and (iv) asking and answering questions without language is possible using graphical templates. In this paper we present our findings and make recommendations for designing children{\textquoteright}s cross-cultural online communities.}, keywords = {children, Cross-cultural, Evaluation and design, International Children{\textquoteright}s Digital Library, Online communities}, isbn = {0953-5438}, doi = {10.1016/j.intcom.2007.03.001}, url = {http://www.sciencedirect.com/science/article/pii/S0953543807000240}, author = {Komlodi,Anita and Hou,Weimin and Preece,Jenny and Druin, Allison and Golub,Evan and Alburo,Jade and Liao,Sabrina and Elkiss,Aaron and Resnik, Philip} } @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 {16427, title = {Evolution of non-uniform cellular automata using a genetic algorithm: diversity and computation}, booktitle = {Proceedings of the 9th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1531 - 1531}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We used a genetic algorithm to evaluate the cost / benefit of diversity in evolving sets of rules for non-uniform cellular automata solving the density classification problem.}, keywords = {diversity, Genetic algorithms, non-uniform cellular automata, search spaces}, isbn = {978-1-59593-697-4}, doi = {10.1145/1276958.1277260}, url = {http://doi.acm.org/10.1145/1276958.1277260}, author = {Sondahl,Forrest and Rand, William} } @article {16408, title = {Examining Group Behavior and Collaboration using ABM and Robots}, journal = {Proc. of Agent}, year = {2007}, month = {2007///}, abstract = {Agent-based modeling has been extensively used by scientists to study complex systems.Participatory simulations are similar to agent-based models except that humans play the role of the virtual agents. The Bifocal modeling approach uses sensors to gather data about the real-world phenomena being modeled and uses that information to affect the model. In this work, we are interested in automatically extracting, analyzing and modeling group behaviors in problem solving. Combining these three systems into one unified platform would be useful for those purposes, since it would facilitate a synthesis of their main affordances: understanding the role of locality, mapping human action to emergent behaviors, and controlling embedded physical objects in noisy environments while receiving sensory feedback. We will demonstrate a technological platform based on the NetLogo/HubNet architecture that supports simulated agents, participatory agents and physical agents. We place this platform within a more general framework that we call Human, Embedded and Virtual agents in Mediation (HEV-M). We have run several studies using an instantiation of this platform that consists of a robot-car with four users who navigate a maze. We believe that this tool has potential for three main reasons (1) it facilitates logging of participant{\textquoteright}s actions, so as to identify patterns, (2) it offers researchers in the field of computer-supported collaborative learning an easy-to-use tool to design engaging collaborative learning activities and, (3) it foregrounds the role of individual actions within the accomplishment of a collective goal, highlighting the connections between simple individual actions and the resultant macroscopic behaviors of the system. }, author = {Blikstein,P. and Rand, William and Wilensky,Uri} } @article {12134, title = {Experimenting with software testbeds for evaluating new technologies}, journal = {Empirical Software Engineering}, volume = {12}, year = {2007}, month = {2007///}, pages = {417 - 444}, abstract = {The evolution of a new technology depends upon a good theoretical basis for developing the technology, as well as upon its experimental validation. In order to provide for this experimentation, we have investigated the creation of a software testbed and the feasibility of using the same testbed for experimenting with a broad set of technologies. The testbed is a set of programs, data, and supporting documentation that allows researchers to test their new technology on a standard software platform. An important component of this testbed is the Unified Model of Dependability (UMD), which was used to elicit dependability requirements for the testbed software. With a collection of seeded faults and known issues of the target system, we are able to determine if a new technology is adept at uncovering defects or providing other aids proposed by its developers. In this paper, we present the Tactical Separation Assisted Flight Environment (TSAFE) testbed environment for which we modeled and evaluated dependability requirements and defined faults to be seeded for experimentation. We describe two completed experiments that we conducted on the testbed. The first experiment studies a technology that identifies architectural violations and evaluates its ability to detect the violations. The second experiment studies model checking as part of design for verification. We conclude by describing ongoing experimental work studying testing, using the same testbed. Our conclusion is that even though these three experiments are very different in terms of the studied technology, using and re-using the same testbed is beneficial and cost effective.}, doi = {10.1007/s10664-006-9034-0}, author = {Lindvall,M. and Rus,I. and Donzelli,P. and Memon, Atif M. and Zelkowitz, Marvin V and Betin-Can,A. and Bultan,T. and Ackermann,C. and Anders,B. and Asgari, S. and Basili, Victor R.} } @article {16738, title = {Extended wavelets for multiple measures}, journal = {ACM Transactions on Database SystemsACM Trans. Database Syst.}, volume = {32}, year = {2007}, month = {2007/06//}, pages = {10-es - 10-es}, isbn = {03625915}, doi = {10.1145/1242524.1242527}, url = {http://dl.acm.org/citation.cfm?id=1242527}, author = {Deligiannakis,Antonios and Garofalakis,Minos and Roussopoulos, Nick} } @article {13998, title = {A fast algorithm for learning large scale preference relations}, journal = {Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics (AISTATS 2007)}, volume = {2}, year = {2007}, month = {2007///}, pages = {388 - 395}, abstract = {We consider the problem of learning the rank-ing function that maximizes a generalization of the Wilcoxon-Mann-Whitney statistic on training data. Relying on an ϵ-exact approx- imation for the error-function, we reduce the computational complexity of each iteration of a conjugate gradient algorithm for learn- ing ranking functions from O(m2), to O(m), where m is the size of the training data. Experiments on public benchmarks for ordi- nal regression and collaborative filtering show that the proposed algorithm is as accurate as the best available methods in terms of rank- ing accuracy, when trained on the same data, and is several orders of magnitude faster. }, author = {Raykar,V.C. and Duraiswami, Ramani and Krishnapuram,B.} } @conference {12576, title = {Fast Bilinear SfM with Side Information}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {We study the beneficial effect of side information on the Structure from Motion (SfM) estimation problem. The side information that we consider is measurement of a {\textquoteright}reference vector{\textquoteright} and distance from fixed plane perpendicular to that reference vector. Firstly, we show that in the presence of this information, the SfM equations can be rewritten similar to a bilinear form in its unknowns. Secondly, we describe a fast iterative estimation procedure to recover the structure of both stationary scenes and moving objects that capitalizes on this information. We also provide a refinement procedure in order to tackle incomplete or noisy side information. We characterize the algorithm with respect to its reconstruction accuracy, memory requirements and stability. Finally, we describe two classes of commonly occurring real-world scenarios in which this algorithm will be effective: (a) presence of a dominant ground plane in the scene and (b) presence of an inertial measurement unit on board. Experiments using both real data and rigorous simulations show the efficacy of the algorithm.}, keywords = {bilinear, Estimation, estimation;, estimation;reference, information;image, methods;motion, procedure;motion, procedure;side, reconstruction;iterative, recovery;image, structure, vector;refinement}, doi = {10.1109/ICCV.2007.4408874}, author = {Ramachandran, M. and Veeraraghavan,A. and Chellapa, Rama} } @article {13999, title = {Fast computation of sums of Gaussians}, journal = {Journal of Machine Learning Research (submitted)}, volume = {4}, year = {2007}, month = {2007///}, abstract = {Evaluating sums of multivariate Gaussian kernels is a key computational task in manyproblems in computational statistics and machine learning. The computational cost of the direct evaluation of such sums scales as the product of the number of kernel functions and the evaluation points. The fast Gauss transform proposed by Greengard and Strain (1991) is a ǫ-exact approximation algorithm that reduces the computational complexity of the evaluation of the sum of N Gaussians at M points in d dimensions from O(MN) to O(M + N). However, the constant factor in O(M + N) grows exponentially with increasing dimensionality d, which makes the algorithm impractical for dimensions greater than three. In this paper we present a new algorithm where the constant factor is reduced to asymptotically polynomial order. The reduction is based on a new multivariate Taylor{\textquoteright}s series expansion (which can act both as a local as well as a far field expansion) scheme combined with the efficient space subdivision using the k-center algorithm. The proposed method differs from the original fast Gauss transform in terms of a different factorization, efficient space subdivision, and the use of different error bounds for each source point. Algorithm details, error bounds, a procedure to choose the parameters, and numerical experiments are presented. We also compare our algorithm with the dual-tree algorithm of Gray and Moore (2003). As an example we show how the proposed method can be used for very fast ǫ-exact multivariate kernel density estimation. }, author = {Raykar,V.C. and Duraiswami, Ramani and Gumerov, Nail A.} } @article {14001, title = {Fast large scale Gaussian process regression using approximate matrix-vector products}, journal = {Learning workshop}, year = {2007}, month = {2007///}, author = {Raykar,V.C. and Duraiswami, Ramani} } @article {13997, title = {Fast weighted summation of erfc functions}, journal = {Technical Reports from UMIACS UMIACS-TR-2007-03}, year = {2007}, month = {2007/01/08/}, abstract = {Abstract: Direct computation of the weighted sum of N complementaryerror functions at M points scales as O(MN). We present a O(M + N) $\epsilon$-exact approximation algorithm to compute the same. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/7535}, author = {Raykar,Vikas C. and Duraiswami, Ramani and Krishnapuram,B.} } @conference {18570, title = {Filtering spam with behavioral blacklisting}, booktitle = {Proceedings of the 14th ACM conference on Computer and communications security}, series = {CCS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {342 - 351}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Spam filters often use the reputation of an IP address (or IP address range) to classify email senders. This approach worked well when most spam originated from senders with fixed IP addresses, but spam today is also sent from IP addresses for which blacklist maintainers have outdated or inaccurate information (or no information at all). Spam campaigns also involve many senders, reducing the amount of spam any particular IP address sends to a single domain; this method allows spammers to stay "under the radar". The dynamism of any particular IP address begs for blacklisting techniques that automatically adapt as the senders of spam change. This paper presents SpamTracker, a spam filtering system that uses a new technique called behavioral blacklisting to classify email senders based on their sending behavior rather than their identity. Spammers cannot evade SpamTracker merely by using "fresh" IP addresses because blacklisting decisions are based on sending patterns, which tend to remain more invariant. SpamTracker uses fast clustering algorithms that react quickly to changes in sending patterns. We evaluate SpamTracker{\textquoteright}s ability to classify spammers using email logs for over 115 email domains; we find that SpamTracker can correctly classify many spammers missed by current filtering techniques. Although our current datasets prevent us from confirming SpamTracker{\textquoteright}s ability to completely distinguish spammers from legitimate senders, our evaluation shows that SpamTracker can identify a significant fraction of spammers that current IP-based blacklists miss. SpamTracker{\textquoteright}s ability to identify spammers before existing blacklists suggests that it can be used in conjunction with existing techniques (e.g., as an input to greylisting). SpamTracker is inherently distributed and can be easily replicated; incorporating it into existing email filtering infrastructures requires only small modifications to mail server configurations.}, keywords = {blacklists, botnets, clustering, Security, spam}, isbn = {978-1-59593-703-2}, doi = {10.1145/1315245.1315288}, url = {http://doi.acm.org/10.1145/1315245.1315288}, author = {Ramachandran,Anirudh and Feamster, Nick and Vempala,Santosh} } @article {16405, title = {Full Spectrum Modeling: From Simplicity to Elaboration and Realism in Urban Pattern Formation}, journal = {North american association computational social and organization sciences conference (NAACSOS)}, year = {2007}, month = {2007///}, abstract = {There is a dichotomy between researchers who utilize elaborated and realistic agent-basedmodels and those who prefer simple models. Researchers who use realistic agent-based models (ABMs) argue that their realism makes them more useful, while those who utilize simple models claim that they are more general and provide more global knowledge. We believe that it is better to embrace both of these modeling approaches at the same time. Creating richly, detailed, empirically validated models to explore complex systems at a high level, and at the same time extracting general principles to create simplified models that help explore the most important general principles of the phenomena. We call this approach full spectrum modeling and we examine its use through a particular project concerned with understanding urban pattern formation. }, author = {Rand, William and Wilensky,U.} } @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} } @article {14581, title = {GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo}, journal = {Development}, volume = {134}, year = {2007}, month = {2007/01/01/}, pages = {189 - 198}, abstract = {In vitro studies have suggested that members of the GATA and Nkx transcription factor families physically interact, and synergistically activate pulmonary epithelial- and cardiac-gene promoters. However, the relevance of this synergy has not been demonstrated in vivo. We show that Gata6-Titf1 (Gata6-Nkx2.1) double heterozygous (G6-Nkx DH) embryos and mice have severe defects in pulmonary epithelial differentiation and distal airway development, as well as reduced phospholipid production. The defects in G6-Nkx DH embryos and mice are similar to those observed in human neonates with respiratory distress syndromes, including bronchopulmonary dysplasia, and differential gene expression analysis reveals essential developmental pathways requiring synergistic regulation by both Gata6 and Titf1 (Nkx2.1). These studies indicate that Gata6 and Nkx2.1 act in a synergistic manner to direct pulmonary epithelial differentiation and development in vivo, providing direct evidence that interactions between these two transcription factor families are crucial for the development of the tissues in which they are co-expressed.}, doi = {10.1242/dev.02720}, url = {http://dev.biologists.org/content/134/1/189.abstract}, author = {Zhang,Yuzhen and Rath,Nibedita and Hannenhalli, Sridhar and Wang,Zhishan and Cappola,Thomas and Kimura,Shioko and Atochina-Vasserman,Elena and Lu,Min Min and Beers,Michael F. and Morrisey,Edward E.} } @conference {19637, title = {Geometry and Charge State of Mixed-Ligand Au13 Nanoclusters}, booktitle = {X-RAY ABSORPTION FINE STRUCTURE - XAFS13: 13th International Conference}, volume = {882}, year = {2007}, month = {2007/02/02/}, pages = {749 - 751}, publisher = {AIP Publishing}, organization = {AIP Publishing}, abstract = {The integration of synthetic, experimental and theoretical tools into a self-consistent data analysis methodology allowed us to develop unique new levels of detail in nanoparticle characterization. We describe our methods using an example of Au 13 monolayer-protected clusters (MPCs), synthesized by ligand exchange methods. The combination of atom counting methods of scanning transmission electron microscopy and Au L3-edge EXAFS allowed us to characterize these clusters as icosahedral, with surface strain reduced from 5\% (as in ideal, regular icosahedra) to 3\%, due to the interaction with ligands. Charge transfer from Au to the thiol and phosphine ligands was evidenced by S and P K-edge XANES. A comparison of total energies of bare clusters of different geometries was performed by equivalent crystal theory calculations.}, keywords = {Atom surface interactions, Charge transfer, Data analysis, Extended X-ray absorption fine structure spectroscopy, Gold, nanoparticles, Scanning transmission electron microscopy, Surface strains, Total energy calculations, X-ray absorption near edge structure}, url = {http://scitation.aip.org/content/aip/proceeding/aipcp/10.1063/1.2644652}, author = {Frenkel, A. I. and Menard, L. D. and Northrup, P. and Rodriguez, J. A. and Zypman, F. and Dana Dachman-Soled and Gao, S.-P. and Xu, H. and Yang, J. C. and Nuzzo, R. G.} } @conference {13348, title = {A graph-based approach to vehicle tracking in traffic camera video streams}, booktitle = {Proceedings of the 4th workshop on Data management for sensor networks: in conjunction with 33rd International Conference on Very Large Data Bases}, series = {DMSN {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {19 - 24}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Vehicle tracking has a wide variety of applications from law enforcement to traffic planning and public safety. However, the image resolution of the videos available from most traffic camera systems, make it difficult to track vehicles based on unique identifiers like license plates. In many cases, vehicles with similar attributes are indistinguishable from one another due to image quality issues. Often, network bandwidth and power constraints limit the frame rate, as well. In this paper, we discuss the challenges of performing vehicle tracking queries over video streams from ubiquitous traffic cameras. We identify the limitations of tracking vehicles individually in such conditions and provide a novel graph-based approach using the identity of neighboring vehicles to improve the performance. We evaluate our approach using streaming video feeds from live traffic cameras available on the Internet. The results show that vehicle tracking is feasible, even for low quality and low frame rate traffic cameras. Additionally, exploitation of the attributes of neighboring vehicles significantly improves the performance.}, isbn = {978-159593-911-1}, doi = {10.1145/1286380.1286386}, url = {http://doi.acm.org/10.1145/1286380.1286386}, author = {Shahri,Hamid Haidarian and Namata,Galileo and Navlakha,Saket and Deshpande, Amol and Roussopoulos, Nick} } @conference {19449, title = {Grow and Know: Understanding Record-keeping Needs for Tracking the Development of Young Children}, booktitle = {SIGCHI {\textquoteright}07}, series = {CHI {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {1351 - 1360}, publisher = {ACM}, organization = {ACM}, abstract = {From birth through age five, children undergo rapid development and learn skills that will influence them their entire lives. Regular visits to the pediatrician and detailed record-keeping can ensure that children are progressing and can identify early warning signs of developmental delay or disability. However, new parents are often overwhelmed with new responsibilities, and we believe there is an opportunity for computing technology to assist in this process. In this paper, we present a qualitative study aimed at uncovering some specific needs for record-keeping and analysis for new parents and their network of caregivers. Through interviews and focus groups, we have confirmed assumptions about the rationales parents have and the functions required for using technology for record-keeping. We also identify new themes, potential prototypes, and design guidelines for this domain.}, keywords = {children, design requirements, developmental delay, healthcare, qualitative study}, isbn = {978-1-59593-593-9}, url = {http://doi.acm.org/10.1145/1240624.1240830}, author = {Kientz, Julie A. and Arriaga, Rosa I. and Marshini Chetty and Hayes, Gillian R. and Richardson, Jahmeilah and Patel, Shwetak N. and Abowd, Gregory D.} } @article {12579, title = {Guest Editorial: Special Issue on Human Detection and Recognition}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {2}, year = {2007}, month = {2007/09//}, pages = {489 - 490}, abstract = {The 12 regular papers and three correspondences in this special issue focus on human detection and recognition. The papers represent gait, face (3-D, 2-D, video), iris, palmprint, cardiac sounds, and vulnerability of biometrics and protection against the spoof attacks.}, isbn = {1556-6013}, doi = {10.1109/TIFS.2007.905740}, author = {Bhanu, B. and Ratha,N. K and Kumar, V. and Chellapa, Rama and Bigun, J.} } @article {13437, title = {Heuristic Search and Information Visualization Methods for School Redistricting}, journal = {AI Magazine}, volume = {28}, year = {2007}, month = {2007/09/15/}, pages = {59 - 59}, abstract = {We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives, such as school capacity, busing costs, and socioeconomic distribution, must be considered. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different trade-offs in the decision space. We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans.}, isbn = {0738-4602}, doi = {10.1609/aimag.v28i3.2055}, url = {https://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/2055}, author = {desJardins, Marie and Bulka,Blazej and Carr,Ryan and Jordan,Eric and Rheingans,Penny} } @article {18574, title = {How to lease the internet in your spare time}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {37}, year = {2007}, month = {2007/01//}, pages = {61 - 64}, abstract = {Today{\textquoteright}s Internet Service Providers (ISPs) serve two roles: managing their network infrastructure and providing (arguably limited) services to end users. We argue that coupling these roles impedes the deployment of new protocols and architectures, and that the future Internet should support two separate entities: infrastructure providers (who manage the physical infrastructure) and service providers (who deploy network protocols and offer end-to-end services). We present a high-level design for Cabo, an architecture that enables this separation; we also describe challenges associated with realizing this architecture.}, isbn = {0146-4833}, doi = {10.1145/1198255.1198265}, url = {http://doi.acm.org/10.1145/1198255.1198265}, author = {Feamster, Nick and Gao,Lixin and Rexford,Jennifer} } @conference {12585, title = {Human Identification using Gait and Face}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 2}, abstract = {In general the visual-hull approach for performing integrated face and gait recognition requires at least two cameras. In this paper we present experimental results for fusion of face and gait for the single camera case. We considered the NIST database which contains outdoor face and gait data for 30 subjects. In the NIST database, subjects walk along an inverted Sigma pattern. In (A. Kale, et al., 2003), we presented a view-invariant gait recognition algorithm for the single camera case along with some experimental evaluations. In this chapter we present the results of our view-invariant gait recognition algorithm in (A. Kale, et al., 2003) on the NIST database. The algorithm is based on the planar approximation of the person which is valid when the person walks far away from the camera. In (S. Zhou et al., 2003), an algorithm for probabilistic recognition of human faces from video was proposed and the results were demonstrated on the NIST database. Details of these methods can be found in the respective papers. We give an outline of the fusion strategy here.}, keywords = {algorithm;visual-hull, analysis;image, approach;cameras;face, approximation;probabilistic, database;camera;face, databases;, fusion;face, fusion;human, fusion;probability;video, Gait, identification;planar, NIST, processing;visual, recognition, recognition;gait, recognition;view-invariant, signal}, doi = {10.1109/CVPR.2007.383523}, author = {Chellapa, Rama and Roy-Chowdhury, A.K. and Kale, A.} } @article {14150, title = {IFISS: A Matlab toolbox for modelling incompressible flow}, journal = {ACM Transactions on Mathematical Software}, volume = {33}, year = {2007}, month = {2007///}, author = {Elman, Howard and Ramage, A. and Silvester, D. J} } @article {14000, title = {The improved fast Gauss transform with applications to machine learning}, journal = {Large Scale Kernel Machines}, year = {2007}, month = {2007///}, pages = {175 - 201}, author = {Raykar,V.C. and Duraiswami, Ramani} } @conference {16424, title = {Just a cog in the machine: participatory robotics as a tool for understanding collaborative learning and decision-making}, booktitle = {Proceedings of the 8th iternational conference on Computer supported collaborative learning}, series = {CSCL{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {84 - 86}, publisher = {International Society of the Learning Sciences}, organization = {International Society of the Learning Sciences}, abstract = {We will demonstrate the integration of a software-based multi-agent modeling platform with a participatory simulation environment and a real-time control system for a physical robotic agent. Both real and virtual participants will be able to act collaboratively in a simulation that will control a physical agent. The backbone of this demonstration is a widely used, freely available, mature modeling platform (NetLogo). We posit that this technological platform can be of use for researchers interested in investigating collaborative learning and decision-making, as well as to design collaborative learning activities. We will present preliminary findings from pilot studies with the tool.}, isbn = {978-0-6151-5436-7}, url = {http://dl.acm.org/citation.cfm?id=1599600.1599614}, author = {Blikstein,Paulo and Rand, William and Wilensky,Uri} } @conference {12254, title = {Large-scale byzantine fault tolerance: safe but not always live}, booktitle = {Proceedings of the 3rd workshop on on Hot Topics in System Dependability}, series = {HotDep{\textquoteright}07}, year = {2007}, month = {2007///}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {The overall correctness of large-scale systems composed of many groups of replicas executing BFT protocols scales poorly with the number of groups. This is because the probability of at least one group being compromised (more than 1/3 faulty replicas) increases rapidly as the number of groups increases. In this paper we address this problem with a simple modification to Castro and Liskov{\textquoteright}s BFT replication that allows for arbitrary choice of n (number of replicas) and f (failure threshold). The price to pay is a more restrictive liveness requirement, and we present the design of a large-scale BFT replicated system that obviates this problem.}, url = {http://dl.acm.org/citation.cfm?id=1323140.1323157}, author = {Rodrigues,Rodrigo and Kouznetsov,Petr and Bhattacharjee, Bobby} } @article {16402, title = {Making models match: Replicating an agent-based model}, journal = {Journal of Artificial Societies and Social Simulation}, volume = {10}, year = {2007}, month = {2007///}, pages = {2 - 2}, abstract = {Scientists have increasingly employed computer models in their work. Recent years have seen a proliferation of agent-based models in the natural and social sciences. But with the exception of a few "classic" models, most of these models have never been replicated by anyone but the original developer. As replication is a critical component of the scientific method and a core practice of scientists, we argue herein for an increased practice of replication in the agent-based modeling community, and for widespread discussion of the issues surrounding replication. We begin by clarifying the concept of replication as it applies to ABM. Furthermore we argue that replication may have even greater benefits when applied to computational models than when applied to physical experiments. Replication of computational models affects model verification and validation and fosters shared understanding about modeling decisions. To facilitate replication, we must create standards for both how to replicate models and how to evaluate the replication. In this paper, we present a case study of our own attempt to replicate a classic agent-based model. We begin by describing an agent-based model from political science that was developed by Axelrod and Hammond. We then detail our effort to replicate that model and the challenges that arose in recreating the model and in determining if the replication was successful. We conclude this paper by discussing issues for (1) researchers attempting to replicate models and (2) researchers developing models in order to facilitate the replication of their results.}, author = {Wilensky,U. and Rand, William} } @conference {13145, title = {Multimodal Tracking for Smart Videoconferencing and Video Surveillance}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 2}, abstract = {Many applications require the ability to track the 3-D motion of the subjects. We build a particle filter based framework for multimodal tracking using multiple cameras and multiple microphone arrays. In order to calibrate the resulting system, we propose a method to determine the locations of all microphones using at least five loudspeakers and under assumption that for each loudspeaker there exists a microphone very close to it. We derive the maximum likelihood (ML) estimator, which reduces to the solution of the non-linear least squares problem. We verify the correctness and robustness of the multimodal tracker and of the self-calibration algorithm both with Monte-Carlo simulations and on real data from three experimental setups.}, keywords = {(numerical, 3D, algorithm;smart, analysis;least, approximations;particle, arrays;nonlinear, cameras;multiple, Carlo, estimator;multimodal, filter;self-calibration, Filtering, least, likelihood, methods);teleconferencing;video, methods;image, microphone, MOTION, motion;Monte-Carlo, problem;particle, processing;video, signal, simulations;maximum, squares, surveillance;, surveillance;Monte, tracking;multiple, videoconferencing;video}, doi = {10.1109/CVPR.2007.383525}, author = {Zotkin,Dmitry N and Raykar,V.C. and Duraiswami, Ramani and Davis, Larry S.} } @article {18590, title = {Network-Wide Prediction of BGP Routes}, journal = {Networking, IEEE/ACM Transactions on}, volume = {15}, year = {2007}, month = {2007/04//}, pages = {253 - 266}, abstract = {This paper presents provably correct algorithms for computing the outcome of the BGP route-selection process for each router in a network, without simulating the complex details of BGP message passing. The algorithms require only static inputs that can be easily obtained from the routers: the BGP routes learned from neighboring domains, the import policies configured on the BGP sessions, and the internal topology. Solving the problem would be easy if the route-selection process were deterministic and every router received all candidate BGP routes. However, two important features of BGP-the Multiple Exit Discriminator (MED) attribute and route reflectors-violate these properties. After presenting a simple route-prediction algorithm for networks that do not use these features, we present algorithms that capture the effects of the MED attribute and route reflectors in isolation. Then, we explain why the interaction between these two features precludes efficient route prediction. These two features also create difficulties for the operation of BGP itself, leading us to suggest improvements to BGP that achieve the same goals as MED and route reflection without introducing the negative side effects}, keywords = {BGP message passing, BGP route-selection process, border gateway protocol, Message passing, multiple exit discriminator attribute, network-wide prediction, route reflectors, route-prediction algorithm, routing protocols, telecommunication network topology}, isbn = {1063-6692}, doi = {10.1109/TNET.2007.892876}, author = {Feamster, Nick and Rexford,J.} } @article {14074, title = {New Trypanosoma cruzi Repeated Element That Shows Site Specificity for Insertion}, journal = {Eukaryotic Cell}, volume = {6}, year = {2007}, month = {2007/07/01/}, pages = {1228 - 1238}, abstract = {A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5{\textquoteright} end of the element and a sequence domain of [~]500 bp without a well-defined borderline at the 3{\textquoteright} end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of [~]0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be [~]173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.}, doi = {

10.1128/EC.00036-07

}, url = {http://ec.asm.org/cgi/content/abstract/6/7/1228}, author = {Souza,Renata T. and Santos,Marcia R. M. and Lima,Fabio M. and El-Sayed, Najib M. and Myler,Peter J. and Ruiz,Jeronimo C. and da Silveira,Jose Franco} } @article {14555, title = {Oblivious routing on node-capacitated and directed graphs}, journal = {ACM Transactions on Algorithms (TALG)}, volume = {3}, year = {2007}, month = {2007///}, pages = {51{\textendash}es - 51{\textendash}es}, author = {Hajiaghayi, Mohammad T. and Kleinberg,R. D and R\{\"a}cke,H. and Leighton,T.} } @conference {12970, title = {Optimizing mpf queries}, booktitle = {Proceedings of the 2007 ACM SIGMOD international conference on Management of data - SIGMOD {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {701 - 701}, address = {Beijing, China}, doi = {10.1145/1247480.1247558}, url = {http://dl.acm.org/citation.cfm?id=1247558}, author = {Corrada Bravo, Hector and Ramakrishnan,Raghu} } @article {13150, title = {Pedestrian detection via periodic motion analysis}, journal = {International Journal of Computer Vision}, volume = {71}, year = {2007}, month = {2007///}, pages = {143 - 160}, abstract = {We describe algorithms for detecting pedestrians in videos acquired by infrared (and color) sensors. Two approaches are proposed based on gait. The first employs computationally efficient periodicity measurements. Unlike other methods, it estimates a periodic motion frequency using two cascading hypothesis testing steps to filter out non-cyclic pixels so that it works well for both radial and lateral walking directions. The extraction of the period is efficient and robust with respect to sensor noise and cluttered background. In order to integrate shape and motion, we convert the cyclic pattern into a binary sequence by Maximal Principal Gait Angle (MPGA) fitting in the second method. It does not require alignment and continuously estimates the period using a Phase-locked Loop. Both methods are evaluated by experimental results that measure performance as a function of size, movement direction, frame rate and sequence length.}, author = {Ran, Y. and Weiss, I. and Zheng,Q. and Davis, Larry S.} } @article {15572, title = {A practical approximation algorithm for the LMS line estimator}, journal = {Computational Statistics \& Data Analysis}, volume = {51}, year = {2007}, month = {2007/02/01/}, pages = {2461 - 2486}, abstract = {The problem of fitting a straight line to a finite collection of points in the plane is an important problem in statistical estimation. Robust estimators are widely used because of their lack of sensitivity to outlying data points. The least median-of-squares (LMS) regression line estimator is among the best known robust estimators. Given a set of n points in the plane, it is defined to be the line that minimizes the median squared residual or, more generally, the line that minimizes the residual of any given quantile q, where 0 \< q ⩽ 1 . This problem is equivalent to finding the strip defined by two parallel lines of minimum vertical separation that encloses at least half of the points.The best known exact algorithm for this problem runs in O ( n 2 ) time. We consider two types of approximations, a residual approximation, which approximates the vertical height of the strip to within a given error bound ε r ⩾ 0 , and a quantile approximation, which approximates the fraction of points that lie within the strip to within a given error bound ε q ⩾ 0 . We present two randomized approximation algorithms for the LMS line estimator. The first is a conceptually simple quantile approximation algorithm, which given fixed q and ε q \> 0 runs in O ( n log n ) time. The second is a practical algorithm, which can solve both types of approximation problems or be used as an exact algorithm. We prove that when used as a quantile approximation, this algorithm{\textquoteright}s expected running time is O ( n log 2 n ) . We present empirical evidence that the latter algorithm is quite efficient for a wide variety of input distributions, even when used as an exact algorithm. }, keywords = {Approximation algorithms, least median-of-squares regression, line arrangements, line fitting, randomized algorithms, robust estimation}, isbn = {0167-9473}, doi = {10.1016/j.csda.2006.08.033}, url = {http://www.sciencedirect.com/science/article/pii/S0167947306002921}, author = {Mount, Dave and Netanyahu,Nathan S. and Romanik,Kathleen and Silverman,Ruth and Wu,Angela Y.} } @article {16806, title = {Probabilistic wavelet synopses for multiple measures}, volume = {11/225,539}, year = {2007}, month = {2007/03/15/}, abstract = {A technique for building probabilistic wavelet synopses for multi-measure data sets is provided. In the presence of multiple measures, it is demonstrated that the problem of exact probabilistic coefficient thresholding becomes significantly more complex. An algorithmic formulation for probabilistic multi-measure wavelet thresholding based on the idea of partial-order dynamic programming (PODP) is provided. A fast, greedy approximation algorithm for probabilistic multi-measure thresholding based on the idea of marginal error gains is provided. An empirical study with both synthetic and real-life data sets validated the approach, demonstrating that the algorithms outperform naive approaches based on optimizing individual measures independently and the greedy thresholding scheme provides near-optimal and, at the same time, fast and scalable solutions to the probabilistic wavelet synopsis construction problem.}, url = {http://www.google.com/patents?id=IHWbAAAAEBAJ}, author = {Deligiannakis,Antonios and Garofalakis,Minos N. and Roussopoulos, Nick} } @conference {18688, title = {Profiling Attacker Behavior Following SSH Compromises}, year = {2007}, month = {2007/06//}, pages = {119 - 124}, abstract = {This practical experience report presents the results of an experiment aimed at building a profile of attacker behavior following a remote compromise. For this experiment, we utilized four Linux honeypot computers running SSH with easily guessable passwords. During the course of our research, we also determined the most commonly attempted usernames and passwords, the average number of attempted logins per day, and the ratio of failed to successful attempts. To build a profile of attacker behavior, we looked for specific actions taken by the attacker and the order in which they occurred. These actions were: checking the configuration, changing the password, downloading a file, installing/running rogue code, and changing the system configuration.}, keywords = {Linux, Linux honeypot computers, profiling attacker behavior, remote compromise, rogue code, security of data, SSH compromises, system configuration}, doi = {10.1109/DSN.2007.76}, author = {Ramsbrock,D. and Berthier,R. and Michel Cukier} } @inbook {12601, title = {Recognizing Faces Across Age Progression}, booktitle = {Face Biometrics for Personal IdentificationFace Biometrics for Personal Identification}, series = {Signals and Communication Technology}, year = {2007}, month = {2007///}, pages = {27 - 42}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-540-49346-4}, url = {http://dx.doi.org/10.1007/978-3-540-49346-4_3}, author = {Ramanathan,Narayanan and Chellapa, Rama}, editor = {Hammoud,Riad and Abidi,Besma and Abidi,Mongi} } @article {15841, title = {Searching spontaneous conversational speech}, journal = {ACM SIGIR Forum}, volume = {41}, year = {2007}, month = {2007/12/01/}, pages = {104 - 104}, isbn = {01635840}, doi = {10.1145/1328964.1328982}, url = {http://dl.acm.org/citation.cfm?id=1328982}, author = {Jong,Franciska De and Oard, Douglas and Ordelman,Roeland and Raaijmakers,Stephan} } @article {12262, title = {Secure lookup without (constrained) flooding}, journal = {WRAITS 2007}, year = {2007}, month = {2007///}, author = {Bhattacharjee, Bobby and Rodrigues,R. and Kouznetsov,P.} } @conference {17780, title = {Sentiment analysis: Adjectives and adverbs are better than adjectives alone}, booktitle = {Proceedings of the International Conference on Weblogs and Social Media (ICWSM)}, year = {2007}, month = {2007///}, abstract = {Most past work on determining the strength of subjective expres-sions within a sentence or a document use specific parts of speech such as adjectives, verbs and nouns. To date, there is almost no work on the use of adverbs in sentiment analysis, nor has there been any work on the use of adverb-adjective combinations (AACs). We propose an AAC-based sentiment analysis technique that uses a lin- guistic analysis of adverbs of degree. We define a set of general axioms (based on a classification of adverbs of degree into five cat- egories) that all adverb scoring techniques must satisfy. Instead of aggregating scores of both adverbs and adjectives using simple scor- ing functions, we propose an axiomatic treatment of AACs based on the linguistic classification of adverbs. Three specific AAC scor- ing methods that satisfy the axioms are presented. We describe the results of experiments on an annotated set of 200 news articles (an- notated by 10 students) and compare our algorithms with some exist- ing sentiment analysis algorithms. We show that our results lead to higher accuracy based on Pearson correlation with human subjects. }, author = {Benamara,F. and Cesarano,C. and Picariello, A. and Reforgiato,D. and V.S. Subrahmanian} } @article {14143, title = {Some observations on multigrid convergence for convection{\textendash}diffusion equations}, journal = {Computing and Visualization in Science}, volume = {10}, year = {2007}, month = {2007///}, pages = {43 - 56}, author = {Ramage, A. and Elman, Howard} } @conference {16426, title = {A spatial model of the red queen effect}, booktitle = {Proceedings of the 9th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {490 - 491}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Van Valen first discovered the "Red Queen Effect" (RQE), where two species can dramatically co-evolve their phenotypes over time but never gain a relative advantage [2]. In the ideal version of the RQE, regardless of the actual values that the species evolve to obtain, they have not moved in relation to each other. Though previous models of the RQE exist, we developed an agent-based model (ABM) which has a base ontology more similar to real world coevolutionary systems than equation-based models (EBMs). For instance, this model contains spatial information and an individuallevel reproduction mechanism. Yet this model recreates traditional EBM results. For instance Dieckmann et al show that there are three possible outcomes of competitive coevolution: predator dominance, prey dominance and evolutionary cycling (RQE) [1]. By reconceptualizing this EBM using an ABM, we make it easier for students and researchers to understand, manipulate, and modify this model [4]. The model is written in the NetLogo agent-based modeling environment [3]. The model is initialized with 150 predator and 150 prey agents. Predator agents have a resistance level r and prey agents have a poison p. The agents are initially randomly distributed on a toroidal real-valued 35 by 35 grid. The initial resistance and poison values for the predators and prey are drawn from normal distributions with means {\textmu}r and {\textmu}p and a standard deviation of 1. During a model timestep, each agent moves one unit at a random heading. If at the end of its move a predator is within 1 unit of a prey, then it will challenge the prey. The predator will compare its resistance value to the prey{\textquoteright}s poison value and which ever agent has the larger value will win the challenge and the other agent will be killed. At the end of an agent{\textquoteright}s turn if the total number of agents is less than the maximum carrying capacity the agent will reproduce with a 50\% probability. The new agent{\textquoteright}s initial poison / resistance will be drawn from a normal distribution with the parent{\textquoteright}s poison / resistance as the mean value and a standard deviation of 1. Our goal was to investigate whether this ABMwould replicate the results of the EBM of [1]. Our parameter of interest was {\textmu}p; we held {\textmu}r constant at 25 and varied {\textmu}p from 0 to 50 at increments of 5. For each value we ran the model 10 times for 5000 timesteps. Figure 1 illustrates the final average values of both the resistance and the poison for the various initial values. If there are no predators or prey then a value of 0 is plotted for the respective final trait. In most cases, one species drives the other to extinction, and there is little change in the initial trait values. However when the value of {\textmu}p is similar to {\textmu}r then neither species is completely destroyed, but if there is any significant difference between {\textmu}r and {\textmu}p then one species will die off. The highest final trait values are found when {\textmu}p = {\textmu}r, in this case we see the results of the RQE since the final trait values are much higher than the initial values. These final values are more than 1.5 orders of magnitude larger than the initial values. This model reproduces classical models of the RQE, but has two different mobile species interacting on a spatial grid over time which is a closer representation of reality than traditional models. This closer representation makes ABMs excellent teaching and experimental tools because their basic assumptions can easily be manipulated and explored. Acknowledgments: We thank the National Science Foundation and NICO for supporting this research.}, keywords = {Agent-based modeling, coevolution, red queen effect, spatial modeling}, isbn = {978-1-59593-697-4}, doi = {10.1145/1276958.1277064}, url = {http://doi.acm.org/10.1145/1276958.1277064}, author = {Ottino-Loffler,Jules and Rand, William and Wilensky,Uri} } @conference {14862, title = {A Study of Face Recognition as People Age}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {In this paper we study face recognition across ages within a real passport photo verification task. First, we propose using the gradient orientation pyramid for this task. Discarding the gradient magnitude and utilizing hierarchical techniques, we found that the new descriptor yields a robust and discriminative representation. With the proposed descriptor, we model face verification as a two-class problem and use a support vector machine as a classifier. The approach is applied to two passport data sets containing more than 1,800 image pairs from each person with large age differences. Although simple, our approach outperforms previously tested Bayesian technique and other descriptors, including the intensity difference and gradient with magnitude. In addition, it works as well as two commercial systems. Second, for the first time, we empirically study how age differences affect recognition performance. Our experiments show that, although the aging process adds difficulty to the recognition task, it does not surpass illumination or expression as a confounding factor.}, keywords = {Bayesian, difference;passport, machine;face, machines;, magnitude;gradient, orientation, photo, pyramid;hierarchical, recognition;face, recognition;support, representation;face, task;support, technique;discriminative, techniques;intensity, vector, verification, verification;gradient}, doi = {10.1109/ICCV.2007.4409069}, author = {Ling,Haibin and Soatto,S. and Ramanathan,N. and Jacobs, David W.} } @article {12586, title = {Super-Resolution of Face Images Using Kernel PCA-Based Prior}, journal = {Multimedia, IEEE Transactions on}, volume = {9}, year = {2007}, month = {2007/06//}, pages = {888 - 892}, abstract = {We present a learning-based method to super-resolve face images using a kernel principal component analysis-based prior model. A prior probability is formulated based on the energy lying outside the span of principal components identified in a higher-dimensional feature space. This is used to regularize the reconstruction of the high-resolution image. We demonstrate with experiments that including higher-order correlations results in significant improvements}, keywords = {analysis;learning-based, analysis;probability;, component, Face, image, method;prior, model;face, principal, probability, recognition;image, reconstruction;image, reconstruction;kernel, resolution;principal, super-resolution;high-resolution}, isbn = {1520-9210}, doi = {10.1109/TMM.2007.893346}, author = {Chakrabarti,Ayan and Rajagopalan, AN and Chellapa, Rama} } @article {16523, title = {Swarm Intelligence Systems Using Guided Self-Organization for Collective Problem Solving}, journal = {Advances in Complex Systems}, volume = {10}, year = {2007}, month = {2007///}, pages = {5 - 34}, author = {RodrIGuez,A. and Grushin,A. and Reggia, James A. and HAUPTMAN,AMI and SIPPER,M. and PAN,Z. and Reggia, James A. and GAO,D. and DARABOS,C. and GIACOBINI,M. and others} } @article {16807, title = {System for 802.11 connectivity at high speed}, volume = {UMIACS-TR-2007-27}, year = {2007}, month = {2007/05/13/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Measurements and ongoing research have shown that WLANconnection for moving vehicles is feasible. However none of the previous work suggests a solution addressing a complete array of the challenges in vehicular WLAN communications. To amend this we designed a system that provides wireless connection roaming at high velocities transparent to user level applications, and does not impose additional requirements to existing infrastructures. It offers simple deployment, security, and scalability. It remains efficient under - intermittent connectivity conditions and supports heterogeneous network mediums for increased robustness. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/4374}, author = {Frangiadakis,Nikolaos and Kuklov,Danila and Roussopoulos, Nick} } @article {16386, title = {Understanding the Semantics of the Genetic Algorithm in Dynamic Environments}, journal = {Applications of Evolutionary Computing}, year = {2007}, month = {2007///}, pages = {657 - 667}, abstract = {Researchers examining genetic algorithms (GAs) in applied settings rarely have access to anything other than fitness values of the best individuals to observe the behavior of the GA. In particular, researchers do not know what schemata are present in the population. Even when researchers look beyond best fitness values, they concentrate on either performance related measures like average fitness and robustness, or low-level descriptions like bit-level diversity measures. To understand the behavior of the GA on dynamic problems, it would be useful to track what is occurring on the {\textquotedblleft}semantic{\textquotedblright} level of schemata. Thus in this paper we examine the evolving {\textquotedblleft}content{\textquotedblright} in terms of schemata, as the GA solves dynamic problems. This allows us to better understand the behavior of the GA in dynamic environments. We finish by summarizing this knowledge and speculate about future work to address some of the new problems that we discovered during these experiments.}, doi = {10.1007/978-3-540-71805-5_72}, author = {Alharbi,A. and Rand, William and Riolo,R} } @conference {16449, title = {Using annotations from controlled vocabularies to find meaningful associations}, booktitle = {Proceedings of the 4th international conference on Data integration in the life sciences}, year = {2007}, month = {2007///}, pages = {247 - 263}, author = {Lee,W. J and Raschid, Louiqa and Srinivasan,P. and Shah,N. and Rubin,D. and Noy,N.} } @conference {13889, title = {Using paraphrases for parameter tuning in statistical machine translation}, booktitle = {Proceedings of the Second Workshop on Statistical Machine Translation}, series = {StatMT {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {120 - 127}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Most state-of-the-art statistical machine translation systems use log-linear models, which are defined in terms of hypothesis features and weights for those features. It is standard to tune the feature weights in order to maximize a translation quality metric, using held-out test sentences and their corresponding reference translations. However, obtaining reference translations is expensive. In this paper, we introduce a new full-sentence paraphrase technique, based on English-to-English decoding with an MT system, and we demonstrate that the resulting paraphrases can be used to drastically reduce the number of human reference translations needed for parameter tuning, without a significant decrease in translation quality.}, url = {http://dl.acm.org/citation.cfm?id=1626355.1626371}, author = {Madnani,Nitin and Ayan,Necip Fazil and Resnik, Philip and Dorr, Bonnie J} } @conference {16662, title = {Using paraphrases for parameter tuning in statistical machine translation}, booktitle = {Proceedings of the Second Workshop on Statistical Machine Translation}, year = {2007}, month = {2007///}, pages = {120 - 127}, author = {Madnani,N. and Ayan,N.F. and Resnik, Philip and Dorr, Bonnie J} } @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} } @article {16492, title = {Adaptive pull-based policies for wide area data delivery}, journal = {ACM Transactions on Database Systems (TODS)}, volume = {31}, year = {2006}, month = {2006///}, pages = {631 - 671}, author = {Bright,L. and Gal,A. and Raschid, Louiqa} } @article {17784, title = {Annotated rdf}, journal = {The Semantic Web: Research and Applications}, volume = {4011}, year = {2006}, month = {2006///}, pages = {487 - 501}, abstract = {There are numerous extensions of RDF that support temporal reasoning, reasoning about pedigree, reasoning about uncertainty, and so on. In this paper, we present Annotated RDF (or aRDF for short) in which RDF triples are annotated by members of a partially ordered set (with bottom element) that can be selected in any way desired by the user. We present a formal declarative semantics (model theory) for annotated RDF and develop algorithms to check consistency of aRDF theories and to answer queries to aRDF theories. We show that annotated RDF captures versions of all the forms of reasoning mentioned above within a single unified framework. We develop a prototype aRDF implementation and show that our algorithms work very fast indeed {\textendash} in fact, in just a matter of seconds for theories with over 100,000 nodes.}, doi = {10.1007/11762256_36}, author = {Udrea,O. and Recupero,D. and V.S. Subrahmanian} } @article {15248, title = {Approximating the minimal sensor selection for supervisory control}, journal = {Discrete Event Dynamic Systems}, volume = {16}, year = {2006}, month = {2006///}, pages = {143 - 170}, abstract = {This paper discusses the problem of selecting a set of sensors of minimum cost that can be used for the synthesis of a supervisory controller. It is shown how this sensor selection problem is related to a type of directed graph st-cut problem that has not been previously discussed in the literature. Approximation algorithms to solve the sensor selection problem can be used to solve the graph cutting problem and vice-versa. Polynomial time algorithms to find good approximate solutions to either problem most likely do not exist (under certain complexity assumptions), but a time efficient approximation algorithm is shown that solves a special case of these problems. It is also shown how to convert the sensor selection problem into an integer programming problem.}, doi = {10.1007/s10626-006-6187-3}, author = {Rohloff,K. R and Khuller, Samir and Kortsarz,G.} } @article {18653, title = {An architecture for adaptive intrusion-tolerant applications}, journal = {Software: Practice and Experience}, volume = {36}, year = {2006}, month = {2006///}, pages = {1331 - 1354}, abstract = {Applications that are part of a mission-critical information system need to maintain a usable level of key services through ongoing cyber-attacks. In addition to the well-publicized denial of service (DoS) attacks, these networked and distributed applications are increasingly threatened by sophisticated attacks that attempt to corrupt system components and violate service integrity. While various approaches have been explored to deal with DoS attacks, corruption-inducing attacks remain largely unaddressed. We have developed a collection of mechanisms based on redundancy, Byzantine fault tolerance, and adaptive middleware that help distributed, object-based applications tolerate corruption-inducing attacks. In this paper, we present the ITUA architecture, which integrates these mechanisms in a framework for auto-adaptive intrusion-tolerant systems, and we describe our experience in using the technology to defend a critical application that is part of a larger avionics system as an example. We also motivate the adaptive responses that are key to intrusion tolerance, and explain the use of the ITUA architecture to support them in an architectural framework. Copyright {\textcopyright} 2006 John Wiley \& Sons, Ltd.}, keywords = {adaptive defense, adaptive middleware, Byzantine fault tolerance, intrusion tolerance, redundancy, survivability architecture}, isbn = {1097-024X}, doi = {10.1002/spe.747}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.747/abstract}, author = {Pal,Partha and Rubel,Paul and Atighetchi,Michael and Webber,Franklin and Sanders,William H. and Seri,Mouna and Ramasamy,HariGovind and Lyons,James and Courtney,Tod and Agbaria,Adnan and Michel Cukier and Gossett,Jeanna and Keidar,Idit} } @article {18491, title = {Can DNS-based blacklists keep up with bots}, journal = {Conference on email and anti-spam}, year = {2006}, month = {2006///}, author = {Ramachandran,A. and Dagon,D. and Feamster, Nick} } @article {15340, title = {Characterization of the turbulence structure in supersonic boundary layers using DNS data}, journal = {AIAA Paper}, volume = {3539}, year = {2006}, month = {2006///}, author = {Ringuette,M. J and Martin, M.P and Smits,A. J. and Wu,M.} } @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} } @inbook {13751, title = {Cross-Language Access to Recorded Speech in the MALACH Project}, booktitle = {Text, Speech and DialogueText, Speech and Dialogue}, series = {Lecture Notes in Computer Science}, volume = {2448}, year = {2006}, month = {2006///}, pages = {197 - 212}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The MALACH project seeks to help users find information in a vast multilingual collections of untranscribed oral history interviews. This paper introduces the goals of the project and focuses on supporting access by users who are unfamiliar with the interview language. It begins with a review of the state of the art in crosslanguage speech retrieval; approaches that will be investigated in the project are then described. Czech was selected as the first non-English language to be supported, so results of an initial experiment with Czech/English cross-language retrieval are reported.}, isbn = {978-3-540-44129-8}, url = {http://dx.doi.org/10.1007/3-540-46154-X_8}, author = {Oard, Douglas and Demner-Fushman,Dina and Haji{\v c},Jan and Ramabhadran,Bhuvana and Gustman,Samuel and Byrne,William and Soergel,Dagobert and Dorr, Bonnie J and Resnik, Philip and Picheny,Michael}, editor = {Sojka,Petr and Kopecek,Ivan and Pala,Karel} } @article {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} } @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 {16792, title = {Dissemination of compressed historical information in sensor networks}, journal = {The VLDB JournalThe VLDB Journal}, volume = {16}, year = {2006}, month = {2006/07//}, pages = {439 - 461}, isbn = {1066-8888}, doi = {10.1007/s00778-005-0173-5}, url = {http://dl.acm.org/citation.cfm?id=1285903}, author = {Deligiannakis,Antonios and Kotidis,Yannis and Roussopoulos, Nick} } @article {16812, title = {Dwarf cube architecture for reducing storage sizes of multidimensional data}, volume = {10/157,960}, year = {2006}, month = {2006/11/07/}, abstract = {The invention relates to data warehouses and the ability to create and maintain data cubes of multi-dimensional data. More specifically, the invention pertains to data cube architectures that permit significant reduction of storage, exhibit very efficient retrieval and provide a very efficient incremental update of the data cubes.}, url = {http://www.google.com/patents?id=PGl7AAAAEBAJ}, author = {Roussopoulos, Nick and Sismanis,John and Deligiannakis,Antonios}, editor = {The University of Maryland College Park} } @conference {12643, title = {Edge Suppression by Gradient Field Transformation Using Cross-Projection Tensors}, booktitle = {Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on}, volume = {2}, year = {2006}, month = {2006///}, pages = {2301 - 2308}, abstract = {We propose a new technique for edge-suppressing operations on images. We introduce cross projection tensors to achieve affine transformations of gradient fields. We use these tensors, for example, to remove edges in one image based on the edge-information in a second image. Traditionally, edge suppression is achieved by setting image gradients to zero based on thresholds. A common application is in the Retinex problem, where the illumination map is recovered by suppressing the reflectance edges, assuming it is slowly varying. We present a class of problems where edge-suppression can be a useful tool. These problems involve analyzing images of the same scene under variable illumination. Instead of resetting gradients, the key idea in our approach is to derive local tensors using one image and to transform the gradient field of another image using them. Reconstructed image from the modified gradient field shows suppressed edges or textures at the corresponding locations. All operations are local and our approach does not require any global analysis. We demonstrate the algorithm in the context of several applications such as (a) recovering the foreground layer under varying illumination, (b) estimating intrinsic images in non-Lambertian scenes, (c) removing shadows from color images and obtaining the illumination map, and (d) removing glass reflections.}, doi = {10.1109/CVPR.2006.106}, author = {Agrawal,A. and Raskar, R. and Chellapa, Rama} } @article {16388, title = {The effect of building block construction on the behavior of the ga in dynamic environments: A case study using the shaky ladder hyperplane-defined functions}, journal = {Applications of Evolutionary Computing}, year = {2006}, month = {2006///}, pages = {776 - 787}, abstract = {The shaky ladder hyperplane-defined functions (sl-hdf{\textquoteright}s) are a test suite utilized for exploring the behavior of the genetic algorithm (GA) in dynamic environments. We present three ways of constructing the sl-hdf{\textquoteright}s by manipulating the way building blocks are constructed, combined, and changed. We examine the effect of the length of elementary building blocks used to create higher building blocks, and the way in which those building blocks are combined. We show that the effects of building block construction on the behavior of the GA are complex. Our results suggest that construction routines which increase the roughness of the changes in the environment allow the GA to perform better by preventing premature convergence. Moreover, short length elementary building blocks permit early rapid progress.}, doi = {10.1007/11732242_75}, author = {Rand, William and Riolo,R} } @conference {16423, title = {The effect of crossover on the behavior of the GA in dynamic environments: a case study using the shaky ladder hyperplane-defined functions}, booktitle = {Proceedings of the 8th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1289 - 1296}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {One argument as to why the hyperplane-defined functions (hdf{\textquoteright}s) are a good testbed for the genetic algorithm (GA) is that the hdf{\textquoteright}s are built in the same way that the GA works. In this paper we test that hypothesis in a new setting by exploring the GA on a subset of the hdf{\textquoteright}s which are dynamic---the shaky ladder hyperplane-defined functions (sl-hdf{\textquoteright}s). In doing so we gain insight into how the GA makes use of crossover during its traversal of the sl-hdf search space. We begin this paper by explaining the sl-hdf{\textquoteright}s. We then conduct a series of experiments with various crossover rates and various rates of environmental change. Our results show that the GA performs better with than without crossover in dynamic environments. Though these results have been shown on some static functions in the past, they are re-confirmed and expanded here for a new type of function (the hdf) and a new type of environment (dynamic environments). Moreover we show that crossover is even more beneficial in dynamic environments than it is in static environments. We discuss how these results can be used to develop a richer knowledge about the use of building blocks by the GA.}, keywords = {crossover, dynamic environments, Genetic algorithms, hyperplane-defined functions, search}, isbn = {1-59593-186-4}, doi = {10.1145/1143997.1144198}, url = {http://doi.acm.org/10.1145/1143997.1144198}, author = {Rand, William and Riolo,Rick and Holland,John H.} } @article {17931, title = {An Efficient Computational Method for Predicting Rotational Diffusion Tensors of Globular Proteins Using an Ellipsoid Representation}, journal = {Journal of the American Chemical Society}, volume = {128}, year = {2006}, month = {2006///}, pages = {15432 - 15444}, abstract = {We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138?146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins.We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138?146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins. }, isbn = {0002-7863}, doi = {10.1021/ja062715t}, url = {http://dx.doi.org/10.1021/ja062715t}, author = {Ryabov,Yaroslav E. and Geraghty,Charles and Varshney, Amitabh and Fushman, David} } @conference {12348, title = {Efficient simulation of critical synchronous dataflow graphs}, booktitle = {Proceedings of the 43rd annual Design Automation Conference}, year = {2006}, month = {2006///}, pages = {893 - 898}, author = {Hsu,C. J and Ramasubbu,S. and Ko,M. Y and Pino,J. L and Bhattacharyya, Shuvra S.} } @article {16578, title = {Evolutionary design of neural network architectures using a descriptive encoding language}, journal = {Evolutionary Computation, IEEE Transactions on}, volume = {10}, year = {2006}, month = {2006///}, pages = {676 - 688}, author = {Jung,J. Y and Reggia, James A.} } @conference {16087, title = {Exploring erotics in Emily Dickinson{\textquoteright}s correspondence with text mining and visual interfaces}, booktitle = {Proceedings of the 6th ACM/IEEE-CS joint conference on Digital libraries}, series = {JCDL {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {141 - 150}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a system to support humanities scholars in their interpretation of literary work. It presents a user interface and web architecture that integrates text mining, a graphical user interface and visualization, while attempting to remain easy to use by non specialists. Users can interactively read and rate documents found in a digital libraries collection, prepare training sets, review results of classification algorithms and explore possible indicators and explanations. Initial evaluation steps suggest that there is a rationale for "provocational" text mining in literary interpretation.}, keywords = {case studies, humanities, literary criticism, text mining, user interface, Visualization}, isbn = {1-59593-354-9}, doi = {10.1145/1141753.1141781}, url = {http://doi.acm.org/10.1145/1141753.1141781}, author = {Plaisant, Catherine and Rose,James and Yu,Bei and Auvil,Loretta and Kirschenbaum,Matthew G. and Smith,Martha Nell and Clement,Tanya and Lord,Greg} } @article {12603, title = {Face Verification Across Age Progression}, journal = {Image Processing, IEEE Transactions on}, volume = {15}, year = {2006}, month = {2006/11//}, pages = {3349 - 3361}, abstract = {Human faces undergo considerable amounts of variations with aging. While face recognition systems have been proven to be sensitive to factors such as illumination and pose, their sensitivity to facial aging effects is yet to be studied. How does age progression affect the similarity between a pair of face images of an individual? What is the confidence associated with establishing the identity between a pair of age separated face images? In this paper, we develop a Bayesian age difference classifier that classifies face images of individuals based on age differences and performs face verification across age progression. Further, we study the similarity of faces across age progression. Since age separated face images invariably differ in illumination and pose, we propose preprocessing methods for minimizing such variations. Experimental results using a database comprising of pairs of face images that were retrieved from the passports of 465 individuals are presented. The verification system for faces separated by as many as nine years, attains an equal error rate of 8.5\%}, keywords = {age, Aging, Bayesian, classification;, classification;face, classifier;age, difference, effects;preprocessing, Face, image, images;error, methods;Bayes, methods;error, progression;age, rate;face, recognition, recognition;image, separated, statistics;face, systems;face, verification;facial}, isbn = {1057-7149}, doi = {10.1109/TIP.2006.881993}, author = {Ramanathan,N. and Chellapa, Rama} } @article {14011, title = {Fast optimal bandwidth selection for kernel density estimation}, journal = {Proceedings of the sixth SIAM International Conference on Data Mining}, year = {2006}, month = {2006///}, pages = {524 - 528}, abstract = {We propose a computationally efficient ϵ-exact approxima-tion algorithm for univariate Gaussian kernel based density derivative estimation that reduces the computational com- plexity from O(MN) to linear O(N +M). We apply the pro- cedure to estimate the optimal bandwidth for kernel density estimation. We demonstrate the speedup achieved on this problem using the {\textquotedblright}solve-the-equation plug-in{\textquotedblright} method, and on exploratory projection pursuit techniques. }, author = {Raykar,V.C. and Duraiswami, Ramani} } @conference {12626, title = {Finding Gait in Space and Time}, booktitle = {Pattern Recognition, 2006. ICPR 2006. 18th International Conference on}, volume = {4}, year = {2006}, month = {2006///}, pages = {586 - 589}, abstract = {We describe an approach to characterize the signatures generated by walking humans in spatio-temporal domain. To describe the computational model for this periodic pattern, we take the mathematical theory of geometry group theory, which is widely used in crystallographic structure research. Both empirical and theoretical analyses prove that spatio-temporal helical patterns generated by legs belong to the Frieze Groups because they can be characterized by a repetitive motif along the direction of walking. The theory is applied to an automatic detection-and-tracking system capable of counting heads and handling occlusion by recognizing such patterns. Experimental results for videos acquired from both static and moving ground sensors are presented. Our algorithm demonstrates robustness to non-rigid human deformation as well as background clutter}, keywords = {analysis;, analysis;geometry, analysis;group, characterization;occlusion, counting;mathematical, detection-and-tracking, domain;spatiotemporal, Frieze, group, groups;automatic, handling;pattern, helical, humans;computer, MOTION, pattern;spatiotemporal, patterns;walking, recognition;periodic, signature, system;computer, theory;head, theory;image, theory;motion, vision;gait}, doi = {10.1109/ICPR.2006.562}, author = {Yang Ran and Chellapa, Rama and Qinfen Zheng} } @article {14909, title = {First Steps Toward an Electronic Field Guide for Plants}, journal = {Taxon}, volume = {55}, year = {2006}, month = {2006///}, pages = {597 - 610}, abstract = {this paper, we will describe our progress towards building a digital collection of the Smithsonian{\textquoteright}s type specimens, developing recognition algorithms that can match an image of a leaf to the species of plant from which it comes, and designing user interfaces for interacting with an electronic field guide. To start, we are developing a prototype electronic field guide for the flora of Plummers Island, a small, well-studied island in the Potomac River. This prototype system contains multiple images for each of about 130 species of plants on the island, and should soon grow to cover all 200+ species currently recorded (Shetler et al., 2005). Images of full specimens are available, as well as images of isolated leaves of each species. A zoomable user interface allows a user to browse these images, zooming in on ones of interest. Visual recognition algorithms assist a botanist in locating the specimens that are most relevant to identify the species of a plant. The system currently runs on a small hand-held computer. We will describe the components of this prototype, and also describe some of the future challenges we anticipate if we are to provide botanists in the field with all the resources that are now currently available in the world{\textquoteright}s museums and herbaria. Type Specimen Digital Collection The first challenge in producing our electronic field guide is to create a digital collection covering all of the Smithsonian{\textquoteright}s 85,000 vascular plant type specimens. For each type specimen, the database should eventually include systematically acquired high-resolution digital images of the specimen, textual descriptions, links to decision trees, images of live plants, and 3D models. Figure 1: On the left, our set-up at the Smithsonian for digitally photographing type specimens. On the...}, author = {Haibin,Gaurav Agarwal and Agarwal,Gaurav and Ling,Haibin and Jacobs, David W. and Shirdhonkar,Sameer and Kress,W. John and Russell,Rusty and Belhumeur,Peter and Dixit,An and Feiner,Steve and Mahajan,Dhruv and Sunkavalli,Kalyan and Ramamoorthi,Ravi and White,Sean} } @article {14146, title = {Fourier analysis of multigrid for a model two-dimensional convection-diffusion equation}, journal = {BIT Numerical Mathematics}, volume = {46}, year = {2006}, month = {2006///}, pages = {283 - 306}, author = {Elman, Howard and Ramage, A.} } @conference {12622, title = {The Function Space of an Activity}, booktitle = {Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on}, volume = {1}, year = {2006}, month = {2006///}, pages = {959 - 968}, abstract = {An activity consists of an actor performing a series of actions in a pre-defined temporal order. An action is an individual atomic unit of an activity. Different instances of the same activity may consist of varying relative speeds at which the various actions are executed, in addition to other intra- and inter- person variabilities. Most existing algorithms for activity recognition are not very robust to intra- and inter-personal changes of the same activity, and are extremely sensitive to warping of the temporal axis due to variations in speed profile. In this paper, we provide a systematic approach to learn the nature of such time warps while simultaneously allowing for the variations in descriptors for actions. For each activity we learn an $\#$145;average $\#$146; sequence that we denote as the nominal activity trajectory. We also learn a function space of time warpings for each activity separately. The model can be used to learn individualspecific warping patterns so that it may also be used for activity based person identification. The proposed model leads us to algorithms for learning a model for each activity, clustering activity sequences and activity recognition that are robust to temporal, intra- and inter-person variations. We provide experimental results using two datasets.}, doi = {10.1109/CVPR.2006.304}, author = {Veeraraghavan,A. and Chellapa, Rama and Roy-Chowdhury, A.K.} } @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} } @article {15681, title = {Fuzzy svm ensembles for relevance feedback in image retrieval}, journal = {Image and Video Retrieval}, year = {2006}, month = {2006///}, pages = {350 - 359}, author = {Rao,Y. and Mundur, Padma and Yesha,Y.} } @article {12160, title = {The Goal Question Metric Approach}, journal = {5th ACM-IEEE International Symposium on Empirical Software Engineering (ISESE{\textquoteright}06)}, year = {2006}, month = {2006///}, author = {Basili, Victor R. and Caldiera,G. and Rombach,H. D} } @conference {13436, title = {Heuristic search and information visualization methods for school redistricting}, booktitle = {Proceedings of the 18th conference on Innovative applications of artificial intelligence - Volume 2}, series = {IAAI{\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1774 - 1781}, publisher = {AAAI Press}, organization = {AAAI Press}, abstract = {We describe an application of AI search and information visualization techniques to the problem of school redistricting, in which students are assigned to home schools within a county or school district. This is a multicriteria optimization problem in which competing objectives must be considered, such as school capacity, busing costs, and socioeconomic distribution. Because of the complexity of the decision-making problem, tools are needed to help end users generate, evaluate, and compare alternative school assignment plans. A key goal of our research is to aid users in finding multiple qualitatively different redistricting plans that represent different tradeoffs in the decision space.We present heuristic search methods that can be used to find a set of qualitatively different plans, and give empirical results of these search methods on population data from the school district of Howard County, Maryland. We show the resulting plans using novel visualization methods that we have developed for summarizing and comparing alternative plans. }, isbn = {978-1-57735-281-5}, url = {http://dl.acm.org/citation.cfm?id=1597122.1597136}, author = {desJardins, Marie and Bulka,Blazej and Carr,Ryan and Hunt,Andrew and Rathod,Priyang and Rheingans,Penny} } @article {12814, title = {High-confidence medical device software and systems}, journal = {Computer}, volume = {39}, year = {2006}, month = {2006/04//}, pages = {33 - 38}, abstract = {Given the shortage of caregivers and the increase in an aging US population, the future of US healthcare quality does not look promising and definitely is unlikely to be cheaper. Advances in health information systems and healthcare technology offer a tremendous opportunity for improving the quality of care while reducing costs. The development and production of medical device software and systems is a crucial issue, both for the US economy and for ensuring safe advances in healthcare delivery. As devices become increasingly smaller in physical terms but larger in software terms, the design, testing, and eventual Food and Drug Administration (FDA) device approval is becoming much more expensive for medical device manufacturers both in terms of time and cost. Furthermore, the number of devices that have recently been recalled due to software and hardware problems is increasing at an alarming rate. As medical devices are becoming increasingly networked, ensuring even the same level of health safety seems a challenge.}, keywords = {Aging, biomedical equipment, Clinical software engineering, Costs, FDA device, Food and Drug Administration device, health and safety, health care, health information system, health safety, healthcare delivery, Healthcare technology, Information systems, medical computing, medical device manufacturing, medical device software development, medical device systems development, medical information systems, Medical services, Medical software, Medical tests, networked medical devices, Production systems, Software design, Software safety, Software systems, Software testing, US healthcare quality}, isbn = {0018-9162}, doi = {10.1109/MC.2006.127}, author = {Lee,I. and Pappas,G. J and Cleaveland, Rance and Hatcliff,J. and Krogh,B. H and Lee,P. and Rubin,H. and Sha,L.} } @conference {16451, title = {Implementing a bioinformatics pipeline (bip) on a mediator platform: Comparing cost and quality of alternate choices}, booktitle = {Data Engineering Workshops, 2006. Proceedings. 22nd International Conference on}, year = {2006}, month = {2006///}, pages = {67 - 67}, author = {Eckman,B. A and Gaasterland,T. and Lacroix,Z. and Raschid, Louiqa and Snyder,B. and Vidal,M. E} } @article {18577, title = {In VINI veritas: realistic and controlled network experimentation}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {36}, year = {2006}, month = {2006/08//}, pages = {3 - 14}, abstract = {This paper describes VINI, a virtual network infrastructure that allows network researchers to evaluate their protocols and services in a realistic environment that also provides a high degree of control over network conditions. VINI allows researchers to deploy and evaluate their ideas with real routing software, traffic loads, and network events. To provide researchers flexibility in designing their experiments, VINI supports simultaneous experiments with arbitrary network topologies on a shared physical infrastructure. This paper tackles the following important design question: What set of concepts and techniques facilitate flexible, realistic, and controlled experimentation (e.g., multiple topologies and the ability to tweak routing algorithms) on a fixed physical infrastructure? We first present VINI{\textquoteright}s high-level design and the challenges of virtualizing a single network. We then present PL-VINI, an implementation of VINI on PlanetLab, running the "Internet In a Slice". Our evaluation of PL-VINI shows that it provides a realistic and controlled environment for evaluating new protocols and services.}, keywords = {architecture, experimentation, Internet, Routing, virtualization}, isbn = {0146-4833}, doi = {10.1145/1151659.1159916}, url = {http://doi.acm.org/10.1145/1151659.1159916}, author = {Bavier,Andy and Feamster, Nick and Huang,Mark and Peterson,Larry and Rexford,Jennifer} } @inbook {14593, title = {An Interaction-Dependent Model for Transcription Factor Binding}, booktitle = {Systems Biology and Regulatory GenomicsSystems Biology and Regulatory Genomics}, series = {Lecture Notes in Computer Science}, volume = {4023}, year = {2006}, month = {2006///}, pages = {225 - 234}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Transcriptional regulation is accomplished by several transcription factor proteins that bind to specific DNA elements in the relative vicinity of the gene, and interact with each other and with Polymerase enzyme. Thus the determination of transcription factor-DNA binding is an important step toward understanding transcriptional regulation. An effective way to experimentally determine the genomic regions bound by a transcription factor is by a ChIP-on-chip assay. Then, given the putative genomic regions, computational motif finding algorithms are applied to estimate the DNA binding motif or positional weight matrix for the TF. The a priori expectation is that the presence or absence of the estimated motif in a promoter should be a good indicator of the binding of the TF to that promoter. This association between the presence of the transcription factor motif and its binding is however weak in a majority of cases where the whole genome ChIP experiments have been performed. One possible reason for this is that the DNA binding of a particular transcription factor depends not only on its own motif, but also on synergistic or antagonistic action of neighboring motifs for other transcription factors. We believe that modeling this interaction-dependent binding with linear regression can better explain the observed binding data. We assess this hypothesis based on the whole genome ChIP-on-chip data for Yeast. The derived interactions are largely consistent with previous results that combine ChIP-on-chip data with expression data. We additionally apply our method to determine interacting partners for CREB and validate our findings based on published experimental results.}, isbn = {978-3-540-48293-2}, url = {http://dx.doi.org/10.1007/978-3-540-48540-7_19}, author = {Wang,Li-San and Jensen,Shane and Hannenhalli, Sridhar}, editor = {Eskin,Eleazar and Ideker,Trey and Raphael,Ben and Workman,Christopher} } @article {18705, title = {Interdomain mobility in di-ubiquitin revealed by NMR}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {63}, year = {2006}, month = {2006///}, pages = {787 - 796}, abstract = {Domain orientation and dynamics can play an essential role in the function of multidomain proteins. Lys48-linked polyubiquitin chains, the principal signal for proteasomal protein degradation, adopt a closed conformation at physiological conditions, in which the functionally important residues Leu8, Ile44, and Val70 are sequestered at the interdomain interface. This interface must open in order for these groups to become available for interactions with various chain-recognition factors. Knowledge of the mechanism of domain motion leading to the opening of the interdomain interface in polyubiqutin is, therefore, essential for the understanding of the processes controlling molecular recognition events in polyubiquitin signaling. Here we use NMR to characterize the interdomain dynamics that open the interface in a di-ubiquitin chain. This process occurs via domain reorientations on a 10-ns time scale and with the amplitudes that are sufficient for making functionally important hydrophobic residues in polyubiquitin available for direct interactions with various ubiquitin-binding factors. The analysis revealed the structures of the interconverting conformational states of di-ubiquitin and the rates and amplitudes of this process at near-physiological and acidic pH. The proposed mechanism of domain reorientation is quite general and could serve as a paradigm of interdomain mobility in other multidomain systems. Proteins 2006. {\textcopyright} 2006 Wiley-Liss, Inc.}, keywords = {anisotropic diffusion, domain motion, interdomain orientation, polyubiquitin, spin relaxation}, isbn = {1097-0134}, doi = {10.1002/prot.20917}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.20917/abstract}, author = {Ryabov,Yaroslav and Fushman, David} } @article {16409, title = {Machine Learning Meets Agent-Based Modeling: When not to go to A Bar}, journal = {Proceedings of Agent Based Simulation}, year = {2006}, month = {2006///}, abstract = {One of the promises of ABM is the ability to have adaptive agents make decisions inchanging environments. Though great work has been done using adaptive agents in ABM, more research into the theoretical understanding of these systems would be useful. Adaptive agents have already been studied within machine learning (ML){\textemdash}an area of artificial intelligence specifically concerned with adaptation and building internal models. The first part of this paper presents a framework for understanding ML as a component of ABM, and describes how different ML techniques can be incorporated into some ABMs. At the high level this framework consists of two cycles that involve evaluating input, making decisions and then generating output. Within this generalized framework, the ML algorithm is using the ABM as an environment and a reward generator, while the ABM is using the ML algorithm to refine the internal models of the agents. There are many details that must be answered before any ML technique can be incorporated into an ABM. In this paper I start to explore some guidelines for how to more closely integrate ABM and ML and will discuss complications that arise when combining ABM and ML techniques. To illustrate some of these issues, I will describe an integration of a ML technique within the El Farol Bar Problem. I will conclude with some discussion of this integration and a look toward future research. }, author = {Rand, William} } @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.} } @article {12602, title = {Method and System for Object Surveillance and Real Time Activity Recognition}, volume = {12/086,118}, year = {2006}, month = {2006/12/05/}, abstract = {Method and system for objects surveillance and real-time activity recognition is based on analysis of spatio-temporal images of individuals under surveillance where a spatio-temporal volume occupied by each individual is decomposed by crossing the same at specific heights to form 2-dimensional slices, each containing representation of trajectory of the motion of corresponding portions of the individual body. The symmetry of the trajectories (Gait DNA) is analyzed and classified to generate data indicative of a type of activity of the individual based on the symmetry or asymmetry of the Gait DNA in each 2-dimensional slice. An effective occlusion handling ability is implemented which permits to restore the occluded silhouette of an individual.}, url = {http://www.google.com/patents?id=IArMAAAAEBAJ}, author = {Yang Ran and Chellapa, Rama and Qinfen Zheng} } @conference {12838, title = {Model based verification and validation of distributed control architectures}, booktitle = {Proceedings of Convergence Convergence International Congress and Exposition on Transportation Electronics, Detroit, USA}, year = {2006}, month = {2006///}, author = {Ray,A. and Cleaveland, Rance and Jiang,S. and Fuhrman,T.} } @article {16933, title = {A model for computer frustration: the role of instrumental and dispositional factors on incident, session, and post-session frustration and mood}, journal = {Computers in Human Behavior}, volume = {22}, year = {2006}, month = {2006/11//}, pages = {941 - 961}, abstract = {Frustration is almost universally accepted as the emotional outcome of a negative computing experience. Despite the wide use of the term, however, it has not been rigorously conceptualized as a factor in the study of the human{\textendash}computer interface. This project sets out to explicate frustration as a pre-emotional state generated by the user{\textquoteright}s appraisal of the interface as an impediment to goal attainment, and looks at how user characteristics, such as self-efficacy, relate to it. This project employed episode report methodology to capture data from 144 computer users{\textquoteright} reports of actual frustrating events as they took place. Diaries taken as users worked at their everyday tasks yield detailed data about the problems they encountered and included information about session length and an estimate of the time lost due to the experiences. Outcomes were measured as either situational or dispositional factors. Situational factors, having to do with specific events, predicted incident frustration. However, disposition variables, especially user self-efficacy, were much stronger, predicting incident and session frustration, and post-session mood. One surprising outcome was the failure of demographic variables as predictors of frustration.}, keywords = {Efficacy, Emotion, Frustration, Mood, problem solving, usability}, isbn = {0747-5632}, doi = {10.1016/j.chb.2004.03.015}, url = {http://www.sciencedirect.com/science/article/pii/S0747563204000615}, author = {Bessi{\`e}re,Katie and Newhagen,John E. and Robinson,John P. and Shneiderman, Ben} } @conference {12614, title = {Modeling Age Progression in Young Faces}, booktitle = {Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on}, volume = {1}, year = {2006}, month = {2006/06//}, pages = {387 - 394}, abstract = {We propose a craniofacial growth model that characterizes growth related shape variations observed in human faces during formative years. The model draws inspiration from the $\#$145;revised $\#$146; cardioidal strain transformation model proposed in psychophysical studies related to craniofacial growth. The model takes into account anthropometric evidences collected on facial growth and hence is in accordance with the observed growth patterns in human faces across years. We characterize facial growth by means of growth parameters defined over facial landmarks often used in anthropometric studies. We illustrate how the age-based anthropometric constraints on facial proportions translate into linear and non-linear constraints on facial growth parameters and propose methods to compute the optimal growth parameters. The proposed craniofacial growth model can be used to predict one $\#$146;s appearance across years and to perform face recognition across age progression. This is demonstrated on a database of age separated face images of individuals under 18 years of age.}, doi = {10.1109/CVPR.2006.187}, author = {Ramanathan,N. and Chellapa, Rama} } @article {18643, title = {Modeling and Simulation of the Escalation Archetype in Computer Security}, journal = {Symposium on Simulation Software Security (SSSS 06)}, volume = {38}, year = {2006}, month = {2006///}, pages = {495 - 495}, abstract = {To support decision-making for mitigating computer security risks, we developed and used a system dynamics model of security aspects of an enterprise system. We describe the notion of archetypes in general and the escalation archetype specifically, showing how it can arise in computer security. We show the effects of this instance of escalation through simulation of our model, consider the effects of changes in the simulation, and discuss the prognoses drawn from the archetype literature and their applicability to security.}, url = {https://www.scs.org/confernc/springsim/springsim06/prelimProgram/ssss/2.html}, author = {Rosenfeld,S. N. and Rus,I. and Michel Cukier} } @conference {18679, title = {Modeling the Symptomatic Fixes Archetype in Enterprise Computer Security}, volume = {1}, year = {2006}, month = {2006/09//}, pages = {178 - 188}, abstract = {To support decision-making for security-risk mitigation and the appropriate selection of security countermeasures, we propose a system dynamics model of the security aspects of an enterprise system. We developed such an executable model, incorporating the concept of archetypes. We present here one archetype for computer security, namely symptomatic fixes (or shifting the burden). Using simulation, we show one instance of how this archetype can be used for recognizing and diagnosing typical situations, as well as for fixing problems. The global effects of changes and behavioral trends are examined, and other instances of symptomatic fixes in security are described as well}, keywords = {business data processing, decision making, decision-making, enterprise computer security, human factors, security of data, security-risk mitigation, symptomatic fixes archetype modeling, system dynamics model, system modeling}, doi = {10.1109/COMPSAC.2006.62}, author = {Rosenfeld,S. N. and Rus,I. and Michel Cukier} } @conference {14557, title = {New lower bounds for oblivious routing in undirected graphs}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {918 - 927}, author = {Hajiaghayi, Mohammad T. and Kleinberg,R. D and Leighton,T. and R\{\"a}cke,H.} } @article {14004, title = {Numerical computation of the Green?s function for two-dimensional finite-size photonic crystals of infinite length}, journal = {Optics ExpressOpt. Express}, volume = {14}, year = {2006}, month = {2006/11/13/}, pages = {11362 - 11371}, abstract = {We develop a numerical algorithm that computes the Green{\textquoteright}s function of Maxwell equation for a 2D finite-size photonic crystal, composed of rods of arbitrary shape. The method is based on the boundary integral equation, and a Nystr{\"o}m discretization is used for the numerical solution. To provide an exact solution that validates our code we derive multipole expansions for circular cylinders using our integral equation approach. The numerical method performs very well on the test case. We then apply it to crystals of arbitrary shape and discuss the convergence.}, keywords = {Diffraction and gratings, Multiple scattering}, doi = {10.1364/OE.14.011362}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-14-23-11362}, author = {Seydou,F. and Ramahi,Omar M. and Duraiswami, Ramani and Sepp{\"a}nen,T.} } @conference {14554, title = {Oblivious network design}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {970 - 979}, author = {Gupta,A. and Hajiaghayi, Mohammad T. and R\{\"a}cke,H.} } @conference {17788, title = {Opinion Analysis in Document Databases}, booktitle = {Proc. AAAI Spring Symposium on Computational Approaches to Analyzing Weblogs, Stanford, CA}, year = {2006}, month = {2006///}, abstract = {There are numerous applications in which we would like toassess what opinions are being expressed in text documents. Forr example, Martha Stewart{\textquoteright}s company may have wished to assess the degree of harshness of news articles about her in the recent past. Likewise, a World Bank official may wish to as- sess the degree of criticism of a proposed dam in Bangladesh. The ability to gauge opinion on a given topic is therefore of critical interest. In this paper, we develop a suite of algo- rithms which take as input, a set D of documents as well as a topic t, and gauge the degree of opinion expressed about topic t in the set D of documents. Our algorithms can return both a number (larger the number, more positive the opinion) as well as a qualitative opinion (e.g. harsh, complimentary). We as- sess the accuracy of these algorithms via human experiments and show that the best of these algorithms can accurately re- flect human opinions. We have also conducted performance experiments showing that our algorithms are computationally fast. }, author = {Cesarano,C. and Dorr, Bonnie J and Picariello, A. and Reforgiato,D. and Sagoff,A. and V.S. Subrahmanian} } @article {13839, title = {Parallel syntactic annotation of multiple languages}, journal = {Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC2006). Genoa, Italy}, year = {2006}, month = {2006///}, abstract = {This paper describes an effort to investigate the incrementally deepening development of an interlingua notation, validated by humanannotation of texts in English plus six languages. We begin with deep syntactic annotation, and in this paper present a series of annotation manuals for six different languages at the deep-syntactic level of representation. Many syntactic differences between languages are removed in the proposed syntactic annotation, making them useful resources for multilingual NLP projects with semantic components. }, author = {Rambow,O. and Dorr, Bonnie J and Farwell,D. and Green,R. and Habash,N. and Helmreich,S. and Hovy,E. and Levin,L. and Miller,K.J. and Mitamura,T. and others} } @conference {16429, title = {Participatory, embodied, multi-agent simulation}, booktitle = {Proceedings of the fifth international joint conference on Autonomous agents and multiagent systems}, series = {AAMAS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1457 - 1458}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We will demonstrate the integration of a software-based multi-agent modeling platform with a participatory simulation environment and real-time control over a physical agent (robot). Both real and virtual participants will be able to act as agents in a simulation that will control a physical agent. The backbone of this demonstration is a widely used, freely available, mature modeling platform known as NetLogo.}, keywords = {embedded agents, multi-agent simulation, participatory simulation, ROBOTICS, Sensors}, isbn = {1-59593-303-4}, doi = {10.1145/1160633.1160913}, url = {http://doi.acm.org/10.1145/1160633.1160913}, author = {Blikstein,Paulo and Rand, William and Wilensky,Uri} } @conference {13841, title = {PCFGs with syntactic and prosodic indicators of speech repairs}, booktitle = {Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics}, series = {ACL-44}, year = {2006}, month = {2006///}, pages = {161 - 168}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {A grammatical method of combining two kinds of speech repair cues is presented. One cue, prosodic disjuncture, is detected by a decision tree-based ensemble classifier that uses acoustic cues to identify where normal prosody seems to be interrupted (Lickley, 1996). The other cue, syntactic parallelism, codifies the expectation that repairs continue a syntactic category that was left unfinished in the reparandum (Levelt, 1983). The two cues are combined in a Treebank PCFG whose states are split using a few simple tree transformations. Parsing performance on the Switchboard and Fisher corpora suggests that these two cues help to locate speech repairs in a synergistic way.}, doi = {10.3115/1220175.1220196}, url = {http://dx.doi.org/10.3115/1220175.1220196}, author = {Hale,John and Shafran,Izhak and Yung,Lisa and Dorr, Bonnie J and Harper,Mary and Krasnyanskaya,Anna and Lease,Matthew and Liu,Yang and Roark,Brian and Snover,Matthew and Stewart,Robin} } @article {14383, title = {Probabilistic, Logical and Relational Learning-Towards a Synthesis}, journal = {Dagstuhl Seminar Proceedings}, volume = {5051}, year = {2006}, month = {2006///}, author = {De Raedt,L. and Dietterich,T. and Getoor, Lise and Muggleton,S. H and Lloyd,J. W and Sears,T. D and Milch,B. and Marthi,B. and Russell,S. and Sontag,D.} } @article {16794, title = {Processing approximate aggregate queries in wireless sensor networks}, journal = {Information Systems}, volume = {31}, year = {2006}, month = {2006/12//}, pages = {770 - 792}, abstract = {In-network data aggregation has been recently proposed as an effective means to reduce the number of messages exchanged in wireless sensor networks. Nodes of the network form an aggregation tree, in which parent nodes aggregate the values received from their children and propagate the result to their own parents. However, this schema provides little flexibility for the end-user to control the operation of the nodes in a data sensitive manner. For large sensor networks with severe energy constraints, the reduction (in the number of messages exchanged) obtained through the aggregation tree might not be sufficient. In this paper, we present new algorithms for obtaining approximate aggregate statistics from large sensor networks. The user specifies the maximum error that he is willing to tolerate and, in turn, our algorithms program the nodes in a way that seeks to minimize the number of messages exchanged in the network, while always guaranteeing that the produced estimate lies within the specified error from the exact answer. A key ingredient to our framework is the notion of the residual mode of operation that is used to eliminate messages from sibling nodes when their cumulative change to the computed aggregate is small. We introduce two new algorithms, based on potential gains, which adaptively redistribute the error thresholds to those nodes that benefit the most and try to minimize the total number of transmitted messages in the network. Our techniques significantly reduce the number of messages, often by a factor of 10 for a modest 2\% relative error bound, and consistently outperform previous techniques for computing approximate aggregates, which we have adapted for sensor networks.}, keywords = {Aggregate queries, approximation, sensor networks}, isbn = {0306-4379}, doi = {16/j.is.2005.02.001}, url = {http://www.sciencedirect.com/science/article/pii/S0306437905000177}, author = {Deligiannakis,Antonios and Kotidis,Yannis and Roussopoulos, Nick} } @article {16498, title = {ProMo-A Scalable and Efficient Framework for Online Data Delivery}, journal = {Lecture notes in computer science}, volume = {4032}, year = {2006}, month = {2006///}, pages = {359 - 359}, author = {Roitman,H. and Gal,A. and Raschid, Louiqa} } @article {15245, title = {Query planning in the presence of overlapping sources}, journal = {Advances in Database Technology-EDBT 2006}, year = {2006}, month = {2006///}, pages = {811 - 828}, abstract = {Navigational queries on Web-accessible life science sources pose unique query optimization challenges. The objects in these sources are interconnected to objects in other sources, forming a large and complex graph, and there is an overlap of objects in the sources. Answering a query requires the traversal of multiple alternate paths through these sources. Each path can be associated with the benefit or the cardinality of the target object set (TOS) of objects reached in the result. There is also an evaluation cost of reaching the TOS.We present dual problems in selecting the best set of paths. The first problem is to select a set of paths that satisfy a constraint on the evaluation cost while maximizing the benefit (number of distinct objects in the TOS). The dual problem is to select a set of paths that satisfies a threshold of the TOS benefit with minimal evaluation cost. The two problems can be mapped to the budgeted maximum coverage problem and the maximal set cover with a threshold. To solve these problems, we explore several solutions including greedy heuristics, a randomized search, and a traditional IP/LP formulation with bounds. We perform experiments on a real-world graph of life sciences objects from NCBI and report on the computational overhead of our solutions and their performance compared to the optimal solution. }, doi = {10.1007/11687238_48}, author = {Bleiholder,J. and Khuller, Samir and Naumann,F. and Raschid, Louiqa and Wu,Y.} } @article {16469, title = {Query planning in the presence of overlapping sources}, journal = {Advances in Database Technology-EDBT 2006}, year = {2006}, month = {2006///}, pages = {811 - 828}, author = {Bleiholder,J. and Khuller, Samir and Naumann,F. and Raschid, Louiqa and Wu,Y.} } @conference {16472, title = {Query Rewriting in the Semantic Web7}, booktitle = {Data Engineering Workshops, 22nd International Conference on}, year = {2006}, month = {2006///}, pages = {7 - 7}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {The widespread explosion of Web accessible resources has lead to a new challenge of locating all relevant resources and identifying the best ones to answer a query. This challenge has to address the difficult task of ranking the resources based on user needs, as well as the more expensive computational task of determining all the solutions to answer a query. In this paper, we define a Top K problem for query rewriting on the Semantic Web. We first introduce a three level data model composed of the ontology level, the physical level of the physical resources, and the data level composed of the entries in the different resources. We present a query language for Top K navigational queries over ontology concepts. We then sketch the outline of an efficient search algorithm to compute an approximation of the Top K rewriting options to produce source paths among the physical resources. We briefly discuss the results of an experimental study}, isbn = {0-7695-2571-7}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDEW.2006.124}, author = {Vidal,Maria Esther and Raschid, Louiqa and Marquez,Natalia and Cardenas,Marelis and Yao Wu} } @book {13182, title = {Real-Time Distributed Algorithms for Visual and Battlefield Reasoning}, year = {2006}, month = {2006///}, publisher = {MARYLAND UNIV COLLEGE PARK OFFICE OF RESEARCH ADMINISTRATION AND ADVANCEMENT}, organization = {MARYLAND UNIV COLLEGE PARK OFFICE OF RESEARCH ADMINISTRATION AND ADVANCEMENT}, abstract = {Information is key to the success of the next generation battlefield. There is a critical need to determine, in real-time, what the enemy is doing, and to interpret that information in the context of past related events. In this project we examined two aspects of this issue: development of a high-level task definition language for tasking a network of sensors to carry out given objectives, and interpreting recounted events so that past related scenarios could be automatically identified from a case database.}, author = {Davis, Larry S. and Basili, Victor R. and V.S. Subrahmanian and Reggia, James A. and Aloimonos, J.} } @conference {13169, title = {Real-Time Human Detection, Tracking, and Verification in Uncontrolled Camera Motion Environments}, booktitle = {Computer Vision Systems, 2006 ICVS {\textquoteright}06. IEEE International Conference on}, year = {2006}, month = {2006/01//}, pages = {41 - 41}, abstract = {In environments where a camera is installed on a freely moving platform, e.g. a vehicle or a robot, object detection and tracking becomes much more difficult. In this paper, we presents a real time system for human detection, tracking, and verification in such challenging environments. To deliver a robust performance, the system integrates several computer vision algorithms to perform its function: a human detection algorithm, an object tracking algorithm, and a motion analysis algorithm. To utilize the available computing resources to the maximum possible extent, each of the system components is designed to work in a separate thread that communicates with the other threads through shared data structures. The focus of this paper is more on the implementation issues than on the algorithmic issues of the system. Object oriented design was adopted to abstract algorithmic details away from the system structure.}, doi = {10.1109/ICVS.2006.52}, author = {Hussein,M. and Abd-Almageed, Wael and Yang Ran and Davis, Larry S.} } @conference {13849, title = {Reranking for Sentence Boundary Detection in Conversational Speech}, booktitle = {2006 IEEE International Conference on Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings}, volume = {1}, year = {2006}, month = {2006/05/14/19}, pages = {I-I - I-I}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a reranking approach to sentence-like unit (SU) boundary detection, one of the EARS metadata extraction tasks. Techniques for generating relatively small n-best lists with high oracle accuracy are presented. For each candidate, features are derived from a range of information sources, including the output of a number of parsers. Our approach yields significant improvements over the best performing system from the NIST RT-04F community evaluation}, keywords = {Automatic speech recognition, conversational speech, data mining, Ear, EARS metadata extraction tasks, Feature extraction, hidden Markov models, meta data, Model driven engineering, NIST, NIST RT-04F community evaluation, oracle accuracy, performance evaluation, reranking, sentence-like unit boundary detection, Speech processing, Speech recognition, Telephony}, isbn = {1-4244-0469-X}, doi = {10.1109/ICASSP.2006.1660078}, author = {Roark,B. and Liu,Yang and Harper,M. and Stewart,R. and Lease,M. and Snover,M. and Shafran,I. and Dorr, Bonnie J and Hale,J. and Krasnyanskaya,A. and Yung,L.} } @conference {18487, title = {Revealing botnet membership using DNSBL counter-intelligence}, booktitle = {Proc. 2nd USENIX Steps to Reducing Unwanted Traffic on the Internet}, year = {2006}, month = {2006///}, pages = {49 - 54}, abstract = {Botnets{\textemdash}networks of (typically compromised) machines{\textemdash}are often used for nefarious activities (e.g., spam, click fraud, denial-of-service attacks, etc.). Identifying members of botnets could help stem these attacks, but passively detecting botnet membership (i.e., without disrupting the operation of the botnet) proves to be difficult. This paper studies the effectiveness of monitoring lookups to a DNS-based blackhole list (DNSBL) to expose botnet membership. We perform counter-intelligence based on the insight that botmasters themselves perform DNSBL lookups to determine whether their spamming bots are blacklisted. Using heuristics to identify which DNSBL lookups are perpetrated by a botmaster performing such reconnaissance, we are able to compile a list of likely bots. This paper studies the prevalence of DNSBL reconnaissance observed at a mirror of a well-known blacklist for a 45-day period, identifies the means by which botmasters are performing reconnaissance, and suggests the possibility of using counter-intelligence to discover likely bots. We find that bots are performing reconnaissance on behalf of other bots. Based on this finding, we suggest counter-intelligence techniques that may be useful for early bot detection. }, author = {Ramachandran,A. and Feamster, Nick and Dagon,D.} } @article {15075, title = {Robust fuzzy extractors and authenticated key agreement from close secrets}, journal = {Advances in Cryptology-CRYPTO 2006}, year = {2006}, month = {2006///}, pages = {232 - 250}, abstract = {Consider two parties holding correlated random variables W and W', respectively, that are within distance t of each other in some metric space. These parties wish to agree on a uniformly distributed secret key R by sending a single message over an insecure channel controlled by an all-powerful adversary. We consider both the keyless case, where the parties share no additional secret information, and the keyed case, where the parties share a long-term secret SK that they can use to generate a sequence of session keys {R j } using multiple pairs {(W j , W' j )}. The former has applications to, e.g., biometric authentication, while the latter arises in, e.g., the bounded storage model with errors.Our results improve upon previous work in several respects: {\textendash} The best previous solution for the keyless case with no errors (i.e., t=0) requires the min-entropy of W to exceed 2|W|/3. We show a solution when the min-entropy of W exceeds the minimal threshold |W|/2. {\textendash} Previous solutions for the keyless case in the presence of errors (i.e., t>0) required random oracles. We give the first constructions (for certain metrics) in the standard model. {\textendash} Previous solutions for the keyed case were stateful. We give the first stateless solution. }, doi = {10.1007/11818175_14}, author = {Dodis,Y. and Katz, Jonathan and Reyzin,L. and Smith,A.} } @article {12924, title = {Septaplex PCR assay for rapid identification of Vibrio cholerae including detection of virulence and int SXT genes}, journal = {FEMS Microbiology Letters}, volume = {265}, year = {2006}, month = {2006/12/01/}, pages = {208 - 214}, abstract = {In this study, we describe a septaplex PCR assay for rapid identification of Vibrio cholerae including detection of the virulence and intsxt genes. Conditions were optimized to amplify fragments of ISRrRNA (encoding for 16S{\textendash}23S rRNA gene, Intergenic spacer regions), O1rfb (O1 serogroup specific rfb), O139rfb (O139 serogroup specific rfb), ctxA (cholera toxin subunit A), tcpA (toxin coregulated pilus), and intsxt (sxt integron) simultaneously in a single PCR. The septaplex PCR was evaluated using 211 strains of V. cholerae and six water samples for in situ testing. PCR results were correlated with genotype data obtained by individual PCR and slot-blot assays. The one-step PCR described here can be used to identify V. cholerae accurately and rapidly. Also, the virulence and intsxt genes can be simultaneously detected, providing a useful method for monitoring pathogenic, intsxt-positive and nonpathogenic, intsxt-negative V. cholerae serogroups both in the environment and clinical settings.}, keywords = {DETECTION, intsxt, septaplex PCR, Vibrio cholerae, virulence}, isbn = {1574-6968}, doi = {10.1111/j.1574-6968.2006.00491.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2006.00491.x/full}, author = {Mantri,Chinmay K. and Mohapatra,Saswat S. and Ramamurthy,Thandavarayan and Ghosh,Raikamal and Rita R Colwell and Singh,Durg V.} } @conference {12830, title = {A Software Architectural Approach to Security by Design}, booktitle = {Computer Software and Applications Conference, 2006. COMPSAC {\textquoteright}06. 30th Annual International}, volume = {2}, year = {2006}, month = {2006/09/17/21}, pages = {83 - 86}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper shows how an architecture description notation that has support for timed events can be used to provide a meta-language for specifying exact communication semantics. The advantages of such an approach is that a designer is made fully aware of the ramifications of her design choices so that an attacker can no longer take advantage of hidden assumptions}, keywords = {architecture description notation, Clocks, communication semantics, Computer architecture, computer crime, computer security, Connectors, Costs, Degradation, Delay, Educational institutions, security design, security of data, Software architecture, software engineering}, isbn = {0-7695-2655-1}, doi = {10.1109/COMPSAC.2006.102}, author = {Ray,A. and Cleaveland, Rance} } @article {13864, title = {SParseval: Evaluation metrics for parsing speech}, journal = {Proc. LREC}, year = {2006}, month = {2006///}, abstract = {While both spoken and written language processing stand to benefit from parsing, the standard Parseval metrics (Black et al., 1991) andtheir canonical implementation (Sekine and Collins, 1997) are only useful for text. The Parseval metrics are undefined when the words input to the parser do not match the words in the gold standard parse tree exactly, and word errors are unavoidable with automatic speech recognition (ASR) systems. To fill this gap, we have developed a publicly available tool for scoring parses that implements a variety of metrics which can handle mismatches in words and segmentations, including: alignment-based bracket evaluation, alignment-based dependency evaluation, and a dependency evaluation that does not require alignment. We describe the different metrics, how to use the tool, and the outcome of an extensive set of experiments on the sensitivity of the metrics. }, author = {Roark,B. and Harper,M. and Charniak,E. and Dorr, Bonnie J and Johnson,M. and Kahn,J. and Liu,Y. and Ostendorf,M. and Hale,J. and Krasnyanskaya,A. and others} } @article {12605, title = {Special Issue on Biometrics: Algorithms and Applications}, journal = {Proceedings of the IEEE}, volume = {94}, year = {2006}, month = {2006/11//}, pages = {1912 - 1914}, isbn = {0018-9219}, doi = {10.1109/JPROC.2006.886016}, author = {Chellapa, Rama and Phillips, J. and Reynolds, D.} } @conference {12609, title = {Stabilization and Mosaicing of Airborne Videos}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {345 - 348}, abstract = {We present an algorithm for stabilizing low-quality and low-resolution video sequences obtained from UAVs and MAVs flying over a predominantly planar terrain. The problem is important for the processing of videos captured from airborne platforms where most of the image region gives little information about the image-motion. The algorithm consists of approximately aligning the images using phase correlation, then refining the transformation parameters using available optical flow measurements and finally performing a minimization of the image difference by carefully selecting the image regions to make the iterations converge. In the second part of the paper, we describe an algorithm for camera ego-motion estimation by incorporating available metadata along with the video sequence. The availability of metadata such as IMU measurements provides a good initial solution for the camera orientation and helps the iterations converge faster by reducing the search space}, keywords = {airborne, analysis;image, cameras;, convergence;low-resolution, ego-motion, estimation;iterations, flow, measurement;video, mosaicing;camera, MOTION, resolution;image, segmentation;image, sequence;optical, sequences;video, stabilization;image, video, Videos}, doi = {10.1109/ICIP.2006.313164}, author = {Ramachandran, M. and Chellapa, Rama} } @article {16522, title = {Stigmergic self-assembly of prespecified artificial structures in a constrained and continuous environment}, journal = {Integrated Computer-Aided Engineering}, volume = {13}, year = {2006}, month = {2006///}, pages = {289 - 312}, author = {Grushin,A. and Reggia, James A.} } @conference {15343, title = {The turbulence structure of shockwave and boundary layer interaction in a compression corner}, booktitle = {44th AIAA Aerospace Meeting and Exhibit}, volume = {2006}, year = {2006}, month = {2006///}, address = {Reno, NV}, abstract = {Shockwave and turbulent boundary layer interactions (STBLI) result in intense localizedheating rates and pressure loads, making them extremely important flow features that must be identified for engineering design. The absence of detailed and complete experimental and numerical data at the same flow and boundary conditions is one of the major stumbling blocks in the development of accurate turbulence models for the prediction of STBLI. We use a set of direct numerical simulation data (Wu \& Martin, 2006) that has been validated against experiments (Bookey et al., 2005) at the same conditions to present detailed flow features of the STBLI over a compression corner at Mach 3 and low Reynolds number with Reθ=2100. Details regarding the evolution of the turbulence structure angle, characteristic streamwise length scales, and hairpin packets through the interaction are presented. The three-dimensionality of the turbulence field and main shock are illustrated and the strength of shocks and shocklets through the interaction are considered. }, author = {Martin, M.P and Smits,A. and Wu,M. and Ringuette,M.} } @conference {18610, title = {Understanding the network-level behavior of spammers}, booktitle = {Proceedings of the 2006 conference on Applications, technologies, architectures, and protocols for computer communications}, series = {SIGCOMM {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {291 - 302}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper studies the network-level behavior of spammers, including: IP address ranges that send the most spam, common spamming modes (e.g., BGP route hijacking, bots), how persistent across time each spamming host is, and characteristics of spamming botnets. We try to answer these questions by analyzing a 17-month trace of over 10 million spam messages collected at an Internet "spam sinkhole", and by correlating this data with the results of IP-based blacklist lookups, passive TCP fingerprinting information, routing information, and botnet "command and control" traces.We find that most spam is being sent from a few regions of IP address space, and that spammers appear to be using transient "bots" that send only a few pieces of email over very short periods of time. Finally, a small, yet non-negligible, amount of spam is received from IP addresses that correspond to short-lived BGP routes, typically for hijacked prefixes. These trends suggest that developing algorithms to identify botnet membership, filtering email messages based on network-level properties (which are less variable than email content), and improving the security of the Internet routing infrastructure, may prove to be extremely effective for combating spam.}, keywords = {BGP, botnet, network management, Security, spam}, isbn = {1-59593-308-5}, doi = {10.1145/1159913.1159947}, url = {http://doi.acm.org/10.1145/1159913.1159947}, author = {Ramachandran,Anirudh and Feamster, Nick} } @article {16406, title = {Verification and Validation through Replication: A Case Study Using Axelrod and Hammond{\textquoteright}s Ethnocentrism Model}, journal = {North American Association for Computational Social and Organization Sciences (NAACSOS)}, year = {2006}, month = {2006///}, abstract = {Recent years have seen a proliferation of agent-based models (ABMs), but with the exceptionof a few "classic" models, most of these models have never been replicated. We argue that replication has even greater benefits when applied to computational models than when applied to physical experiments. Replication affects model verification, in that it aids in determining if the implemented model reflects the conceptual model. It affects model validation, since a replication of a conceptual model may change the output from an implemented model and thus alter the correspondence between the model and the real world. Replication also affects validation by forcing the model developer and replicator to re-examine assumptions made in the original model. In addition replication fosters shared understanding of the details of modeling decisions within the research community. To facilitate the practice of replication, we argue for the creation of standards for both how to replicate models and how to evaluate the replication. In this paper, we present a case study of our attempt to replicate an ABM developed by Axelrod and Hammond. We detail our effort to replicate that model and the challenges that arose in recreating the model and in determining if the replication was successful. }, author = {Rand, William and Wilensky,U.} } @article {14008, title = {Very fast optimal bandwidth selection for univariate kernel density estimation}, journal = {Technical Reports from UMIACS UMIACS-TR-2005-73}, year = {2006}, month = {2006/01/03/T15:1}, abstract = {Most automatic bandwidth selection procedures for kernel density estimates require estimation of quantities involvingthe density derivatives. Estimation of modes and inflexion points of densities also require derivative estimates. The computational complexity of evaluating the density derivative at M evaluation points given N sample points from the density is O(MN). In this paper we propose a computationally efficient $\epsilon$-exact approximation algorithm for univariate, Gaussian kernel based, density derivative estimation that reduces the computational complexity from O(MN) to linear order (O(N+M)). The constant depends on the desired arbitrary accuracy, $\epsilon$. We apply the density derivative evaluation procedure to estimate the optimal bandwidth for kernel density estimation, a process that is often intractable for large data sets. For example for N = M = 409,600 points while the direct evaluation of the density derivative takes around 12.76 hours the fast evaluation requires only 65 seconds with an error of around $10^{-12)$. Algorithm details, error bounds, procedure to choose the parameters and numerical experiments are presented. We demonstrate the speedup achieved on the bandwidth selection using the {\textquoteleft}{\textquoteleft}solve-the-equation plug-in method{\textquoteright}{\textquoteright} [18]. We also demonstrate that the proposed procedure can be extremely useful for speeding up exploratory projection pursuit techniques. }, keywords = {Approximation algorithms, computational statistics, fast gauss transform, kernel density estimation, projection pursuit}, url = {http://drum.lib.umd.edu/handle/1903/3028}, author = {Raykar,Vikas Chandrakant and Duraiswami, Ramani} } @conference {13481, title = {Visualization Support for Fusing Relational, Spatio-Temporal Data: Building Career Histories}, booktitle = {Information Fusion, 2006 9th International Conference on}, year = {2006}, month = {2006/07//}, pages = {1 - 7}, publisher = {IEEE}, organization = {IEEE}, abstract = {Many real-world domains resist analysis because they are best characterized by a variety of data types, including relational, spatial, and temporal components. Examples of such domains include disease outbreaks, criminal networks, and the World-Wide Web. We present two types of visualizations based on physical metaphors that facilitate fusion, analysis, and deep understanding of relational, spatio-temporal data. The first visualization is based on the metaphor of fluid flow through elastic pipes, and the second on wave propagation. We discuss both types of visualizations in the context of fusing information about the activities of scientists over time with the goal of constructing career histories}, isbn = {1-4244-0953-5, 0-9721844-6-5}, doi = {10.1109/ICIF.2006.301772}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4086058}, author = {Blythe,Jim and Patwardhan,Mithila and Oates,Tim and desJardins, Marie and Rheingans,Penny} } @inbook {12642, title = {What Is the Range of Surface Reconstructions from a Gradient Field?}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3951}, year = {2006}, month = {2006///}, pages = {578 - 591}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We propose a generalized equation to represent a continuum of surface reconstruction solutions of a given non-integrable gradient field. We show that common approaches such as Poisson solver and Frankot-Chellappa algorithm are special cases of this generalized equation. For a N {\texttimes} N pixel grid, the subspace of all integrable gradient fields is of dimension N 2 {\textendash} 1. Our framework can be applied to derive a range of meaningful surface reconstructions from this high dimensional space. The key observation is that the range of solutions is related to the degree of anisotropy in applying weights to the gradients in the integration process. While common approaches use isotropic weights, we show that by using a progression of spatially varying anisotropic weights, we can achieve significant improvement in reconstructions. We propose (a) α-surfaces using binary weights, where the parameter α allows trade off between smoothness and robustness, (b) M-estimators and edge preserving regularization using continuous weights and (c) Diffusion using affine transformation of gradients. We provide results on photometric stereo, compare with previous approaches and show that anisotropic treatment discounts noise while recovering salient features in reconstructions.}, isbn = {978-3-540-33832-1}, url = {http://dx.doi.org/10.1007/11744023_45}, author = {Agrawal,Amit and Raskar,Ramesh and Chellapa, Rama}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @article {16414, title = {Widgets, Planets, and Demons: the Case for the Integration of Human, Embedded, and Virtual Agents via Mediation}, journal = {Proceedings of Swarmfest}, year = {2006}, month = {2006///}, author = {Rand, William and Blikstein,P. and Wilensky,U.} } @conference {16705, title = {Word-based alignment, phrase-based translation: What{\textquoteright}s the link}, booktitle = {Proc. of AMTA}, year = {2006}, month = {2006///}, pages = {90 - 99}, author = {Lopez,A. and Resnik, Philip} } @article {12672, title = {3D face modeling from monocular video sequences}, journal = {Face Processing: Advanced Modeling and Methods}, year = {2005}, month = {2005///}, abstract = {In this chapter we present two algorithms for 3D face modeling from a monocular video sequence. The firstmethod is based on Structure from Motion (SfM), while the second one relies on contour adaptation over time. The SfM based method incorporates statistical measures of quality of the 3D estimate into the reconstruction algorithm. The initial multi-frame SfM estimate is smoothed using a generic face model in an energy function minimization framework. Such a strategy avoids excessively biasing the final 3D estimate towards the generic model. The second method relies on matching a generic 3D face model to the outer contours of a face in the input video sequence, and integrating this strategy over all the frames in the sequence. It consists of an edge-based head pose estimation step, followed by global and local deformations of the generic face model in order to adapt it to the actual 3D face. This contour adaptation approach is able to separate the geometric subtleties of the human head from the variations in shading and texture, and it does not rely on finding accurate point correspondences across frames. Detailed experimental evaluation of both the methods along with reconstructed 3D models is presented. }, author = {Roy-Chowdhury, A. and Chellapa, Rama and Gupta, R.} } @article {17791, title = {Aggregate operators in probabilistic databases}, journal = {J. ACM}, volume = {52}, year = {2005}, month = {2005/01//}, pages = {54 - 101}, abstract = {Though extensions to the relational data model have been proposed in order to handle probabilistic information, there has been very little work to date on handling aggregate operators in such databases. In this article, we present a very general notion of an aggregate operator and show how classical aggregation operators (such as COUNT, SUM, etc.) as well as statistical operators (such as percentiles, variance, etc.) are special cases of this general definition. We devise a formal linear programming based semantics for computing aggregates over probabilistic DBMSs, develop algorithms that satisfy this semantics, analyze their complexity, and introduce several families of approximation algorithms that run in polynomial time. We implemented all of these algorithms and tested them on a large set of data to help determine when each one is preferable.}, keywords = {Aggregates, probabilistic relational databases}, isbn = {0004-5411}, doi = {10.1145/1044731.1044734}, url = {http://doi.acm.org/10.1145/1044731.1044734}, author = {Ross,Robert and V.S. Subrahmanian and Grant,John} } @conference {12650, title = {An algebraic approach to surface reconstruction from gradient fields}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {1}, year = {2005}, month = {2005/10//}, pages = {174 - 181 Vol. 1 - 174 - 181 Vol. 1}, abstract = {Several important problems in computer vision such as shape from shading (SFS) and photometric stereo (PS) require reconstructing a surface from an estimated gradient field, which is usually non-integrable, i.e. have non-zero curl. We propose a purely algebraic approach to enforce integrability in discrete domain. We first show that enforcing integrability can be formulated as solving a single linear system Ax =b over the image. In general, this system is under-determined. We show conditions under which the system can be solved and a method to get to those conditions based on graph theory. The proposed approach is non-iterative, has the important property of local error confinement and can be applied to several problems. Results on SFS and PS demonstrate the applicability of our method.}, keywords = {algebra;, algebraic, approach;, Computer, confinement;, discrete, domain, error, field;, from, gradient, graph, image, integrability;, linear, local, methods;, photometric, reconstruction;, shading;, SHAPE, stereo;, surface, system;, theory;, vision;}, doi = {10.1109/ICCV.2005.31}, author = {Agrawal,A. and Chellapa, Rama and Raskar, R.} } @article {12813, title = {An Algebraic Theory Of Boundary Crossing Transitions}, journal = {Electronic Notes in Theoretical Computer Science}, volume = {115}, year = {2005}, month = {2005/01/18/}, pages = {69 - 88}, abstract = {This paper gives a process-algebraic semantics for the hierarchical state machine (HSM) fragment of Statecharts, in which state transitions are permitted to cross state boundaries. Although frowned upon by researchers as promoting unstructured modeling, such transitions are used extensively in practice to model parameterized start states and conditional exit states. The purpose of this work is to develop a compositional semantics for HSMs that may be fit together with compositional semantic accounts for Statecharts without boundary-crossing transitions in order to arrive at a compositional theory for virtually the whole Statecharts language. Our technical development consists of a process algebra for HSMs that is equipped with an operational semantics, an argument that bisimulation is a congruence for the algebra, a syntax-directed translation procedure for HSMs into the process algebra, and an equational axiomatization of the algebra.}, keywords = {Compositional Semantics, Formal Methods, Process algebra, Statecharts}, isbn = {1571-0661}, doi = {10.1016/j.entcs.2004.09.029}, url = {http://www.sciencedirect.com/science/article/pii/S1571066104053186}, author = {Ray,Arnab and Cleaveland, Rance and Skou,Arne} } @conference {14024, title = {Approximate expressions for the mean and the covariance of the maximum likelihood estimator for acoustic source localization}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {3}, year = {2005}, month = {2005/03//}, pages = {iii/73 - iii/76 Vol. 3 - iii/73 - iii/76 Vol. 3}, abstract = {Acoustic source localization using multiple microphones can be formulated as a maximum likelihood estimation problem. The estimator is implicitly defined as the minimum of a certain objective function. As a result, we cannot get explicit expressions for the mean and the covariance of the estimator. We derive approximate expressions for the mean vector and covariance matrix of the estimator using Taylor{\textquoteright}s series expansion of the implicitly defined estimator. The validity of our expressions is verified by Monte-Carlo simulations. We also study the performance of the estimator for different microphone array configurations.}, keywords = {(mathematics);, acoustic, approximate, approximation, array, array;, covariance, estimation;, expansion;, expressions;, function;, likelihood, localization;, matrices;, matrix;, maximum, mean, microphone, objective, processing;, series, signal, source, Taylor, theory;, vector;, vectors;}, doi = {10.1109/ICASSP.2005.1415649}, author = {Raykar,V.C. and Duraiswami, Ramani} } @inbook {19486, title = {Architecting and Implementing Versatile Dependability}, booktitle = {Architecting Dependable Systems III}, series = {Lecture Notes in Computer Science}, year = {2005}, month = {2005/01/01/}, pages = {212 - 231}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Distributed applications must often consider and select the appropriate trade-offs among three important aspects {\textendash} fault-tolerance, performance and resources. We introduce a novel concept, called versatile dependability, that provides a framework for analyzing and reasoning about these trade-offs in dependable software architectures. We present the architecture of a middleware framework that implements versatile dependability by providing the appropriate {\textquotedblright}knobs{\textquotedblright} to tune and re-calibrate the trade-offs. Our framework can adjust the properties and the behavior of the system at development-time, at deployment-time, and throughout the application{\textquoteright}s life-cycle. This renders the versatile dependability approach useful both to applications that require static fault-tolerance configurations supporting the loss/addition of resources and changing workloads, as well as to applications that evolve in terms of their dependability requirements. Through a couple of specific examples, one on adapting the replication style at runtime and the other on tuning the system scalability under given constraints, we demonstrate concretely how versatile dependability can provide an extended coverage of the design space of dependable distributed systems.}, keywords = {Operating systems, software engineering}, isbn = {978-3-540-28968-5, 978-3-540-31648-0}, url = {http://link.springer.com/chapter/10.1007/11556169_10}, author = {Tudor Dumitras and Srivastava, Deepti and Narasimhan, Priya}, editor = {Lemos, Rog{\'e}rio de and Gacek, Cristina and Romanovsky, Alexander} } @article {12656, title = {Background learning for robust face recognition with PCA in the presence of clutter}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/06//}, pages = {832 - 843}, abstract = {We propose a new method within the framework of principal component analysis (PCA) to robustly recognize faces in the presence of clutter. The traditional eigenface recognition (EFR) method, which is based on PCA, works quite well when the input test patterns are faces. However, when confronted with the more general task of recognizing faces appearing against a background, the performance of the EFR method can be quite poor. It may miss faces completely or may wrongly associate many of the background image patterns to faces in the training set. In order to improve performance in the presence of background, we argue in favor of learning the distribution of background patterns and show how this can be done for a given test image. An eigenbackground space is constructed corresponding to the given test image and this space in conjunction with the eigenface space is used to impart robustness. A suitable classifier is derived to distinguish nonface patterns from faces. When tested on images depicting face recognition in real situations against cluttered background, the performance of the proposed method is quite good with fewer false alarms.}, keywords = {Automated;Principal Component Analysis;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Biological;Models, Computer-Assisted;Information Storage and Retrieval;Models, Computer-Assisted;Subtraction Technique;, PCA;background learning;clutter;eigenface recognition method;face recognition;linear discriminant;principal component analysis;clutter;eigenvalues and eigenfunctions;face recognition;learning (artificial intelligence);principal component analysis;Algorith, Statistical;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.847288}, author = {Rajagopalan, AN and Chellapa, Rama and Koterba, N.T.} } @article {14423, title = {Bayesian network learning with abstraction hierarchies and context-specific independence}, journal = {Machine Learning: ECML 2005}, year = {2005}, month = {2005///}, pages = {485 - 496}, abstract = {Context-specific independence representations, such as tree-structured conditional probability tables (TCPTs), reduce the number of parameters in Bayesian networks by capturing local independence relationships and improve the quality of learned Bayesian networks. We previously presented Abstraction-Based Search (ABS), a technique for using attribute value hierarchies during Bayesian network learning to remove unimportant distinctions within the CPTs. In this paper, we introduce TCPT ABS (TABS), which integrates ABS with TCPT learning. Since expert-provided hierarchies may not be available, we provide a clustering technique for deriving hierarchies from data. We present empirical results for three real-world domains, finding that (1) combining TCPTs and ABS provides a significant increase in the quality of learned Bayesian networks (2) combining TCPTs and ABS provides a dramatic reduction in the number of parameters in the learned networks, and (3) data-derived hierarchies perform as well or better than expert-provided hierarchies.}, doi = {10.1007/11564096_46}, author = {desJardins, Marie and Rathod,P. and Getoor, Lise} } @article {16696, title = {The Bible and multilingual optical character recognition}, journal = {Communications of the ACM}, volume = {48}, year = {2005}, month = {2005///}, pages = {124 - 130}, author = {Kanungo,T. and Resnik, Philip and Mao,S. and Kim,D.W. and Zheng,Q.} } @article {18939, title = {Bootstrapping parsers via syntactic projection across parallel texts}, journal = {Nat. Lang. Eng.}, volume = {11}, year = {2005}, month = {2005/09//}, pages = {311 - 325}, abstract = {Broad coverage, high quality parsers are available for only a handful of languages. A prerequisite for developing broad coverage parsers for more languages is the annotation of text with the desired linguistic representations (also known as {\textquotedblleft}treebanking{\textquotedblright}). However, syntactic annotation is a labor intensive and time-consuming process, and it is difficult to find linguistically annotated text in sufficient quantities. In this article, we explore using parallel text to help solving the problem of creating syntactic annotation in more languages. The central idea is to annotate the English side of a parallel corpus, project the analysis to the second language, and then train a stochastic analyzer on the resulting noisy annotations. We discuss our background assumptions, describe an initial study on the {\textquotedblleft}projectability{\textquotedblright} of syntactic relations, and then present two experiments in which stochastic parsers are developed with minimal human intervention via projection from English.}, isbn = {1351-3249}, doi = {10.1017/S1351324905003840}, url = {http://dx.doi.org/10.1017/S1351324905003840}, author = {Hwa,Rebecca and Resnik, Philip and Weinberg, Amy and Cabezas,Clara and Kolak,Okan} } @article {18928, title = {Breaking the resource bottleneck for multilingual parsing}, year = {2005}, month = {2005///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We propose a framework that enables the acquisition of annotation-heavy resources such as syntacfic dependency tree corpora for low-resource languages by importing linguistic annotations from high-quality English resources. We present a large-scale experiment showing that Chinese dependency trees can be induced by using an English parser, a word alignment package, and a large corpus of sentence-aligned bilingual text. As a part of the experiment, we evaluate the quality of a Chinese parser trained on the induced dependency treebank. We find that a parser trained in this manner out-performs some simple baselines inspite of the noise in the induced treebank. The results suggest that projecting syntactic structures from English is a viable option for acquiring annotated syntactic structures quickly and cheaply. We expect the quality of the induced treebank to improve when more sophisticated filtering and error-correction techniques are applied.}, url = {http://oai.dtic.mil/oai/oai?verb=getRecord\&metadataPrefix=html\&identifier=ADA440432}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy} } @conference {14460, title = {Capital and benefit in social networks}, booktitle = {Proceedings of the 3rd international workshop on Link discovery}, series = {LinkKDD {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {44 - 51}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Recently there has been a surge of interest in social networks. Email traffic, disease transmission, and criminal activity can all be modeled as social networks. In this paper, we introduce a particular form of social network which we call a friendship-event network. A friendship-event network describes two inter-related networks. One is a friendship network among a set of actors. The other is an event network that describes events, event organizers and event participants. Within these types of networks, we formulate the notion of capital based on the actor-organizer friendship relationship and the notion of benefit, based on event participation. We ground these definitions in a real-world example of academic collaboration networks, where the actors are researchers, the friendships are collaborations, the events are conferences, the organizers are program committee members and the participants are conference authors. We incorporate a temporal component by considering the notion of an event series. We explore the use of these measures on a data set describing three computer science conferences over the past ten years.}, isbn = {1-59593-215-1}, doi = {10.1145/1134271.1134278}, url = {http://doi.acm.org/10.1145/1134271.1134278}, author = {Licamele,Louis and Bilgic,Mustafa and Getoor, Lise and Roussopoulos, Nick} } @article {16593, title = {Collective-movement teams for cooperative problem solving}, journal = {Integrated Computer-Aided Engineering}, volume = {12}, year = {2005}, month = {2005///}, pages = {217 - 235}, author = {Rodr{\'\i}guez,A. and Reggia, James A.} } @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} } @article {17030, title = {Content Index to Volume 18}, journal = {INTERNATIONAL JOURNAL OF HUMAN{\textendash}COMPUTER INTERACTION}, volume = {18}, year = {2005}, month = {2005///}, pages = {367 - 368}, author = {Kuniavsky,M. and Vaughan,M. and Bederson, Benjamin B. and Shneiderman, Ben and Rau,P.L.P. and from Menus,T. and Lane,D.M. and Napier,H.A. and Peres,S.C. and S{\'a}ndor,A.} } @mastersthesis {16438, title = {Controlled observations of the genetic algorithm in a changing environment: case studies using the shaky ladder hyperplane-defined functions}, year = {2005}, month = {2005///}, school = {The University of Michigan}, author = {Rand, William} } @conference {16482, title = {A data model and query language to explore enhanced links and paths in life science sources}, booktitle = {Proceedings of the ACM SIGMOD Workshop on The Web and Databases (WebDB)}, year = {2005}, month = {2005///}, author = {Mihaila,G. and Naumann,F. and Raschid, Louiqa and Vidal,M. E} } @conference {18560, title = {Design and implementation of a routing control platform}, booktitle = {Proceedings of the 2nd conference on Symposium on Networked Systems Design \& Implementation - Volume 2}, series = {NSDI{\textquoteright}05}, year = {2005}, month = {2005///}, pages = {15 - 28}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {The routers in an Autonomous System (AS) must distribute the information they learn about how to reach external destinations. Unfortunately, today{\textquoteright}s internal Border Gateway Protocol (iBGP) architectures have serious problems: a "full mesh" iBGP configuration does not scale to large networks and "route reflection" can introduce problems such as protocol oscillations and persistent loops. Instead, we argue that a Routing Control Platform (RCP) should collect information about external destinations and internal topology and select the BGP routes for each router in an AS. RCP is a logically-centralized platform, separate from the IP forwarding plane, that performs route selection on behalf of routers and communicates selected routes to the routers using the unmodified iBGP protocol. RCP provides scalability without sacrificing correctness. In this paper, we present the design and implementation of an RCP prototype on commodity hardware. Using traces of BGP and internal routing data from a Tier-1 backbone, we demonstrate that RCP is fast and reliable enough to drive the BGP routing decisions for a large network. We show that RCP assigns routes correctly, even when the functionality is replicated and distributed, and that networks using RCP can expect comparable convergence delays to those using today{\textquoteright}s iBGP architectures.}, url = {http://dl.acm.org/citation.cfm?id=1251203.1251205}, author = {Caesar,Matthew and Caldwell,Donald and Feamster, Nick and Rexford,Jennifer and Shaikh,Aman and van der Merwe,Jacobus} } @conference {19032, title = {Detection of denial-of-message attacks on sensor network broadcasts}, year = {2005}, month = {2005}, pages = {64 - 78}, abstract = {So far sensor network broadcast protocols assume a trustworthy environment. However in safety and mission-critical sensor networks this assumption may not be valid and some sensor nodes might be adversarial. In these environments, malicious sensor nodes can deprive other nodes from receiving a broadcast message. We call this attack a denial-of-message attack (DoM). In this paper we model and analyze this attack, and present countermeasures. We present SIS, a secure implicit sampling scheme that permits a broadcasting base station to probabilistically detect the failure of nodes to receive its broadcast, even if these failures result from an attacker motivated to induce these failures undetectably. SIS works by eliciting authenticated acknowledgments from a subset of nodes per broadcast, where the subset is unpredictable to the attacker and tunable so as to mitigate acknowledgment implosion on the base station. We use a game-theoretic approach to evaluate this scheme in the face of an optimal attacker that attempts to maximize the number of nodes it denies the broadcast while remaining undetected by the base station, and show that SIS significantly constrains such an attacker even in sensor networks exhibiting high intrinsic loss rates. We also discuss extensions that permit more targeted detection capabilities.}, keywords = {authenticated acknowledgments, broadcast channels, broadcast protocols, broadcasting base station, countermeasures, denial-of-message attacks, DoM, game theory, game-theoretic approach, malicious sensor nodes, Mobile computing, optimal attacker, probabilistic detection, probability, Protocols, Sampling methods, secure implicit sampling, sensor network broadcasts, SIS, telecommunication security, Wireless sensor networks}, author = {McCune, J.M. and Elaine Shi and Perrig, A. and Reiter, M.K.} } @article {17079, title = {Determining Causes and Severity of End-User Frustration (2002)}, year = {2005}, month = {2005///}, abstract = {While computers are beneficial to individuals and society, frequently, users encounter frustrating experiences when using computers. This study attempts to measure, through 111 participants, the frequency, cause, and the level of severity of frustrating experiences. The data showed that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47-53\% of time spent on a computer depending on the location and study method. After discarding extreme cases the time lost was still above 38\%. These disturbing results should be a basis for future study.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6493}, author = {Ceaparu,Irina and Lazar,Jonathan and Bessiere,Katie and Robinson,John and Shneiderman, Ben} } @conference {16558, title = {Diagnostic problem solving using swarm intelligence}, booktitle = {Swarm Intelligence Symposium, 2005. SIS 2005. Proceedings 2005 IEEE}, year = {2005}, month = {2005///}, pages = {365 - 372}, author = {Lapizco-Encinas,G. C and Reggia, James A.} } @article {15869, title = {Dictionary-based cross-language retrieval}, journal = {Information Processing and Management}, volume = {41}, year = {2005}, month = {2005///}, pages = {523 - 547}, author = {Levow,G.A. and Oard, Douglas and Resnik, Philip} } @article {16689, title = {Dictionary-based techniques for cross-language information retrieval}, journal = {Information Processing \& Management}, volume = {41}, year = {2005}, month = {2005/05//}, pages = {523 - 547}, abstract = {Cross-language information retrieval (CLIR) systems allow users to find documents written in different languages from that of their query. Simple knowledge structures such as bilingual term lists have proven to be a remarkably useful basis for bridging that language gap. A broad array of dictionary-based techniques have demonstrated utility, but comparison across techniques has been difficult because evaluation results often span only a limited range of conditions. This article identifies the key issues in dictionary-based CLIR, develops unified frameworks for term selection and term translation that help to explain the relationships among existing techniques, and illustrates the effect of those techniques using four contrasting languages for systematic experiments with a uniform query translation architecture. Key results include identification of a previously unseen dependence of pre- and post-translation expansion on orthographic cognates and development of a query-specific measure for translation fanout that helps to explain the utility of structured query methods.}, keywords = {Cross-language information retrieval, Dictionary-based translation, Ranked retrieval}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2004.06.012}, url = {http://www.sciencedirect.com/science/article/pii/S0306457304000810}, author = {Levow,Gina-Anne and Oard, Douglas and Resnik, Philip} } @article {18699, title = {Diverse polyubiquitin interaction properties of ubiquitin-associated domains}, journal = {Nature Structural \& Molecular Biology}, volume = {12}, year = {2005}, month = {2005///}, pages = {708 - 714}, abstract = {The ubiquitin-associated (UBA) domain occurs frequently in proteins involved in ubiquitin-dependent signaling pathways. Although polyubiquitin chain binding is considered to be a defining feature of the UBA domain family, the generality of this property has not been established. Here we have surveyed the polyubiquitin interaction properties of 30 UBA domains, including 16 of 17 occurrences in budding yeast. The UBA domains sort into four classes that include linkage-selective polyubiquitin binders and domains that bind different chains (and monoubiquitin) in a nondiscriminatory manner; one notable class (30\%) did not bind any ubiquitin ligand surveyed. The properties of a given UBA domain are conserved from yeast to mammals. Their functional relevance is further suggested by the ability of an ectopic UBA domain to alter the specificity of a deubiquitylating enzyme in a predictable manner. Conversely, non-UBA sequences can modulate the interaction properties of a UBA domain.}, keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation}, isbn = {1545-9993}, doi = {10.1038/nsmb962}, url = {http://www.nature.com/nsmb/journal/v12/n8/full/nsmb962.html}, author = {Raasi,Shahri and Varadan,Ranjani and Fushman, David and Pickart,Cecile M.} } @article {14680, title = {Dynamic inference of polymorphic lock types}, journal = {Science of Computer Programming}, volume = {58}, year = {2005}, month = {2005/12//}, pages = {366 - 383}, abstract = {We present FindLocks, an approach for automatically proving the absence of data races in multi-threaded Java programs, using a combination of dynamic and static analysis. The program in question is instrumented so that when executed it will gather information about locking relationships. This information is then used to automatically generate annotations needed to type check the program using the Race-Free Java type system. Programs that type check are sure to be free from races. We call this technique dynamic annotation inference. We describe the design and implementation of our approach, and our experience applying the tool to a variety of Java programs. We have found that when using a reasonably comprehensive test suite, which is easy for small programs but harder for larger ones, the approach generates useful annotations.}, keywords = {Data races, Dynamic analysis, java, Multithreading, Type inference}, isbn = {0167-6423}, doi = {10.1016/j.scico.2005.03.003}, url = {http://www.sciencedirect.com/science/article/pii/S0167642305000705}, author = {Rose,James and Swamy,Nikhil and Hicks, Michael W.} } @article {16295, title = {An empirical study of regression test application frequency}, journal = {Software Testing, Verification and Reliability}, volume = {15}, year = {2005}, month = {2005///}, pages = {257 - 279}, author = {Kim,J. M and Porter, Adam and Rothermel,G.} } @article {16613, title = {Evolutionary discovery of arbitrary self-replicating structures}, journal = {Computational Science{\textendash}ICCS 2005}, year = {2005}, month = {2005///}, pages = {404 - 411}, author = {PAN,Z. and Reggia, James A.} } @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.} } @article {16516, title = {Evolving processing speed asymmetries and hemispheric interactions in a neural network model}, journal = {Neurocomputing}, volume = {65}, year = {2005}, month = {2005///}, pages = {47 - 53}, author = {Grushin,A. and Reggia, James A.} } @article {16389, title = {EvoSTOC Contributions}, journal = {Applications of evolutionary computing: EvoWorkshops 2005, EvoBIO, EvoCOMNET, EvoHOT, EvoIASP, EvoMUSART, and EvoSTOC}, year = {2005}, month = {2005///}, author = {Merkle,D. and Middendorf,M. and Scheidler,A. and Avigad,G. and Moshaiov,A. and Brauner,N. and Parsopoulos,K.E. and Vrahatis,M.N. and Rand, William and Riolo,R} } @conference {12071, title = {Exploiting partially overlapping channels in wireless networks: Turning a peril into an advantage}, booktitle = {Proceedings of the 5th ACM SIGCOMM conference on Internet Measurement}, year = {2005}, month = {2005///}, pages = {29 - 29}, author = {Mishra,A. and Rozner,E. and Banerjee,S. and Arbaugh, William A.} } @article {14028, title = {Extracting the frequencies of the pinna spectral notches in measured head related impulse responses}, journal = {The Journal of the Acoustical Society of America}, volume = {118}, year = {2005}, month = {2005///}, pages = {364 - 374}, abstract = {The head related impulse response (HRIR) characterizes the auditory cues created by scattering of sound off a person{\textquoteright}s anatomy. The experimentally measured HRIR depends on several factors such as reflections from body parts (torso, shoulder, and knees), head diffraction, and reflection/diffraction effects due to the pinna. Structural models (Algazi et al., 2002; Brown and Duda, 1998) seek to establish direct relationships between the features in the HRIR and the anatomy. While there is evidence that particular features in the HRIR can be explained by anthropometry, the creation of such models from experimental data is hampered by the fact that the extraction of the features in the HRIR is not automatic. One of the prominent features observed in the HRIR, and one that has been shown to be important for elevation perception, are the deep spectral notches attributed to the pinna. In this paper we propose a method to robustly extract the frequencies of the pinna spectral notches from the measured HRIR, distinguishing them from other confounding features. The method also extracts the resonances described by Shaw (1997). The techniques are applied to the publicly available CIPIC HRIR database (Algazi et al., 2001c). The extracted notch frequencies are related to the physical dimensions and shape of the pinna.}, keywords = {acoustic wave reflection, acoustic wave scattering, anthropometry, Ear, hearing, physiological models}, doi = {10.1121/1.1923368}, url = {http://link.aip.org/link/?JAS/118/364/1}, author = {Raykar,Vikas C. and Duraiswami, Ramani and Yegnanarayana,B.} } @conference {16793, title = {A fast approximation scheme for probabilistic wavelet synopses}, booktitle = {Proceedings of the 17th International Conference on Scientific and Statistical Database Management (SSDBM)}, year = {2005}, month = {2005///}, author = {Deligiannakis,A. and Garofalakis,M. and Roussopoulos, Nick} } @article {14018, title = {Fast Computation of Sums of Gaussians in High Dimensions}, journal = {Technical Reports from UMIACS UMIACS-TR-2005-69}, year = {2005}, month = {2005/11/15/T19:2}, abstract = {Evaluating sums of multivariate Gaussian kernels is a key computational task in many problems in computational statistics andmachine learning. The computational cost of the direct evaluation of such sums scales as the product of the number of kernel functions and the evaluation points. The fast Gauss transform proposed by Greengard and Strain (1991) is a $\epsilon$-exact approximation algorithm that reduces the computational complexity of the evaluation of the sum of $N$ Gaussians at $M$ points in $d$ dimensions from $\mathcal{O}(MN)$ to $\mathcal{O}(M+N)$. However, the constant factor in $\mathcal{O}(M+N)$ grows exponentially with increasing dimensionality $d$, which makes the algorithm impractical for dimensions greater than three. In this paper we present a new algorithm where the constant factor is reduced to asymptotically polynomial order. The reduction is based on a new multivariate Taylor{\textquoteright}s series expansion (which can act both as a local as well as a far field expansion) scheme combined with the efficient space subdivision using the $k$-center algorithm. The proposed method differs from the original fast Gauss transform in terms of a different factorization, efficient space subdivision, and the use of point-wise error bounds. Algorithm details, error bounds, procedure to choose the parameters and numerical experiments are presented. As an example we shows how the proposed method can be used for very fast $\epsilon$-exact multivariate kernel density estimation. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3020}, author = {Raykar,Vikas Chandrakant and Yang,Changjaing and Duraiswami, Ramani and Gumerov, Nail A.} } @article {12969, title = {A framework for set-oriented computation in inductive logic programming and its application in generalizing inverse entailment}, journal = {Inductive Logic Programming}, year = {2005}, month = {2005///}, pages = {69 - 86}, author = {Corrada Bravo, Hector and Page,D. and Ramakrishnan,R. and Shavlik,J. and Costa,V. S} } @article {12674, title = {Gait-based human identification using appearance matching}, journal = {Optical and Digital Techniques for Information Security}, year = {2005}, month = {2005///}, pages = {271 - 295}, abstract = {In this chapter, we present an appearance-based approach for recognizing human gait. Given the gait video of an individual, the images are binarized and the width of the outer contour of the silhouette of that individual is obtained for each image frame. Several gait features are derived from this basic width vector. Temporally ordered sequences of the feature vectors are then used to represent the gait of a person. While matching the feature templates for recognition, dynamic time-warping (DTW), which is a nonlinear time-normalization technique, is used to deal with naturally occurring changes in the walking speeds of individuals. The performance of the proposed method is tested on indoor as well as outdoor gait databases, and the efficacy of different gait features and their noise resilience is studied. The experiments also demonstrate the effect of change in the viewing angle and frame rate of data capture on the accuracy of gait recognition.}, author = {Kale, A. and Cuntoor, N. and Yegnanarayana,B. and Rajagopalan, A. and Chellapa, Rama} } @article {14092, title = {The genome of the African trypanosome Trypanosoma brucei}, journal = {Science}, volume = {309}, year = {2005}, month = {2005///}, pages = {416 - 416}, author = {Berriman,M. and Ghedin,E. and Hertz-Fowler,C. and Blandin,G. and Renauld,H. and Bartholomeu,D. C and Lennard,N. J and Caler,E. and Hamlin,N. E and Haas,B. and others} } @article {19077, title = {The genome of the protist parasite Entamoeba histolytica}, journal = {Nature}, volume = {433}, year = {2005}, month = {2005}, pages = {865 - 868}, author = {Loftus,B. and Anderson,I. and Davies,R. and Alsmark,U. C.M and Samuelson,J. and Amedeo,P. and Roncaglia,P. and Berriman,M. and Hirt,R. P and Mann,B. J and others} } @article {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} } @conference {17794, title = {A graph theoretical foundation for integrating RDF ontologies}, booktitle = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {20}, year = {2005}, month = {2005///}, pages = {1442 - 1442}, abstract = {RDF ontologies are rapidly increasing in number. We studythe problem of integrating two RDF ontologies under a given set H of Horn clauses that specify semantic relationships be- tween terms in the ontology, as well as under a given set of negative constraints. We formally define the notion of a {\textquotedblleft}wit- ness{\textquotedblright} to the integrability of two RDF ontologies under such constraints. A witness represents a way of integrating the ontologies together. We define a {\textquotedblleft}minimal{\textquotedblright} witnesses and provide the polynomial CROW (Computing RDF Ontology Witness) algorithm to find a witness. We report on the per- formance of CROW both on DAML, SchemaWeb and Onto- Broker ontologies as well as on synthetically generated data. The experiments show that CROW works very well on real- life ontologies and scales to massive ontologies. }, author = {Udrea,O. and Deng,Y. and Ruckhaus,E. and V.S. Subrahmanian} } @article {17187, title = {Help! I{\textquoteright}m Lost: User Frustration in Web Navigation (2003)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {Computers can be valuable tools, and networked resources via the Internet can be beneficial to many different populations and communities. Unfortunately, when people are unable to reach their task goals due to frustrating experiences, this can hinder the effectiveness of technology. This research summary provides information about the user frustration research that has been performed at the University of Maryland and Towson University. Causes of user frustration are discussed in this research summary, along with the surprising finding that nearly one-third to one-half of the time spent in front of the computer is wasted due to frustrating experiences. Furthermore, when interfaces are planned to be deceptive and confusing, this}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6508}, author = {Lazar,Jonathan and Bessiere,Katie and Ceaparu,Irina and Robinson,John and Shneiderman, Ben} } @conference {16668, title = {The Hiero machine translation system: Extensions, evaluation, and analysis}, booktitle = {Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing}, year = {2005}, month = {2005///}, pages = {779 - 786}, author = {Chiang,D. and Lopez,A. and Madnani,N. and Monz,C. and Resnik, Philip and Subotin,M.} } @article {13927, title = {How do I find blue books about dogs? The errors and frustrations of young digital library users}, journal = {Proceedings of HCII 2005}, year = {2005}, month = {2005///}, author = {Hutchinson,H. and Druin, Allison and Bederson, Benjamin B. and Reuter,K. and Rose,A. and Weeks,A. C} } @article {15155, title = {Identity-based zero-knowledge}, journal = {Security in Communication Networks}, year = {2005}, month = {2005///}, pages = {180 - 192}, abstract = {We introduce and define the notion of identity-based zero-knowledge, concentrating on the non-interactive setting. In this setting, our notion allows any prover to widely disseminate a proof of a statement while protecting the prover from plagiarism in the following sense: although proofs are transferable (i.e., publicly verifiable), they are also bound to the identity of the prover in a way which is recognizable to any verifier. Furthermore, an adversary is unable to change this identity (i.e., to claim the proof as his own, or to otherwise change the authorship), unless he could have proved the statement on his own.While we view the primary contribution of this work as a formal definition of the above notion, we also explore the relation of this notion to that of non-malleable (non-interactive) zero-knowledge. On the one hand, we show that these two notions are incomparable: that is, there are proof systems which are non-malleable but not identity-based, and vice versa. On the other hand, we show that a proof system of either type essentially implies a proof system of the other type. }, doi = {10.1007/978-3-540-30598-9_13}, author = {Katz, Jonathan and Ostrovsky,R. and Rabin,M.} } @article {16107, title = {Immediate Usability: A Case Study of Public Access Design for a Community Photo Library (2003)}, year = {2005}, month = {2005///}, abstract = {This paper describes a novel instantiation of a digital photo library in a public access system. It demonstrates how designers can utilize characteristics of a target user community (social constraints, trust, and a lack of anonymity) to provide capabilities that would be impractical in other types of public access systems. It also presents a compact set of design principles and guidelines for ensuring the immediate usability of public access information systems. These principles and guidelines were derived from our experience developing PhotoFinder Kiosk, a community photo library. Attendees of a major HCI conference (CHI 2001 Conference on Human Factors in Computing Systems) successfully used the tool to browse and annotate collections of photographs spanning 20 years of HCI-related conferences, producing a richly annotated photo history of the field of human-computer interaction. Observations and log data were used to evaluate the tool and develop the guidelines. They provide specific guidance for practitioners, as well as a useful framework for additional research in public access interfaces.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6504}, author = {Kules,Bill and Kang,Hyunmo and Plaisant, Catherine and Rose,Anne and Shneiderman, Ben} } @article {16106, title = {Immediate Usability: Kiosk design principles from the CHI 2001 Photo Library (2001)}, year = {2005}, month = {2005///}, abstract = {This paper describes a novel set of design principles and guidelines for ensuring the immediate usability of public access systems. These principles and guidelines were formulated while developing PhotoFinder Kiosk, a community photo library. Attendees of CHI 2001 successfully used the tool to browse and annotate collections of photographs spanning 20 years of CHI and related conferences, producing a richly annotated photo history of the field of human-computer interaction. We used observations and log data to evaluate the tool and refine the guidelines. They provide specific guidance for practitioners, as well as a useful framework for additional research in public access interfaces.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6488}, author = {Kules,Bill and Kang,Hyunmo and Plaisant, Catherine and Rose,Anne and Shneiderman, Ben} } @conference {16676, title = {Improved HMM alignment models for languages with scarce resources}, booktitle = {Proceedings of the ACL Workshop on Building and Using Parallel Texts}, year = {2005}, month = {2005///}, pages = {83 - 86}, author = {Lopez,A. and Resnik, Philip} } @conference {13920, title = {The International Children{\textquoteright}s Digital Library: A Case Study in Designing for a MultiLingual}, booktitle = {Multi-Cultural, Multi-Generational Audience. Information Technology and Libraries}, year = {2005}, month = {2005///}, author = {Hutchinson,H.B. and Rose,A. and Bederson, Benjamin B. and Weeks,A. C and Druin, Allison} } @article {13806, title = {Johns Hopkins summer workshop final report on parsing and spoken structural event detection}, journal = {Johns Hopkins University, Tech. Rep}, year = {2005}, month = {2005///}, abstract = {This report describes research conducted by the Parsing and Spoken Structural Event Detection(PaSSED) team as part of the 2005 Johns Hopkins Summer Workshop on Language Engineering. This project investigated the interaction between parsing and the detection of structural metadata in conversational speech, including sentence boundaries, edits (the reparandum portion of speech repairs), and fillers. In terms of parsing, we explored alternative methods of exploiting metadata information in parsing models and measured how varying accuracy in transcription and metadata information affects parsing accuracy. In the other direction, we similarly considered how syntactic and prosodic knowledge could be leveraged in metadata detection, measuring how this knowledge impacts metadata detection accuracy. As part of this work, we investigated metrics for evaluating parse accuracy in the presence of tran- scription and metadata detection errors, and we report on our experience using these metrics with several parsers and across varying experimental conditions. A range of methods for handling edits during pars- ing were evaluated in this research (excision, addition of markups to the input string, and grammar modification). We also developed a ToBI (a prosodic structure annotation scheme [SBP+92]) prosodic event classifier and describe its evaluation. Finally, we present methods for effective n-best sentence boundary candidate generation and reranking using syntactic, prosodic, and other features. These stud- ies are complemented by a second set of reranking investigations wherein we optimize sentence boundary detection explicitly to improve parse accuracy. The PaSSED project has: {\textbullet} investigated various techniques to enhance parsing of speech given metadata detection on conver- sational speech; {\textbullet} defined metrics for evaluating speech parsing accuracy, implemented them in the publically avail- able SParseval software package, and evaluated them under a wide variety of conditions; {\textbullet} recast SU detection as an n-best reranking problem with a relatively small n. Using this approach, we demonstrated significant improvements over a very strong baseline SU detection system. {\textbullet} reported on the interaction between parsing and metadata detection and their synergy; {\textbullet} fostered new collaborations and identified a number of interesting avenues for future work. }, author = {Harper,MP and Dorr, Bonnie J and Hale,J. and Roark,B. and Shafran,I. and Lease,M. and Liu,Y. and Snover,M. and Yung,L. and Krasnyanskaya,A.} } @inbook {16931, title = {A Knowledge Integration Framework for Information Visualization}, booktitle = {From Integrated Publication and Information Systems to Information and Knowledge EnvironmentsFrom Integrated Publication and Information Systems to Information and Knowledge Environments}, series = {Lecture Notes in Computer Science}, volume = {3379}, year = {2005}, month = {2005///}, pages = {207 - 220}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Users can better understand complex data sets by combining insights from multiple coordinated visual displays that include relevant domain knowledge. When dealing with multidimensional data and clustering results, the most familiar displays and comprehensible are 1- and 2-dimensional projections (histograms, and scatterplots). Other easily understood displays of domain knowledge are tabular and hierarchical information for the same or related data sets. The novel parallel coordinates view [6] powered by a direct-manipulation search, offers strong advantages, but requires some training for most users. We provide a review of related work in the area of information visualization, and introduce new tools and interaction examples on how to incorporate users{\textquoteright} domain knowledge for understanding clustering results. Our examples present hierarchical clustering of gene expression data, coordinated with a parallel coordinates view and with the gene annotation and gene ontology.}, isbn = {978-3-540-24551-3}, url = {http://dx.doi.org/10.1007/978-3-540-31842-2_21}, author = {Seo,Jinwook and Shneiderman, Ben}, editor = {Hemmje,Matthias and Nieder{\'e}e,Claudia and Risse,Thomas} } @conference {16681, title = {The linguist{\textquoteright}s search engine: an overview}, booktitle = {Proceedings of the ACL 2005 on Interactive poster and demonstration sessions}, year = {2005}, month = {2005///}, pages = {33 - 36}, author = {Resnik, Philip and Elkiss,A.} } @conference {16734, title = {Maintaining Implicated Statistics in Constrained Environments}, booktitle = {Data Engineering, International Conference on}, year = {2005}, month = {2005///}, pages = {730 - 741}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Aggregated information regarding implicated entities is critical for online applications like network management, traffic characterization or identifying patters of resource consumption. Recently there has been a flurry of research for online aggregation on streams (like quantiles, hot items, hierarchical heavy hitters) but surprizingly the problem of summarizing implicated information in stream data has received no attention. As an example, consider an IP-network and the implication source {\textrightarrow} destination. Flash crowds, {\textemdash} such as those that follow recent sport events (like the olympics) or seek information regarding catastrophic events {\textemdash} or denial of service attacks direct a large volume of traffic from a huge number of sources to a very small number of destinations. In this paper we present novel randomized algorithms for monitoring such implications with constraints in both memory and processing power for environments like network routers. Our experiments demonstrate several factors of improvements over straightforward approaches.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDE.2005.84}, author = {Sismanis,Yannis and Roussopoulos, Nick} } @conference {14026, title = {The manifolds of spatial hearing}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {3}, year = {2005}, month = {2005/03//}, pages = {iii/285 - iii/288 Vol. 3 - iii/285 - iii/288 Vol. 3}, abstract = {We present exploratory studies on learning the non-linear manifold structure, in head related impulse responses (HRIRs). We use the recently popular locally linear embedding technique. The lower dimensional manifold encodes the perceptual information in the HRIRs, namely the direction of the sound source. Based on this, we propose a new method for HRIR interpolation. We also propose that the distance between two HRIRs of an individual be taken as the geodesic distance on the learned manifold.}, keywords = {acoustics;, dimensional, direction, distance;, EMBEDDING, encoding;, geodesic, Head, hearing, hearing;, HRIR, impulse, information, interpolation;, learned, linear, localization;, locally, low, manifold, manifold;, manifolds;, nonlinear, perceptual, related, response;, responses;, sound, source, spatial, structure;, technique;, transient}, doi = {10.1109/ICASSP.2005.1415702}, author = {Duraiswami, Ramani and Raykar,V.C.} } @article {12645, title = {Matching shape sequences in video with applications in human movement analysis}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {27}, year = {2005}, month = {2005/12//}, pages = {1896 - 1909}, abstract = {We present an approach for comparing two sequences of deforming shapes using both parametric models and nonparametric methods. In our approach, Kendall{\textquoteright}s definition of shape is used for feature extraction. Since the shape feature rests on a non-Euclidean manifold, we propose parametric models like the autoregressive model and autoregressive moving average model on the tangent space and demonstrate the ability of these models to capture the nature of shape deformations using experiments on gait-based human recognition. The nonparametric model is based on dynamic time-warping. We suggest a modification of the dynamic time-warping algorithm to include the nature of the non-Euclidean space in which the shape deformations take place. We also show the efficacy of this algorithm by its application to gait-based human recognition. We exploit the shape deformations of a person{\textquoteright}s silhouette as a discriminating feature and provide recognition results using the nonparametric model. Our analysis leads to some interesting observations on the role of shape and kinematics in automated gait-based person authentication.}, keywords = {Automated;Photography;Reproducibility of Results;Sensitivity and Specificity;Subtraction Technique;Video Recording;, autoregressive moving average model;deforming shapes;dynamic time-warping;feature extraction;gait-based human recognition;human movement analysis;matching shape sequences;video;autoregressive moving average processes;feature extraction;image matching;imag, Biological;Models, Computer-Assisted;Imaging, Statistical;Movement;Pattern Recognition, Three-Dimensional;Leg;Models}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2005.246}, author = {A,Veeraraghavan and Roy-Chowdhury, A.K. and Chellapa, Rama} } @article {19499, title = {MEAD: support for Real-Time Fault-Tolerant CORBA}, journal = {Concurrency and Computation: Practice and Experience}, volume = {17}, year = {2005}, month = {2005///}, pages = {1527 - 1545}, abstract = {The OMG{\textquoteright}s Real-Time CORBA (RT-CORBA) and Fault-Tolerant CORBA (FT-CORBA) specifications make it possible for today{\textquoteright}s CORBA implementations to exhibit either real-time or fault tolerance in isolation. While real-time requires a priori knowledge of the system{\textquoteright}s temporal operation, fault tolerance necessarily deals with faults that occur unexpectedly, and with possibly unpredictable fault recovery times. The MEAD (Middleware for Embedded Adaptive Dependability) system attempts to identify and to reconcile the conflicts between real-time and fault tolerance, in a resource-aware manner, for distributed CORBA applications. MEAD supports transparent yet tunable fault tolerance in real-time, proactive dependability, resource-aware system adaptation to crash, communication and timing faults with bounded fault detection and fault recovery. Copyright {\textcopyright} 2005 John Wiley \& Sons, Ltd.}, keywords = {CORBA, Fault tolerance, non-determinism, predictability, real-time, recovery, trade-offs}, isbn = {1532-0634}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cpe.882/abstract}, author = {Narasimhan, P. and Tudor Dumitras and Paulos, A. M. and Pertet, S. M. and Reverte, C. F. and Slember, J. G. and Srivastava, D.} } @conference {16420, title = {Measurements for understanding the behavior of the genetic algorithm in dynamic environments: a case study using the Shaky Ladder Hyperplane-Defined Functions}, booktitle = {Proceedings of the 2005 workshops on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {32 - 38}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe a set of measures to examine the behavior of the Genetic Algorithm (GA) in dynamic environments. We describe how to use both average and best measures to look at performance, satisficability, robustness, and diversity. We use these measures to examine GA behavior with a recently devised dynamic test suite, the Shaky Ladder Hyperplane-Defined Functions (sl-hdf{\textquoteright}s). This test suite can generate random problems with similar levels of difficulty and provides a platform allowing systematic controlled observations of the GA in dynamic environments. We examine the results of these measures in two different versions of the sl-hdf{\textquoteright}s, one static and one regularly-changing. We provide explanations for the observations in these two different environments, and give suggestions as to future work.}, keywords = {dynamic environments, Genetic algorithms, hyperplane-defined functions, measurement}, doi = {10.1145/1102256.1102263}, url = {http://doi.acm.org/10.1145/1102256.1102263}, author = {Rand, William and Riolo,Rick} } @conference {12659, title = {A method for converting a smiling face to a neutral face with applications to face recognition}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/03//}, pages = {ii/977 - ii/980 Vol. 2 - ii/977 - ii/980 Vol. 2}, abstract = {The human face displays a variety of expressions, like smile, sorrow, surprise, etc. All these expressions constitute nonrigid motions of various features of the face. These expressions lead to a significant change in the appearance of a facial image which leads to a drop in the recognition accuracy of a face-recognition system trained with neutral faces. There are other factors like pose and illumination which also lead to performance drops. Researchers have proposed methods to tackle the effects of pose and illumination; however, there has been little work on how to tackle expressions. We attempt to address the issue of expression invariant face-recognition. We present preprocessing steps for converting a smiling face to a neutral face. We expect that this would in turn make the vector in the feature space to be closer to the correct vector in the gallery, in an appearance-based face recognition. This conjecture is supported by our recognition results which demonstrate that the accuracy goes up if we include the expression-normalization block.}, keywords = {appearance-based, Expression, Face, face;, feature, invariant, motion;, neutral, nonrigid, normalization;, recognition;, smiling}, doi = {10.1109/ICASSP.2005.1415570}, author = {Ramachandran, M. and Zhou,S. K and Jhalani, D. and Chellapa, Rama} } @article {16646, title = {Mirror symmetric topographic maps can arise from activity-dependent synaptic changes}, journal = {Neural computation}, volume = {17}, year = {2005}, month = {2005///}, pages = {1059 - 1083}, author = {Schulz,R. and Reggia, James A.} } @conference {16675, title = {OCR post-processing for low density languages}, booktitle = {Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing}, year = {2005}, month = {2005///}, pages = {867 - 874}, author = {Kolak,O. and Resnik, Philip} } @article {16399, title = {Path dependence and the validation of agent-based spatial models of land use}, journal = {International Journal of Geographical Information Science}, volume = {19}, year = {2005}, month = {2005///}, pages = {153 - 174}, author = {Corresponding,D.G.B. and Page,S and Riolo,R and Zellner,M and Rand, William} } @article {16398, title = {Path dependence and the validation of agent-based spatial models of land use}, journal = {International Journal of Geographical Information Science}, volume = {19}, year = {2005}, month = {2005///}, pages = {153 - 174}, abstract = {In this paper, we identify two distinct notions of accuracy of land?use models and highlight a tension between them. A model can have predictive accuracy: its predicted land?use pattern can be highly correlated with the actual land?use pattern. A model can also have process accuracy: the process by which locations or land?use patterns are determined can be consistent with real world processes. To balance these two potentially conflicting motivations, we introduce the concept of the invariant region, i.e., the area where land?use type is almost certain, and thus path independent; and the variant region, i.e., the area where land use depends on a particular series of events, and is thus path dependent. We demonstrate our methods using an agent?based land?use model and using multi?temporal land?use data collected for Washtenaw County, Michigan, USA. The results indicate that, using the methods we describe, researchers can improve their ability to communicate how well their model performs, the situations or instances in which it does not perform well, and the cases in which it is relatively unlikely to predict well because of either path dependence or stochastic uncertainty.}, isbn = {1365-8816}, doi = {10.1080/13658810410001713399}, url = {http://www.tandfonline.com/doi/abs/10.1080/13658810410001713399}, author = {Brown,Daniel G. and Page,Scott and Riolo,Rick and Zellner,Moira and Rand, William} } @conference {13192, title = {Pedestrian classification from moving platforms using cyclic motion pattern}, booktitle = {Image Processing, 2005. ICIP 2005. IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/09//}, pages = {II - 854-7 - II - 854-7}, abstract = {This paper describes an efficient pedestrian detection system for videos acquired from moving platforms. Given a detected and tracked object as a sequence of images within a bounding box, we describe the periodic signature of its motion pattern using a twin-pendulum model. Then a principle gait angle is extracted in every frame providing gait phase information. By estimating the periodicity from the phase data using a digital phase locked loop (dPLL), we quantify the cyclic pattern of the object, which helps us to continuously classify it as a pedestrian. Past approaches have used shape detectors applied to a single image or classifiers based on human body pixel oscillations, but ours is the first to integrate a global cyclic motion model and periodicity analysis. Novel contributions of this paper include: i) development of a compact shape representation of cyclic motion as a signature for a pedestrian, ii) estimation of gait period via a feedback loop module, and iii) implementation of a fast online pedestrian classification system which operates on videos acquired from moving platforms.}, keywords = {analysis;, angle;, body, classification;, compact, cyclic, DETECTION, detection;, digital, Feedback, Gait, human, image, information;, locked, loop, loop;, loops;, module;, MOTION, object, oscillations;, pattern;, pedestrian, phase, Pixel, principle, representation;, sequence;, sequences;, SHAPE, system;}, doi = {10.1109/ICIP.2005.1530190}, author = {Yang Ran and Qinfen Zheng and Weiss, I. and Davis, Larry S. and Abd-Almageed, Wael and Liang Zhao} } @conference {11908, title = {Pedestrian classification from moving platforms using cyclic motion pattern}, booktitle = {IEEE International Conference on Image Processing, 2005. ICIP 2005}, volume = {2}, year = {2005}, month = {2005/09//}, pages = {II- 854-7 - II- 854-7}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper describes an efficient pedestrian detection system for videos acquired from moving platforms. Given a detected and tracked object as a sequence of images within a bounding box, we describe the periodic signature of its motion pattern using a twin-pendulum model. Then a principle gait angle is extracted in every frame providing gait phase information. By estimating the periodicity from the phase data using a digital phase locked loop (dPLL), we quantify the cyclic pattern of the object, which helps us to continuously classify it as a pedestrian. Past approaches have used shape detectors applied to a single image or classifiers based on human body pixel oscillations, but ours is the first to integrate a global cyclic motion model and periodicity analysis. Novel contributions of this paper include: i) development of a compact shape representation of cyclic motion as a signature for a pedestrian, ii) estimation of gait period via a feedback loop module, and iii) implementation of a fast online pedestrian classification system which operates on videos acquired from moving platforms.}, keywords = {compact shape representation, cyclic motion pattern, data mining, Detectors, digital phase locked loop, digital phase locked loops, feedback loop module, gait analysis, gait phase information, human body pixel oscillations, HUMANS, image classification, Image motion analysis, image representation, image sequence, Image sequences, Motion detection, Object detection, pedestrian classification, pedestrian detection system, Phase estimation, Phase locked loops, principle gait angle, SHAPE, tracking, Videos}, isbn = {0-7803-9134-9}, doi = {10.1109/ICIP.2005.1530190}, author = {Yang Ran and Qinfen Zheng and Weiss, I. and Davis, Larry S. and Abd-Almageed, Wael and Liang Zhao} } @conference {16419, title = {The problem with a self-adaptative mutation rate in some environments: a case study using the shaky ladder hyperplane-defined functions}, booktitle = {Proceedings of the 2005 conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {1493 - 1500}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Dynamic environments have periods of quiescence and periods of change. In periods of quiescence a Genetic Algorithm (GA) should (optimally) exploit good individuals while in periods of change the GA should (optimally) explore new solutions. Self-adaptation is a mechanism which allows individuals in the GA to choose their own mutation rate, and thus allows the GA to control when it explores new solutions or exploits old ones. We examine the use of this mechanism on a recently devised dynamic test suite, the Shaky Ladder Hyperplane-Defined Functions (sl-hdf{\textquoteright}s). This test suite can generate random problems with similar levels of difficulty and provides a platform allowing systematic controlled observations of the GA in dynamic environments. We show that in a variety of circumstances self-adaptation fails to allow the GA to perform better on this test suite than fixed mutation, even when the environment is static. We also show that mutation is beneficial throughout the run of a GA, and that seeding a population with known good genetic material is not always beneficial to the results. We provide explanations for these observations, with particular emphasis on comparing our results to other results [2] which have shown the GA to work in static environments. We conclude by giving suggestions as to how to change the simple GA to solve these problems.}, keywords = {dynamic environments, Genetic algorithms, hyperplane-defined functions, self-adaptation}, isbn = {1-59593-010-8}, doi = {10.1145/1068009.1068245}, url = {http://doi.acm.org/10.1145/1068009.1068245}, author = {Rand, William and Riolo,Rick} } @conference {17890, title = {Query planning for the grid: adapting to dynamic resource availability}, booktitle = {Cluster Computing and the Grid, IEEE International Symposium on}, volume = {2}, year = {2005}, month = {2005///}, pages = {751 - 758}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {The availability of massive datasets, comprising sensor measurements or the results of scientific simulations, has had a significant impact on the methodology of scientific reasoning. Scientists require storage, bandwidth and computational capacity to query and analyze these datasets, to understand physical phenomena or to test hypotheses. This paper addresses the challenge of identifying and selecting resources to develop an evaluation plan for large scale data analysis queries when data processing capabilities and datasets are dispersed across nodes in one or more computing and storage clusters. We show that generating an optimal plan is hard and we propose heuristic techniques to find a good choice of resources. We also consider heuristics to cope with dynamic resource availability; in this situation we have stale information about reusable cached results (datasets) and the load on various nodes.}, isbn = {0-7803-9074-1}, doi = {http://doi.ieeecomputersociety.org/10.1109/CCGRID.2005.1558638}, author = {Zhang,K. and Andrade,H. and Raschid, Louiqa and Sussman, Alan} } @article {12663, title = {Recognition of Humans and Their Activities Using Video}, journal = {Synthesis Lectures on Image, Video, and Multimedia Processing}, volume = {1}, year = {2005}, month = {2005/01//}, pages = {1 - 173}, abstract = {The recognition of humans and their activities from video sequences is currently a very active area of research because of its applications in video surveillance, design of realistic entertainment systems, multimedia communications, and medical diagnosis. In this lecture, we discuss the use of face and gait signatures for human identification and recognition of human activities from video sequences. We survey existing work and describe some of the more well-known methods in these areas. We also describe our own research and outline future possibilities.In the area of face recognition, we start with the traditional methods for image-based analysis and then describe some of the more recent developments related to the use of video sequences, 3D models, and techniques for representing variations of illumination. We note that the main challenge facing researchers in this area is the development of recognition strategies that are robust to changes due to pose, illumination, disguise, and aging. Gait recognition is a more recent area of research in video understanding, although it has been studied for a long time in psychophysics and kinesiology. The goal for video scientists working in this area is to automatically extract the parameters for representation of human gait. We describe some of the techniques that have been developed for this purpose, most of which are appearance based. We also highlight the challenges involved in dealing with changes in viewpoint and propose methods based on image synthesis, visual hull, and 3D models. In the domain of human activity recognition, we present an extensive survey of various methods that have been developed in different disciplines like artificial intelligence, image processing, pattern recognition, and computer vision. We then outline our method for modeling complex activities using 2D and 3D deformable shape theory. The wide application of automatic human identification and activity recognition methods will require the fusion of different modalities like face and gait, dealing with the problems of pose and illumination variations, and accurate computation of 3D models. The last chapter of this lecture deals with these areas of future research. }, isbn = {1559-8136, 1559-8144}, doi = {10.2200/S00002ED1V01Y200508IVM001}, url = {http://www.morganclaypool.com/doi/abs/10.2200/S00002ED1V01Y200508IVM001}, author = {Chellapa, Rama and Roy-Chowdhury,Amit K. and Zhou,S. Kevin} } @article {19025, title = {Recovering from Intrusions in the OSPF Data-plane}, year = {2005}, month = {2005}, institution = {School of Computer Science, Carnegie Mellon University}, abstract = {In this paper, we propose CONS-ROUTE, a data-plane intrusion recoverymechanism for securing the OSPF routing protocol. CONS-ROUTE allows routers to perform intrusion detection in a distributed manner. The intrusion detection outcome can be used globally to reevaluate routing decisions in a way that is resilient to the slandering attack, where a malicious router claims that a legitimate router is misbehaving. We evaluate CONS-ROUTE through simulation and compare it with several simple OSPF data plane resilience techniques. }, doi = {Technical Report}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.60.5274\&rep=rep1\&type=pdf$\#$page=51}, author = {Elaine Shi and Lu, Yong and Reid, Matt} } @article {13203, title = {Reliable Segmentation of Pedestrians in Moving Scenes}, journal = {The 2005 International Conference on Acoustics, Speech, and Signal Processing (ICASSP2005)}, year = {2005}, month = {2005///}, abstract = {This paper describes a periodic motion based pedestriansegmentation algorithm for videos acquired from moving platforms. Given a sequence of bounding boxes containing the detected and tracked walking human, the goal is to analyze the low dimension structure by considering every object sample as a point in the high dimensional manifold space and use the learned structure for segmentation. In this work, unlike the traditional top- down dimension reduction (manifold learning) methods such as Isomap and locally linear embedding (LLE) [9], we introduce a novel bottom-up learning approach. We represent the human stride as a cascade of models with increasing parameter numbers. These parameters describe the dynamics of pedestrians from coarse to fine. By applying the learned manifold structure, we can predict the location of body parts, especially legs, with high accuracy at every frame. The segmentation in consecutive images is done by EM clustering. With the accuracy for prediction using twin-pendulum model, EM is more likely to converge to global maximums. Experimental results for real videos are presented. The algorithm has demonstrated a reliable performance for videos acquired from moving platforms. }, author = {Ran, Y. and Zheng,Q. and Weiss, I. and Davis, Larry S.} } @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 {12775, title = {Secure requirements elicitation through triggered message sequence charts}, journal = {Distributed Computing and Internet Technology}, year = {2005}, month = {2005///}, pages = {273 - 282}, author = {Ray,A. and Sengupta,B. and Cleaveland, Rance} } @article {16387, title = {Shaky ladders, hyperplane-defined functions and genetic algorithms: Systematic controlled observation in dynamic environments}, journal = {Applications of Evolutionary Computing}, year = {2005}, month = {2005///}, pages = {600 - 609}, abstract = {Though recently there has been interest in examining genetic algorithms (GAs) in dynamic environments, work still needs to be done in investigating the fundamental behavior of these algorithms in changing environments. When researching the GA in static environments, it has been useful to use test suites of functions that are designed for the GA so that the performance can be observed under systematic controlled conditions. One example of these suites is the hyperplane-defined functions (hdfs) designed by Holland [1]. We have created an extension of these functions, specifically designed for dynamic environments, which we call the shaky ladder functions. In this paper, we examine the qualities of this suite that facilitate its use in examining the GA in dynamic environments, describe the construction of these functions and present some preliminary results of a GA operating on these functions.}, doi = {10.1007/978-3-540-32003-6_63}, author = {Rand, William and Riolo,R} } @article {12647, title = {"Shape Activity": a continuous-state HMM for moving/deforming shapes with application to abnormal activity detection}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/10//}, pages = {1603 - 1616}, abstract = {The aim is to model "activity" performed by a group of moving and interacting objects (which can be people, cars, or different rigid components of the human body) and use the models for abnormal activity detection. Previous approaches to modeling group activity include co-occurrence statistics (individual and joint histograms) and dynamic Bayesian networks, neither of which is applicable when the number of interacting objects is large. We treat the objects as point objects (referred to as "landmarks") and propose to model their changing configuration as a moving and deforming "shape" (using Kendall{\textquoteright}s shape theory for discrete landmarks). A continuous-state hidden Markov model is defined for landmark shape dynamics in an activity. The configuration of landmarks at a given time forms the observation vector, and the corresponding shape and the scaled Euclidean motion parameters form the hidden-state vector. An abnormal activity is then defined as a change in the shape activity model, which could be slow or drastic and whose parameters are unknown. Results are shown on a real abnormal activity-detection problem involving multiple moving objects.}, keywords = {abnormal activity detection;activity recognition;co-occurrence statistics;continuous-state hidden Markov model;dynamic Bayesian networks;hidden-state vector;particle filtering;scaled Euclidean motion parameter;shape deforming;belief networks;filtering the, Automated;Subtraction Technique;Video Recording;, Biological;Models, Computer-Assisted;Information Storage and Retrieval;Markov Chains;Models, Statistical;Movement;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.852197}, author = {Vaswani, N. and Roy-Chowdhury, A.K. and Chellapa, Rama} } @article {17368, title = {Social and Psychological Influences on Computer User Frustration (Newhagen book chapter, 2002)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {As computer usage has proliferated, so has user frustration. Even devoted and knowledgeable users encounter annoying delays, incomprehensible messages, incompatible files, and indecipherable menus. The frustration generated by these problems can be personally disturbing and socially disruptive. Psychological and social perspectives on frustration may clarify the relationships among variables such as personality types, cultural factors, goal attainment, workplace anger, and computer anxiety. These perspectives may also help designers, managers, and users understand the range of responses to frustration, which could lead to effective interventions such as redesign of software, improved training, better online help, user discipline, and even resetting of national research priorities.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6497}, author = {Bessiere,Katie and Ceaparu,Irina and Lazar,Jonathan and Robinson,John and Shneiderman, Ben} } @article {16403, title = {Spatial process and data models: Toward integration of agent-based models and GIS}, journal = {Journal of Geographical Systems}, volume = {7}, year = {2005}, month = {2005///}, pages = {25 - 47}, abstract = {The use of object-orientation for both spatial data and spatial process models facilitates their integration, which can allow exploration and explanation of spatial-temporal phenomena. In order to better understand how tight coupling might proceed and to evaluate the possible functional and efficiency gains from such a tight coupling, we identify four key relationships affecting how geographic data (fields and objects) and agent-based process models can interact: identity, causal, temporal and topological. We discuss approaches to implementing tight integration, focusing on a middleware approach that links existing GIS and ABM development platforms, and illustrate the need and approaches with example agent-based models.}, doi = {10.1007/s10109-005-0148-5}, author = {Brown,D.G. and Riolo,R and Robinson,D.T. and North,M. and Rand, William} } @article {14023, title = {Speaker Localization Using Excitation Source Information in Speech}, journal = {Speech and Audio Processing, IEEE Transactions on}, volume = {13}, year = {2005}, month = {2005/09//}, pages = {751 - 761}, abstract = {This paper presents the results of simulation and real room studies for localization of a moving speaker using information about the excitation source of speech production. The first step in localization is the estimation of time-delay from speech collected by a pair of microphones. Methods for time-delay estimation generally use spectral features that correspond mostly to the shape of vocal tract during speech production. Spectral features are affected by degradations due to noise and reverberation. This paper proposes a method for localizing a speaker using features that arise from the excitation source during speech production. Experiments were conducted by simulating different noise and reverberation conditions to compare the performance of the time-delay estimation and source localization using the proposed method with the results obtained using the spectrum-based generalized cross correlation (GCC) methods. The results show that the proposed method shows lower number of discrepancies in the estimated time-delays. The bias, variance and the root mean square error (RMSE) of the proposed method is consistently equal or less than the GCC methods. The location of a moving speaker estimated using the time-delays obtained by the proposed method are closer to the actual values, than those obtained by the GCC method.}, keywords = {correlation, correlation;, cross, Delay, error, error;, estimation;, excitation, generalized, information;, localization;, mean, methods;, processing;, production;, root, source, speaker, speech, square, TIME}, isbn = {1063-6676}, doi = {10.1109/TSA.2005.851907}, author = {Raykar,V.C. and Yegnanarayana,B. and Prasanna,S. R.M and Duraiswami, Ramani} } @article {12654, title = {Statistical bias in 3-D reconstruction from a monocular video}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/08//}, pages = {1057 - 1062}, abstract = {The present state-of-the-art in computing the error statistics in three-dimensional (3-D) reconstruction from video concentrates on estimating the error covariance. A different source of error which has not received much attention is the fact that the reconstruction estimates are often significantly statistically biased. In this paper, we derive a precise expression for the bias in the depth estimate, based on the continuous (differentiable) version of structure from motion (SfM). Many SfM algorithms, or certain portions of them, can be posed in a linear least-squares (LS) framework Ax=b. Examples include initialization procedures for bundle adjustment or algorithms that alternately estimate depth and camera motion. It is a well-known fact that the LS estimate is biased if the system matrix A is noisy. In SfM, the matrix A contains point correspondences, which are always difficult to obtain precisely; thus, it is expected that the structure and motion estimates in such a formulation of the problem would be biased. Existing results on the minimum achievable variance of the SfM estimator are extended by deriving a generalized Cramer-Rao lower bound. A detailed analysis of the effect of various camera motion parameters on the bias is presented. We conclude by presenting the effect of bias compensation on reconstructing 3-D face models from rendered images.}, keywords = {3D face models, 3D video reconstruction, algorithms, artifacts, Artificial intelligence, Automated;Signal Processing, bias compensation, bundle adjustment, camera motion estimation, Computer simulation, Computer-Assisted;Imaging, Computer-Assisted;Subtraction Technique;Video Recording;, depth estimate, error covariance estimation, error statistics, generalized Cramer-Rao lower bound, Image Enhancement, Image Interpretation, Image reconstruction, initialization procedures, least squares approximations, linear least-squares framework, monocular video, motion compensation, Motion estimation, statistical bias, Statistical;Pattern Recognition, structure from motion algorithms, Three-Dimensional;Information Storage and Retrieval;Models, video signal processing}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.849775}, author = {Roy-Chowdhury, A.K. and Chellapa, Rama} } @article {18718, title = {Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain}, journal = {Molecular Cell}, volume = {18}, year = {2005}, month = {2005/06/10/}, pages = {687 - 698}, abstract = {SummaryAlthough functional diversity in polyubiquitin chain signaling has been ascribed to the ability of differently linked chains to bind in a distinctive manner to effector proteins, structural models of such interactions have been lacking. Here, we use NMR to unveil the structural basis of selective recognition of Lys48-linked di- and tetraubiquitin chains by the UBA2 domain of hHR23A. Although the interaction of UBA2 with Lys48-linked diubiquitin involves the same hydrophobic surface on each ubiquitin unit as that utilized in monoubiquitin:UBA complexes, our results show how the {\textquotedblleft}closed{\textquotedblright} conformation of Lys48-linked diubiquitin is crucial for high-affinity binding. Moreover, recognition of Lys48-linked diubiquitin involves a unique epitope on UBA, which allows the formation of a sandwich-like diubiqutin:UBA complex. Studies of the UBA-tetraubiquitin interaction suggest that this mode of UBA binding to diubiquitin is relevant for longer chains. }, isbn = {1097-2765}, doi = {10.1016/j.molcel.2005.05.013}, url = {http://www.sciencedirect.com/science/article/pii/S1097276505013195}, author = {Varadan,Ranjani and Assfalg,Michael and Raasi,Shahri and Pickart,Cecile and Fushman, David} } @article {13865, title = {Structural metadata and parsing speech}, year = {2005}, month = {2005///}, institution = {JHU Language Engineering Workshop}, author = {Harper,M. and Dorr, Bonnie J and Hale,J. and Roark,B. and Shafran,I. and Lease,M. and Liu,Y. and Snover,M. and Yung,L. and Krasnyanskaya,A. and others} } @article {12932, title = {Temperature-Driven Campylobacter Seasonality in England and Wales}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {71}, year = {2005}, month = {2005/01/01/}, pages = {85 - 92}, abstract = {Campylobacter incidence in England and Wales between 1990 and 1999 was examined in conjunction with weather conditions. Over the 10-year interval, the average annual rate was determined to be 78.4 {\textpm} 15.0 cases per 100,000, with an upward trend. Rates were higher in males than in females, regardless of age, and highest in children less than 5 years old. Major regional differences were detected, with the highest rates in Wales and the southwest and the lowest in the southeast. The disease displayed a seasonal pattern, and increased campylobacter rates were found to be correlated with temperature. The most marked seasonal effect was observed for children under the age of 5. The seasonal pattern of campylobacter infections indicated a linkage with environmental factors rather than food sources. Therefore, public health interventions should not be restricted to food-borne approaches, and the epidemiology of the seasonal peak in human campylobacter infections may best be understood through studies in young children.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.71.1.85-92.2005}, url = {http://aem.asm.org/content/71/1/85}, author = {Louis,Val{\'e}rie R. and Gillespie,Iain A. and O{\textquoteright}Brien,Sarah J. and Russek-Cohen,Estelle and Pearson,Andrew D. and Rita R Colwell} } @conference {13471, title = {Temporal visualization of planning polygons for e~cient partitioning of geo-spatial data}, booktitle = {Information Visualization, 2005. INFOVIS 2005. IEEE Symposium on}, year = {2005}, month = {2005///}, pages = {211 - 218}, publisher = {IEEE}, organization = {IEEE}, abstract = {Partitioning of geo-spatial data for efficient allocation of resources such as schools and emergency health care services is driven by a need to provide better and more effective services. Partitioning of spatial data is a complex process that depends on numerous factors such as population, costs incurred in deploying or utilizing resources and target capacity of a resource. Moreover, complex data such as population distributions are dynamic i.e. they may change over time. Simple animation may not effectively show temporal changes in spatial data. We propose the use of three temporal visualization techniques -wedges, rings and time slices - to display the nature of change in temporal data in a single view. Along with maximizing resource utilization and minimizing utilization costs, a partition should also ensure the long term effectiveness of the plan. We use multi-attribute visualization techniques to highlight the strengths and identify the weaknesses of a partition. Comparative visualization techniques allow multiple partitions to be viewed simultaneously. Users can make informed decisions about how to partition geo spatial data by using a combination of our techniques for multi-attribute visualization, temporal visualization and comparative visualization.}, isbn = {0-7803-9464-X}, doi = {10.1109/INFVIS.2005.1532149}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1532149}, author = {Shanbhag,P. and Rheingans,P. and desJardins, Marie} } @article {16412, title = {Toward a graphical ABM toolkit with GIS integration}, journal = {Proceedings of Agent2005}, year = {2005}, month = {2005///}, abstract = {Agent-based modeling (ABM) has proved useful in a number of fields. Many of theearly successes of ABM were due to its ability to represent the processes of a phenomenon. However, less emphasis has been placed in ABM on developing its ability to replicate spatial patterns of phenomena. In order to do that, more powerful spatial modeling techniques, like those within geographical information systems (GIS), are necessary. The integration of these two tool sets into a cohesive package would allow for elegant modeling of both process and pattern. One problem with an integrated toolkit is that most GIS users are not programmers, but most GIS users are familiar with the use of detailed graphical user interfaces (GUIs) in order to create complex visualizations of data. Thus providing a detailed GUI to access an integrated ABM-GIS toolkit would vastly expand the number of users for such a toolkit. This paper is a first step toward that goal. We first outline several design principles for an ABM-GIS toolkit and then describe a survey of extant toolkits (RepastPy, NetLogo, and MobiDyc) that were selected based on the design principles. The toolkits were surveyed to see how well they fulfill some of the design principles. This survey is not meant to be a comparative review of these toolkits but rather it was conducted to determine what useful design principles can be gathered from them that might inform a new {\textquotedblleft}ideal{\textquotedblright} ABM-GIS toolkit. Finally, the paper concludes with some design recommendations for such a toolkit. }, author = {Rand, William and Brown,D and Riolo,R and Robinson,D} } @conference {17444, title = {Turning information visualization innovations into commercial products: lessons to guide the next success}, booktitle = {IEEE Symposium on Information Visualization, 2005. INFOVIS 2005}, year = {2005}, month = {2005/10/23/25}, pages = {241 - 244}, publisher = {IEEE}, organization = {IEEE}, abstract = {As information visualization matures as an academic research field, commercial spinoffs are proliferating, but success stories are harder to find. This is the normal process of emergence for new technologies, but the panel organizers believe that there are certain strategies that facilitate success. To teach these lessons, we have invited several key figures who are seeking to commercialize information visualization tools. The panelists make short presentations, engage in a moderated discussion, and respond to audience questions.}, keywords = {Books, commercial development, commercial product, Computer interfaces, Computer science, data visualisation, Data visualization, Educational institutions, exploratory data analysis, information visualization innovation, information visualization tool, innovation management, Laboratories, Management training, new technology emergence, Technological innovation, technology transfer, Turning, User interfaces}, isbn = {0-7803-9464-X}, doi = {10.1109/INFVIS.2005.1532153}, author = {Shneiderman, Ben and Rao,R. and Andrews,K. and Ahlberg,C. and Brodbeck,D. and Jewitt,T. and Mackinlay,J.} } @conference {16601, title = {Using aggregate motion in multi-agent teams to solve search and transport problems}, booktitle = {Swarm Intelligence Symposium, 2005. SIS 2005. Proceedings 2005 IEEE}, year = {2005}, month = {2005///}, pages = {373 - 380}, author = {RodrIGuez,A. and Reggia, James A.} } @article {16475, title = {Using Non-random Associations for Predicting Latency in WANs}, journal = {Web Information Systems Engineering {\textendash} WISE 2005}, year = {2005}, month = {2005///}, abstract = {In this paper, we propose a scalable performance management tool for Wide Area Applications. Our objective is to scalably identify non-random associations between pairs of individual Latency Profiles (iLPs) (i.e., latency distributions experienced by clients when connecting to a server) and exploit them in latency prediction. Our approach utilizes Relevance Networks (RNs) to manage tens of thousands of iLPs. Non-random associations between iLPs can be identified by topology-independent measures such as correlation and mutual information. We demonstrate that these non-random associations do indeed have a significant impact in improving the error of latency prediction.}, doi = {10.1007/11581062_48}, author = {Raschid, Louiqa and Ye,Q. and Zadorozhny,V. and Gal,A. and Murthy,H.} } @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 {12713, title = {3d modelling of human motion using kinematic chains and multiple cameras for tracking}, journal = {Proc. of Eighth International Symposium on the}, year = {2004}, month = {2004///}, author = {Sundaresan, A. and RoyChowdhury, A. and Chellapa, Rama} } @article {16392, title = {Agent-based and analytical modeling to evaluate the effectiveness of greenbelts}, journal = {Environmental Modelling \& Software}, volume = {19}, year = {2004}, month = {2004/12//}, pages = {1097 - 1109}, abstract = {We present several models of residential development at the rural{\textendash}urban fringe to evaluate the effectiveness of a greenbelt located beside a developed area, for delaying development outside the greenbelt. First, we develop a mathematical model, under two assumptions about the distributions of service centers, that represents the trade-off between greenbelt placement and width, their effects on the rate of development beyond the greenbelt, and how these interact with spatial patterns of aesthetic quality and the locations of services. Next, we present three agent-based models (ABMs) that include agents with the potential for heterogeneous preferences and a landscape with the potential for heterogeneous attributes. Results from experiments run with a one-dimensional ABM agree with the starkest of the results from the mathematical model, strengthening the support for both models. Further, we present two different two-dimensional ABMs and conduct a series of experiments to supplement our mathematical analysis. These include examining the effects of heterogeneous agent preferences, multiple landscape patterns, incomplete or imperfect information available to agents, and a positive aesthetic quality impact of the greenbelt on neighboring locations. These results suggest how width and location of the greenbelt could help determine the effectiveness of greenbelts for slowing sprawl, but that these relationships are sensitive to the patterns of landscape aesthetic quality and assumptions about service center locations.}, keywords = {Agent-based modeling, Land-use change, Landscape ecology, Urban sprawl}, isbn = {1364-8152}, doi = {10.1016/j.envsoft.2003.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S1364815203002664}, author = {Brown,Daniel G. and Page,Scott E. and Riolo,Rick and Rand, William} } @conference {14035, title = {Automatic position calibration of multiple microphones}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {4}, year = {2004}, month = {2004/05//}, pages = {iv-69 - iv-72 vol.4 - iv-69 - iv-72 vol.4}, abstract = {We describe a method to determine automatically the relative three dimensional positions of multiple microphones using at least five loudspeakers in unknown positions. The only assumption we make is that there is a microphone which is very close to a loudspeaker. In our experimental setup, we attach one microphone to each loudspeaker. We derive the maximum likelihood estimator and the solution turns out to be a non-linear least squares problem. A closed form solution which can be used as the initial guess for the minimization routine is derived. We also derive an approximate expression for the covariance of the estimator using the implicit function theorem. Using this, we analyze the performance of the estimator with respect to the positions of the loudspeakers. The algorithm is validated using both Monte-Carlo simulations and a real-time experimental setup.}, keywords = {approximations;, array, audio, AUTOMATIC, calibration;, closed, covariance;, dimensional, estimation;, form, function, implicit, least, likelihood, loudspeakers;, maximum, microphone, microphones;, minimisation;, minimization;, multiple, nonlinear, position, positions;, problem;, processing;, signal, solution;, squares, theorem;, three}, doi = {10.1109/ICASSP.2004.1326765}, author = {Raykar,V.C. and Duraiswami, Ramani} } @article {13508, title = {Automatic recognition of spontaneous speech for access to multilingual oral history archives}, journal = {IEEE Transactions on Speech and Audio Processing, Special Issue on Spontaneous Speech Processing}, volume = {12}, year = {2004}, month = {2004/07//}, pages = {420 - 435}, abstract = {The MALACH project has the goal of developing the technologies needed to facilitate access to large collections of spontaneous speech. Its aim is to dramatically improve the state of the art in key Automatic Speech Recognition (ASR), Natural Language Processing (NLP) technologies for use in large-scale retrieval systems. The project leverages a unique collection of oral history interviews with survivors of the Holocaust that has been assembled and extensively annotated by the Survivors of the Shoah Visual History Foundation. This paper describes the collection, 116,000 hours of interviews in 32 languages, and the way in which system requirements have been discerned through user studies. It discusses ASR methods for very difficult speech (heavily accented, emotional, and elderly spontaneous speech), including transcription to create training data and methods for language modeling and speaker adaptation. Results are presented for for English and Czech. NLP results are presented for named entity tagging, topic segmentation, and supervised topic classification, and the architecture of an integrated search system that uses these results is described.}, author = {Byrne,W. and David Doermann and Franz,M. and Gustman,S. and Hajic,J. and Oard, Douglas and Picheny,M. and Psutka,J. and Ramabhadran,B.} } @conference {15690, title = {Automatic video summarization for wireless and mobile environments}, booktitle = {2004 IEEE International Conference on Communications}, volume = {3}, year = {2004}, month = {2004/06/20/24}, pages = {1532- 1536 Vol.3 - 1532- 1536 Vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we propose a novel video summarization technique using which we can automatically generate high quality video summaries suitable for wireless and mobile environments. The significant contribution of this paper lies in the proposed clustering scheme. We use Delaunay diagrams to cluster multidimensional point data corresponding to the frame contents of the video. In contrast to the existing clustering techniques used for summarization, our clustering algorithm is fully automatic and well suited for batch processing. We illustrate the quality of our clustering and summarization scheme in an experiment using several video clips.}, keywords = {automatic video summarization, batch processing, batch processing (computers), Clustering algorithms, Clustering methods, clustering scheme, Computer science, Delaunay diagram, graph theory, Gunshot detection systems, Image sequences, mesh generation, Mobile computing, mobile radio, multidimensional point data cluster, Multidimensional systems, Multimedia communication, video clip, video frame content, Video sequences, video signal processing, wireless mobile environment}, isbn = {0-7803-8533-0}, doi = {10.1109/ICC.2004.1312767}, author = {Yong Rao and Mundur, Padma and Yesha,Y.} } @conference {18552, title = {BorderGuard: detecting cold potatoes from peers}, booktitle = {Proceedings of the 4th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {213 - 218}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Internet Service Providers often establish contractual "peering" agreements, where they agree to forward traffic to each other{\textquoteright}s customers at no cost. Consistent route advertisement at all peering points is a common provision in these agreements, because it gives an AS the flexibility to select egress points for the traffic (e.g., performing "hot potato" routing). Verifying "consistent export" is challenging because route advertisements are exchanged at multiple peering points and may be modified by routing policies. In this paper, we propose two algorithms to detect inconsistent routes using routing and configuration data from an AS{\textquoteright}s border routers. The first algorithm requires access to all eBGP routes advertised by a peer. Because this data is often unavailable, we propose another algorithm that detects inconsistencies using readily available data. We have applied our algorithms to the routes advertised by the peers of AT\&T{\textquoteright}s commercial IP backbone. Although a peer may intentionally send inconsistent advertisements to prevent its neighbor from performing hot-potato routing, we also discuss several configuration scenarios where a peer may inadvertently advertise inconsistent routes, despite having consistent export policies. Finally, we explain how simple modifications to the routers could make detection of inconsistent advertisements much easier than it is today.}, keywords = {anomalies, BGP, inconsistent advertisement, peering}, isbn = {1-58113-821-0}, doi = {10.1145/1028788.1028815}, url = {http://doi.acm.org/10.1145/1028788.1028815}, author = {Feamster, Nick and Mao,Zhuoqing Morley and Rexford,Jennifer} } @article {13935, title = {Bringing together children and books: An initial descriptive study of children{\textquoteright}s book searching and selection behavior in a digital library}, journal = {Proceedings of the American Society for Information science and Technology}, volume = {41}, year = {2004}, month = {2004///}, pages = {339 - 348}, author = {Reuter,K. and Druin, Allison} } @conference {15901, title = {Building an information retrieval test collection for spontaneous conversational speech}, booktitle = {Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {41 - 48}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Test collections model use cases in ways that facilitate evaluation of information retrieval systems. This paper describes the use of search-guided relevance assessment to create a test collection for retrieval of spontaneous conversational speech. Approximately 10,000 thematically coherent segments were manually identified in 625 hours of oral history interviews with 246 individuals. Automatic speech recognition results, manually prepared summaries, controlled vocabulary indexing, and name authority control are available for every segment. Those features were leveraged by a team of four relevance assessors to identify topically relevant segments for 28 topics developed from actual user requests. Search-guided assessment yielded sufficient inter-annotator agreement to support formative evaluation during system development. Baseline results for ranked retrieval are presented to illustrate use of the collection.}, keywords = {assessment, Automatic speech recognition, oral history, search-guided relevance}, isbn = {1-58113-881-4}, doi = {10.1145/1008992.1009002}, url = {http://doi.acm.org/10.1145/1008992.1009002}, author = {Oard, Douglas and Soergel,Dagobert and David Doermann and Huang,Xiaoli and Murray,G. Craig and Wang,Jianqiang and Ramabhadran,Bhuvana and Franz,Martin and Gustman,Samuel and Mayfield,James and Kharevych,Liliya and Strassel,Stephanie} } @conference {18602, title = {The case for separating routing from routers}, booktitle = {Proceedings of the ACM SIGCOMM workshop on Future directions in network architecture}, series = {FDNA {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {5 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Over the past decade, the complexity of the Internet{\textquoteright}s routing infrastructure has increased dramatically. This complexity and the problems it causes stem not just from various new demands made of the routing infrastructure, but also from fundamental limitations in the ability of today{\textquoteright}s distributed infrastructure to scalably cope with new requirements.The limitations in today{\textquoteright}s routing system arise in large part from the fully distributed path-selection computation that the IP routers in an autonomous system (AS) must perform. To overcome this weakness, interdomain routing should be separated from today{\textquoteright}s IP routers, which should simply forward packets (for the most part). Instead, a separate Routing Control Platform (RCP) should select routes on behalf of the IP routers in each AS and exchange reachability information with other domains.Our position is that an approach like RCP is a good way of coping with complexity while being responsive to new demands and can lead to a routing system that is substantially easier to manage than today. We present a design overview of RCP based on three architectural principles path computation based on a consistent view of network state, controlled interactions between routing protocol layers, and expressive specification of routing policies and discuss the architectural strengths and weaknesses of our proposal.}, keywords = {BGP, interdomain routing, routing architecture}, isbn = {1-58113-942-X}, doi = {10.1145/1016707.1016709}, url = {http://doi.acm.org/10.1145/1016707.1016709}, author = {Feamster, Nick and Balakrishnan,Hari and Rexford,Jennifer and Shaikh,Aman and van der Merwe,Jacobus} } @conference {16447, title = {Challenges in selecting paths for navigational queries: Trade-off of benefit of path versus cost of plan}, booktitle = {Proceedings of the 7th International Workshop on the Web and Databases: colocated with ACM SIGMOD/PODS 2004}, year = {2004}, month = {2004///}, pages = {61 - 66}, author = {Vidal,M. E and Raschid, Louiqa and Mestre,J.} } @conference {14289, title = {A comparison of bug finding tools for Java}, booktitle = {Software Reliability Engineering, 2004. ISSRE 2004. 15th International Symposium on}, year = {2004}, month = {2004///}, pages = {245 - 256}, author = {Rutar,N. and Almazan,C.B. and Foster, Jeffrey S.} } @conference {16785, title = {Compressing historical information in sensor networks}, booktitle = {Proceedings of the 2004 ACM SIGMOD international conference on Management of data - SIGMOD {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {527 - 527}, address = {Paris, France}, doi = {10.1145/1007568.1007628}, url = {http://dl.acm.org/citation.cfm?id=1007628}, author = {Deligiannakis,Antonios and Kotidis,Yannis and Roussopoulos, Nick} } @conference {14034, title = {Computation of Green{\textquoteright}s function for finite-size photonic crystals by boundary element method}, booktitle = {Antennas and Propagation Society International Symposium, 2004. IEEE}, volume = {4}, year = {2004}, month = {2004/06//}, pages = {4320 - 4323 Vol.4 - 4320 - 4323 Vol.4}, abstract = {We have derived a new integral equation method for computing the Green{\textquoteright}s function for 2D electromagnetic wave propagation in a finite size photonic crystal. The method is also used for deriving the multipole expansions for the case of circular cylinders. This derivation is different from the ones in the literature. Our numerical results show an excellent agreement of the two algorithms. In the future we would like to expand the method to the numerical solution of the three-dimensional electromagnetic problem.}, keywords = {2D, boundary, boundary-elements, circular, crystals;, cylinders;, electromagnetic, element, equation, equations;, expansions;, finite-size, function, function;, Green, Green{\textquoteright}s, integral, method;, methods;, multipole, photonic, propagation;, wave}, doi = {10.1109/APS.2004.1330307}, author = {Seydou,F. and Ramahi,O. and Duraiswami, Ramani and Seppdnen,T.} } @conference {12716, title = {Contour-based 3D Face Modeling from a Monocular Video}, booktitle = {Proceedings of the British Machine Vision Conference}, year = {2004}, month = {2004///}, pages = {39.1-39.10 - 39.1-39.10}, publisher = {British Machine Vision Association}, organization = {British Machine Vision Association}, abstract = {In this paper, we present a novel 3D face modeling approach from a monoc-ular video captured using a conventional camera. The proposed algorithm relies on matching a generic 3D face model to the outer contours of the face to be modeled and a few of its internal features. At the first stage of the method, we estimate the head pose by comparing the edges extracted from video frames, with the contours extracted from a generic face model. Next, the generic face model is adapted to the actual 3D face by global and local deformations. An affine model is used for global deformation. The 3D model is locally deformed by computing the optimal perturbations of a sparse set of control points using a stochastic search optimization method. The deforma- tions are integrated over a set of poses in the video sequence, leading to an accurate 3D model. }, isbn = {1-901725-25-1}, doi = {10.5244/C.18.39}, url = {http://www.bmva.org/bmvc/2004/papers/paper_136.html}, author = {Gupta, H. and Roy Chowdhury, A.K. and Chellapa, Rama} } @article {12210, title = {DateLens: A fisheye calendar interface for PDAs}, journal = {ACM Transactions on Computer-Human Interaction (TOCHI)}, volume = {11}, year = {2004}, month = {2004///}, pages = {90 - 119}, author = {Bederson, Benjamin B. and Clamage,A. and Czerwinski,M.P. and Robertson,G.G.} } @article {18381, title = {Defect evolution in a product line environment}, journal = {Journal of Systems and Software}, volume = {70}, year = {2004}, month = {2004/02//}, pages = {143 - 154}, abstract = {One mechanism used for monitoring the development of the Space Shuttle flight control software, in order to minimize any risks to the missions, is the independent verification and validation (IV\&V) process. Using data provided by both the Shuttle software developer and the IV\&V contractor, in this paper we describe the overall IV\&V process as used on the Space Shuttle program and provide an analysis of the use of metrics to document and control this process over multiple releases of this software. Our findings reaffirm the value of IV\&V, show the impact of IV\&V on multiple releases of a large complex software system, and indicate that some of the traditional measures of defect detection and repair are not applicable in a multiple-release environment such as this one.}, keywords = {Evolutionary software, Life and mission critical software, metrics, Process characterization, Product line development, Software independent verification and validation, Software safety and reliability, Space Shuttle program}, isbn = {0164-1212}, doi = {10.1016/S0164-1212(03)00013-X}, url = {http://www.sciencedirect.com/science/article/pii/S016412120300013X}, author = {Zelkowitz, Marvin V and Rus,Ioana} } @conference {16631, title = {A descriptive encoding language for evolving modular neural networks}, booktitle = {Genetic and Evolutionary Computation{\textendash}GECCO 2004}, year = {2004}, month = {2004///}, pages = {519 - 530}, author = {Jung,J. Y and Reggia, James A.} } @article {17078, title = {Determining Causes and Severity of End-User Frustration}, journal = {International Journal of Human-Computer Interaction}, volume = {17}, year = {2004}, month = {2004///}, pages = {333 - 356}, abstract = {Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47\% to 53\% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38\%. These disturbing results should be a basis for future study.Although computers are beneficial to individuals and society, frequently users encounter frustrating experiences when using computers. This study represents an attempt to measure, in 111 participants, the frequency, the cause, and the level of severity of frustrating experiences. The data show that frustrating experiences happen on a frequent basis. The applications in which the frustrating experiences happened most frequently were Web browsing, e-mail, and word processing. The most-cited causes of frustrating experiences were error messages, dropped network connections, long download times, and hard-to-find features. The time lost due to frustrating experiences ranged from 47\% to 53\% of time spent on a computer, depending on the location and study method. After extreme cases were discarded, the time lost was still above 38\%. These disturbing results should be a basis for future study. }, isbn = {1044-7318}, doi = {10.1207/s15327590ijhc1703_3}, url = {http://www.tandfonline.com/doi/abs/10.1207/s15327590ijhc1703_3}, author = {Ceaparu,Irina and Lazar,Jonathan and Bessiere,Katie and Robinson,John and Shneiderman, Ben} } @conference {13218, title = {An Efficient and Robust Human Classification Algorithm using Finite Frequencies Probing}, booktitle = {Computer Vision and Pattern Recognition Workshop, 2004. CVPRW {\textquoteright}04. Conference on}, year = {2004}, month = {2004/06//}, pages = {132 - 132}, abstract = {This paper describes a periodicity motion detection based object classification algorithm for infrared videos. Given a detected and tracked object, the goal is to analyze the periodic signature of its motion pattern. We propose an efficient and robust solution, which is related to the frequency estimation in speech recognition. Periodic reference functions are correlated with the video signal. Experimental results for both infrared and visible videos acquired by ground-based as well as airborne moving sensors are presented.}, doi = {10.1109/CVPR.2004.25}, author = {Yang Ran and Weiss, I. and Qinfen Zheng and Davis, Larry S.} } @conference {16467, title = {Efficient techniques to explore and rank paths in life science data sources}, booktitle = {Data Integration in the Life Sciences}, year = {2004}, month = {2004///}, pages = {187 - 202}, author = {Lacroix,Z. and Raschid, Louiqa and Vidal,M. E} } @conference {12131, title = {Empirical-based estimation of the effect on software dependability of a technique for architecture conformance verification}, booktitle = {Proceedings of the ICSE 2004 Workshop on Architecting Dependable Systems, Edinburgh, UK}, year = {2004}, month = {2004///}, abstract = {The High Dependability Computing Program (HDCP)project is a NASA initiative for increasing dependability of software-based systems. It researches achieving high dependability by introducing new technologies. We focus on the evaluation of the effectiveness of technologies with respect to dependability. We employ empirical evaluation methods along with evaluation testbeds. In this paper, our technology evaluation approach is described. A testbed representative of air traffic control applications is used. An experiment to evaluate a technology to for identification of architectural violations is presented. }, author = {Asgari, S. and Basili, Victor R. and Costa,P. and Donzelli,P. and Hochstein, L. and Lindvall,M. and Rus,I. and Shull, F. and Tvedt,R. and Zelkowitz, Marvin V} } @conference {16462, title = {Exploiting multiple paths to express scientific queries}, booktitle = {16th International Conference on Scientific and Statistical Database Management, 2004. Proceedings}, year = {2004}, month = {2004/06/21/23}, pages = {357 - 360}, publisher = {IEEE}, organization = {IEEE}, abstract = {The purpose of this demonstration is to present the main features of the BioNavigation system. Scientific data collection needed in various stages of scientific discovery is typically performed manually. For each scientific object of interest (e.g., a gene, a sequence), scientists query a succession of Web resources following links between retrieved entries. Each of the steps provides part of the intended characterization of the scientific object. This process is sometimes partially supported by hard-coded scripts or complex queries that will be evaluated by a mediation-based data integration system or against a data warehouse. These approaches fail in guiding the scientists during the collection process. In contrast, the BioNavigation approach presented in the paper provides the scientists with information on the available alternative resources, their provenance, and the costs of data collection. The BioNavigation system enhances a mediation-based integration system and provides scientists with support for the following: to ask queries at a high conceptual level; to visualize the multiple alternative resources that may be exploited to execute their data collection queries; to choose the final execution path to evaluate their queries.}, keywords = {access protocols, biology computing, BioNavigation system, complex queries, Costs, Data analysis, data handling, Data visualization, data warehouse, Data warehouses, Databases, diseases, distributed databases, hard-coded scripts, information resources, Information retrieval, mediation-based data integration system, multiple paths, query evaluation, Query processing, scientific data collection, scientific discovery, scientific information, scientific information systems, scientific object of interest, scientific queries, sequences, Web resources}, isbn = {0-7695-2146-0}, doi = {10.1109/SSDM.2004.1311231}, author = {Lacroix,Z. and Moths,T. and Parekh,K. and Raschid, Louiqa and Vidal,M. -E} } @article {16802, title = {Exploring the tradeoff between performance and data freshness in database-driven web servers}, journal = {The VLDB Journal}, volume = {13}, year = {2004}, month = {2004///}, pages = {240 - 255}, author = {Labrinidis,A. and Roussopoulos, Nick} } @article {16645, title = {Extending self-organizing particle systems to problem solving}, journal = {Artificial Life}, volume = {10}, year = {2004}, month = {2004///}, pages = {379 - 395}, author = {Rodr{\'\i}guez,A. and Reggia, James A.} } @article {14041, title = {Extracting the frequencies of the pinna spectral notches from measured head-related impulse responses}, journal = {The Journal of the Acoustical Society of America}, volume = {116}, year = {2004}, month = {2004///}, pages = {2625 - 2625}, abstract = {Experimental data are available for the Head-related impulse response (HRIR) for several azimuth and elevation angles, and for several subjects. The measured HRIR depends on several factors such as reflections from body parts (torso, shoulder, and knees), head diffraction, and reflection/diffraction effects due to the external ear (pinna). Due to the combined influence of these factors on the HRIR, it is difficult to isolate features thought to be perceptually important (such as the frequencies of pinna spectral notches) using standard signal-processing techniques. Signal-processing methods to extract the frequencies of the pinna spectral notches from the HRIR are presented. The techniques are applied to extracting the frequencies of the pinna spectral notches from the publicly available HRIR databases. A brief discussion relating the notch frequencies to the physical dimensions and the shape of the pinna is given. [The support of NSF Award ITR-0086075 is gratefully acknowledged.]}, url = {http://link.aip.org/link/?JAS/116/2625/2}, author = {Raykar,Vikas C. and Duraiswami, Ramani and Yegnanarayana,B.} } @conference {12685, title = {Facial similarity across age, disguise, illumination and pose}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {3}, year = {2004}, month = {2004/10//}, pages = {1999 - 2002 Vol. 3 - 1999 - 2002 Vol. 3}, abstract = {Illumination, pose variations, disguises, aging effects and expression variations are some of the key factors that affect the performance of face recognition systems. Face recognition systems have always been studied from a recognition perspective. Our emphasis is on deriving a measure of similarity between faces. The similarity measure provides insights into the role each of the above mentioned variations play in affecting the performance of face recognition systems. In the process of computing the similarity measure between faces, we suggest a framework to compensate for pose variations and introduce the notion of {\textquoteright}half-faces{\textquoteright} to circumvent the problem of non-uniform illumination. We used the similarity measure to retrieve similar faces from a database containing multiple images of individuals. Moreover, we devised experiments to study the effect age plays in affecting facial similarity. In conclusion, the similarity measure helps in studying the significance facial features play in affecting the performance of face recognition systems.}, keywords = {Aging, database, databases;, disguise;, effect;, Expression, Face, half-face;, illumination;, image, lighting;, pose, recognition, recognition;, retrieval;, system;, variation;, visual}, doi = {10.1109/ICIP.2004.1421474}, author = {Ramanathan,N. and Chellapa, Rama and Roy Chowdhury, A.K.} } @article {12805, title = {Formal Modeling Of Middleware-based Distributed Systems}, journal = {Electronic Notes in Theoretical Computer Science}, volume = {108}, year = {2004}, month = {2004/12/13/}, pages = {21 - 37}, abstract = {Effective design of middleware-based systems requires modeling notations that allow the use of process-interaction schemes provided by different middleware packages directly in designs. Traditional design notations typically only support a fixed class of interprocess interaction schemes, and designers wishing to use them for modeling middleware-based systems must devote significant effort to encoding the middleware primitives in the notation. In this paper, we demonstrate how a new graphical design notation, Architectural Interaction Diagrams (AIDs), which provides parameterized support for different interaction schemes, may be used to model a real-life middleware-based system like the Event Heap coordination infrastructure of the i-Room ubiquitous computing environment.}, keywords = {distributed systems, Formal Methods, Middleware, Software architecture}, isbn = {1571-0661}, doi = {10.1016/j.entcs.2004.01.010}, url = {http://www.sciencedirect.com/science/article/pii/S1571066104051989}, author = {Ray,Arnab and Cleaveland, Rance} } @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} } @conference {12704, title = {Fusion of gait and face for human identification}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {5}, year = {2004}, month = {2004/05//}, pages = {V - 901-4 vol.5 - V - 901-4 vol.5}, abstract = {Identification of humans from arbitrary view points is an important requirement for different tasks including perceptual interfaces for intelligent environments, covert security and access control etc. For optimal performance, the system must use as many cues as possible and combine them in meaningful ways. In this paper, we discuss fusion of face and gait cues for the single camera case. We present a view invariant gait recognition algorithm for gait recognition. We employ decision fusion to combine the results of our gait recognition algorithm and a face recognition algorithm based on sequential importance sampling. We consider two fusion scenarios: hierarchical and holistic. The first involves using the gait recognition algorithm as a filter to pass on a smaller set of candidates to the face recognition algorithm. The second involves combining the similarity scores obtained individually from the face and gait recognition algorithms. Simple rules like the SUM, MIN and PRODUCT are used for combining the scores. The results of fusion experiments are demonstrated on the NIST database which has outdoor gait and face data of 30 subjects.}, keywords = {access, algorithm;, analysis;, combining, control;, covert, cues;, data, decision, Environment, Face, fusion;, Gait, hierarchical, holistic, human, identification;, importance, intelligent, interfaces;, invariant, perceptual, recognition, recognition;, rules;, sampling;, score, scores;, security;, sensor, sequential, similarity, view}, doi = {10.1109/ICASSP.2004.1327257}, author = {Kale, A. and Roy Chowdhury, A.K. and Chellapa, Rama} } @article {12715, title = {Gait-based human identification from a monocular video sequence}, journal = {Handbook on Pattern Recognition and Computer Vision}, year = {2004}, month = {2004///}, abstract = {Human gait is a spatio-temporal phenomenon that characterizes the motion char-acteristics of an individual. It is possible to detect and measure gait even in low- resolution video. In this chapter, we discuss algorithms for identifying people by their gait from a monocular video sequence. Human identification using gait, sim- ilar to text-based speaker identification, involves different individuals performing the same task and a template-matching approach is suitable for such problems. In situations where the amount of training data is limited, we demonstrate the utility of a simple width feature for gait recognition. By virtue of their determin- istic nature, template matching methods have limited noise resilience. In order to deal with noise we introduce a systematic approach to gait recognition by building representations for the structural and dynamic components of gait using exemplars and hidden Markov models (HMMs). The above methods assume that an exact side-view of the subject is available in the probe sequence. For the case when the person walks at an arbitrary angle far away from the camera we present a view invariant gait recognition algorithm which is based on synthesizing a side view of a person from an arbitrary monocular view. }, author = {Kale, A. and Sundaresan, A. and Roy Chowdhury, A.K. and Chellapa, Rama} } @article {16753, title = {Hierarchical in-network data aggregation with quality guarantees}, journal = {Advances in Database Technology-EDBT 2004}, year = {2004}, month = {2004///}, pages = {577 - 578}, author = {Deligiannakis,A. and Kotidis,Y. and Roussopoulos, Nick} } @article {12690, title = {Identification of humans using gait}, journal = {Image Processing, IEEE Transactions on}, volume = {13}, year = {2004}, month = {2004/09//}, pages = {1163 - 1173}, abstract = {We propose a view-based approach to recognize humans from their gait. Two different image features have been considered: the width of the outer contour of the binarized silhouette of the walking person and the entire binary silhouette itself. To obtain the observation vector from the image features, we employ two different methods. In the first method, referred to as the indirect approach, the high-dimensional image feature is transformed to a lower dimensional space by generating what we call the frame to exemplar (FED) distance. The FED vector captures both structural and dynamic traits of each individual. For compact and effective gait representation and recognition, the gait information in the FED vector sequences is captured in a hidden Markov model (HMM). In the second method, referred to as the direct approach, we work with the feature vector directly (as opposed to computing the FED) and train an HMM. We estimate the HMM parameters (specifically the observation probability B) based on the distance between the exemplars and the image features. In this way, we avoid learning high-dimensional probability density functions. The statistical nature of the HMM lends overall robustness to representation and recognition. The performance of the methods is illustrated using several databases.}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, binary silhouette;frame to exemplar distance;gait databases;gait recognition;hidden Markov model;human identification;image features;observation probability;observation vector;hidden Markov models;image recognition;image representation;image sequences;pro, Biological;Models, Computer-Assisted;Models, Computer-Assisted;Subtraction Technique;Task Performance and Analysis;Video Recording;, Statistical;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2004.832865}, author = {Kale, A. and Sundaresan, A. and Rajagopalan, AN and Cuntoor, N.P. and Roy-Chowdhury, A.K. and Kruger, V. and Chellapa, Rama} } @article {16115, title = {Immediate usability: a case study of public access design for a community photo library}, journal = {Interacting with Computers}, volume = {16}, year = {2004}, month = {2004/12//}, pages = {1171 - 1193}, abstract = {This paper describes a novel instantiation of a digital photo library in a public access system. It demonstrates how designers can utilize characteristics of a target user community (social constraints, trust, and a lack of anonymity) to provide capabilities, such as unrestricted annotation and uploading of photos, which would be impractical in other types of public access systems. It also presents a compact set of design principles and guidelines for ensuring the immediate usability of public access information systems. These principles and guidelines were derived from our experience developing PhotoFinder Kiosk, a community photo library. Attendees of a major HCI conference (CHI 2001 Conference on Human Factors in Computing Systems) successfully used the tool to browse and annotate collections of photographs spanning 20 years of HCI-related conferences, producing a richly annotated photo history of the field of human{\textendash}computer interaction. Observations and usage log data were used to evaluate the tool and develop the guidelines. They provide specific guidance for practitioners, as well as a useful framework for additional research in public access interfaces.}, keywords = {Casual use, Community photo library, direct annotation, direct manipulation, Drag-and-drop, Group annotation, Immediate usability, Photo collection, Public access system, Walk-up-and-use, Zero-trial learning}, isbn = {0953-5438}, doi = {10.1016/j.intcom.2004.07.005}, url = {http://www.sciencedirect.com/science/article/pii/S0953543804000840}, author = {Kules,Bill and Kang,Hyunmo and Plaisant, Catherine and Rose,Anne and Shneiderman, Ben} } @conference {13792, title = {Inducing frame semantic verb classes from WordNet and LDOCE}, booktitle = {Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics}, year = {2004}, month = {2004///}, pages = {375 - 375}, abstract = {This paper presents SemFrame, a systemthat induces frame semantic verb classes from WordNet and LDOCE. Semantic frames are thought to have significant potential in resolving the paraphrase problem challenging many language- based applications. When compared to the handcrafted FrameNet, SemFrame achieves its best recall-precision balance with 83.2\% recall (based on SemFrame{\textquoteright}s coverage of FrameNet frames) and 73.8\% precision (based on SemFrame verbs{\textquoteright} semantic relatedness to frame-evoking verbs). The next best performing semantic verb classes achieve 56.9\% recall and 55.0\% precision. }, author = {Green,R. and Dorr, Bonnie J and Resnik, Philip} } @article {12698, title = {An information theoretic criterion for evaluating the quality of 3-D reconstructions from video}, journal = {Image Processing, IEEE Transactions on}, volume = {13}, year = {2004}, month = {2004/07//}, pages = {960 - 973}, abstract = {Even though numerous algorithms exist for estimating the three-dimensional (3-D) structure of a scene from its video, the solutions obtained are often of unacceptable quality. To overcome some of the deficiencies, many application systems rely on processing more data than necessary, thus raising the question: how is the accuracy of the solution related to the amount of data processed by the algorithm? Can we automatically recognize situations where the quality of the data is so bad that even a large number of additional observations will not yield the desired solution? Previous efforts to answer this question have used statistical measures like second order moments. They are useful if the estimate of the structure is unbiased and the higher order statistical effects are negligible, which is often not the case. This paper introduces an alternative information-theoretic criterion for evaluating the quality of a 3-D reconstruction. The accuracy of the reconstruction is judged by considering the change in mutual information (MI) (termed as the incremental MI) between a scene and its reconstructions. An example of 3-D reconstruction from a video sequence using optical flow equations and known noise distribution is considered and it is shown how the MI can be computed from first principles. We present simulations on both synthetic and real data to demonstrate the effectiveness of the proposed criterion.}, keywords = {3D reconstruction, algorithms, Artificial intelligence, Automated;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer Graphics, Computer-Assisted;Imaging, Computer-Assisted;Software Validation;Subtraction Technique;Video Recording;, Image Enhancement, Image Interpretation, Image reconstruction, Image sequences, information theoretic criterion, Mutual information, NOISE, noise distribution, optical flow equations, second order moments, statistical analysis, Three-Dimensional;Information Storage and Retrieval;Information Theory;Movement;Pattern Recognition, Video sequences, video signal processing}, isbn = {1057-7149}, doi = {10.1109/TIP.2004.827240}, author = {Roy-Chowdhury, A.K. and Chellapa, Rama} } @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} } @article {13796, title = {Interlingual annotation of multilingual text corpora}, journal = {Proceedings of the North American Chapter of the Association for Computational Linguistics Workshop on Frontiers in Corpus Annotation}, year = {2004}, month = {2004///}, pages = {55 - 62}, abstract = {This paper describes a multi-site project toannotate six sizable bilingual parallel corpora for interlingual content. After presenting the background and objectives of the effort, we describe the data set that is being annotated, the interlingua representation language used, an interface environment that supports the an- notation task and the annotation process itself. We will then present a preliminary version of our evaluation methodology and conclude with a summary of the current status of the project along with a number of issues which have arisen. }, author = {Farwell,D. and Helmreich,S. and Dorr, Bonnie J and Habash,N. and Reeder,F. and Miller,K. and Levin,L. and Mitamura,T. and Hovy,E. and Rambow,O. and others} } @conference {16487, title = {Links and paths through life sciences data sources}, booktitle = {Data Integration in the Life Sciences}, year = {2004}, month = {2004///}, pages = {203 - 211}, author = {Lacroix,Z. and Murthy,H. and Naumann,F. and Raschid, Louiqa} } @article {17624, title = {Method of designing signaling networks for internet telephony}, volume = {:~09/517,658}, year = {2004}, month = {2004/02/03/}, abstract = {A method is disclosed for designing a signaling network of call coordinators (CCs) for internet telephony. The new method can be used to design a CC network of arbitrary size that satisfies, with high probability, limitations on the maximum number of sockets per CC and on the maximum number of hops between an arbitrary pair of switches in the network. According to the disclosed method, the network of CCs is treated initially as a collection of isolated points, one point for each CC. Then, links are added between pairs of CCs, excluding pairs lying within the same switch. The links are added randomly, but with a particular probability p, which may be different for different pairs. Thus, whether a given link is added depends, in effect, upon the outcome of a loaded coin toss in which the probability of a positive outcome is p.}, url = {http://www.google.com/patents?id=VTsSAAAAEBAJ}, author = {Aravamudan,Murali and Kumaran,Krishnan and Ramakrishnan,Kajamalai Gopalaswamy and Srinivasan, Aravind}, editor = {Lucent Technologies Inc.} } @article {18542, title = {A model of BGP routing for network engineering}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {32}, year = {2004}, month = {2004/06//}, pages = {331 - 342}, abstract = {The performance of IP networks depends on a wide variety of dynamic conditions. Traffic shifts, equipment failures, planned maintenance, and topology changes in other parts of the Internet can all degrade performance. To maintain good performance, network operators must continually reconfigure the routing protocols. Operators configure BGP to control how traffic flows to neighboring Autonomous Systems (ASes), as well as how traffic traverses their networks. However, because BGP route selection is distributed, indirectly controlled by configurable policies, and influenced by complex interactions with intradomain routing protocols, operators cannot predict how a particular BGP configuration would behave in practice. To avoid inadvertently degrading network performance, operators need to evaluate the effects of configuration changes before deploying them on a live network. We propose an algorithm that computes the outcome of the BGP route selection process for each router in a single AS, given only a static snapshot of the network state, without simulating the complex details of BGP message passing. We describe a BGP emulator based on this algorithm; the emulator exploits the unique characteristics of routing data to reduce computational overhead. Using data from a large ISP, we show that the emulator correctly computes BGP routing decisions and has a running time that is acceptable for many tasks, such as traffic engineering and capacity planning.}, keywords = {BGP, modeling, Routing, traffic engineering}, isbn = {0163-5999}, doi = {10.1145/1012888.1005726}, url = {http://doi.acm.org/10.1145/1012888.1005726}, author = {Feamster, Nick and Winick,Jared and Rexford,Jennifer} } @article {18520, title = {Modeling BGP route selection within an AS}, journal = {IEEE/ACM Transactions on Networking}, year = {2004}, month = {2004///}, abstract = {This paper presents a provably correct model that computes the out-come of the BGP decision process for each router in a single AS, without simulating the complex details of BGP message passing. The model requires only static inputs that can be easily obtained from the routers: the set of candidate routes to a destination (and the routers in the AS at which they were learned), import policies and other session-level parameters, and internal topology. We pro- pose algorithms for computing route selection under four different network configurations: with the MED attribute compared across all routes, and compared only across routes from the same neigh- boring AS; and with a {\textquotedblleft}full mesh{\textquotedblright} internal BGP (iBGP) topology versus an iBGP topology that uses a scalability technique called {\textquotedblleft}route reflection{\textquotedblright}. For each scenario, we derive general properties of the routes that routers ultimately select, present an efficient al- gorithm for computing the outcome of BGP route selection, and prove the algorithm{\textquoteright}s correctness. Studying the general properties and computational overhead of modeling the route selection pro- cess in each of these cases provides insights into the unnecessary complexity introduced by the MED attribute and route reflection; we use these insights to propose improvements to BGP that achieve the same goals as MED and route reflection without introducing the negative side effects of these features. We have implemented some of the algorithms from this paper in a prototype and have shown them to be efficient and accurate enough for many traffic engineer- ing tasks. }, author = {Feamster, Nick and Rexford,J.} } @conference {12683, title = {Multiple view tracking of humans modelled by kinematic chains}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {2}, year = {2004}, month = {2004/10//}, pages = {1009 - 1012 Vol.2 - 1009 - 1012 Vol.2}, abstract = {We use a kinematic chain to model human body motion. We estimate the kinematic chain motion parameters using pixel displacements calculated from video sequences obtained from multiple calibrated cameras to perform tracking. We derive a linear relation between the 2D motion of pixels in terms of the 3D motion parameters of various body parts using a perspective projection model for the cameras, a rigid body motion model for the base body and the kinematic chain model for the body parts. An error analysis of the estimator is provided, leading to an iterative algorithm for calculating the motion parameters from the pixel displacements. We provide experimental results to demonstrate the accuracy of our formulation. We also compare our iterative algorithm to the noniterative algorithm and discuss its robustness in the presence of noise.}, keywords = {3D, algorithm;, analysis;, body, calibrated, cameras;, chain, displacement;, error, estimation;, human, image, iterative, kinematic, kinematics;, methods;, model;, MOTION, motion;, multiple, parameters;, perspective, Pixel, processing;, projection, sequences;, signal, tracking;, video, view}, doi = {10.1109/ICIP.2004.1419472}, author = {Sundaresan, A. and Chellapa, Rama and RoyChowdhury, R.} } @article {13308, title = {Multi-resolution modeling, visualization and streaming of volume meshes}, journal = {Eurographics 2004, Tutorials 2: Multi-resolution Modeling, Visualization and Streaming of Volume Meshes}, year = {2004}, month = {2004///}, author = {Cignoni,P. and De Floriani, Leila and Lindstrom,P. and Pascucci,V. and Rossignac,J. and Silva,C.} } @conference {17805, title = {Oasys: An opinion analysis system}, booktitle = {AAAI Spring symposium on Computational Approaches to Analyzing Weblogs}, year = {2004}, month = {2004///}, abstract = {There are numerous applications in which we would like toassess what opinions are being expressed in text documents. For example, Martha Stewart{\textquoteright}s company may have wished to assess the degree of harshness of news articles about her in the recent past. Likewise, a World Bank official may wish to as- sess the degree of criticism of a proposed dam in Bangladesh. The ability to gauge opinion on a given topic is therefore of critical interest. In this paper, we develop a suite of algo- rithms which take as input, a set D of documents as well as a topic t, and gauge the degree of opinion expressed about topic t in the set D of documents. Our algorithms can return both a number (larger the number, more positive the opinion) as well as a qualitative opinion (e.g. harsh, complimentary). We as- sess the accuracy of these algorithms via human experiments and show that the best of these algorithms can accurately re- flect human opinions. We have also conducted performance experiments showing that our algorithms are computationally fast. }, author = {Cesarano,C. and Dorr, Bonnie J and Picariello, A. and Reforgiato,D. and Sagoff,A. and V.S. Subrahmanian} } @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.} } @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 {16493, title = {Querying Web-Accessible Life Science Sources: Which paths to choose?}, booktitle = {Proceedings of VLDB Workshop on Information Integration on the Web (IIWeb-2004)}, year = {2004}, month = {2004///}, pages = {83 - 83}, author = {Bleiholder,J. and Naumann,F. and Raschid, Louiqa and Vidal,M. E} } @article {18989, title = {Reducing storage requirements for biological sequence comparison}, journal = {BioinformaticsBioinformatics}, volume = {20}, year = {2004}, month = {2004/12/12/}, pages = {3363 - 3369}, abstract = {Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the {\textquoteleft}seed-and-extend{\textquoteright} approach, in which occurrences of short subsequences called {\textquoteleft}seeds{\textquoteright} are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process.Results: We present a simple and elegant method in which only a small fraction of seeds, called {\textquoteleft}minimizers{\textquoteright}, needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds. }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/bth408}, url = {http://bioinformatics.oxfordjournals.org/content/20/18/3363}, author = {Roberts,Michael and Hayes,Wayne and Hunt,Brian R. and Mount, Stephen M. and Yorke,James A.} } @article {14768, title = {Resource policing to support fine-grain cycle stealing in networks of workstations}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {15}, year = {2004}, month = {2004/10//}, pages = {878 - 892}, abstract = {We present the design, implementation, and performance evaluation of a suite of resource policing mechanisms that allow guest processes to efficiently and unobtrusively exploit otherwise idle workstation resources. Unlike traditional policies that harvest cycles only from unused machines, we employ fine-grained cycle stealing to exploit resources even from machines that have active users. We developed a suite of kernel extensions that enable these policies to operate without significantly impacting host processes: 1) a new starvation-level CPU priority for guest jobs, 2) a new page replacement policy that imposes hard bounds on physical memory usage by guest processes, and 3) a new I/O scheduling mechanism called rate windows that throttle guest processes{\textquoteright} usage of I/O and network bandwidth. We evaluate both the individual impacts of each mechanism, and their utility for our fine-grain cycle stealing.}, keywords = {65, Application software, Bandwidth, cluster computing, Computer networks, Computer Society, Concurrent computing, cycle stealing, cycle stealing., grid computing, I/O scheduling, Intelligent networks, Kernel, network bandwidth, networks of workstations, page replacement policy, parallel computing, performance evaluation, Processor scheduling, resource allocation, resource scheduling, starvation-level CPU priority, workstation clusters, workstation resources, Workstations}, isbn = {1045-9219}, doi = {10.1109/TPDS.2004.58}, author = {Ryu, K. D and Hollingsworth, Jeffrey K} } @article {13854, title = {Semantic annotation and lexico-syntactic paraphrase}, journal = {Proceedings of the 4th International Conference on Language Resources and Evaluation (LREC) Workshop on Building Lexical Resources from Semantically Annotated Corpora}, year = {2004}, month = {2004///}, pages = {47 - 52}, abstract = {The IAMTC project (Interlingual Annotation of Multilingual Translation Corpora) is developing an interlingual representation frameworkfor annotation of parallel corpora (English paired with Arabic, French, Hindi, Japanese, Korean, and Spanish) with deep-semantic representations. In particular, we are investigating meaning equivalent paraphrases involving conversives and non-literal language use, as well as extended paraphrases involving syntax, lexicon, and grammatical features. The interlingua representation has three levels of depth. Each level is characterized by the types of meaning equivalent paraphrases that receive identical representations at that level. }, author = {Dorr, Bonnie J and Green,R. and Levin,L. and Rambow,O. and Farwell,D. and Habash,N. and Helmreich,S. and Hovy,E. and Miller,K.J. and Mitamura,T. and others} } @article {13855, title = {Semantic Annotation for Interlingual Representation of Multilingual Texts}, journal = {Workshop Programme}, year = {2004}, month = {2004///}, pages = {19 - 19}, abstract = {This paper describes the annotation process being used in a multi-site project to create six sizable bilingual parallel corpora annotated with a consistent interlingua representation. After presenting the background and objectives of the effort, we describe the multilingual corpora and the three stages of interlingual representation being developed. We then focus on the annotation process itself, including an interface environment that supports the annotation task, and the methodology for evaluating the interlingua representation. Finally, we discuss some issues encountered during the annotation tasks. The resulting annotated multilingual corpora will be useful for a wide range of natural language processing research tasks, including machine translation, question answering, text summarization, and information extraction.}, author = {Mitamura,T. and Miller,K. and Dorr, Bonnie J and Farwell,D. and Habash,N. and Helmreich,S. and Hovy,E. and Levin,L. and Rambow,O. and Reeder,F. and others} } @inbook {17367, title = {Social and psychological influences on computer user frustration}, booktitle = {Media access: Social and psychological dimensions of new technology useMedia access: Social and psychological dimensions of new technology use}, year = {2004}, month = {2004///}, pages = {91 - 103}, author = {Bessiere,K. and Ceaparu,I. and Lazar,J. and Robinson,J. and Shneiderman, Ben} } @article {18713, title = {Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, volume = {279}, year = {2004}, month = {2004/02/20/}, pages = {7055 - 7063}, abstract = {Diverse cellular events are regulated by post-translational modification of substrate proteins via covalent attachment of one or a chain of ubiquitin molecules. The outcome of (poly)ubiquitination depends upon the specific lysine residues involved in the formation of polyubiquitin chains. Lys48-linked chains act as a universal signal for proteasomal degradation, whereas Lys63-linked chains act as a specific signal in several non-degradative processes. Although it has been anticipated that functional diversity between alternatively linked polyubiquitin chains relies on linkage-dependent differences in chain conformation/topology, direct structural evidence in support of this model has been lacking. Here we use NMR methods to determine the structure of a Lys63-linked di-ubiquitin chain. The structure is characterized by an extended conformation, with no direct contact between the hydrophobic residues Leu8, Ile44, and Val70 on the ubiquitin units. This structure contrasts with the closed conformation observed for Lys48-linked di-ubiquitin wherein these residues form the interdomain interface (Cook, W. J., Jeffrey, L. C., Carson, M., Zhijian, C., and Pickart, C. M. (1992) J. Biol. Chem. 267, 16467-16471; Varadan, R., Walker, O., Pickart, C., and Fushman, D. (2002) J. Mol. Biol. 324, 637-647). Consistent with the open conformation of the Lys63-linked di-ubiquitin, our binding studies show that both ubiquitin domains in this chain can bind a ubiquitin-associated domain from HHR23A independently and in a mode similar to that for mono-ubiquitin. In contrast, Lys48-linked di-ubiquitin binds in a different, higher affinity mode that has yet to be determined. This is the first experimental evidence that alternatively linked polyubiquitin chains adopt distinct conformations.}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.M309184200}, url = {http://www.jbc.org/content/279/8/7055}, author = {Varadan,Ranjani and Assfalg,Michael and Haririnia,Aydin and Raasi,Shahri and Pickart,Cecile and Fushman, David} } @article {18490, title = {Some foundational problems in interdomain routing}, journal = {Proceedings of Third Workshop on Hot Topics in Networks (HotNets-III)}, year = {2004}, month = {2004///}, abstract = {The substantial complexity of interdomain routing in theInternet comes from the need to support flexible poli- cies while scaling to a large number of Autonomous Systems. Despite impressive progress in characterizing the various ills of the Border Gateway Protocol (BGP), many problems remain unsolved, and the behavior of the routing system is still poorly understood. This paper argues that we must understand interdomain routing in terms of: (1) intrinsic properties and design tradeoffs of policy-based routing, independent of the specific routing protocol and (2) properties that relate to artifacts in to- day{\textquoteright}s protocol. We pose open questions for the research community that, if answered, should help us understand why BGP{\textquoteright}s many problems are so difficult to fix. Un- derstanding the fundamental properties of interdomain routing will help us decide how to make progress, be it making backward-compatible modifications to BGP or designing a radically different protocol. }, author = {Feamster, Nick and Balakrishnan,H. and Rexford,J.} } @article {14042, title = {A study of the pinna anthropometry and the spectral notch frequencies}, journal = {The Journal of the Acoustical Society of America}, volume = {116}, year = {2004}, month = {2004///}, pages = {2625 - 2625}, abstract = {The head-related transfer function (HRTF) varies significantly between individuals due to the different sizes and shapes of different anatomical parts like the pinnae, head, and torso. Applications in the creation of virtual auditory displays require individual HRTFs for perceptual fidelity. A generic HRTF would not work satisfactorily, since it has been shown that nonindividual HRTFs result in poor elevation perception. While good geometrical models exist for the effects of head, torso, and shoulders, a simple model for the pinna that connects the anthropometry to the features in the HRTF does not exist. One of the prominent cues contributed by the pinna are the sharp spectral notches, which encode the elevation of the sound source. Recently, we proposed a method to extract the frequencies of the pinna spectral notches from the HRTF. In this paper we study the relationship between the extracted notch frequency and pinna anthropometry. Based on these observations new approaches for HRTF customization can be developed. [The support of NSF Award ITR-0086075 is gratefully acknowledged.]}, url = {http://link.aip.org/link/?JAS/116/2625/3}, author = {Raykar,Vikas C. and Duraiswami, Ramani and Yegnanarayana,B.} } @article {16480, title = {Techniques for optimization of queries on integrated biological resources}, journal = {Journal of bioinformatics and computational biology}, volume = {2}, year = {2004}, month = {2004///}, pages = {375 - 412}, author = {Lacroix,Z. and Raschid, Louiqa and Eckman,B. A} } @article {16566, title = {Temporally asymmetric learning supports sequence processing in multi-winner self-organizing maps}, journal = {Neural Computation}, volume = {16}, year = {2004}, month = {2004///}, pages = {535 - 561}, author = {Schulz,R. and Reggia, James A.} } @article {14376, title = {Understanding tuberculosis epidemiology using structured statistical models}, journal = {Artificial Intelligence in Medicine}, volume = {30}, year = {2004}, month = {2004/03//}, pages = {233 - 256}, abstract = {Molecular epidemiological studies can provide novel insights into the transmission of infectious diseases such as tuberculosis. Typically, risk factors for transmission are identified using traditional hypothesis-driven statistical methods such as logistic regression. However, limitations become apparent in these approaches as the scope of these studies expand to include additional epidemiological and bacterial genomic data. Here we examine the use of Bayesian models to analyze tuberculosis epidemiology. We begin by exploring the use of Bayesian networks (BNs) to identify the distribution of tuberculosis patient attributes (including demographic and clinical attributes). Using existing algorithms for constructing BNs from observational data, we learned a BN from data about tuberculosis patients collected in San Francisco from 1991 to 1999. We verified that the resulting probabilistic models did in fact capture known statistical relationships. Next, we examine the use of newly introduced methods for representing and automatically constructing probabilistic models in structured domains. We use statistical relational models (SRMs) to model distributions over relational domains. SRMs are ideally suited to richly structured epidemiological data. We use a data-driven method to construct a statistical relational model directly from data stored in a relational database. The resulting model reveals the relationships between variables in the data and describes their distribution. We applied this procedure to the data on tuberculosis patients in San Francisco from 1991 to 1999, their Mycobacterium tuberculosis strains, and data on contact investigations. The resulting statistical relational model corroborated previously reported findings and revealed several novel associations. These models illustrate the potential for this approach to reveal relationships within richly structured data that may not be apparent using conventional statistical approaches. We show that Bayesian methods, in particular statistical relational models, are an important tool for understanding infectious disease epidemiology.}, keywords = {Bayesian networks, epidemiology, Probabilistic and statistical relational models, Tuberculosis}, isbn = {0933-3657}, doi = {10.1016/j.artmed.2003.11.003}, url = {http://www.sciencedirect.com/science/article/pii/S0933365703001337}, author = {Getoor, Lise and Rhee,Jeanne T and Koller,Daphne and Small,Peter} } @article {12792, title = {Unit verification: the CARA experience}, journal = {International Journal on Software Tools for Technology Transfer (STTT)}, volume = {5}, year = {2004}, month = {2004///}, pages = {351 - 369}, author = {Ray,A. and Cleaveland, Rance} } @conference {14817, title = {Unobtrusiveness and efficiency in idle cycle stealing for PC grids}, booktitle = {Parallel and Distributed Processing Symposium, 2004. Proceedings. 18th International}, year = {2004}, month = {2004/04/26/30}, publisher = {IEEE}, organization = {IEEE}, abstract = {Summary form only given. Studies have shown that for a significant fraction of the time desktop PCs and workstations are under-utilized. To exploit these idle resources, various desktop/workstation grid systems have been developed. The ultimate goal of such systems is to maximize efficiency of resource usage while maintaining low obtrusiveness to machine owners. To this end, we created a new fine-grain cycle stealing approach and conducted a performance comparison study against the traditional coarse-grain cycle stealing. We developed a prototype of fine-grain cycle stealing, the Linger-Longer system, on a Linux cluster. The experiments on a cluster of desktop Linux PCs with benchmark applications show that, overall, fine-grain cycle stealing can improve efficiency of idle cycle usage by increasing the guest job throughput by 50\% to 70\%, while limiting obtrusiveness with no more than 3\% of host job slowdown.}, keywords = {Biological system modeling, Computational modeling, Computer science, Computer simulation, Contracts, desktop grid system, fine-grain cycle stealing approach, grid computing, idle cycle stealing, Linger-Longer system, Linux, Linux cluster, microcomputers, PC grids, Personal communication networks, Prototypes, resource allocation, Throughput, workstation clusters, workstation grid systems, Workstations}, isbn = {0-7695-2132-0}, doi = {10.1109/IPDPS.2004.1302987}, author = {Ryu, K. D and Hollingsworth, Jeffrey K} } @article {16591, title = {Using distributed partial memories to improve self-organizing collective movements}, journal = {Systems, Man, and Cybernetics, Part B: Cybernetics, IEEE Transactions on}, volume = {34}, year = {2004}, month = {2004///}, pages = {1697 - 1707}, author = {Winder,R. and Reggia, James A.} } @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} } @article {12936, title = {Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {70}, year = {2004}, month = {2004/12/01/}, pages = {7481 - 7486}, abstract = {In Argentina, as in other countries of Latin America, cholera has occurred in an epidemic pattern. Vibrio cholerae O1 is native to the aquatic environment, and it occurs in both culturable and viable but nonculturable (VNC) forms, the latter during interepidemic periods. This is the first report of the presence of VNC V. cholerae O1 in the estuarine and marine waters of the R{\'\i}o de la Plata and the Argentine shelf of the Atlantic Ocean, respectively. Employing immunofluorescence and PCR methods, we were able to detect reservoirs of V. cholerae O1 carrying the virulence-associated genes ctxA and tcpA. The VNC forms of V. cholerae O1 were identified in samples of water, phytoplankton, and zooplankton; the latter organisms were mainly the copepods Acartia tonsa, Diaptomus sp., Paracalanus crassirostris, and Paracalanus parvus. We found that under favorable conditions, the VNC form of V. cholerae can revert to the pathogenic, transmissible state. We concluded that V. cholerae O1 is a resident of Argentinean waters, as has been shown to be the case in other geographic regions of the world.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.70.12.7481-7486.2004}, url = {http://aem.asm.org/content/70/12/7481}, author = {Binsztein,Norma and Costagliola,Marcela C. and Pichel,Mariana and Jurquiza,Ver{\'o}nica and Ram{\'\i}rez,Fernando C. and Akselman,Rut and Vacchino,Marta and Huq,Anwarul and Rita R Colwell} } @article {16497, title = {Wide area performance monitoring using aggregate latency profiles}, journal = {Web Engineering}, year = {2004}, month = {2004///}, pages = {771 - 775}, author = {Zadorozhny,V. and Gal,A. and Raschid, Louiqa and Ye,Q.} } @article {12699, title = {Wide baseline image registration with application to 3-D face modeling}, journal = {Multimedia, IEEE Transactions on}, volume = {6}, year = {2004}, month = {2004/06//}, pages = {423 - 434}, abstract = {Establishing correspondence between features in two images of the same scene taken from different viewing angles is a challenging problem in image processing and computer vision. However, its solution is an important step in many applications like wide baseline stereo, three-dimensional (3-D) model alignment, creation of panoramic views, etc. In this paper, we propose a technique for registration of two images of a face obtained from different viewing angles. We show that prior information about the general characteristics of a face obtained from video sequences of different faces can be used to design a robust correspondence algorithm. The method works by matching two-dimensional (2-D) shapes of the different features of the face (e.g., eyes, nose etc.). A doubly stochastic matrix, representing the probability of match between the features, is derived using the Sinkhorn normalization procedure. The final correspondence is obtained by minimizing the probability of error of a match between the entire constellation of features in the two sets, thus taking into account the global spatial configuration of the features. The method is applied for creating holistic 3-D models of a face from partial representations. Although this paper focuses primarily on faces, the algorithm can also be used for other objects with small modifications.}, keywords = {2D, 3D, algorithm;, baseline, biometrics;, Computer, configuration;, correspondence, doubly, error, extraction;, Face, feature, holistic, image, matching;, matrix;, minimization;, modeling;, models;, normalization, probability, probability;, procedure;, processes;, processing;, recognition;, registration;, representation;, sequences;, shapes;, Sinkhorn, spatial, statistics;, Stochastic, video, vision;, wide}, isbn = {1520-9210}, doi = {10.1109/TMM.2004.827511}, author = {Roy-Chowdhury, A.K. and Chellapa, Rama and Keaton, T.} } @book {18790, title = {19th Biennial Conference on Mechanical Vibration and Noise}, year = {2003}, month = {2003///}, publisher = {American Society of Mechanical Engineers}, organization = {American Society of Mechanical Engineers}, author = {Gupta,A. K. and Fadel,G. M. and Lewicki,D. G. and Shabana,A. A. and Royston,T. J. and Gupta,S.K. and Hayes,C. and Herrmann,J.W. and Dym,C. L. and Schmidt,L. C.} } @article {12719, title = {Accurate dense optical flow estimation using adaptive structure tensors and a parametric model}, journal = {Image Processing, IEEE Transactions on}, volume = {12}, year = {2003}, month = {2003/10//}, pages = {1170 - 1180}, abstract = {An accurate optical flow estimation algorithm is proposed in this paper. By combining the three-dimensional (3D) structure tensor with a parametric flow model, the optical flow estimation problem is converted to a generalized eigenvalue problem. The optical flow can be accurately estimated from the generalized eigenvectors. The confidence measure derived from the generalized eigenvalues is used to adaptively adjust the coherent motion region to further improve the accuracy. Experiments using both synthetic sequences with ground truth and real sequences illustrate our method. Comparisons with classical and recently published methods are also given to demonstrate the accuracy of our algorithm.}, keywords = {3D, accuracy;, adaptive, and, coherent, confidence, dense, eigenfunctions;, eigenvalue, eigenvalues, eigenvectors;, estimation;, flow, generalized, ground, image, measure;, model;, MOTION, optical, parameter, parametric, problem;, real, region;, sequences;, structure, synthetic, tensor;, tensors;, three-dimensional, truth;}, isbn = {1057-7149}, doi = {10.1109/TIP.2003.815296}, author = {Liu,Haiying and Chellapa, Rama and Rosenfeld, A.} } @conference {12729, title = {Activity recognition using the dynamics of the configuration of interacting objects}, booktitle = {Computer Vision and Pattern Recognition, 2003. Proceedings. 2003 IEEE Computer Society Conference on}, volume = {2}, year = {2003}, month = {2003/06//}, pages = {II - 633-40 vol.2 - II - 633-40 vol.2}, abstract = {Monitoring activities using video data is an important surveillance problem. A special scenario is to learn the pattern of normal activities and detect abnormal events from a very low resolution video where the moving objects are small enough to be modeled as point objects in a 2D plane. Instead of tracking each point separately, we propose to model an activity by the polygonal {\textquoteright}shape{\textquoteright} of the configuration of these point masses at any time t, and its deformation over time. We learn the mean shape and the dynamics of the shape change using hand-picked location data (no observation noise) and define an abnormality detection statistic for the simple case of a test sequence with negligible observation noise. For the more practical case where observation (point locations) noise is large and cannot be ignored, we use a particle filter to estimate the probability distribution of the shape given the noisy observations up to the current time. Abnormality detection in this case is formulated as a change detection problem. We propose a detection strategy that can detect both {\textquoteright}drastic{\textquoteright} and {\textquoteright}slow{\textquoteright} abnormalities. Our framework can be directly applied for object location data obtained using any type of sensors - visible, radar, infrared or acoustic.}, keywords = {2D, abnormal, abnormality, abnormality;, acoustic, activity, analysis;, change;, Computer, configuration, configuration;, data;, DETECTION, detection;, distribution;, drastic, dynamics;, event;, filter;, hand-picked, image, infrared, interacting, learning;, location, low, mean, model;, monitoring;, MOTION, moving, noise;, noisy, object, object;, observation, observation;, particle, pattern, plane;, point, polygonal, probability, probability;, problem;, processing;, radar, recognition;, resolution, sensor;, sensors;, sequence;, SHAPE, shape;, signal, slow, statistic;, strategy;, Surveillance, surveillance;, target, test, tracking;, video, video;, visible, vision;}, doi = {10.1109/CVPR.2003.1211526}, author = {Vaswani, N. and RoyChowdhury, A. and Chellapa, Rama} } @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 {14108, title = {An Analysis of Smoothing Effects of Upwinding Strategies for the Convection-Diffusion Equation}, journal = {SIAM Journal on Numerical Analysis}, volume = {40}, year = {2003}, month = {2003/01/01/}, pages = {254 - 281}, abstract = {Using a technique for constructing analytic expressions for discrete solutions to the convection-diffusion equation, we examine and characterize the effects of upwinding strategies on solution quality. In particular, for grid-aligned flow and discretization based on bilinear finite elements with streamline upwinding, we show precisely how the amount of upwinding included in the discrete operator affects solution oscillations and accuracy when different types of boundary layers are present. This analysis provides a basis for choosing a streamline upwinding parameter which also gives accurate solutions for problems with non-grid-aligned and variable speed flows. In addition, we show that the same analytic techniques provide insight into other discretizations, such as a finite difference method that incorporates streamline diffusion and the isotropic artificial diffusion method.}, isbn = {0036-1429}, url = {http://www.jstor.org/stable/4100953}, author = {Elman, Howard and Alison Ramage} } @inbook {17558, title = {Approximation Algorithms for Channel Allocation Problems in Broadcast Networks}, booktitle = {Approximation, Randomization, and Combinatorial Optimization: Algorithms and Techniques}, series = {Lecture Notes in Computer Science}, volume = {2764}, year = {2003}, month = {2003///}, pages = {821 - 826}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We study two packing problems that arise in the area of dissemination-based information systems; a second theme is the study of distributed approximation algorithms. The problems considered have the property that the space occupied by a collection of objects together could be significantly less than the sum of the sizes of the individual objects. In the Channel Allocation Problem , there are users who request subsets of items. There are a fixed number of channels that can carry an arbitrary amount of information. Each user must get all of the requested items from one channel, i.e., all the data items of each request must be broadcast on some channel. The load on any channel is the number of items that are broadcast on that channel; the objective is to minimize the maximum load on any channel. We present approximation algorithms for this problem and also show that the problem is MAX-SNP hard. The second problem is the Edge Partitioning Problem addressed by Goldschmidt, Hochbaum, Levin, and Olinick ( Networks, 41:13-23, 2003 ). Each channel here can deliver information to at most k users, and we aim to minimize the total load on all channels. We present an O ( n 1/3 ){\textendash}approximation algorithm and also show that the algorithm can be made fully distributed with the same approximation guarantee; we also generalize to the case of hypergraphs.}, isbn = {978-3-540-40770-6}, url = {http://dx.doi.org/10.1007/978-3-540-45198-3_5}, author = {Gandhi,Rajiv and Khuller, Samir and Srinivasan, Aravind and Wang,Nan}, editor = {Arora,Sanjeev and Jansen,Klaus and Rolim,Jos{\'e} and Sahai,Amit} } @article {18661, title = {AQuA: an adaptive architecture that provides dependable distributed objects}, journal = {Computers, IEEE Transactions on}, volume = {52}, year = {2003}, month = {2003/01//}, pages = {31 - 50}, abstract = {Building dependable distributed systems from commercial off-the-shelf components is of growing practical importance. For both cost and production reasons, there is interest in approaches and architectures that facilitate building such systems. The AQuA architecture is one such approach; its goal is to provide adaptive fault tolerance to CORBA applications by replicating objects. The AQuA architecture allows application programmers to request desired levels of dependability during applications{\textquoteright} runtimes. It provides fault tolerance mechanisms to ensure that a CORBA client can always obtain reliable services, even if the CORBA server object that provides the desired services suffers from crash failures and value faults. AQuA includes a replicated dependability manager that provides dependability management by configuring the system in response to applications{\textquoteright} requests and changes in system resources due to faults. It uses Maestro/Ensemble to provide group communication services. It contains a gateway to intercept standard CORBA IIOP messages to allow any standard CORBA application to use AQuA. It provides different types of replication schemes to forward messages reliably to the remote replicated objects. All of the replication schemes ensure strong, data consistency among replicas. This paper describes the AQuA architecture and presents, in detail, the active replication pass-first scheme. In addition, the interface to the dependability manager and the design of the dependability manager replication are also described. Finally, we describe performance measurements that were conducted for the active replication pass-first scheme, and we present results from our study of fault detection, recovery, and blocking times.}, keywords = {active replication pass-first scheme, adaptive architecture, adaptive fault tolerance, AQuA, CORBA, data consistency, data integrity, dependable distributed objects, distributed object management, performance measurements, quality of service, replicated dependability manager, replication schemes, software fault tolerance, system resources}, isbn = {0018-9340}, doi = {10.1109/TC.2003.1159752}, author = {Ren,Yansong and Bakken,D. E. and Courtney,T. and Michel Cukier and Karr,D. A. and Rubel,P. and Sabnis,C. and Sanders,W. H. and Schantz,R.E. and Seri,M.} } @conference {12801, title = {Architectural Interaction Diagrams: AIDs for System Modeling}, booktitle = {Software Engineering, International Conference on}, year = {2003}, month = {2003///}, pages = {396 - 396}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper develops a modeling paradigm called Architectural Interaction Diagrams, or AIDs, for the high-level design of systems containing concurrent, interacting components. The novelty of AIDs is that they introduce interaction mechanisms, or buses, as first-class entities into the modeling vocabulary. Users then have the capability, in their modeling, of using buses whose behavior captures interaction at a higher level of abstraction than that afforded by modeling notations such as Message Sequence Charts or process algebra, which typically provide only one fixed interaction mechanism. This paper defines AIDs formally by giving them an operational semantics that describes how buses combine subsystem transitions into system-level transitions. This semantics enables AIDs to be simulated; to incorporate subsystems given in different modeling notations into a single system model; and to use testing, debugging and model checking early in the system design cycle in order to catch design errors before they are implemented.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICSE.2003.1201218}, author = {Ray,Arnab and Cleaveland, Rance} } @article {13250, title = {AUDIO-P2. 1: PITCH AND TIMBRE MANIPULATIONS USING CORTICAL REPRESENTATION OF SOUND}, journal = {IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS SPEECH AND SIGNAL PROCESSING}, volume = {5}, year = {2003}, month = {2003///}, author = {Zotkin,Dmitry N and Shamma,S.A. and Ru,P. and Duraiswami, Ramani and Davis, Larry S.} } @conference {16784, title = {Balancing performance and data freshness in web database servers}, booktitle = {Proceedings of the 29th international conference on Very large data bases-Volume 29}, year = {2003}, month = {2003///}, pages = {393 - 404}, author = {Labrinidis,A. and Roussopoulos, Nick} } @article {14161, title = {A characterisation of oscillations in the discrete two-dimensional convection-diffusion equation}, journal = {Mathematics of computation}, volume = {72}, year = {2003}, month = {2003///}, pages = {263 - 288}, author = {Elman, Howard and Ramage, A.} } @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} } @article {13911, title = {A collaborative digital library for children}, journal = {Journal of Computer Assisted Learning}, volume = {19}, year = {2003}, month = {2003///}, pages = {239 - 248}, author = {Druin, Allison and Revelle,G. and Bederson, Benjamin B. and Hourcade,J. P and Farber,A. and Lee,J. and Campbell,D.} } @article {12985, title = {Comparing bootstrap and posterior probability values in the four-taxon case}, journal = {Syst Biol}, volume = {52}, year = {2003}, month = {2003/08//}, pages = {477 - 487}, abstract = {Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. We used simulated data and the four-taxon case to explore the relationship between nonparametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified: (1) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not significant, (2) near the two-branch corner, and (3) deep in the two-branch corner. In the last two regions, significant differences occur between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star topologies revealed that both bootstrap and posterior probability values differ significantly from theoretical expectations; in particular, there are more posterior probability values in the range 0.85-1 than expected by theory. Therefore, our results corroborate the findings of others that posterior probability values are excessively high. Our results also suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probability values.}, author = {Cummings, Michael P. and Handley,S. A and Myers,D. S and Reed,D. L and Rokas,A. and Winka,K.} } @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} } @article {16515, title = {Cost minimization during simulated evolution of paired neural networks leads to asymmetries and specialization}, journal = {Cognitive Systems Research}, volume = {4}, year = {2003}, month = {2003///}, pages = {365 - 383}, author = {Shkuro,Y. and Reggia, James A.} } @inbook {17639, title = {On the Covering Steiner Problem}, booktitle = {FST TCS 2003: Foundations of Software Technology and Theoretical Computer ScienceFST TCS 2003: Foundations of Software Technology and Theoretical Computer Science}, series = {Lecture Notes in Computer Science}, volume = {2914}, year = {2003}, month = {2003///}, pages = {244 - 251}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The Covering Steiner problem is a common generalization of the k -MST and Group Steiner problems. An instance of the Covering Steiner problem consists of an undirected graph with edge-costs, and some subsets of vertices called groups , with each group being equipped with a non-negative integer value (called its requirement ); the problem is to find a minimum-cost tree which spans at least the required number of vertices from every group. When all requirements are equal to 1, this is the Group Steiner problem. While many covering problems (e.g., the covering integer programs such as set cover) become easier to approximate as the requirements increase, the Covering Steiner problem remains at least as hard to approximate as the Group Steiner problem; in fact, the best guarantees previously known for the Covering Steiner problem were worse than those for Group Steiner as the requirements became large. In this work, we present an improved approximation algorithm whose guarantee equals the best known guarantee for the Group Steiner problem.}, isbn = {978-3-540-20680-4}, url = {http://dx.doi.org/10.1007/978-3-540-24597-1_21}, author = {Gupta,Anupam and Srinivasan, Aravind}, editor = {Pandya,Paritosh and Radhakrishnan,Jaikumar} } @article {12194, title = {Designing a digital library for young children: An intergenerational partnership}, journal = {The craft of information visualization: readings and reflections}, volume = {178}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Hourcade,J. P and Sherman,L. and Revelle,G. and Platner,M. and Weng,S.} } @article {13754, title = {Desparately seeking cebuano}, journal = {Third Conference on Human Language Technologies}, year = {2003}, month = {2003///}, abstract = {This paper describes an effort to rapidly de-velop language resources and component tech- nology to support searching Cebuano news sto- ries using English queries. Results from the first 60 hours of the exercise are presented. }, author = {Oard, Douglas and David Doermann and Dorr, Bonnie J and He,D. and Resnik, Philip and Weinberg, Amy and Byrne,W. and Khudanpur,S. and Yarowsky,D. and Leuski,A. and others} } @article {12948, title = {Direct Detection of Vibrio Cholerae and ctxA in Peruvian Coastal Water and Plankton by PCR}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {69}, year = {2003}, month = {2003/06/01/}, pages = {3676 - 3680}, abstract = {Seawater and plankton samples were collected over a period of 17 months from November 1998 to March 2000 along the coast of Peru. Total DNA was extracted from water and from plankton grouped by size into two fractions (64 μm to 202 μm and >202 μm). All samples were assayed for Vibrio cholerae, V. cholerae O1, V. cholerae O139, and ctxA by PCR. Of 50 samples collected and tested, 33 (66.0\%) were positive for V. cholerae in at least one of the three fractions. Of these, 62.5\% (n = 32) contained V. cholerae O1; ctxA was detected in 25\% (n = 20) of the V. cholerae O1-positive samples. None were positive for V. cholerae O139. Thus, PCR was successfully employed in detecting toxigenic V. cholerae directly in seawater and plankton samples and provides evidence for an environmental reservoir for this pathogen in Peruvian coastal waters.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.69.6.3676-3680.2003}, url = {http://aem.asm.org/content/69/6/3676}, author = {Lipp,Erin K. and Rivera,Irma N. G. and Gil,Ana I. and Espeland,Eric M. and Choopun,Nipa and Louis,Val{\'e}rie R. and Russek-Cohen,Estelle and Huq,Anwar and Rita R Colwell} } @article {19078, title = {The dog genome: survey sequencing and comparative analysis}, journal = {Science}, volume = {301}, year = {2003}, month = {2003}, author = {Kirkness,E. F and Bafna,V. and Halpern,A. L and Levy,S. and Remington,K. and Rusch,D. B and Delcher,A. L and Pop, Mihai and Wang,W. and Fraser,C. M and others} } @article {16289, title = {The Dog Genome: Survey Sequencing and Comparative Analysis}, journal = {ScienceScience}, volume = {301}, year = {2003}, month = {2003/09/26/}, pages = {1898 - 1903}, abstract = {A survey of the dog genome sequence (6.22 million sequence reads; 1.5{\texttimes} coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25\%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1086432}, url = {http://www.sciencemag.org/content/301/5641/1898}, author = {Kirkness,Ewen F. and Bafna,Vineet and Halpern,Aaron L. and Levy,Samuel and Remington,Karin and Rusch,Douglas B and Delcher,Arthur L. and Pop, Mihai and Wang,Wei and Fraser,Claire M. and Venter,J. Craig} } @conference {16772, title = {Efficient dissemination of aggregate data over the wireless web}, booktitle = {International Workshop on the Web and Databases (WebDB)}, year = {2003}, month = {2003///}, pages = {93 - 98}, author = {Sharaf,M. A and Sismanis,Y. and Labrinidis,A. and Chrysanthis,P. and Roussopoulos, Nick} } @article {12129, title = {Eight lessons learned during COTS-based systems maintenance}, journal = {Software, IEEE}, volume = {20}, year = {2003}, month = {2003/10//sept}, pages = {94 - 96}, abstract = {To make better decisions relative to CBSs, we need empirical knowledge. To gain this knowledge, we must more fully understand the lifecycle processes people use when harnessing COTS packages. The initial findings reported here are but the first step in our attempts to capture this empirical knowledge. We plan to continue collecting data and investigating the phenomenology of COTS-based systems.}, keywords = {COTS, COTS-based, cycle, life, lifecycle, Maintenance, maintenance;, object-oriented, packages;, phase;, processes;, programming;, reusability;, software, systems}, isbn = {0740-7459}, doi = {10.1109/MS.2003.1231161}, author = {Reifer,D.J. and Basili, Victor R. and Boehm,B.W. and Clark,B.} } @inbook {17136, title = {Errors}, booktitle = {Encyclopedia of Computer ScienceEncyclopedia of Computer Science}, year = {2003}, month = {2003///}, pages = {677 - 680}, publisher = {John Wiley and Sons Ltd.}, organization = {John Wiley and Sons Ltd.}, address = {Chichester, UK}, abstract = {The indignant customer who receives an incorrect bill from a department store probably does not care what the source of the error was or even that, almost certainly, the fault was not a computer{\textquoteright}s but rather that of its data entry personnel or programmers. Neither is the astronaut who is descending toward the surface of the Moon very concerned about the precise source of the error that caused the onboard computer to fail. But an understanding of the sources of errors in computers is important to anyone who wishes to use or comprehend digital computers.}, isbn = {0-470-86412-5}, url = {http://dl.acm.org/citation.cfm?id=1074100.1074382}, author = {Ralston,Anthony and Shneiderman, Ben} } @article {18938, title = {Evaluating Translational Correspondence using Annotation Projection}, volume = {UMIACS-TR-2003-25}, year = {2003}, month = {2003///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Recently, statistical machine translation models have begun to take advantage of higherlevel linguistic structures such as syntactic dependencies. Underlying these models is an assumption about the directness of translational correspondence between sentences in the two languages; however, the extent to which this assumption is valid and useful is not well understood. In this paper, we present an empirical study that quantifies the degree to which syntactic dependencies are preserved when parses are projected directly from En- glish to Chinese. Our results show that although the direct correspondence assumption is often too restrictive, a small set of principled, elementary linguistic transformations can boost the quality of the projected Chinese parses by 76\% relative to the unimproved baseline. }, url = {http://lampsrv02.umiacs.umd.edu/pubs/TechReports/LAMP_100/LAMP_100.pdf}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy and Kolak,O.} } @article {14060, title = {Extracting significant features from the HRTF}, journal = {Proceedings of the 2003 International Conference on Auditory Display}, year = {2003}, month = {2003///}, abstract = {The Head Related Transfer Function (HRTF) characterizes the au-ditory cues created by scattering of sound off a person{\textquoteright}s anatomy. While it is known that features in the HRTF can be associated with various phenomena, such as head diffraction, head and torso re- flection, knee reflection and pinna resonances and anti resonances, identification of these phenomena are usually qualitative and/or heuristic. The objective of this paper is to attempt to decompose the HRTF and extract significant features that are perceptually im- portant for source localization. Some of the significant features that have been identified are the pinna resonances and the notches in the spectrum caused by various parts of the body. We develop signal processing algorithms to decompose the HRTF into compo- nents, and extract the features corresponding to each component. The support of NSF award ITR-0086075 is gratefully acknowl- edged }, author = {Raykar,V.C. and Duraiswami, Ramani and Davis, Larry S. and Yegnanarayana,B.} } @article {13251, title = {Extracting significant features from the hrtf}, journal = {Proceedings of the 2003 International Conference on Auditory Display}, year = {2003}, month = {2003///}, abstract = {The Head Related Transfer Function (HRTF) characterizes the au-ditory cues created by scattering of sound off a person{\textquoteright}s anatomy. While it is known that features in the HRTF can be associated with various phenomena, such as head diffraction, head and torso re- flection, knee reflection and pinna resonances and anti resonances, identification of these phenomena are usually qualitative and/or heuristic. The objective of this paper is to attempt to decompose the HRTF and extract significant features that are perceptually im- portant for source localization. Some of the significant features that have been identified are the pinna resonances and the notches in the spectrum caused by various parts of the body. We develop signal processing algorithms to decompose the HRTF into compo- nents, and extract the features corresponding to each component. The support of NSF award ITR-0086075 is gratefully acknowl- edged }, author = {Raykar,V.C. and Duraiswami, Ramani and Davis, Larry S. and Yegnanarayana,B.} } @article {12717, title = {Face recognition: A literature survey}, journal = {ACM Comput. Surv.}, volume = {35}, year = {2003}, month = {2003/12//}, pages = {399 - 458}, abstract = {As one of the most successful applications of image analysis and understanding, face recognition has recently received significant attention, especially during the past several years. At least two reasons account for this trend: the first is the wide range of commercial and law enforcement applications, and the second is the availability of feasible technologies after 30 years of research. Even though current machine recognition systems have reached a certain level of maturity, their success is limited by the conditions imposed by many real applications. For example, recognition of face images acquired in an outdoor environment with changes in illumination and/or pose remains a largely unsolved problem. In other words, current systems are still far away from the capability of the human perception system.This paper provides an up-to-date critical survey of still- and video-based face recognition research. There are two underlying motivations for us to write this survey paper: the first is to provide an up-to-date review of the existing literature, and the second is to offer some insights into the studies of machine recognition of faces. To provide a comprehensive survey, we not only categorize existing recognition techniques but also present detailed descriptions of representative methods within each category. In addition, relevant topics such as psychophysical studies, system evaluation, and issues of illumination and pose variation are covered.}, keywords = {face recognition, person identification}, isbn = {0360-0300}, doi = {10.1145/954339.954342}, url = {http://doi.acm.org/10.1145/954339.954342}, author = {Zhao, W. and Chellapa, Rama and Phillips,P.J. and Rosenfeld, A.} } @article {12726, title = {Face reconstruction from monocular video using uncertainty analysis and a generic model}, journal = {Computer Vision and Image Understanding}, volume = {91}, year = {2003}, month = {2003/07//}, pages = {188 - 213}, abstract = {Reconstructing a 3D model of a human face from a monocular video sequence is an important problem in computer vision, with applications to recognition, surveillance, multimedia, etc. However, the quality of 3D reconstructions using structure from motion (SfM) algorithms is often not satisfactory. One of the reasons is the poor quality of the input video data. Hence, it is important that 3D face reconstruction algorithms take into account the statistics representing the quality of the video. Also, because of the structural similarities of most faces, it is natural that the performance of these algorithms can be improved by using a generic model of a face. Most of the existing work using this approach initializes the reconstruction algorithm with this generic model. The problem with this approach is that the algorithm can converge to a solution very close to this initial value, resulting in a reconstruction which resembles the generic model rather than the particular face in the video which needs to be modeled. In this paper, we propose a method of 3D reconstruction of a human face from video in which the 3D reconstruction algorithm and the generic model are handled separately. We show that it is possible to obtain a reasonably good 3D SfM estimate purely from the video sequence, provided the quality of the input video is statistically assessed and incorporated into the algorithm. The final 3D model is obtained after combining the SfM estimate and the generic model using an energy function that corrects for the errors in the estimate by comparing the local regions in the two models. The main advantage of our algorithm over others is that it is able to retain the specific features of the face in the video sequence even when these features are different from those of the generic model and it does so even as the quality of the input video varies. The evolution of the 3D model through the various stages of the algorithm and an analysis of its accuracy are presented.}, keywords = {Energy function minimization, Face modeling, Generic model, stochastic approximation, structure from motion, uncertainty analysis}, isbn = {1077-3142}, doi = {10.1016/S1077-3142(03)00079-1}, url = {http://www.sciencedirect.com/science/article/pii/S1077314203000791}, author = {Roy Chowdhury,Amit K. and Chellapa, Rama} } @article {12740, title = {Fast two-frame multiscale dense optical flow estimation using discrete wavelet filters}, journal = {Journal of the Optical Society of America AJ. Opt. Soc. Am. A}, volume = {20}, year = {2003}, month = {2003///}, pages = {1505 - 1515}, abstract = {A multiscale algorithm with complexity O(N) (where N is the number of pixels in one image) using wavelet filters is proposed to estimate dense optical flow from two frames. Hierarchical image representation by wavelet decomposition is integrated with differential techniques in a new multiscale framework. It is shown that if a compactly supported wavelet basis with one vanishing moment is carefully selected, hierarchical image, first-order derivative, and corner representations can be obtained from the wavelet decomposition. On the basis of this result, three of the four components of the wavelet decomposition are employed to estimate dense optical flow with use of only two frames. This overcomes the {\textquotedblleft}flattening-out{\textquotedblright} problem in traditional pyramid methods, which produce large errors when low-texture regions become flat at coarse levels as a result of blurring. A two-dimensional affine motion model is used to formulate the optical flow problem as a linear system, with all resolutions simultaneously (i.e., coarse-and-fine) rather than the traditional coarse-to-fine approach, which unavoidably propagates errors from the coarse level. This not only helps to improve the accuracy but also makes the hardware implementation of our algorithm simple. Experiments on different types of image sequences, together with quantitative and qualitative comparisons with several other optical flow methods, are given to demonstrate the effectiveness and the robustness of our algorithm.}, keywords = {digital image processing, Image analysis, optical flow}, doi = {10.1364/JOSAA.20.001505}, url = {http://josaa.osa.org/abstract.cfm?URI=josaa-20-8-1505}, author = {Liu,Haiying and Chellapa, Rama and Rosenfeld,Azriel} } @article {18638, title = {Formal verification of an intrusion-tolerant group membership protocol}, journal = {IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS E SERIES D}, volume = {86}, year = {2003}, month = {2003///}, pages = {2612 - 2622}, abstract = {The traditional approach for establishing thecorrectness of group communication protocols is through rigor- ous arguments. While this is a valid approach, the likelihood of subtle errors in the design and implementation of such complex distributed protocols is not negligible. The use of formal verifi- cation methods has been widely advocated to instill confidence in the correctness of protocols. In this paper, we describe how we used the SPIN model checker to formally verify a group mem- bership protocol that is part of an intrusion-tolerant group com- munication system. We describe how we successfully tackled the state-space explosion problem by determining the right abstrac- tion level for formally specifying the protocol. The verification exercise not only formally showed that the protocol satisfies its correctness claims, but also provided information that will help us make the protocol more efficient without violating correctness. key words: intrusion tolerance, group communication systems, validation, formal methods }, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/03RAM01.pdf}, author = {Ramasamy,H. V. and Michel Cukier and Sanders,W. H.} } @inbook {12741, title = {Gait Analysis for Human Identification}, booktitle = {Audio- and Video-Based Biometric Person AuthenticationAudio- and Video-Based Biometric Person Authentication}, series = {Lecture Notes in Computer Science}, volume = {2688}, year = {2003}, month = {2003///}, pages = {1058 - 1058}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Human gait is an attractive modality for recognizing people at a distance. In this paper we adopt an appearance-based approach to the problem of gait recognition. The width of the outer contour of the binarized silhouette of a walking person is chosen as the basic image feature. Different gait features are extracted from the width vector such as the dowsampled, smoothed width vectors, the velocity profile etc. and sequences of such temporally ordered feature vectors are used for representing a person{\textquoteright}s gait. We use the dynamic time-warping (DTW) approach for matching so that non-linear time normalization may be used to deal with the naturally-occuring changes in walking speed. The performance of the proposed method is tested using different gait databases.}, isbn = {978-3-540-40302-9}, url = {http://dx.doi.org/10.1007/3-540-44887-X_82}, author = {Kale, A. and Cuntoor, N. and Yegnanarayana,B. and Rajagopalan, AN and Chellapa, Rama}, editor = {Kittler,Josef and Nixon,Mark} } @conference {16703, title = {A generative probabilistic OCR model for NLP applications}, booktitle = {Proceedings of the 2003 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology-Volume 1}, year = {2003}, month = {2003///}, pages = {55 - 62}, author = {Kolak,O. and Byrne,W. and Resnik, Philip} } @article {16290, title = {The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria}, journal = {Nature}, volume = {423}, year = {2003}, month = {2003/05/01/}, pages = {81 - 86}, abstract = {Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax1. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity{\textemdash}including haemolysins, phospholipases and iron acquisition functions{\textemdash}and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax4. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.}, isbn = {0028-0836}, doi = {10.1038/nature01586}, url = {http://www.nature.com/nature/journal/v423/n6935/full/nature01586.html}, author = {Read,Timothy D. and Peterson,Scott N. and Tourasse,Nicolas and Baillie,Les W. and Paulsen,Ian T. and Nelson,Karen E. and Tettelin,Herv|[eacute]| and Fouts,Derrick E. and Eisen,Jonathan A. and Gill,Steven R. and Holtzapple,Erik K. and |[Oslash]|kstad,Ole Andreas and Helgason,Erlendur and Rilstone,Jennifer and Wu,Martin and Kolonay,James F. and Beanan,Maureen J. and Dodson,Robert J. and Brinkac,Lauren M. and Gwinn,Michelle and DeBoy,Robert T. and Madpu,Ramana and Daugherty,Sean C. and Durkin,A. Scott and Haft,Daniel H. and Nelson,William C. and Peterson,Jeremy D. and Pop, Mihai and Khouri,Hoda M. and Radune,Diana and Benton,Jonathan L. and Mahamoud,Yasmin and Jiang,Lingxia and Hance,Ioana R. and Weidman,Janice F. and Berry,Kristi J. and Plaut,Roger D. and Wolf,Alex M. and Watkins,Kisha L. and Nierman,William C. and Hazen,Alyson and Cline,Robin and Redmond,Caroline and Thwaite,Joanne E. and White,Owen and Salzberg,Steven L. and Thomason,Brendan and Friedlander,Arthur M. and Koehler,Theresa M. and Hanna,Philip C. and Kolst|[oslash]|,Anne-Brit and Fraser,Claire M.} } @article {18572, title = {Guidelines for interdomain traffic engineering}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {33}, year = {2003}, month = {2003/10//}, pages = {19 - 30}, abstract = {Network operators must have control over the flow of traffic into, out of, and across their networks. However, the Border Gateway Protocol (BGP) does not facilitate common traffic engineering tasks, such as balancing load across multiple links to a neighboring AS or directing traffic to a different neighbor. Solving these problems is difficult because the number of possible changes to routing policies is too large to exhaustively test all possibilities, some changes in routing policy can have an unpredictable effect on the flow of traffic, and the BGP decision process implemented by router vendors limits an operator{\textquoteright}s control over path selection.We propose fundamental objectives for interdomain traffic engineering and specific guidelines for achieving these objectives within the context of BGP. Using routing and traffic data from the AT\&T backbone we show how certain BGP policy changes can move traffic in a predictable fashion, despite limited knowledge about the routing policies in neighboring AS{\textquoteright}s. Then, we show how operators can gain greater flexibility by relaxing some steps in the BGP decision process and ensuring that neighboring AS{\textquoteright}s send consistent advertisements at each peering location. Finally, we show that an operator can manipulate traffic efficiently by changing the routes for a small number of prefixes (or groups of related prefixes) that consistently receive a large amount of traffic.}, isbn = {0146-4833}, doi = {10.1145/963985.963988}, url = {http://doi.acm.org/10.1145/963985.963988}, author = {Feamster, Nick and Borkenhagen,Jay and Rexford,Jennifer} } @article {17188, title = {Help! I{\textquoteright}m lost: User frustration in web navigation}, journal = {IT \& Society}, volume = {1}, year = {2003}, month = {2003///}, pages = {18 - 26}, abstract = {Computers can be valuable tools, and networked resources via the Internet can be beneficial to many different populations and communities. Unfortunately, when people are unable to reach their task goals due to frustrating experiences, this can hinder the effectiveness of technology. This research summary provides information about the user frustration research that has been performed at the University of Maryland and Towson University. Causes of user frustration are discussed in this research summary, along with the surprising finding that nearly one-third to one-half of the time spent in front of the computer is wasted due to frustrating experiences. Furthermore, when interfaces are planned to be deceptive and confusing, this can lead to increased frustration. Implications for designers and users are discussed.}, author = {Lazar,J. and Bessiere,K. and Ceaparu,I. and Robinson,J. and Shneiderman, Ben} } @conference {12720, title = {A hidden Markov model based framework for recognition of humans from gait sequences}, booktitle = {Image Processing, 2003. ICIP 2003. Proceedings. 2003 International Conference on}, volume = {2}, year = {2003}, month = {2003/09//}, pages = {II - 93-6 vol.3 - II - 93-6 vol.3}, abstract = {In this paper we propose a generic framework based on hidden Markov models (HMMs) for recognition of individuals from their gait. The HMM framework is suitable, because the gait of an individual can be visualized as his adopting postures from a set, in a sequence which has an underlying structured probabilistic nature. The postures that the individual adopts can be regarded as the states of the HMM and are typical to that individual and provide a means of discrimination. The framework assumes that, during gait, the individual transitions between N discrete postures or states but it is not dependent on the particular feature vector used to represent the gait information contained in the postures. The framework, thus, provides flexibility in the selection of the feature vector. The statistical nature of the HMM lends robustness to the model. In this paper we use the binarized background-subtracted image as the feature vector and use different distance metrics, such as those based on the L1 and L2 norms of the vector difference, and the normalized inner product of the vectors, to measure the similarity between feature vectors. The results we obtain are better than the baseline recognition rates reported before.}, keywords = {analysis;, background-subtracted, binarized, discrete, distance, feature, Gait, hidden, human, image, image;, Markov, metrics;, model;, models;, postures;, recognition;, sequences;, vector;}, doi = {10.1109/ICIP.2003.1246624}, author = {Sundaresan,Aravind and RoyChowdhury,Amit and Chellapa, Rama} } @conference {16758, title = {Hierarchical dwarfs for the rollup cube}, booktitle = {Proceedings of the 6th ACM international workshop on Data warehousing and OLAP - DOLAP {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {17 - 17}, address = {New Orleans, Louisiana, USA}, doi = {10.1145/956060.956064}, url = {http://dl.acm.org/citation.cfm?id=956064}, author = {Sismanis,Yannis and Deligiannakis,Antonios and Kotidis,Yannis and Roussopoulos, Nick} } @article {16125, title = {Immediate Usability: Kiosk design principles from the CHI 2001 Photo Library}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/01/21/}, abstract = {This paper describes a novel set of design principles and guidelines forensuring the immediate usability of public access systems. These principles and guidelines were formulated while developing PhotoFinder Kiosk, a community photo library. Attendees of CHI 2001 successfully used the tool to browse and annotate collections of photographs spanning 20 years of CHI and related conferences, producing a richly annotated photo history of the field of human-computer interaction. We used observations and log data to evaluate the tool and refine the guidelines. They provide specific guidance for practitioners, as well as a useful framework for additional research in public access interfaces. Keywords Photo collection, community photo library, group annotation, public access system, direct annotation, direct manipulation, drag-and-drop, immediate usability, zero-trial learning, walk-up-and-use, casual use. (UMIACS-TR-2001-71) (HCIL-TR-2001-23) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1155}, author = {Kules,Bill and Kang,Hyunmo and Plaisant, Catherine and Rose,Anne and Shneiderman, Ben} } @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 {16418, title = {The interaction between zoning regulations and residential preferences as a driver of urban form}, journal = {Proceedings of the 2003 UTEP Distinguished Faculty and Student Symposium}, year = {2003}, month = {2003///}, author = {Zellner,M.L. and Riolo,R and Rand, William and Page,S.E. and Brown,D.G. and Fernandez,L.E.} } @article {12190, title = {The International Children{\textquoteright}s Digital Library}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13928, title = {The International Children{\textquoteright}s Digital Library: Description and analysis of first use}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, pages = {315 - 315}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13904, title = {The International Children{\textquoteright}s Digital Library: viewing digital books online}, journal = {Interacting with Computers}, volume = {15}, year = {2003}, month = {2003///}, pages = {151 - 167}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison and Rose,A. and Farber,A. and Takayama,Y.} } @conference {11896, title = {Kernel snakes: non-parametric active contour models}, booktitle = {IEEE International Conference on Systems, Man and Cybernetics, 2003}, volume = {1}, year = {2003}, month = {2003/10//}, pages = {240- 244 vol.1 - 240- 244 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, a new non-parametric generalized formulation to statistical pressure snakes is presented. We discuss the shortcomings of the traditional pressure snakes. We then introduce a new generic pressure model that alleviates these shortcomings, based on the Bayesian decision theory. Non-parametric techniques are used to obtain the statistical models that drive the snake. We discuss the advantages of using the proposed non-parametric model compared to other parametric techniques. Multi-colored-target tracking is used to demonstrate the performance of the proposed approach. Experimental results show enhanced, real-time performance.}, keywords = {Active contours, Artificial intelligence, Bayes methods, Bayesian decision theory, Bayesian methods, decision theory, Deformable models, Image edge detection, Image segmentation, Intelligent robots, Kernel, kernel snakes, Laboratories, multicolored target tracking, nonparametric active contour models, nonparametric generalized formulation, nonparametric model, nonparametric statistics, nonparametric techniques, real time performance, Robot vision systems, statistical pressure snakes, target tracking}, isbn = {0-7803-7952-7}, doi = {10.1109/ICSMC.2003.1243822}, author = {Abd-Almageed, Wael and Smith,C.E. and Ramadan,S.} } @conference {16473, title = {Latency Profiles: Performance Monitoring for Wide Area Applications}, booktitle = {Internet Applications, IEEE Workshop on}, year = {2003}, month = {2003///}, pages = {74 - 74}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Recent technological advances have enabled the deployment of wide area applications against Internet accessible sources. A performance challenge to applications in such a setting is the unpredictable end-to-end latency of accessing these sources. We use passive information gathering mechanisms to learn end-to-end latency distributions and construct Latency Profiles (LPs). We hypothesize that a group of clients, within an autonomous system (AS), that are accessing a content server, in another AS, may be represented by (one or more) LPs. Related networking research on IDMaps, points of congestion, and BGP routes support such hypothesis. We develop aggregate LPs to provide coverage of groups (clusters) of client-server pairs. Using data gathered from a (limited) experiment we demonstrate the feasibility of constructing LPs.}, doi = {http://doi.ieeecomputersociety.org/10.1109/WIAPP.2003.1210290}, author = {Raschid, Louiqa and Wen,Hui-Fang and Gal,Avigdor and Zadorozhny,Vladimir} } @article {15847, title = {Making miracles: Interactive translingual search for cebuano and hindi}, journal = {ACM Transactions on Asian Language Information Processing (TALIP)}, volume = {2}, year = {2003}, month = {2003///}, pages = {219 - 244}, author = {He,D. and Oard, Douglas and Wang,J. and Luo,J. and Demner-Fushman,D. and Darwish,K. and Resnik, Philip and Khudanpur,S. and Nossal,M. and Subotin,M. and others} } @article {17706, title = {Matrix Algorithms, Volume II: Eigensystems}, journal = {Applied Mechanics Reviews}, volume = {56}, year = {2003}, month = {2003///}, pages = {B2-B2 - B2-B2}, keywords = {algorithm theory, Eigenvalues and eigenfunctions, linear algebra, matrix algebra, reviews}, doi = {10.1115/1.1523352}, url = {http://link.aip.org/link/?AMR/56/B2/1}, author = {Stewart, G.W. and Author and Mahajan,A. and Reviewer} } @conference {13596, title = {Measuring Structural Similarity of Document Pages for Searching Document Image Databases}, booktitle = {5th IASTEDInternational Conference on Signal and Image Processing}, year = {2003}, month = {2003/08//}, pages = {320 - 325}, abstract = {Current document management and database systems provide text search and retrieval capabilities, but generally lack the ability to utilize the documents{\^a}{\texteuro}{\texttrademark} logical and physical structures. This paper describes a general system for document image retrieval that is able to make use of document structure. It discusses the use of structural similarity for retrieval; it defines a measure of structural similarity between document images based on content area overlap, and also compares similarity ratings based on this measure with human relevance judgments.}, author = {Shin,C. and David Doermann and Rosenfeld, A.} } @article {12946, title = {Method of DNA extraction and application of multiplex polymerase chain reaction to detect toxigenic Vibrio cholerae O1 and O139 from aquatic ecosystems}, journal = {Environmental Microbiology}, volume = {5}, year = {2003}, month = {2003/07/01/}, pages = {599 - 606}, abstract = {Vibrio cholerae is a free-living bacterium found in water and in association with plankton. V. cholerae non-O1/non-O139 strains are frequently isolated from aquatic ecosystems worldwide. Less frequently isolated are V. cholerae O1 and V. cholerae O139, the aetiological agents of cholera. These strains have two main virulence-associated factors, cholera toxin (CT) and toxin co-regulated pilus (TCP). By extracting total DNA from aquatic samples, the presence of pathogenic strains can be determined quickly and used to improve a microbiological risk assessment for cholera in coastal areas. Some methods suggested for DNA extraction from water samples are not applicable to all water types. We describe here a method for DNA extraction from coastal water and a multiplex polymerase chain reaction (PCR) for O1 and O139 serogroups. DNA extraction was successfully accomplished from 117 sea water samples collected from coastal areas of Per{\'u}, Brazil and the USA. DNA concentration in all samples varied from 20~ng to 480~{\textmu}g~{\textmu}l-1. The sensitivity of the DNA extraction method was 100 V. cholerae cells in 250~ml of water. The specificity of multiplex O1/O139 PCR was investigated by analysing 120 strains of V. cholerae, Vibrio and other Bacteria species. All V. cholerae O1 and O139 tested were positive. For cholera surveillance of aquatic environments and ballast water, total DNA extraction, followed by V. cholerae PCR, and O1/O139 serogroup and tcpA/ctxA genes by multiplex PCR offers an efficient system, permitting risk analysis for cholera in coastal areas.}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2003.00443.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2003.00443.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Rivera,Irma N. G. and Lipp,Erin K. and Gil,Ana and Choopun,Nipa and Huq,Anwar and Rita R Colwell} } @article {16722, title = {The Opsis project: materialized views for data warehouses and the web}, journal = {Advances in Informatics}, year = {2003}, month = {2003///}, pages = {64 - 81}, author = {Roussopoulos, Nick and Kotidis,Y. and Labrinidis,A. and Sismanis,Y.} } @conference {18469, title = {Pitch and timbre manipulations using cortical representation of sound}, booktitle = {Multimedia and Expo, IEEE International Conference on}, volume = {3}, year = {2003}, month = {2003///}, pages = {381 - 384}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {The sound receiver at the ears is processed by humans using signal processing that separate the signal along intensity, pitch and timbre dimensions. Conventional Fourier-based signal processing, while endowed with fast algorithms, is unable to easily represent signal along these attributes. In this paper we use a cortical representation to represent the manipulate sound. We briefly overview algorithms for obtaining, manipulating and inverting cortical representation of sound and describe algorithms for manipulating signal pitch and timbre separately. The algorithms are first used to create sound of an instrument between a guitar and a trumpet. Applications to creating maximally separable sounds in auditory user interfaces are discussed.}, isbn = {0-7803-7965-9}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICME.2003.1221328}, author = {Zotkin,Dmitry N and Shamma,S.A. and Ru,P. and Duraiswami, Ramani and Davis, Larry S.} } @article {12949, title = {Predictability of Vibrio Cholerae in Chesapeake Bay}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {69}, year = {2003}, month = {2003/05/01/}, pages = {2773 - 2785}, abstract = {Vibrio cholerae is autochthonous to natural waters and can pose a health risk when it is consumed via untreated water or contaminated shellfish. The correlation between the occurrence of V. cholerae in Chesapeake Bay and environmental factors was investigated over a 3-year period. Water and plankton samples were collected monthly from five shore sampling sites in northern Chesapeake Bay (January 1998 to February 2000) and from research cruise stations on a north-south transect (summers of 1999 and 2000). Enrichment was used to detect culturable V. cholerae, and 21.1\% (n = 427) of the samples were positive. As determined by serology tests, the isolates, did not belong to serogroup O1 or O139 associated with cholera epidemics. A direct fluorescent-antibody assay was used to detect V. cholerae O1, and 23.8\% (n = 412) of the samples were positive. V. cholerae was more frequently detected during the warmer months and in northern Chesapeake Bay, where the salinity is lower. Statistical models successfully predicted the presence of V. cholerae as a function of water temperature and salinity. Temperatures above 19{\textdegree}C and salinities between 2 and 14 ppt yielded at least a fourfold increase in the number of detectable V. cholerae. The results suggest that salinity variation in Chesapeake Bay or other parameters associated with Susquehanna River inflow contribute to the variability in the occurrence of V. cholerae and that salinity is a useful indicator. Under scenarios of global climate change, increased climate variability, accompanied by higher stream flow rates and warmer temperatures, could favor conditions that increase the occurrence of V. cholerae in Chesapeake Bay.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.69.5.2773-2785.2003}, url = {http://aem.asm.org/content/69/5/2773}, author = {Louis,Val{\'e}rie R. and Russek-Cohen,Estelle and Choopun,Nipa and Rivera,Irma N. G. and Gangle,Brian and Jiang,Sunny C. and Rubin,Andrea and Patz,Jonathan A. and Huq,Anwar and Rita R Colwell} } @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} } @article {16486, title = {A query language to support scientific discovery}, journal = {Proc. 2nd IEEE International Computer Society}, year = {2003}, month = {2003///}, author = {Eckman,B. and Deutsch,K. and Janer,M. and Lacroix,Z. and Raschid, Louiqa} } @article {12953, title = {Reduction of Cholera in Bangladeshi Villages by Simple Filtration}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {100}, year = {2003}, month = {2003/02/04/}, pages = {1051 - 1055}, abstract = {Based on results of ecological studies demonstrating that Vibrio cholerae, the etiological agent of epidemic cholera, is commensal to zooplankton, notably copepods, a simple filtration procedure was developed whereby zooplankton, most phytoplankton, and particulates >20 μm were removed from water before use. Effective deployment of this filtration procedure, from September 1999 through July 2002 in 65 villages of rural Bangladesh, of which the total population for the entire study comprised ≈133,000 individuals, yielded a 48\% reduction in cholera (P < 0.005) compared with the control.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0237386100}, url = {http://www.pnas.org/content/100/3/1051}, author = {Rita R Colwell and Huq,Anwar and M. Sirajul Islam and K. M. A. Aziz and Yunus,M. and N. Huda Khan and A. Mahmud and Sack,R. Bradley and Nair,G. B. and J. Chakraborty and Sack,David A. and E. Russek-Cohen} } @inbook {12739, title = {Robust Face Recognition in the Presence of Clutter}, booktitle = {Audio- and Video-Based Biometric Person AuthenticationAudio- and Video-Based Biometric Person Authentication}, series = {Lecture Notes in Computer Science}, volume = {2688}, year = {2003}, month = {2003///}, pages = {1062 - 1062}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We propose a new method within the framework of principal component analysis to robustly recognize faces in the presence of clutter. The traditional eigenface recognition method performs poorly when confronted with the more general task of recognizing faces appearing against a background. It misses faces completely or throws up many false alarms. We argue in favor of learning the distribution of background patterns and show how this can be done for a given test image. An eigenbackground space is constructed and this space in conjunction with the eigenface space is used to impart robustness in the presence of background. A suitable classifier is derived to distinguish non-face patterns from faces. When tested on real images, the performance of the proposed method is found to be quite good.}, isbn = {978-3-540-40302-9}, url = {http://dx.doi.org/10.1007/3-540-44887-X_1}, author = {Rajagopalan, AN and Chellapa, Rama and Koterba,Nathan}, editor = {Kittler,Josef and Nixon,Mark} } @conference {16780, title = {SEB-tree: An approach to index continuously moving objects}, booktitle = {Mobile Data Management}, year = {2003}, month = {2003///}, pages = {340 - 344}, author = {Song,Z. and Roussopoulos, Nick} } @conference {12730, title = {Statistical Error Propagation in 3D Modeling From Monocular Video}, booktitle = {Computer Vision and Pattern Recognition Workshop, 2003. CVPRW {\textquoteright}03. Conference on}, volume = {8}, year = {2003}, month = {2003/06//}, pages = {89 - 89}, abstract = {A significant portion of recent research in computer vision has focused on issues related to sensitivity and robustness of existing techniques. In this paper, we study the classical structure from motion problem and analyze how the statistics representing the quality of the input video propagates through the reconstruction algorithm and affects the quality of the output reconstruction. Specifically, we show that it is possible to derive analytical expressions of the first and second order statistics (bias and error covariance) of the solution as a function of the statistics of the input. We concentrate on the case of reconstruction from a monocular video, where the small baseline makes any algorithm very susceptible to noise in the motion estimates from the video sequence. We derive an expression relating the error covariance of the reconstruction to the error covariance of the feature tracks in the input video. This is done using the implicit function theorem of real analysis and does not require strong statistical assumptions. Next, we prove that the 3D reconstruction is statistically biased, derive an expression for it and show that it is numerically significant. Combining these two results, we also establish a new bound on the minimum error in the depth reconstruction. We present the numerical significance of these analytical results on real video data.}, doi = {10.1109/CVPRW.2003.10092}, author = {RoyChowdhury,Amit and Chellapa, Rama} } @article {16410, title = {Statistical validation of spatial patterns in agent-based models}, journal = {Proceedings of Agent Based Simulation}, volume = {4}, year = {2003}, month = {2003///}, abstract = {We present and evaluate an agent-based model(ABM) of land use change at the rural-urban fringe. This paper is part of a project that links the ABM to surveys of residential preferences and historical patterns of development. Validation is an important issue for such models and we discuss the use of distributional phenomena as a method of validation. We then highlight the ability of our ABM to gen- erate two phenomena evident in empirical analysis of urban development patterns: a power law rela- tionship between frequency and cluster size and a negative exponential relationship between density and distance from city center. We discuss these results in the light of validation of ABMs. }, author = {Rand, William and Brown,D.G. and Page,S.E. and Riolo,R and Fernandez,L.E. and Zellner,M} } @article {18505, title = {Techniques for interdomain traffic engineering}, journal = {Computer Communications Review}, volume = {33}, year = {2003}, month = {2003///}, abstract = {Network operators must have control over the flow of traffic into,out of, and across their networks. However, the Border Gateway Protocol (BGP) does not facilitate common traffic engineering tasks, such as balancing load across multiple links to a neighboring AS or directing traffic to a different neighbor. Solving these problems is difficult because the number of possible changes to routing policies is too large to exhaustively test all possibilities, some changes in routing policy can have an unpredictable effect on the flow of traf- fic, and the BGP decision process implemented by router vendors limits an operator{\textquoteright}s control over path selection. We analyze routing and traffic data from the AT\&T backbone to identify ways to use BGP policy for traffic engineering tasks. First, we show how cer- tain BGP policy changes can move traffic in a predictable fashion, despite limited knowledge about the routing policies in neighboring AS{\textquoteright}s. Then, we show how operators can gain greater flexibility by relaxing some steps in the BGP decision process and ensuring that neighboring AS{\textquoteright}s send consistent advertisements at each peering location. Finally, we show that an operator can manipulate traffic efficiently by changing the routes for a small number of prefixes (or groups of related prefixes) that consistently receive a large amount of traffic. These results can help operators accomplish common traffic engineering tasks using existing BGP features. }, author = {Feamster, Nick and Borkenhagen,J. and Rexford,J.} } @conference {16139, title = {Technology probes: inspiring design for and with families}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {17 - 24}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe a new method for use in the process of co-designing technologies with users called technology probes. Technology probes are simple, flexible, adaptable technologies with three interdisciplinary goals: the social science goal of understanding the needs and desires of users in a real-world setting, the engineering goal of field-testing the technology, and the design goal of inspiring users and researchers to think about new technologies. We present the results of designing and deploying two technology probes, the messageProbe and the videoProbe, with diverse families in France, Sweden, and the U.S. We conclude with our plans for creating new technologies for and with families based on our experiences.}, keywords = {computer mediated communication, ethnography, Home, participatory design and cooperative design}, isbn = {1-58113-630-7}, doi = {10.1145/642611.642616}, url = {http://doi.acm.org/10.1145/642611.642616}, author = {Hutchinson,Hilary and Mackay,Wendy and Westerlund,Bo and Bederson, Benjamin B. and Druin, Allison and Plaisant, Catherine and Beaudouin-Lafon,Michel and Conversy,St{\'e}phane and Evans,Helen and Hansen,Heiko and Roussel,Nicolas and Eiderb{\"a}ck,Bj{\"o}rn} } @article {13344, title = {TelegraphCQ: An architectural status report}, journal = {IEEE Data Engineering Bulletin}, volume = {26}, year = {2003}, month = {2003///}, pages = {11 - 18}, author = {Krishnamurthy, S. and Chandrasekaran,S. and Cooper,O. and Deshpande, Amol and Franklin,M.J. and Hellerstein,J. M and Hong,W. and Madden,S. and Reiss,F. and Shah,M. A} } @conference {13405, title = {TelegraphCQ: continuous dataflow processing}, booktitle = {Proceedings of the 2003 ACM SIGMOD international conference on Management of data}, series = {SIGMOD {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {668 - 668}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-634-X}, doi = {10.1145/872757.872857}, url = {http://doi.acm.org/10.1145/872757.872857}, author = {Chandrasekaran,Sirish and Cooper,Owen and Deshpande, Amol and Franklin,Michael J. and Hellerstein,Joseph M. and Wei Hong and Krishnamurthy,Sailesh and Madden,Samuel R. and Reiss,Fred and Shah,Mehul A.} } @conference {14059, title = {Tracking a moving speaker using excitation source information}, booktitle = {Eighth European Conference on Speech Communication and Technology}, year = {2003}, month = {2003///}, abstract = {Microphone arrays are widely used to detect, locate, and track a stationary or moving speaker. The first step is to estimate the time delay, between the speech signals received by a pair of microphones. Conventional methods like generalized cross-correlation are based on the spectral content of the vocal tract system in the speech signal. The spectral content of the speech signal is affected due to degradations in the speech signal caused by noise and reverberation. However, features corresponding to the excitation source of speech are less affected by such degradations. This paper proposes a novel method to estimate the time delays using the excitation source information in speech. The estimated delays are used to get the position of the moving speaker. The proposed method is compared with the spectrum-based approach using real data from a microphone array setup.}, author = {Raykar,V.C. and Duraiswami, Ramani and Yegnanarayana,B. and Prasanna,S. R.M} } @article {17449, title = {Understanding Computer User Frustration: Measuring and Modeling the Disruption from Poor Designs}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/01/21/}, abstract = {User frustration in the use of information and computing technology is apervasive and persistent problem. When computers crash, network congestion causes delays, and poor user interfaces trigger confusion there are dramatic consequences for individuals, organizations, and society. These frustrations not only cause personal dissatisfaction and loss of self-efficacy, but may disrupt workplaces, slow learning, and reduce participation in local and national communities. We propose a Computing Frustration Model with incident specific and individual variables to guide research. Our study of 108 computer users shows high levels of frustration and loss of 1/3 to 1/2 of time spent. The importance of the users{\textquoteright} goals and the severity of the disruption were correlated with frustration. Those who had strong self-efficacy, indicated by a willingness to stick to solving the problem, reported lower levels of frustration. Implications for users, software developers, managers, and policymakers are discussed. Keywords: user frustration, user interface design, training, helpdesk, computer experience, computer anxiety (UMIACS-TR-2002-89) (HCIL-TR-2002-18) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1233}, author = {Bessiere,Katie and Ceaparu,Irina and Lazar,Jonathan and Robinson,John and Shneiderman, Ben} } @conference {14753, title = {User-specified adaptive scheduling in a streaming media network}, booktitle = {2003 IEEE Conference on Open Architectures and Network Programming}, year = {2003}, month = {2003/04/04/5}, pages = {87 - 96}, publisher = {IEEE}, organization = {IEEE}, abstract = {In disaster and combat situations, mobile cameras and other sensors transmit real-time data, used by many operators or analysis tools. Unfortunately, in the face of limited, unreliable resources, and varying demands, not all users may be able to get the fidelity they require. This paper describes MediaNet, a distributed stream processing system designed with the above scenarios in mind. Unlike past approaches, MediaNet{\textquoteright}s users can intuitively specify how the system should adapt based on their individual needs. MediaNet uses both local and online global resource scheduling to improve user performance and network utilization, and adapts without requiring underlying support for resource reservations. Performance experiments show that our scheduling algorithm is reasonably fast, and that user performance and network utilization are both significantly improved.}, keywords = {Adaptive scheduling, CAMERAS, Computer networks, Computer science, distributed stream processing system, Educational institutions, global resource scheduling, Intelligent networks, MediaNet, Mobile computing, network utilization, Process design, Processor scheduling, quality of service, Streaming media, streaming media network, user performance, user-specified adaptive scheduling}, isbn = {0-7803-7764-8}, doi = {10.1109/OPNARC.2003.1196376}, author = {Hicks, Michael W. and Nagarajan,A. and van Renesse,R.} } @conference {14858, title = {Using specularities for recognition}, booktitle = {Computer Vision, 2003. Proceedings. Ninth IEEE International Conference on}, year = {2003}, month = {2003/10//}, pages = {1512 -1519 vol.2 - 1512 -1519 vol.2}, abstract = {Recognition systems have generally treated specular highlights as noise. We show how to use these highlights as a positive source of information that improves recognition of shiny objects. This also enables us to recognize very challenging shiny transparent objects, such as wine glasses. Specifically, we show how to find highlights that are consistent with a hypothesized pose of an object of known 3D shape. 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 reflectance properties is needed. We first present a method that finds highlights produced by a dominant compact light source, whose position is roughly known. We then show how to estimate the lighting automatically for objects whose reflection is part specular and part Lambertian. We demonstrate this method for two classes of objects. First, we show that specular information alone can suffice to identify objects with no Lambertian reflectance, such as transparent wine glasses. Second, we use our complete system to recognize shiny objects, such as pottery.}, keywords = {3D, formation;object, glass;computer, image, information;specular, light, measurement;reflection;stereo, objects;specular, objects;wine, processing;, property;pottery;recognition, recognition;object, recognition;position, reflectance, reflection;compact, reflection;transparent, shape;Lambertian, source;highlight, systems;shiny, vision;lighting;object}, doi = {10.1109/ICCV.2003.1238669}, author = {Osadchy,M. and Jacobs, David W. and Ramamoorthi,R.} } @conference {13343, title = {Using state modules for adaptive query processing}, booktitle = {19th International Conference on Data Engineering, 2003. Proceedings}, year = {2003}, month = {2003/03/05/8}, pages = {353 - 364}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a query architecture in which join operators are decomposed into their constituent data structures (State Modules, or SteMs), and dataflow among these SteMs is managed adaptively by an eddy routing operator [R. Avnur et al., (2000)]. Breaking the encapsulation of joins serves two purposes. First, it allows the eddy to observe multiple physical operations embedded in a join algorithm, allowing for better calibration and control of these operations. Second, the SteM on a relation serves as a shared materialization point, enabling multiple competing access methods to share results, which can be leveraged by multiple competing join algorithms. Our architecture extends prior work significantly, allowing continuously adaptive decisions for most major aspects of traditional query optimization: choice of access methods and join algorithms, ordering of operators, and choice of a query spanning tree. SteMs introduce significant routing flexibility to the eddy, enabling more opportunities for adaptation, but also introducing the possibility of incorrect query results. We present constraints on eddy routing through SteMs that ensure correctness while preserving a great deal of flexibility. We also demonstrate the benefits of our architecture via experiments in the Telegraph dataflow system. We show that even a simple routing policy allows significant flexibility in adaptation, including novel effects like automatic "hybridization " of multiple algorithms for a single join.}, keywords = {adaptive query processing, Bandwidth, Calibration, data encapsulation, data structure, Data structures, Databases, Dictionaries, eddy routing, eddy routing operator, Encapsulation, join operator, multiple algorithm automatic hybridization, multiple competing join algorithm, query architecture, Query processing, query spanning tree, Routing, routing policy, Runtime, shared materialization point, State Module, SteMs, Telegraph dataflow system, Telegraphy, Tree data structures}, isbn = {0-7803-7665-X}, doi = {10.1109/ICDE.2003.1260805}, author = {Vijayshankar Raman and Deshpande, Amol and Hellerstein,J. M} } @conference {16123, title = {Using Visualization Tools to Gain Insight Into Your Data}, booktitle = {SPE Annual Technical Conference and Exhibition}, year = {2003}, month = {2003/10//}, publisher = {Society of Petroleum Engineers}, organization = {Society of Petroleum Engineers}, abstract = {When the term {\textquoteleft}visualization{\textquoteright} is used in the oil and gas industry, it is usually referring to the viewing of complex geologic structures in three-dimensional space. This paper illustrates insights gained by applying interactive visual environments to petroleum industry data that has traditionally been presented in spreadsheets, line graphs, and bar charts. Two information visualization tools, Treemap and SpaceTree, will be shown applied to a variety of oilfield related data.}, isbn = {9781555631529}, doi = {10.2118/84439-MS}, url = {http://www.onepetro.org/mslib/servlet/onepetropreview?id=00084439}, author = {Plaisant, Catherine and Chintalapani,G. and Lukehart,C. and Schiro,D. and Ryan,J.} } @book {13691, title = {Video Mining}, year = {2003}, month = {2003/08/31/}, publisher = {Springer}, organization = {Springer}, abstract = {Video Mining is an essential reference for the practitioners and academicians in the fields of multimedia search engines.Half a terabyte or 9,000 hours of motion pictures are produced around the world every year. Furthermore, 3,000 television stations broadcasting for twenty-four hours a day produce eight million hours per year, amounting to 24,000 terabytes of data. Although some of the data is labeled at the time of production, an enormous portion remains unindexed. For practical access to such huge amounts of data, there is a great need to develop efficient tools for browsing and retrieving content of interest, so that producers and end users can quickly locate specific video sequences in this ocean of audio-visual data.Video Mining is important because it describes the main techniques being developed by the major players in industry and academic research to address this problem. It is the first time research from these leaders in the field developing the next-generation multimedia search engines is being described in great detail and gathered into a single volume.Video Mining will give valuable insights to all researchers and non-specialists who want to understand the principles applied by the multimedia search engines that are about to be deployed on the Internet, in studios{\textquoteright} multimedia asset management systems, and in video-on-demand systems.}, keywords = {Computers / Client-Server Computing, Computers / Computer Science, Computers / Database Management / Data Mining, Computers / Database Management / General, Computers / Information Technology, Computers / Information Theory, Computers / Intelligence (AI) \& Semantics, Computers / Interactive \& Multimedia, Computers / Networking / General, Computers / Security / Cryptography, data mining, Data mining/ Congresses, Mathematics / General, Medical / General, multimedia systems, Multimedia systems/ Congresses, Technology \& Engineering / Electrical, Technology \& Engineering / Telecommunications}, isbn = {9781402075490}, author = {Rosenfeld,Azriel and David Doermann and DeMenthon,Daniel} } @inbook {16131, title = {The World{\textquoteright}s Information in Digital Libraries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {149 - 149}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Plaisant, Catherine and Marchimini,G. and Bruns,T. and Komlodi,A. and Campbell,L. and Rose,A. and Ding,G.M. and Beale Jr,J. and Nolet,V. and Shneiderman, Ben and others} } @inbook {14589, title = {1.375-Approximation Algorithm for Sorting by Reversals}, booktitle = {Algorithms {\textemdash} ESA 2002Algorithms {\textemdash} ESA 2002}, series = {Lecture Notes in Computer Science}, volume = {2461}, year = {2002}, month = {2002///}, pages = {401 - 408}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analysis of genomes evolving by inversions leads to a general combinatorial problem of Sorting by Reversals , MIN-SBR, the problem of sorting a permutation by a minimum number of reversals. Following a series of preliminary results, Hannenhalli and Pevzner developed the first exact polynomial time algorithm for the problem of sorting signed permutations by reversals, and a polynomial time algorithm for a special case of unsigned permutations. The best known approximation algorithm for MIN-SBR, due to Christie, gives a performance ratio of 1.5. In this paper, by exploiting the polynomial time algorithm for sorting signed permutations and by developing a new approximation algorithm for maximum cycle decomposition of breakpoint graphs, we design a new 1.375-algorithm for the MIN-SBR problem.}, isbn = {978-3-540-44180-9}, url = {http://dx.doi.org/10.1007/3-540-45749-6_21}, author = {Berman,Piotr and Hannenhalli, Sridhar and Karpinski,Marek}, editor = {M{\"o}hring,Rolf and Raman,Rajeev} } @article {13414, title = {AAAI 2002 Workshops}, journal = {AI Magazine}, volume = {23}, year = {2002}, month = {2002/12/15/}, pages = {113 - 113}, isbn = {0738-4602}, doi = {10.1609/aimag.v23i4.1678}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1678}, author = {Blake,Brian and Haigh,Karen and Hexmoor,Henry and Falcone,Rino and Soh,Leen-Kiat and Baral,Chitta and McIlraith,Sheila and Gmytrasiewicz,Piotr and Parsons,Simon and Malaka,Rainer and Krueger,Antonio and Bouquet,Paolo and Smart,Bill and Kurumantani,Koichi and Pease,Adam and Brenner,Michael and desJardins, Marie and Junker,Ulrich and Delgrande,Jim and Doyle,Jon and Rossi,Francesca and Schaub,Torsten and Gomes,Carla and Walsh,Toby and Guo,Haipeng and Horvitz,Eric J and Ide,Nancy and Welty,Chris and Anger,Frank D and Guegen,Hans W and Ligozat,Gerald} } @article {12966, title = {Analysis of 16S-23S rRNA intergenic spacer of Vibrio cholerae and Vibrio mimicus for detection of these species}, journal = {METHODS IN MOLECULAR BIOLOGY}, volume = {179}, year = {2002}, month = {2002///}, pages = {171 - 178}, doi = {10.1385/1-59259-238-4:171}, author = {Chun,J. and Rivera,I. N. G. and Rita R Colwell} } @article {17563, title = {Approximation algorithms for the covering Steiner problem}, journal = {Random Structures \& Algorithms}, volume = {20}, year = {2002}, month = {2002/05/01/}, pages = {465 - 482}, abstract = {The covering Steiner problem is a generalization of both the k-MST and the group Steiner problems: given an edge-weighted graph, with subsets of vertices called the groups, and a nonnegative integer value (called the requirement) for each group, the problem is to find a minimum-weight tree spanning at least the required number of vertices of every group. When all requirements are equal to 1, this becomes the group Steiner problem, while if there is only one group which contains all vertices of the graph the problem reduces to k-MST with k equal to the requirement of this unique group. We discuss two different (but equivalent) linear relaxations of the problem for the case when the given graph is a tree and construct polylogarithmic approximation algorithms based on randomized LP rounding of these relaxations. By using a probabilistic approximation of general metrics by tree metrics due to Bartal, our algorithms also solve the covering Steiner problem on general graphs with a further polylogarithmic worsening in the approximation ratio. {\textcopyright} 2002 Wiley Periodicals, Inc. Random Struct. Alg., 20:465{\textendash}483, 2002}, isbn = {1098-2418}, doi = {10.1002/rsa.10038}, url = {http://onlinelibrary.wiley.com/doi/10.1002/rsa.10038/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+17+March+from+10-14+GMT+\%2806-10+EDT\%29+for+essential+maintenance}, author = {Konjevod,Goran and Ravi,R. and Srinivasan, Aravind} } @conference {18933, title = {Argument structure saturation in a constraint based model}, year = {2002}, month = {2002///}, url = {http://cognet.mit.edu/library/conferences/paper?paper_id=55048}, author = {Drury,J. and Resnik, Philip and Weinberg, Amy and Gennari,S. and Aoshima,S.} } @conference {13729, title = {Automatic transcription of Czech language oral history in the MALACH project: resources and initial experiments}, booktitle = {Proceedings of the The 5th International Conference on Text, Speech and Dialogue}, year = {2002}, month = {2002///}, pages = {57 - 64}, author = {Oard, Douglas and Demner-Fushman,D. and Hajic,J. and Ramabhadran,B. and Gustman,S. and Byrne,WJ and Soergel,D. and Dorr, Bonnie J and Resnik, Philip and Picheny,M.} } @conference {18930, title = {Breaking the resource bottleneck for multilingual applications}, year = {2002}, month = {2002///}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy} } @inbook {14598, title = {Combinatorial Algorithms for Design of DNA Arrays}, booktitle = {Chip TechnologyChip Technology}, series = {Advances in Biochemical Engineering/Biotechnology}, volume = {77}, year = {2002}, month = {2002///}, pages = {1 - 19}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination ( border length minimization problem ) and reducing the complexity of masks ( mask decomposition problem ). We describe algorithms that reduce the number of rectangles in mask decomposition by 20{\textendash}30\% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.}, isbn = {978-3-540-43215-9}, url = {http://dx.doi.org/10.1007/3-540-45713-5_1}, author = {Hannenhalli, Sridhar and Hubbell,Earl and Lipshutz,Robert and Pevzner,Pavel}, editor = {Hoheisel,J{\"o}rg and Brazma,A. and B{\"u}ssow,K. and Cantor,C. and Christians,F. and Chui,G. and Diaz,R. and Drmanac,R. and Drmanac,S. and Eickhoff,H. and Fellenberg,K. and Hannenhalli, Sridhar and Hoheisel,J. and Hou,A. and Hubbell,E. and Jin,H. and Jin,P. and Jurinke,C. and Konthur,Z. and K{\"o}ster,H. and Kwon,S. and Lacy,S. and Lehrach,H. and Lipshutz,R. and Little,D. and Lueking,A. and McGall,G. and Moeur,B. and Nordhoff,E. and Nyarsik,L. and Pevzner,P. and Robinson,A. and Sarkans,U. and Shafto,J. and Sohail,M. and Southern,E. and Swanson,D. and Ukrainczyk,T. and van den Boom,D. and Vilo,J. and Vingron,M. and Walter,G. and Xu,C.} } @article {16250, title = {Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus Anthracis}, journal = {Science}, volume = {296}, year = {2002}, month = {2002/06/14/}, pages = {2028 - 2033}, abstract = {Comparison of the whole-genome sequence ofBacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced B. anthracischromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1071837}, url = {http://www.sciencemag.org/content/296/5575/2028}, author = {Read,Timothy D. and Salzberg,Steven L. and Pop, Mihai and Shumway,Martin and Umayam,Lowell and Jiang,Lingxia and Holtzapple,Erik and Busch,Joseph D and Smith,Kimothy L and Schupp,James M and Solomon,Daniel and Keim,Paul and Fraser,Claire M.} } @article {16411, title = {The complex interaction of agents and environments: An example in urban sprawl}, journal = {Proceedings of Agent Based Simulation}, year = {2002}, month = {2002///}, pages = {149 - 161}, abstract = {We present and evaluate a foundational agent-based model of land use change at therural-urban fringe within the context of a larger project that will link to surveys of the environmental and community preferences of residents with historical data on patterns of development. In this paper, we focus on the dynamics arising from a model of residential location resulting from preferences for services, density, and aesthetics focusing on the relationship between micro level preferences and policy relevant macro phenomena such as scattered development, largest city size, and the number of residential clusters. We consider two representations of agents{\textquoteright} utility functions {\textendash} one additively separable and one multiplicative {\textendash} to see if functional form has any impact on the dynamics of the system, and find that they produce similar results. Our analysis includes both representative agent runs, in which all agents have identical preferences, as well as runs in which the agents have diverse preferences. We find that diversity can increase sprawl through feedbacks associated with the spatial locations of services and agents. In addition, we examine cases in which the agents{\textquoteright} location decisions affect the aesthetic quality of neighboring sites and find that these feedbacks further exacerbate the sprawl effect. }, author = {Rand, William and Zellner,M and Page,S.E. and Riolo,R and Brown,D.G. and Fernandez,L.E.} } @conference {18645, title = {A configurable CORBA gateway for providing adaptable system properties}, year = {2002}, month = {2002///}, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/02SER01.pdf}, author = {Seri,M. and Courtney,T. and Michel Cukier and Gupta,V. and Krishnmamurthy,S. and Lyons,J. and Ramasamy,H. and Ren,J. and Sanders,W. H.} } @inbook {13760, title = {DUSTer: A Method for Unraveling Cross-Language Divergences for Statistical Word-Level Alignment}, booktitle = {Machine Translation: From Research to Real UsersMachine Translation: From Research to Real Users}, series = {Lecture Notes in Computer Science}, volume = {2499}, year = {2002}, month = {2002///}, pages = {31 - 43}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The frequent occurrence of divergenceS {\textemdash}structural differences between languages{\textemdash}presents a great challenge for statistical word-level alignment. In this paper, we introduce DUSTer, a method for systematically identifying common divergence types and transforming an English sentence structure to bear a closer resemblance to that of another language. Our ultimate goal is to enable more accurate alignment and projection of dependency trees in another language without requiring any training on dependency-tree data in that language. We present an empirical analysis comparing the complexities of performing word-level alignments with and without divergence handling. Our results suggest that our approach facilitates word-level alignment, particularly for sentence pairs containing divergences.}, isbn = {978-3-540-44282-0}, url = {http://dx.doi.org/10.1007/3-540-45820-4_4}, author = {Dorr, Bonnie J and Pearl,Lisa and Hwa,Rebecca and Habash,Nizar}, editor = {Richardson,Stephen} } @conference {16797, title = {Dwarf}, booktitle = {Proceedings of the 2002 ACM SIGMOD international conference on Management of data - SIGMOD {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {464 - 464}, address = {Madison, Wisconsin}, doi = {10.1145/564691.564745}, url = {http://dl.acm.org/citation.cfm?id=564745}, author = {Sismanis,Yannis and Deligiannakis,Antonios and Roussopoulos, Nick and Kotidis,Yannis} } @article {16512, title = {Effects of callosal lesions in a model of letter perception}, journal = {Cognitive, Affective, \& Behavioral Neuroscience}, volume = {2}, year = {2002}, month = {2002///}, pages = {37 - 37}, author = {Shevtsova,N. and Reggia, James A.} } @conference {18384, title = {Empirical evaluation of techniques and methods used for achieving and assessing software high dependability}, booktitle = {Proc. DSN Workshop on Dependability Benchmarking}, year = {2002}, month = {2002///}, author = {Rus,I. and Basili, Victor R. and Zelkowitz, Marvin V and Boehm,B.} } @conference {18942, title = {Evaluating translational correspondence using annotation projection}, series = {ACL {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {392 - 399}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Recently, statistical machine translation models have begun to take advantage of higher level linguistic structures such as syntactic dependencies. Underlying these models is an assumption about the directness of translational correspondence between sentences in the two languages; however, the extent to which this assumption is valid and useful is not well understood. In this paper, we present an empirical study that quantifies the degree to which syntactic dependencies are preserved when parses are projected directly from English to Chinese. Our results show that although the direct correspondence assumption is often too restrictive, a small set of principled, elementary linguistic transformations can boost the quality of the projected Chinese parses by 76\% relative to the unimproved baseline.}, doi = {10.3115/1073083.1073149}, url = {http://dx.doi.org/10.3115/1073083.1073149}, author = {Hwa,Rebecca and Resnik, Philip and Weinberg, Amy and Kolak,Okan} } @conference {16669, title = {Evaluating translational correspondence using annotation projection}, booktitle = {Proceedings of the 40th Annual Meeting on Association for Computational Linguistics}, year = {2002}, month = {2002///}, pages = {392 - 399}, author = {Hwa,R. and Resnik, Philip and Weinberg, Amy and Kolak,O.} } @conference {15268, title = {Experimental Construction of Very Large Scale DNA Databases with Associative Search}, booktitle = {DNA computing: 7th International Workshop on DNA-Based Computers, DNA 7, Tampa, FL, USA, June 10-13, 2001: revised papers}, volume = {7}, year = {2002}, month = {2002///}, pages = {231 - 231}, author = {Reif,J. H and LaBean,T. H and Pirrung,M. and Rana,V. S and Guo,B. and Kingsford, Carl and Wickham,G. S} } @conference {11893, title = {Eye tracking using active deformable models}, booktitle = {Proc. of the IIIrd Indian Conference on Computer Vision, Graphics and Image Processing}, year = {2002}, month = {2002///}, author = {Ramadan,S. and Abd-Almageed, Wael and Smith,C.E.} } @conference {18676, title = {Formal specification and verification of a group membership protocol for an intrusion-tolerant group communication system}, year = {2002}, month = {2002/12//}, pages = {9 - 18}, abstract = {We describe a group membership protocol that is part of an intrusion-tolerant group communication system, and present an effort to use formal tools to model and validate our protocol. We describe in detail the most difficult part of the validation exercise, which was the determination of the right level of abstraction of the protocol for formally specifying the protocol. The validation exercise not only formally showed that the protocol satisfies its correctness claims, but also provided information that will help us make the protocol more efficient without violating correctness.}, keywords = {computer network reliability, distributed processing, distributed systems, fault tolerant computing, formal specification, formal verification, group membership protocol, intrusion-tolerant group communication system, PROMELA, Protocols}, doi = {10.1109/PRDC.2002.1185613}, author = {Ramasamy,H. V. and Michel Cukier and Sanders,W. H.} } @article {16270, title = {Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii}, journal = {Nature}, volume = {419}, year = {2002}, month = {2002/10/03/}, pages = {512 - 519}, abstract = {Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.}, isbn = {0028-0836}, doi = {10.1038/nature01099}, url = {http://www.nature.com/nature/journal/v419/n6906/full/nature01099.html}, author = {Carlton,Jane M. and Angiuoli,Samuel V and Suh,Bernard B. and Kooij,Taco W. and Pertea,Mihaela and Silva,Joana C. and Ermolaeva,Maria D. and Allen,Jonathan E and Jeremy D Selengut and Koo,Hean L. and Peterson,Jeremy D. and Pop, Mihai and Kosack,Daniel S. and Shumway,Martin F. and Bidwell,Shelby L. and Shallom,Shamira J. and Aken,Susan E. van and Riedmuller,Steven B. and Feldblyum,Tamara V. and Cho,Jennifer K. and Quackenbush,John and Sedegah,Martha and Shoaibi,Azadeh and Cummings,Leda M. and Florens,Laurence and Yates,John R. and Raine,J. Dale and Sinden,Robert E. and Harris,Michael A. and Cunningham,Deirdre A. and Preiser,Peter R. and Bergman,Lawrence W. and Vaidya,Akhil B. and Lin,Leo H. van and Janse,Chris J. and Waters,Andrew P. and Smith,Hamilton O. and White,Owen R. and Salzberg,Steven L. and Venter,J. Craig and Fraser,Claire M. and Hoffman,Stephen L. and Gardner,Malcolm J. and Carucci,Daniel J.} } @article {12962, title = {Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh}, journal = {Proceedings of the National Academy of Sciences}, volume = {99}, year = {2002}, month = {2002///}, pages = {12409 - 12409}, abstract = {Diversity, relatedness, and ecological interactions of toxigenic Vibrio cholerae O1 populations in two distinctive habitats, the human intestine and the aquatic environment, were analyzed. Twenty environmental isolates and 42 clinical isolates were selected for study by matching serotype, geographic location of isolation in Bangladesh, and season of isolation. Genetic profiling was done by enterobacterial repetitive intergenic consensus sequence{\textendash}PCR, optimized for profiling by using the fully sequenced V. cholerae El Tor N16961 genome. Five significant clonal clusters of haplotypes were found from 57 electrophoretic types. Isolates from different areas or habitats intermingled in two of the five significant clusters. Frequencies of haplotypes differed significantly only between the environmental populations (exact test; P < 0.05). Analysis of molecular variance yielded a population genetic structure reflecting the differentiating effects of geographic area, habitat, and sampling time. Although a parameter confounding the latter differences explained 9\% of the total molecular variance in the entire population (P < 0.01), the net effect of habitat and time could not be separated because of the small number of environmental isolates included in the study. Five subpopulations from a single area were determined, and from these we were able to estimate a relative differentiating effect of habitat, which was small compared with the effect of temporal change. In conclusion, the resulting population structure supports the hypothesis that spatial and temporal fluctuations in the composition of toxigenic V. cholerae populations in the aquatic environment can cause shifts in the dynamics of the disease.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.192426499}, url = {http://www.pnas.org/content/99/19/12409}, author = {Zo,Y. G. and Rivera,I. N. G. and E. Russek-Cohen and Islam,M. S. and Siddique,A. K. and Yunus,M. and Sack,R. B. and Huq,A. and Rita R Colwell} } @inbook {13782, title = {Handling Translation Divergences: Combining Statistical and Symbolic Techniques in Generation-Heavy Machine Translation}, booktitle = {Machine Translation: From Research to Real UsersMachine Translation: From Research to Real Users}, series = {Lecture Notes in Computer Science}, volume = {2499}, year = {2002}, month = {2002///}, pages = {84 - 93}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes a novel approach to handling translation divergences in a Generation-Heavy Hybrid Machine Translation (GHMT) system. The translation divergence problem is usually reserved for Transfer and Interlingual MT because it requires a large combination of complex lexical and structural mappings. A major requirement of these approaches is the accessibility of large amounts of explicit symmetric knowledge for both source and target languages. This limitation renders Transfer and Interlingual approaches ineffective in the face of structurally-divergent language pairs with asymmetric resources. GHMT addresses the more common form of this problem, source-poor/targetrich, by fully exploiting symbolic and statistical target-language resources. This non-interlingual non-transfer approach is accomplished by using target-language lexical semantics, categorial variations and subcategorization frames to overgenerate multiple lexico-structural variations from a target-glossed syntactic dependency of the source-language sentence. The symbolic overgeneration, which accounts for different possible translation divergences, is constrained by a statistical target-language model.}, isbn = {978-3-540-44282-0}, url = {http://dx.doi.org/10.1007/3-540-45820-4_9}, author = {Habash,Nizar and Dorr, Bonnie J}, editor = {Richardson,Stephen} } @conference {13566, title = {Hidden loop recovery for handwriting recognition}, booktitle = {Frontiers in Handwriting Recognition, 2002. Proceedings. Eighth International Workshop on}, year = {2002}, month = {2002///}, pages = {375 - 380}, abstract = {One significant challenge in the recognition of off-line handwriting is in the interpretation of loop structures. Although this information is readily available in online representation, close proximity of strokes often merges their centers making them difficult to identify. In this paper a novel approach to the recovery of hidden loops in off-line scanned document images is presented. The proposed algorithm seeks blobs that resemble truncated ellipses. We use a sophisticated form analysis method based on mutual distance measurements between the two sides of a symmetric shape. The experimental results are compared with the ground truth of the online representations of each off-line word image. More than 86\% percent of the meaningful loops are handled correctly.}, keywords = {analysis;, character, contour, cursive, detection;, distance, edge, ellipses;, form, handwritten, hidden, loop, measurements;, mutual, partitioning;, recognition;, recovery;, SHAPE, shape;, sophisticated, strokes;, symmetric, truncated, word}, doi = {10.1109/IWFHR.2002.1030939}, author = {David Doermann and Intrator,N. and Rivin,E. and Steinherz,T.} } @conference {12746, title = {A hierarchical approach for obtaining structure from two-frame optical flow}, booktitle = {Motion and Video Computing, 2002. Proceedings. Workshop on}, year = {2002}, month = {2002/12//}, pages = {214 - 219}, abstract = {A hierarchical iterative algorithm is proposed for extracting structure from two-frame optical flow. The algorithm exploits two facts: one is that in many applications, such as face and gesture recognition, the depth variation of the visible surface of an object in a scene is small compared to the distance between the optical center and the object; the other is that the time aliasing problem is alleviated at the coarse level for any two-frame optical flow estimate so that the estimate tends to be more accurate. A hierarchical representation for the relationship between the optical flow, depth, and the motion parameters is derived, and the resulting non-linear system is iteratively solved through two linear subsystems. At the coarsest level, the surface of the object tends to be flat, so that the inverse depth tends to be a constant, which is used as the initial depth map. Inverse depth and motion parameters are estimated by the two linear subsystems at each level and the results are propagated to finer levels. Error analysis and experiments using both computer-rendered images and real images demonstrate the correctness and effectiveness of our algorithm.}, keywords = {algorithm;, aliasing;, analysis;, computer-rendered, depth, depth;, error, estimation;, extraction;, Face, feature, flow;, gesture, hierarchical, image, images;, inverse, iterative, methods;, MOTION, nonlinear, optical, parameter, processing;, real, recognition;, sequences;, signal, structure-from-motion;, system;, systems;, TIME, two-frame, variation;, video}, doi = {10.1109/MOTION.2002.1182239}, author = {Liu,Haiying and Chellapa, Rama and Rosenfeld, A.} } @conference {12762, title = {Identification of humans using gait}, booktitle = {IEEE Transactions on Image Processing}, year = {2002}, month = {2002///}, abstract = {We propose a view-based approach to recognize humans from their gait. Two different imagefeatures have been considered: the width of the outer contour of the binarized silhouette of the walking person and the entire binary silhouette itself. To obtain the observation vector from the image features we employ two different methods. In the first method referred to as the indirect approach, the high-dimensional image feature is transformed to a lower-dimensional space by generating what we call the Frame to Exemplar (FED) distance. The FED vector captures both structural and dynamic traits of each individual. For compact and effective gait representation and recognition, the gait information in the FED vector sequences is captured in a hidden Markov model (HMM). In the second method referred to as the direct approach, we work with the feature vector directly (as opposed to computing the FED) and train an HMM. We estimate the HMM parameters (specifically the observation probability B) based on the distance between the exemplars and the image features. In this way we avoid learning high-dimensional probability density functions. The statistical nature of the HMM lends overall robustness to representation and recognition. The performance of the methods is illustrated using several databases. }, author = {Kale, A. and Rajagopalan, AN and Cuntoor, N. and Krueger, V. and Chellapa, Rama} } @article {13444, title = {Interactive, Incremental Scheduling for Virtual Telescopes in Education}, journal = {THIRD INTERNATIONAL NASA WORKSHOP ON PLANNING AND SCHEDULING FOR SPACE}, year = {2002}, month = {2002///}, pages = {27--29 - 27--29}, abstract = {The Telescopes in Education (TIE) project, which began in 1992, provides remote access for students to control large observatory telescopes in real time. TIE began with a single telescope, and with manual evaluation and scheduling of student requests. With the sucess of TIE, 20 or more additional telescopes are expected to come on line. With proportionally more student requests, we anticipate that managing the requests and telescope resources will rapidly become too complex and time-consuming to handle manually. To respond to this problem, the Virtual Telescopes in Education (VTIE) project was begun last year. VTIE will provide networked capabilities for automated proposal preparation and evaluation, scheduling, and data archival. This paper describes the interactive scheduling capability that is under development for VTIE. Accepted observation requests will be incrementally and interactively scheduled by a constraint-based scheduler, and rescheduled as needed in response to dynamically changing weather and telescope conditions. The scheduling system incorporates a novel method for cost-sensitive constraint satisfaction, which will enable modeling of the costs of data gathering and user interaction during schedule repair.}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.134.4105}, author = {Rathod,Priyang and desJardins, Marie and Sansare,Suryakant} } @book {19352, title = {Level of Detail for 3D Graphics}, year = {2002}, month = {2002}, publisher = {Elsevier Science Inc.}, organization = {Elsevier Science Inc.}, address = {New York, NY, USA}, abstract = {Level of detail (LOD) techniques are increasingly used by professional real-time developers to strike the balance between breathtaking virtual worlds and smooth, flowing animation. Level of Detail for 3D Graphics brings together, for the first time, the mechanisms, principles, practices, and theory needed by every graphics developer seeking to apply LOD methods.Continuing advances in level of detail management have brought this powerful technology to the forefront of 3D graphics optimization research. This book, written by the very researchers and developers who have built LOD technology, is both a state-of-the-art chronicle of LOD advances and a practical sourcebook, which will enable graphics developers from all disciplines to apply these formidable techniques to their own work. }, isbn = {1558608389}, author = {Luebke, David and Watson, Benjamin and Cohen, Jonathan D. and Reddy, Martin and Varshney, Amitabh} } @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 {16394, title = {Markov models of literary style for authorship identification}, journal = {Fluctuation and Noise Letters}, volume = {2}, year = {2002}, month = {2002///}, pages = {L299{\textendash}L303 - L299{\textendash}L303}, abstract = {The author introduces a statistical model of literary style that allows for the authorship question to be examined. This model uses Markov modeling to examine underlying patterns in pieces of literature. Different methods for comparing these models are examined. The methods are then applied to an experiment involving the authorship of 16th century sonnets. Finally suggestions for improving on this technique are discussed.}, doi = {10.1142/S0219477502000890}, author = {Rand, William} } @article {16413, title = {Modeling the Effects of Greenbelts at the Urban-Rural Fringe}, journal = {Proceedings of IEMSS 2002}, year = {2002}, month = {2002///}, pages = {190 - 195}, abstract = {We present and evaluate an agent based model (ABM) of land use change at the rural-urban fringe,comparing its performance to a mathematical model of the same process. Our simplified model was developed in Swarm using agents with heterogeneous preferences and a landscape with heterogeneous properties. The context of this work is a larger project that includes surveys of the preferences of residents and data on historical patterns of development. Our broader goal is to use the model to evaluate the ecological effects of alternative policies and designs. We begin by evaluating the influence of a greenbelt, which is located next to a developing area and in which no development is permitted. We present results of a mathematical model that illustrates the necessary trade-off between greenbelt placement and greenbelt width on its effectiveness at delaying develop- ment beyond. Experiments run with the ABM are validated by the mathematical model and illustrate analyses that can be performed by extending to two-dimensions, variable agent preferences, and multiple, and ultimately realistic, patterns of landscape variability. }, author = {Brown,D.G. and Page,S.E. and Riolo,R and Rand, William} } @article {18495, title = {Network-wide BGP route prediction for traffic engineering}, journal = {Proceedings of ITCOM}, year = {2002}, month = {2002///}, abstract = {The Internet consists of about 13,000 Autonomous Systems (AS{\textquoteright}s) that exchange routing information using the BorderGateway Protocol (BGP). The operators of each AS must have control over the flow of traffic through their network and between neighboring AS{\textquoteright}s. However, BGP is a complicated, policy-based protocol that does not include any direct support for traffic engineering. In previous work, we have demonstrated that network operators can adapt the flow of traffic in an efficient and predictable fashion through careful adjustments to the BGP policies running on their edge routers. Nevertheless, many details of the BGP protocol and decision process make predicting the effects of these policy changes difficult. In this paper, we describe a tool that predicts traffic flow at network exit points based on the network topology, the import policy associated with each BGP session, and the routing advertisements received from neighboring AS{\textquoteright}s. We present a linear-time algorithm that computes a network-wide view of the best BGP routes for each destination prefix given a static snapshot of the network state, without simulating the complex details of BGP message passing. We describe how to construct this snapshot using the BGP routing tables and router configuration files available from operational routers. We verify the accuracy of our algorithm by applying our tool to routing and configuration data from AT\&T{\textquoteright}s commercial IP network. Our route prediction techniques help support the operation of large IP backbone networks, where interdomain routing is an important aspect of traffic engineering. }, author = {Feamster, Nick and Rexford,J.} } @conference {16693, title = {OCR error correction using a noisy channel model}, booktitle = {Proceedings of the second international conference on Human Language Technology Research}, year = {2002}, month = {2002///}, pages = {257 - 262}, author = {Kolak,O. and Resnik, Philip} } @article {12748, title = {Optimal edge-based shape detection}, journal = {Image Processing, IEEE Transactions on}, volume = {11}, year = {2002}, month = {2002/11//}, pages = {1209 - 1227}, abstract = {We propose an approach to accurately detecting two-dimensional (2-D) shapes. The cross section of the shape boundary is modeled as a step function. We first derive a one-dimensional (1-D) optimal step edge operator, which minimizes both the noise power and the mean squared error between the input and the filter output. This operator is found to be the derivative of the double exponential (DODE) function, originally derived by Ben-Arie and Rao (1994). We define an operator for shape detection by extending the DODE filter along the shape{\textquoteright}s boundary contour. The responses are accumulated at the centroid of the operator to estimate the likelihood of the presence of the given shape. This method of detecting a shape is in fact a natural extension of the task of edge detection at the pixel level to the problem of global contour detection. This simple filtering scheme also provides a tool for a systematic analysis of edge-based shape detection. We investigate how the error is propagated by the shape geometry. We have found that, under general assumptions, the operator is locally linear at the peak of the response. We compute the expected shape of the response and derive some of its statistical properties. This enables us to predict both its localization and detection performance and adjust its parameters according to imaging conditions and given performance specifications. Applications to the problem of vehicle detection in aerial images, human facial feature detection, and contour tracking in video are presented.}, keywords = {1D, 2D, aerial, analysis;, boundary, conditions;, contour, cross, detection;, DODE, double, edge, edge-based, error, error;, exponential, extraction;, facial, feature, filter, filter;, Filtering, function;, geometry;, global, human, images;, imaging, localization, mean, methods;, NOISE, operator;, optimal, optimisation;, output;, performance;, pixel;, power;, propagation;, properties;, section;, SHAPE, square, squared, statistical, step, theory;, tracking;, two-dimensional, vehicle, video;}, isbn = {1057-7149}, doi = {10.1109/TIP.2002.800896}, author = {Moon, H. and Chellapa, Rama and Rosenfeld, A.} } @conference {18683, title = {Passive replication schemes in AQuA}, year = {2002}, month = {2002/12//}, pages = {125 - 130}, abstract = {Building large-scale distributed object-oriented systems that provide multidimensional quality of service (QoS) in terms of fault tolerance, scalability, and performance is challenging. In order to meet this challenge, we need an architecture that can ensure that applications{\textquoteright} requirements can be met while providing reusable technologies and software solutions. This paper describes techniques, based on the AQuA architecture, that enhance the applications{\textquoteright} dependability and scalability by introducing two types of group members and a novel passive replication scheme. In addition, we describe how to make the management structure itself dependable by using the passive replication scheme. Finally, we provide performance measurements for the passive replication scheme.}, keywords = {AQuA architecture, distributed object management, Fault tolerance, group members, large-scale distributed object-oriented systems, management structure, multidimensional quality of service, passive replication scheme, performance measurements, reusable technologies, scalability, software fault tolerance, software performance evaluation, software reusability, software solutions}, doi = {10.1109/PRDC.2002.1185628}, author = {Ren,Yansong and Rubel,P. and Seri,M. and Michel Cukier and Sanders,W. H. and Courtney,T.} } @article {12754, title = {Performance analysis of a simple vehicle detection algorithm}, journal = {Image and Vision Computing}, volume = {20}, year = {2002}, month = {2002/01/01/}, pages = {1 - 13}, abstract = {We have performed an end-to-end analysis of a simple model-based vehicle detection algorithm for aerial parking lot images. We constructed a vehicle detection operator by combining four elongated edge operators designed to collect edge responses from the sides of a vehicle. We derived the detection and localization performance of this algorithm, and verified them by experiments. Performance degradation due to different camera angles and illuminations was also examined using simulated images. Another important aspect of performance characterization {\textemdash} whether and how much prior information about the scene improves performance {\textemdash} was also investigated. As a statistical diagnostic tool for the detection performance, a computational approach employing bootstrap was used.}, keywords = {Aerial image, Bootstrap, empirical evaluation, Performance analysis, Vehicle detection}, isbn = {0262-8856}, doi = {10.1016/S0262-8856(01)00059-2}, url = {http://www.sciencedirect.com/science/article/pii/S0262885601000592}, author = {Moon, H. and Chellapa, Rama and Rosenfeld, A.} } @article {16148, title = {A photo history of SIGCHI: evolution of design from personal to public}, journal = {interactions}, volume = {9}, year = {2002}, month = {2002/05//}, pages = {17 - 23}, abstract = {For 20 years I have been photographing personalities and events in the emerging discipline of human--computer interaction. Until now, only a few of these photos were published in newsletters or were shown to visitors who sought them out. Now this photo history is going from a personal record to a public archive. This archive should be interesting for professional members of this community who want to reminisce, as well as for historians and journalists who want to understand what happened. Students and Web surfers may also want to look at the people who created better interfaces and more satisfying user experiences.}, isbn = {1072-5520}, doi = {10.1145/506671.506682}, url = {http://doi.acm.org/10.1145/506671.506682}, author = {Shneiderman, Ben and Kang,Hyunmo and Kules,Bill and Plaisant, Catherine and Rose,Anne and Rucheir,Richesh} } @article {16560, title = {Predicting nearest agent distances in artificial worlds}, journal = {Artificial life}, volume = {8}, year = {2002}, month = {2002///}, pages = {247 - 264}, author = {Schulz,R. and Reggia, James A.} } @conference {18690, title = {Quantifying the cost of providing intrusion tolerance in group communication systems}, year = {2002}, month = {2002///}, pages = {229 - 238}, abstract = {Group communication systems that provide consistent group membership and reliable, ordered multicast properties in the presence of faults resulting from malicious intrusions have not been analyzed extensively to quantify the cost of tolerating these intrusions. This paper attempts to quantify this cost by presenting results from an experimental evaluation of three new intrusion-tolerant microprotocols that have been added to an existing crash-fault-tolerant group communication system. The results are analyzed to identify the parts that contribute the most overhead during provision of intrusion tolerance at the group communication system level.}, keywords = {consistent group membership, crash-fault-tolerant group communication system, cryptography, finite state machines, groupware, intrusion-tolerant microprotocols, malicious intrusions, multicast communication, reliable ordered multicast properties, security of data, Transport protocols}, doi = {10.1109/DSN.2002.1028904}, author = {Ramasamy,H. V. and Pandey,P. and Lyons,J. and Michel Cukier and Sanders,W. H.} } @article {18760, title = {Sheet metal bending: forming part families for generating shared press-brake setups}, journal = {Journal of manufacturing systems}, volume = {21}, year = {2002}, month = {2002///}, pages = {329 - 349}, abstract = {Sheet metal bending press-brakes can be setup to produce more than one type of part withoutrequiring a setup change. To exploit this flexibility, we need setup planning techniques so that press-brake setups can be shared among many different parts. In this paper, we describe algorithms for partitioning a given set of parts into setup compatible part families that can be produced on the same setup. First, we present a greedy algorithm to form part family using a bottom-up approach that makes use of the mixed integer linear programming formulation for generating shared setups for each part family. Second, we present a mixed integer linear programming formulation to generate a shared setup for a given set of parts if such a setup exists. We expect that by producing many different types of parts on the same setup, we can significantly reduce the number of setup operations, improve machine tool utilization and enable cost-effective small-batch manufacturing. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.138.8249\&rep=rep1\&type=pdf}, author = {Gupta,S.K. and Rajagopal,D.} } @conference {15897, title = {Supporting access to large digital oral history archives}, booktitle = {Proceedings of the 2nd ACM/IEEE-CS joint conference on Digital libraries}, series = {JCDL {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {18 - 27}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes our experience with the creation, indexing, and provision of access to a very large archive of videotaped oral histories - 116,000 hours of digitized interviews in 32 languages from 52,000 survivors, liberators, rescuers, and witnesses of the Nazi Holocaust. It goes on to identify a set of critical research issues that must be addressed if we are to provide full and detailed access to collections of this size: issues in user requirement studies, automatic speech recognition, automatic classification, segmentation, summarization, retrieval, and user interfaces. The paper ends by inviting others to discuss use of these materials in their own research.}, keywords = {cataloging, oral history, research agenda}, isbn = {1-58113-513-0}, doi = {10.1145/544220.544224}, url = {http://doi.acm.org/10.1145/544220.544224}, author = {Gustman,Samuel and Soergel,Dagobert and Oard, Douglas and Byrne,William and Picheny,Michael and Ramabhadran,Bhuvana and Greenberg,Douglas} } @conference {13661, title = {Temporal Color Correlograms in Video Retrieval}, booktitle = {International Conference on Pattern Recognition}, year = {2002}, month = {2002///}, pages = {267 - 270}, author = {Rautiainen,M. and David Doermann} } @conference {13474, title = {Three-dimensional visualization of hierarchical task network plans}, booktitle = {In Proceedings of the 3rd International NASA Workshop on Planning and Scheduling for}, year = {2002}, month = {2002///}, abstract = {Artificial Intelligence (AI) planning techniques, particularly hierarchical task network (HTN) planners, can produce very complex plans, with many sequential and parallel actions decomposed into multiple levels of abstraction.}, author = {Kundu,K. and Sessions,C. and desJardins, Marie and Rheingans,P.} } @conference {12750, title = {Towards a criterion for evaluating the quality of 3D reconstructions}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-3321 -IV-3324 - IV-3321 -IV-3324}, abstract = {Even though numerous algorithms exist for estimating the structure of a scene from its video, the solutions obtained are often of unacceptable quality. To overcome some of the deficiencies, many application systems rely on processing more information than necessary with the hope that the redundancy will help improve the quality. This raises the question about how the accuracy of the solution is related to the amount of information processed by the algorithm. Can we define the accuracy of the solution precisely enough that we automatically recognize situations where the quality of the data is so bad that even a large number of additional observations will not yield the desired solution? This paper proposes an information theoretic criterion for evaluating the quality of a 3D reconstruction in terms of the statistics of the observed parameters (i.e. the image correspondences). The accuracy of the reconstruction is judged by considering the change in mutual information (or equivalently the conditional differential entropy) between a scene and its reconstructions and its effectiveness is shown through simulations.}, doi = {10.1109/ICASSP.2002.5745364}, author = {Roy Chowdhury,Amit K. and Chellapa, Rama} } @conference {12751, title = {Two-frame multi-scale optical flow estimation using wavelet decomposition}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-3588 -IV-3591 - IV-3588 -IV-3591}, abstract = {A multi-scale algorithm using wavelet decomposition is proposed to estimate dense optical flow using only two frames. Hierarchical image representation by wavelet decomposition is used to exploit the assumption of local rigid motion in a new multi-scale framework. It is shown that if a wavelet basis with one vanishing moment is carefully selected, we can get hierarchical images, edges, and comers from the wavelet decomposition. Based on this result, all the components of the wavelet decomposition are used to estimate relatively accurate optical flow even under the inadequate image sampling condition, and overcome the $\#$x201C;flattening-out $\#$x201D; problem in traditional pyramid methods, which produce high errors when low-texture regions become flat at coarse levels due to blurring. Local affine transforms are also used to speed up flow estimation. Experiments on different types of image sequences together with quantitative and qualitative comparisons with several other optical flow methods are given to demonstrate the effectiveness and robustness of our algorithm.}, doi = {10.1109/ICASSP.2002.5745431}, author = {Liu,Haiying and Rosenfeld,Azriel and Chellapa, Rama} } @conference {16671, title = {An unsupervised method for word sense tagging using parallel corpora}, booktitle = {Proceedings of the 40th Annual Meeting on Association for Computational Linguistics}, year = {2002}, month = {2002///}, pages = {255 - 262}, author = {Diab,M. and Resnik, Philip} } @article {16789, title = {Using Hilbert curve in image storing and retrieving}, journal = {Information Systems}, volume = {27}, year = {2002}, month = {2002/12//}, pages = {523 - 536}, abstract = {In this paper, we propose a method to accelerate the speed of subset query on uncompressed images. First, we change the method to store images: the pixels of images are stored on the disk in the Hilbert order instead of row-wise order that is used in traditional methods. After studying the properties of the Hilbert curve, we give a new algorithm which greatly reduces the number of data segments in subset query range. Although, we have to retrieve more data than necessary, because the speed of sequential readings is much faster than the speed of random access readings, it takes about 10\% less elapsed time in our algorithm than in the traditional algorithms to execute the subset queries. In some systems, the saving is as much as 90\%.}, keywords = {Hilbert order, Row-wise order, Subset query}, isbn = {0306-4379}, doi = {16/S0306-4379(02)00019-4}, url = {http://www.sciencedirect.com/science/article/pii/S0306437902000194}, author = {Song,Zhexuan and Roussopoulos, Nick} } @conference {16484, title = {Using latency-recency profiles for data delivery on the web}, booktitle = {Proceedings of the 28th international conference on Very Large Data Bases}, year = {2002}, month = {2002///}, pages = {550 - 561}, author = {Bright,L. and Raschid, Louiqa} } @conference {13689, title = {Video analysis applications for pervasive environments}, booktitle = {1st International Conference on Mobile and Ubiquitous Multimedia}, year = {2002}, month = {2002///}, pages = {48 - 55}, abstract = {Network capabilities are expanding at arate that will soon allow a much wider range of image and video content to be delivered to and transmitted from mobile wireless devices. Current pervasive applications provide image and video content primarily in high performance networks or by streaming video over low-bandwidth networks. For video to be truly integrated into ubiquitous applications, we must carefully consider the role of automated video analysis to move beyond simple content delivery. Compression and content adaptation have been significant areas of research for some time and deal with the problem of moving media to devices with limited network, software and hardware capabilities. In the near future, mobile wireless devices that have been primarily consumers of image and video will be able to produce such content as well. In this paper, we will review some of the significant issues associated with providing video capabilities in pervasive environments. We consider not only streaming video applications, but point-to- point video and video messaging capabilities as well. We will show how our previous work on content adaptation is being applied to these types of environments, show what role more general video analysis can play and describe a general architecture for video capture, storage, analysis and transmission. }, author = {Karunanidhi,A. and David Doermann and Parekh,N. and Rautio,V.} } @article {12764, title = {View-Based Recognition of Military Vehicles in Ladar Imagery Using CAD Model Matching}, journal = {OPTICAL ENGINEERING-NEW YORK-MARCEL DEKKER INCORPORATED-}, volume = {78}, year = {2002}, month = {2002///}, pages = {151 - 188}, author = {Der, S.Z. and Zheng,Q. and Redman, B. and Chellapa, Rama and Mahmoud, H.} } @conference {18470, title = {Virtual audio system customization using visual matching of ear parameters}, booktitle = {16th International Conference on Pattern Recognition, 2002. Proceedings}, volume = {3}, year = {2002}, month = {2002///}, pages = {1003- 1006 vol.3 - 1003- 1006 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {Applications in the creation of virtual auditory spaces (VAS) and sonification require individualized head related transfer functions (HRTFs) for perceptual fidelity. HRTFs exhibit significant variation from person to person due to differences between their pinnae, and their body sizes. We propose and preliminarily implement a simple HRTF customization based on the use of a published database of HRTFs (Algazi et al., 2001) that also contains geometrical measurements of subject pinnae. We measure some of these features via simple image processing, and select the HRTF that has features most closely corresponding to the individual{\textquoteright}s features. This selection procedure is implemented along with the virtual auditory system described in (Zotkin et al., 2002), and listener tests conducted comparing the customized HRTF and a fixed HRTF. Despite the simplicity of the method, tests reveal average improvement in localization accuracy of about 25 percent, though performance improvement varies with source location and individuals.}, keywords = {acoustic signal processing, Audio systems, Auditory system, Computer vision, database, Ear, ear parameter matching, geometrical measurements, Head, head related transfer functions, HRTF customization, Image databases, IMAGE PROCESSING, medical image processing, performance improvement, Position measurement, sonification, Spatial databases, System testing, Transfer functions, virtual audio system customization, virtual auditory spaces, virtual auditory system, visual matching}, isbn = {0-7695-1695-X}, doi = {10.1109/ICPR.2002.1048207}, author = {Zotkin,Dmitry N and Duraiswami, Ramani and Davis, Larry S. and Mohan,A. and Raykar,V.} } @article {13479, title = {Virtual Telescopes in Education}, journal = {Journal of Digital Information}, volume = {2}, year = {2002}, month = {2002///}, abstract = {Virtual Telescopes in Education is providing the services required to operate a virtual observatory comprising distributed telescopes, including an interactive, constraint-based scheduling service, data and resource archive, proposal preparation and review environment, and a VTIE Journal. A major goal of VTIE is to elicit from learners questions about the nature of celestial objects and the physical processes that give rise to the spectacular imagery that catches their imaginations. Generation of constrained science questions will assist learners in the science process. To achieve interoperability with other NSDL resources, our approach follows the Open Archives Initiative and the W3C Semantic Web activity.}, author = {Hoban,S. and desJardins, Marie and Farrell,N. and Rathod,P. and Sachs,J. and Sansare,S. and Yesha,Y. and Keating,J. and Busschots,B. and Means,J. and others} } @article {12175, title = {A visual search tool for early elementary science students}, journal = {Journal of Science Education and Technology}, volume = {11}, year = {2002}, month = {2002///}, pages = {49 - 57}, author = {Revelle,G. and Druin, Allison and Platner,M. and Bederson, Benjamin B. and Hourcade,J. P and Sherman,L.} } @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 {16720, title = {Word-level Alignment for Multilingual Resource Acquisition}, year = {2002}, month = {2002/04//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We present a simple, one-pass word alignment algorithm for parallel text. Our algorithm utilizes synchronous parsing and takes advantage of existing syntactic annotations. In our experiments the performance of this model is comparable to more complicated iterative methods. We discuss the challenges and potential benefits of using the model to train syntactic parsers for new languages.}, keywords = {*LEARNING MACHINES, *MULTILINGUAL RESOURCES, *WORDS(LANGUAGE), ACQUISITION, algorithms, ALIGNMENT, BENEFITS, ITERATIONS, LANGUAGE, linguistics}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458782}, author = {Lopez,Adam and Nossal,Michael and Hwa,Rebecca and Resnik, Philip} } @article {18650, title = {An adaptive algorithm for tolerating value faults and crash failures}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {12}, year = {2001}, month = {2001/02//}, pages = {173 - 192}, abstract = {The AQuA architecture provides adaptive fault tolerance to CORBA applications by replicating objects and providing a high-level method that an application can use to specify its desired level of dependability. This paper presents the algorithms that AQUA uses, when an application{\textquoteright}s dependability requirements can change at runtime, to tolerate both value faults in applications and crash failures simultaneously. In particular, we provide an active replication communication scheme that maintains data consistency among replicas, detects crash failures, collates the messages generated by replicated objects, and delivers the result of each vote. We also present an adaptive majority voting algorithm that enables the correct ongoing vote while both the number of replicas and the majority size dynamically change. Together, these two algorithms form the basis of the mechanism for tolerating and recovering from value faults and crash failures in AQuA}, keywords = {active replication communication, adaptive algorithm, adaptive fault tolerance, adaptive majority voting algorithm, AQuA architecture, client-server systems, CORBA, crash failures, data consistency, data integrity, Dependability, distributed object management, fault tolerant computing, objects replication, value faults}, isbn = {1045-9219}, doi = {10.1109/71.910872}, author = {Ren,Yansong and Michel Cukier and Sanders,W. H.} } @article {14595, title = {Analysis and prediction of protein functional sub-types from protein sequence alignments}, volume = {EP20000203764}, year = {2001}, month = {2001/05/02/}, abstract = {Here we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. Given an alignment and set of proteins grouped into sub-types according to some definition of function, such as enzymatic specificity, the method identifies positions that are indicative of functional differences by subtraction of sequence profiles, and analysis of positional entropy in the alignment.}, url = {http://www.freepatentsonline.com/EP1096411.html}, author = {Hannenhalli, Sridhar and Russell,Robert B.}, editor = {SMITHKLINE BEECHAM CORP (US) SMITHKLINE BEECHAM PLC (GB)} } @conference {12823, title = {Automated Validation of Software Models}, booktitle = {Automated Software Engineering, International Conference on}, year = {2001}, month = {2001///}, pages = {91 - 91}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper describes the application of an automated verification tool to a software model developed at Ford. Ford already has in place an advanced model-based software development framework that employs the Matlab?, Simulink?, and Stateflow? modeling tools. During this project we applied the invariant checker Salsa to a Simulink?/ Stateflow? model of automotive software to check for nondeterminism, missing cases, dead code, and redundant code. During the analysis, a number of anomalies were detected that had not been found during manual review. We argue that the detection and correction of these problems demonstrates a cost-effective application of formal verification that elevates our level of confidence in the model.}, isbn = {0-7695-1426-X}, doi = {http://doi.ieeecomputersociety.org/10.1109/ASE.2001.989794}, author = {Sims,Steve and Cleaveland, Rance and Butts,Ken and Ranville,Scott} } @article {12123, title = {Building an Experience Base for Software Engineering: A report on the first CeBASE eWorkshop}, journal = {Product Focused Software Process Improvement}, year = {2001}, month = {2001///}, pages = {110 - 125}, abstract = {New information is obtained by research and disseminated by papers in conferences and journals. The synthesis of knowledge depends upon social discourse among the experts in a given domain to discuss the impact of this new information. Meetings among such experts are, however, expensive and time consuming. In this paper we discuss the organization of CeBASE, a center whose goal is the collection and dissemination of empirically-based software engineering knowledge, and the concept of the online workshop or eWorkshop as a way to use the Internet to minimize the needs of face-to-face meetings. We discuss the design of our eWorkshop and give the results of one eWorkshop that discussed the impact of defect reduction strategies.We want to thank Barry Boehm, Scott Henninger, Rayford Vaughn, Winsor Brown, Dan Port and Michael Frey as well as all participants for their contribution to the success of the eWorkshop. We also want to thank students at USC and UMD for their contribution in testing the system and Jennifer Dix for proof reading this paper. }, doi = {10.1007/3-540-44813-6_13}, author = {Basili, Victor R. and Tesoriero,R. and Costa,P. and Lindvall,M. and Rus,I. and Shull, F. and Zelkowitz, Marvin V} } @article {16766, title = {A case for dynamic view management}, journal = {ACM Transactions on Database SystemsACM Trans. Database Syst.}, volume = {26}, year = {2001}, month = {2001/12//}, pages = {388 - 423}, isbn = {03625915}, doi = {10.1145/503099.503100}, url = {http://dl.acm.org/citation.cfm?id=503100}, author = {Kotidis,Yannis and Roussopoulos, Nick} } @article {16536, title = {Conditions enabling the emergence of inter-agent signalling in an artificial world}, journal = {Artificial Life}, volume = {7}, year = {2001}, month = {2001///}, pages = {3 - 32}, author = {Reggia, James A. and Schulz,R. and Wilkinson,G. S and Uriagereka,J.} } @article {16518, title = {Cortical Spreading depression and the pathogenesis of brain disorders: a computational and neural network-based investigation}, journal = {Neurological research}, volume = {23}, year = {2001}, month = {2001///}, pages = {447 - 456}, author = {Ruppin,E. and Reggia, James A.} } @conference {17588, title = {Efficient algorithms for location and sizing problems in network design}, booktitle = {IEEE Global Telecommunications Conference, 2001. GLOBECOM {\textquoteright}01}, volume = {4}, year = {2001}, month = {2001///}, pages = {2586-2590 vol.4 - 2586-2590 vol.4}, publisher = {IEEE}, organization = {IEEE}, abstract = {Large-scale location, sizing and homing problems of distributed network elements, have received much attention recently due to the massive deployment of broadband communication networks for services like Internet telephony and Web caching. Key considerations in designing these networks include modularity of capacity, economies of scale in cost, and reliability. We formulate a general class of such network design problems as Mixed-Integer Programs. These problems are computationally intractable in general; under various asymptotic conditions, we show how to compute near-optimal solutions. To deal with arbitrary instances, we develop new algorithms based on linear programming, as well as greedy randomized adaptive search. These algorithms achieved near-optimal solutions with reasonable computation time for our experiments}, keywords = {Algorithm design and analysis, Broadband communication, broadband communication networks, broadband networks, capacity modularity, Communication networks, computer network reliability, distributed network elements, Economies of scale, greedy randomized adaptive search, homing, integer programming, Intelligent networks, Internet telephony, large-scale location problems, Large-scale systems, Linear programming, mixed-integer programs, near-optimal solutions, network design, Optical switches, randomised algorithms, reliability, search problems, sizing, Technological innovation, telecommunication network planning, Web caching}, isbn = {0-7803-7206-9}, doi = {10.1109/GLOCOM.2001.966243}, author = {Kumaran,K. and Srinivasan, Aravind and Qiong Wang and Lanning,S. and Ramakrishnan,K. G} } @conference {14766, title = {Efficient network and I/O throttling for fine-grain cycle stealing}, booktitle = {Proceedings of the 2001 ACM/IEEE conference on Supercomputing (CDROM) - Supercomputing {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {3 - 3}, address = {Denver, Colorado}, doi = {10.1145/582034.582037}, url = {http://dl.acm.org/citation.cfm?id=582037}, author = {Ryu, Kyung D. and Hollingsworth, Jeffrey K and Keleher, Peter J.} } @article {16324, title = {An empirical study of regression test selection techniques}, journal = {ACM Transactions on Software Engineering and MethodologyACM Trans. Softw. Eng. Methodol.}, volume = {10}, year = {2001}, month = {2001/04//}, pages = {184 - 208}, isbn = {1049331X}, doi = {10.1145/367008.367020}, url = {http://dl.acm.org/citation.cfm?id=367020}, author = {Graves,Todd L. and Harrold,Mary Jean and Kim,Jung-Min and Porter, Adam and Rothermel,Gregg} } @conference {16647, title = {Evolving columnar circuitry for lateral cortical inhibition}, booktitle = {Neural Networks, 2001. Proceedings. IJCNN{\textquoteright}01. International Joint Conference on}, volume = {1}, year = {2001}, month = {2001///}, pages = {278 - 283}, author = {Ayers,D. and Reggia, James A.} } @article {14884, title = {Fragment completion in humans and machines}, journal = {NIPS}, year = {2001}, month = {2001///}, pages = {27 - 34}, author = {Jacobs, David W. and Rokers,B. and Rudra,A. and Liu,Z.} } @conference {16736, title = {Hashing moving objects}, booktitle = {Mobile Data Management}, year = {2001}, month = {2001///}, pages = {161 - 172}, author = {Song,Z. and Roussopoulos, Nick} } @conference {16702, title = {Improved cross-language retrieval using backoff translation}, booktitle = {Proceedings of the first international conference on Human language technology research}, year = {2001}, month = {2001///}, pages = {1 - 3}, author = {Resnik, Philip and Oard, Douglas and Levow,G.} } @article {13374, title = {Independence is good: dependency-based histogram synopses for high-dimensional data}, journal = {SIGMOD Rec.}, volume = {30}, year = {2001}, month = {2001/05//}, pages = {199 - 210}, abstract = {Approximating the joint data distribution of a multi-dimensional data set through a compact and accurate histogram synopsis is a fundamental problem arising in numerous practical scenarios, including query optimization and approximate query answering. Existing solutions either rely on simplistic independence assumptions or try to directly approximate the full joint data distribution over the complete set of attributes. Unfortunately, both approaches are doomed to fail for high-dimensional data sets with complex correlation patterns between attributes. In this paper, we propose a novel approach to histogram-based synopses that employs the solid foundation of statistical interaction models to explicitly identify and exploit the statistical characteristics of the data. Abstractly, our key idea is to break the synopsis into (1) a statistical interaction model that accurately captures significant correlation and independence patterns in data, and (2) a collection of histograms on low-dimensional marginals that, based on the model, can provide accurate approximations of the overall joint data distribution. Extensive experimental results with several real-life data sets verify the effectiveness of our approach. An important aspect of our general, model-based methodology is that it can be used to enhance the performance of other synopsis techniques that are based on data-space partitioning (e.g., wavelets) by providing an effective tool to deal with the {\textquotedblleft}dimensionality curse{\textquotedblright}.}, isbn = {0163-5808}, doi = {10.1145/376284.375685}, url = {http://doi.acm.org/10.1145/376284.375685}, author = {Deshpande, Amol and Garofalakis,Minos and Rastogi,Rajeev} } @conference {16779, title = {Integrating distributed scientific data sources with MOCHA and XRoaster}, booktitle = {Thirteenth International Conference on Scientific and Statistical Database Management, 2001. SSDBM 2001. Proceedings}, year = {2001}, month = {2001///}, pages = {263 - 266}, publisher = {IEEE}, organization = {IEEE}, abstract = {MOCHA is a novel middleware system for integrating distributed data sources that we have developed at the University of Maryland. MOCHA is based on the idea that the code that implements user-defined types and functions should be automatically deployed to remote sites by the middleware system itself. To this end, we have developed an XML-based framework to specify metadata about data sites, data sets, and user-defined types and functions. XRoaster is a graphical tool that we have developed to help the user create all the XML metadata elements to be used in MOCHA}, keywords = {client-server systems, data sets, data sites, Databases, Distributed computing, distributed databases, distributed scientific data source integration, Educational institutions, graphical tool, hypermedia markup languages, IP networks, java, Large-scale systems, Maintenance engineering, meta data, metadata, Middleware, middleware system, MOCHA, Query processing, remote sites, scientific information systems, user-defined types, visual programming, XML, XML metadata elements, XML-based framework, XRoaster}, isbn = {0-7695-1218-6}, doi = {10.1109/SSDM.2001.938560}, author = {Rodriguez-Martinez,M. and Roussopoulos, Nick and McGann,J. M and Kelley,S. and Mokwa,J. and White,B. and Jala,J.} } @conference {18634, title = {Intrusion tolerance approaches in ITUA}, volume = {64}, year = {2001}, month = {2001///}, url = {http://www.dist-systems.bbn.com/papers/2001/ICDSN/01CUK01.pdf}, author = {Michel Cukier and Lyons,J. and Pandey,P. and Ramasamy,H. V. and Sanders,W. H. and Pal,P. and Webber,F. and Schantz,R. and Loyall,J. and Watro,R.} } @article {16756, title = {K-nearest neighbor search for moving query point}, journal = {Advances in Spatial and Temporal Databases}, year = {2001}, month = {2001///}, pages = {79 - 96}, author = {Song,Z. and Roussopoulos, Nick} } @conference {16597, title = {Learning word pronunciations using a recurrent neural network}, booktitle = {Neural Networks, 2001. Proceedings. IJCNN{\textquoteright}01. International Joint Conference on}, volume = {1}, year = {2001}, month = {2001///}, pages = {11 - 15}, author = {Radio,M. J and Reggia, James A. and Berndt,R. S} } @conference {13826, title = {Mapping lexical entries in a verbs database to WordNet senses}, booktitle = {Proceedings of the 39th Annual Meeting on Association for Computational Linguistics}, series = {ACL {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {244 - 251}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper describes automatic techniques for mapping 9611 entries in a database of English verbs to WordNet senses. The verbs were initially grouped into 491 classes based on syntactic features. Mapping these verbs into WordNet senses provides a resource that supports disambiguation in multilingual applications such as machine translation and cross-language information retrieval. Our techniques make use of (1) a training set of 1791 disambiguated entries, representing 1442 verb entries from 167 classes; (2) word sense probabilities, from frequency counts in a tagged corpus; (3) semantic similarity of WordNet senses for verbs within the same class; (4) probabilistic correlations between WordNet data and attributes of the verb classes. The best results achieved 72\% precision and 58\% recall, versus a lower bound of 62\% precision and 38\% recall for assigning the most frequently occurring WordNet sense, and an upper bound of 87\% precision and 75\% recall for human judgment.}, doi = {10.3115/1073012.1073044}, url = {http://dx.doi.org/10.3115/1073012.1073044}, author = {Green,Rebecca and Pearl,Lisa and Dorr, Bonnie J and Resnik, Philip} } @conference {16466, title = {Optimized seamless integration of biomolecular data}, booktitle = {Proceedings of the IEEE 2nd International Symposium on Bioinformatics and Bioengineering Conference, 2001}, year = {2001}, month = {2001/11/04/6}, pages = {23 - 32}, publisher = {IEEE}, organization = {IEEE}, abstract = {Today, scientific data is inevitably digitized, stored in a variety of heterogeneous formats, and is accessible over the Internet. Scientists need to access an integrated view of multiple remote or local heterogeneous data sources. They then integrate the results of complex queries and apply further analysis and visualization to support the task of scientific discovery. Building a digital library for scientific discovery requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web, as well as data that is locally materialized in warehouses or is generated by software. We consider several tasks to provide optimized and seamless integration of biomolecular data. Challenges to be addressed include capturing and representing source capabilities; developing a methodology to acquire and represent metadata about source contents and access costs; and decision support to select sources and capabilities using cost based and semantic knowledge, and generating low cost query evaluation plans}, keywords = {analysis, Bioinformatics, biology computing, cost based knowledge, Costs, Data analysis, data mining, data visualisation, Data visualization, Data warehouses, decision support, digital library, Educational institutions, information resources, Internet, low cost query evaluation plans, Mediation, meta data, metadata, molecular biophysics, multiple local heterogeneous data sources, multiple remote heterogeneous data sources, optimized seamless biomolecular data integration, scientific discovery, scientific information systems, semantic knowledge, software libraries, visual databases, Visualization}, isbn = {0-7695-1423-5}, doi = {10.1109/BIBE.2001.974408}, author = {Eckman,B. A and Lacroix,Z. and Raschid, Louiqa} } @conference {12074, title = {Personal secure booting}, booktitle = {Information Security and Privacy}, year = {2001}, month = {2001///}, pages = {130 - 144}, author = {Itoi,N. and Arbaugh, William A. and Pollack,S. and Reeves,D.} } @article {17828, title = {Probabilistic temporal databases}, journal = {ACM Transaction on Database Systems}, volume = {26}, year = {2001}, month = {2001///}, pages = {41 - 95}, author = {Alex,D. and Robert,R. and V.S. Subrahmanian} } @article {17823, title = {Probabilistic temporal databases, I: algebra}, journal = {ACM Trans. Database Syst.}, volume = {26}, year = {2001}, month = {2001/03//}, pages = {41 - 95}, abstract = {Dyreson and Snodgrass have drawn attention to the fact that, in many temporal database applications, there is often uncertainty about the start time of events, the end time of events, and the duration of events. When the granularity of time is small (e.g., milliseconds), a statement such as {\textquotedblleft}Packet p was shipped sometime during the first 5 days of January, 1998{\textquotedblright} leads to a massive amount of uncertainty (5{\texttimes}24{\texttimes}60{\texttimes}60{\texttimes}1000) possibilities. As noted in Zaniolo et al. [1997], past attempts to deal with uncertainty in databases have been restricted to relatively small amounts of uncertainty in attributes. Dyreson and Snodgrass have taken an important first step towards solving this problem.In this article, we first introduce the syntax of Temporal-Probabilistic (TP) relations and then show how they can be converted to an explicit, significantly more space-consuming form, called Annotated Relations. We then present a theoretical annotated temporal algebra (TATA). Being explicit, TATA is convenient for specifying how the algebraic operations should behave, but is impractical to use because annotated relations are overwhelmingly large. Next, we present a temporal probabilistic algebra (TPA). We show that our definition of the TP-algebra provides a correct implementation of TATA despite the fact that it operates on implicit, succinct TP-relations instead of overwhemingly large annotated relations. Finally, we report on timings for an implementation of the TP-Algebra built on top of ODBC. }, isbn = {0362-5915}, doi = {10.1145/383734.383736}, url = {http://doi.acm.org/10.1145/383734.383736}, author = {Dekhtyar,Alex and Ross,Robert and V.S. Subrahmanian} } @article {17827, title = {Probabilistic Temporal Databases, II: Calculus and Query Processing}, journal = {Technical Reports from UMIACS, UMIACS-TR-2001-79}, year = {2001}, month = {2001///}, abstract = {There is a vast class of applications in which we know that a certain event occurred, but do not know exactly when it occurred. However, as studied by Dyreson and Snodgrass \cite{ds98}, there are many natural scenarios where probability distributions exist and quantify this uncertainty. Dekhtyar et. al. extended Dyreson and Snodgrass{\textquoteright}s work and defined an extension of the relational algebra to handle such data. The first contribution of this paper is a declarative temporal probabilistic (TP for short) calculus which we show is equivalent in expressive power to the temporal probabilistic algebra of Dekhtyar et. al. Our second major contribution is a set of equivalence and containment results for the TP-algebra. Our third contribution is the development of cost models that may be used to estimate the cost of TP-algebra operations. Our fourth contribution is an experimental evaluation of the accuracy of our cost models and the use of the equivalence results as rewrite rules for optimizing queries by using an implementation of TP-databases on top of ODBC.}, author = {Dekhtyar,A. and Ozcan,F. and Ross,R. and V.S. Subrahmanian} } @conference {15898, title = {Rapidly retargetable interactive translingual retrieval}, booktitle = {Proceedings of the first international conference on Human language technology research}, series = {HLT {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {1 - 5}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper describes a system for rapidly retargetable interactive translingual retrieval. Basic functionality can be achieved for a new document language in a single day, and further improvements require only a relatively modest additional investment. We applied the techniques first to search Chinese collections using English queries, and have successfully added French, German, and Italian document collections. We achieve this capability through separation of language-dependent and language-independent components and through the application of asymmetric techniques that leverage an extensive English retrieval infrastructure.}, keywords = {cross-language, information, retrieval}, doi = {10.3115/1072133.1072212}, url = {http://dx.doi.org/10.3115/1072133.1072212}, author = {Levow,Gina-Anne and Oard, Douglas and Resnik, Philip} } @article {18710, title = {Rescuing a destabilized protein fold through backbone cyclization}, journal = {Journal of Molecular Biology}, volume = {308}, year = {2001}, month = {2001/05/18/}, pages = {1045 - 1062}, abstract = {We describe the physicochemical characterization of various circular and linear forms of the \~{}60 residue N-terminal Src homology 3 (SH3) domain from the murine c-Crk adapter protein. Structural, dynamic, thermodynamic, kinetic and biochemical studies reveal that backbone circularization does not prevent the adoption of the natural folded structure in any of the circular proteins. Both the folding and unfolding rate of the protein increased slightly upon circularization. Circularization did not lead to a significant thermodynamic stabilization of the full-length protein, suggesting that destabilizing enthalpic effects (e.g. strain) negate the expected favorable entropic contribution to overall stability. In contrast, we find circularization results in a dramatic stabilization of a truncated version of the SH3 domain lacking a key glutamate residue. The ability to rescue the destabilized mutant indicates that circularization may be a useful tool in protein engineering programs geared towards generating minimized proteins.}, keywords = {circular protein, ligation, SH3 domain}, isbn = {0022-2836}, doi = {10.1006/jmbi.2001.4631}, url = {http://www.sciencedirect.com/science/article/pii/S0022283601946315}, author = {Camarero,Julio A and Fushman, David and Sato,Satoshi and Giriat,Izabela and Cowburn,David and Raleigh,Daniel P and Muir,Tom W} } @conference {18442, title = {The role of independent verification and validation in maintaining a safety critical evolutionary software in a complex environment: the NASA Space Shuttle program}, booktitle = {Software Maintenance, 2001. Proceedings. IEEE International Conference on}, year = {2001}, month = {2001///}, pages = {118 - 126}, abstract = {The National Aeronautics and Space Administration (NASA) Space Shuttle program is a multi-billion dollar activity scheduled to span over 40 years. Maintaining such software with requirements for high reliability and mission safety taxes current development methods. The authors present how independent verification and validation (IV amp;V) activities are used to support these requirements. They also show how the IV amp;V activities for this program differ from those of more traditional software developments}, keywords = {activities;NASA, Administration;complex, Aeronautics, amp;V, and, computing;program, critical, developments;aerospace, environment;development, evolutionary, IV, maintenance;software, maintenance;traditional, methods;high, program;National, prototyping;space, reliability;independent, safety;safety, Shuttle, software, software;software, space, validation;mission, vehicles;, verification, verification;safety-critical}, doi = {10.1109/ICSM.2001.972722}, author = {Zelkowitz, Marvin V and Rus,L.} } @article {16799, title = {Shared index scans for data warehouses}, journal = {Data Warehousing and Knowledge Discovery}, year = {2001}, month = {2001///}, pages = {307 - 316}, author = {Kotidis1*,Y. and Sismanis,Y. and Roussopoulos, Nick} } @article {16463, title = {Source Selection and Ranking in the WebSemantics Architecture Using Quality of Data Metadata-1 Introduction}, journal = {Advances in Computers}, volume = {55}, year = {2001}, month = {2001///}, pages = {89 - 90}, author = {Mihaila,G. A and Raschid, Louiqa and Vidal,M. E} } @article {13863, title = {Spanish Language Processing at University of Maryland: Building Infrastructure for Multilingual Applications}, year = {2001}, month = {2001///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We describe here our construction of lexical resources, tool creation, building of an alignedparallel corpus, and an approach to automatic treebank creation that we have been de- veloping using Spanish data, based on projection of English syntactic dependency infor- mation across a parallel corpus. }, author = {Cabezas,C. and Dorr, Bonnie J and Resnik, Philip} } @conference {16434, title = {Statistical Analysis in Music Information Retrieval}, booktitle = {Proceedings of the Second Annual International Symposium on Music Information Retrieval ISMIR 2001}, volume = {25--26}, year = {2001}, month = {2001///}, pages = {25 - 26}, abstract = {We introduce a statistical model of music that allows for the retrieval of music based upon an audio input. This model uses frequency counts of state transitions to index pieces of music. Several methods of comparing these index values to choose an appropriate match are examined. We describe how this model can serve as the basis for a query-by-humming system. The model is also shown to be robust to several kinds of errors.}, author = {Rand, William and Birmingham,William P.} } @conference {16708, title = {Supervised sense tagging using support vector machines}, booktitle = {Proceedings of the Second International Workshop on Evaluating Word Sense Disambiguation Systems (SENSEVAL-2)}, year = {2001}, month = {2001///}, pages = {59 - 62}, author = {Cabezas,C. and Resnik, Philip and Stevens,J.} } @conference {18447, title = {Understanding IV \& V in a safety critical and complex evolutionary environment: the NASA space shuttle program}, booktitle = {Proceedings of the 23rd International Conference on Software Engineering}, series = {ICSE {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {349 - 357}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {The National Aeronautics and Space Administration is an internationally recognized leader in space science and exploration. NASA recognizes the inherent risk associated with space exploration; however, NASA makes every reasonable effort to minimize that risk. To that end for the Space Shuttle program NASA instituted a software independent verification and validation (IV\&V) process in 1988 to ensure that the Shuttle and its crew are not exposed to any unnecessary risks. Using data provided by both the Shuttle software developer and the IV\&V contractor, in this paper we describe the overall IV\&V process as used on the Space Shuttle program and provide an analysis of the use of metrics to document and control this process. Our findings reaffirm the value of IV\&V and show the impact IV\&V has on multiple releases of a large complex software system.}, keywords = {Evolutionary software, Life and mission critical software, metrics, Process characterization, Software independent verification and validation, Software safety and reliability, Space Shuttle program}, isbn = {0-7695-1050-7}, url = {http://dl.acm.org/citation.cfm?id=381473.381510}, author = {Zelkowitz, Marvin V and Rus,Ioana} } @article {16158, title = {Understanding Manufacturing Systems with a Learning Historian for User-Directed Experimentation}, volume = {CS-TR-4243}, year = {2001}, month = {2001///}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {This paper describes a learning historian to improve user-directed experimentation withdiscrete event simulation models of manufacturing systems. In user-directed experimentation, an analyst conducts simulation runs to estimate system performance. Then the analyst modifies the simulation model to evaluate other possibilities. An important characteristic is the ad hoc nature of the experimentation, as the analyst forms and runs new trials based on the results from previous trials. Through user-directed experimentation designers compare alternatives and students learn the relationships between input parameters and performance measures. Recording and reviewing previous trials while using simulation models enhances their benefits, transforming trial-and-error into learning. The learning historian combines a graphical user interface, a discrete event simulation model, and dynamic data visualization. Usability studies indicate that the learning historian is a usable and useful tool because it allows users to concentrate more on understanding system behavior than on operating simulation software. }, author = {Chipman,G. and Plaisant, Catherine and Gahagan,S. and Herrmann,J.W. and Hewitt,S. and Reaves,L.} } @conference {16761, title = {Update propagation strategies for improving the quality of data on the web}, booktitle = {PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON VERY LARGE DATA BASES}, year = {2001}, month = {2001///}, pages = {391 - 400}, author = {Labrinidis,A. and Roussopoulos, Nick and SCIENCE,MARYLAND UNIV COLLEGE PARK DEPT OF COMPUTER} } @conference {15885, title = {User modeling for information access based on implicit feedback}, booktitle = {3rd Symposium of ISKO-France, Information Filtering and Automatic Summarisation in networds}, year = {2001}, month = {2001///}, author = {Kim,J. and Oard, Douglas and Romanik,K.} } @conference {16488, title = {Validating an access cost model for wide area applications}, booktitle = {Cooperative Information Systems}, year = {2001}, month = {2001///}, pages = {371 - 385}, author = {Zadorozhny,V. and Raschid, Louiqa and Zhan,T. and Bright,L.} } @article {13353, title = {Adaptive query processing: Technology in evolution}, journal = {IEEE Data Engineering Bulletin}, volume = {23}, year = {2000}, month = {2000///}, pages = {7 - 18}, abstract = {As query engines are scaled and federated, they must cope with highly unpredictable and changeableenvironments. In the Telegraph project, we are attempting to architect and implement a continuously adaptive query engine suitable for global-area systems, massive parallelism, and sensor networks. To set the stage for our research, we present a survey of prior work on adaptive query processing, focusing on three characterizations of adaptivity: the frequency of adaptivity, the effects of adaptivity, and the extent of adaptivity. Given this survey, we sketch directions for research in the Telegraph project. }, author = {Hellerstein,J. M and Franklin,M.J. and Chandrasekaran,S. and Deshpande, Amol and Hildrum,K. and Madden,S. and Raman,V. and Shah,M. A} } @article {14594, title = {Analysis and prediction of functional sub-types from protein sequence alignments}, journal = {Journal of Molecular Biology}, volume = {303}, year = {2000}, month = {2000/10/13/}, pages = {61 - 76}, abstract = {The increasing number and diversity of protein sequence families requires new methods to define and predict details regarding function. Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. Given an alignment and set of proteins grouped into sub-types according to some definition of function, such as enzymatic specificity, the method identifies positions that are indicative of functional differences by comparison of sub-type specific sequence profiles, and analysis of positional entropy in the alignment. Alignment positions with significantly high positional relative entropy correlate with those known to be involved in defining sub-types for nucleotidyl cyclases, protein kinases, lactate/malate dehydrogenases and trypsin-like serine proteases. We highlight new positions for these proteins that suggest additional experiments to elucidate the basis of specificity. The method is also able to predict sub-type for unclassified sequences. We assess several variations on a prediction method, and compare them to simple sequence comparisons. For assessment, we remove close homologues to the sequence for which a prediction is to be made (by a sequence identity above a threshold). This simulates situations where a protein is known to belong to a protein family, but is not a close relative of another protein of known sub-type. Considering the four families above, and a sequence identity threshold of 30 \%, our best method gives an accuracy of 96 \% compared to 80 \% obtained for sequence similarity and 74 \% for BLAST. We describe the derivation of a set of sub-type groupings derived from an automated parsing of alignments from PFAM and the SWISSPROT database, and use this to perform a large-scale assessment. The best method gives an average accuracy of 94 \% compared to 68 \% for sequence similarity and 79 \% for BLAST. We discuss implications for experimental design, genome annotation and the prediction of protein function and protein intra-residue distances.}, keywords = {prediction, protein function, protein structure, sequence alignment}, isbn = {0022-2836}, doi = {10.1006/jmbi.2000.4036}, url = {http://www.sciencedirect.com/science/article/pii/S0022283600940361}, author = {Hannenhalli, Sridhar and Russell,Robert B.} } @article {15230, title = {Approximation algorithms with bounded performance guarantees for the clustered traveling salesman problem}, journal = {Algorithmica}, volume = {28}, year = {2000}, month = {2000///}, pages = {422 - 437}, abstract = {Let G=(V,E) be a complete undirected graph with vertex set V , edge set E , and edge weights l(e) satisfying triangle inequality. The vertex set V is partitioned into clusters V 1 , . . ., V k . The clustered traveling salesman problem is to compute a shortest Hamiltonian cycle (tour) that visits all the vertices, and in which the vertices of each cluster are visited consecutively. Since this problem is a generalization of the traveling salesman problem, it is NP-hard. In this paper we consider several variants of this basic problem and provide polynomial time approximation algorithms for them.}, doi = {10.1007/s004530010045}, author = {Guttmann-Beck,N. and Hassin,R. and Khuller, Samir and Raghavachari,B.} } @article {16725, title = {Automatic deployment of application-specific metadata and code in MOCHA}, journal = {Advances in Database Technology{\textemdash}EDBT 2000}, year = {2000}, month = {2000///}, pages = {69 - 85}, author = {Rodriguez-Martinez,M. and Roussopoulos, Nick} } @article {15235, title = {Centers of sets of pixels}, journal = {Discrete Applied Mathematics}, volume = {103}, year = {2000}, month = {2000/07/15/}, pages = {297 - 306}, abstract = {The center of a connected graph G is the set of nodes of G for which the maximum distance to any other node of G is as small as possible. If G is a simply connected set of lattice points ({\textquotedblleft}pixels{\textquotedblright}) with graph structure defined by 4-neighbor adjacency, we show that the center of G is either a 2{\texttimes}2 square block, a diagonal staircase, or a (dotted) diagonal line with no gaps.}, keywords = {Center, Chessboard distance, City block distance, Intrinsic distance, Simply connected set}, isbn = {0166-218X}, doi = {10.1016/S0166-218X(99)00248-6}, url = {http://www.sciencedirect.com/science/article/pii/S0166218X99002486}, author = {Khuller, Samir and Rosenfeld,Azriel and Wu,Angela} } @article {16552, title = {A computational model of lateralization and asymmetries in cortical maps}, journal = {Neural computation}, volume = {12}, year = {2000}, month = {2000///}, pages = {2037 - 2062}, author = {Levitan,S. and Reggia, James A.} } @conference {16617, title = {Cortical inhibition as explained by the competitive distribution hypothesis}, booktitle = {Network models for control and processing}, year = {2000}, month = {2000///}, pages = {31 - 62}, author = {Reggia, James A. and Sutton III,G. G. and Lynne,C. and D{\textquoteright}Autrechy,S. C and Armentrout,S. L} } @article {15547, title = {Efficient expected-case algorithms for planar point location}, journal = {Algorithm Theory-SWAT 2000}, year = {2000}, month = {2000///}, pages = {537 - 543}, doi = {10.1007/3-540-44985-X_31}, author = {Arya,S. and Cheng,S. W and Mount, Dave and Ramesh,H.} } @conference {16444, title = {Efficient remote data access in a mobile computing environment}, booktitle = {ICPP}, year = {2000}, month = {2000///}, pages = {57 - 57}, author = {Bright,L. and Raschid, Louiqa} } @conference {16341, title = {An empirical study of regression test application frequency}, booktitle = {Proceedings of the 22nd international conference on Software engineering - ICSE {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {126 - 135}, address = {Limerick, Ireland}, doi = {10.1145/337180.337196}, url = {http://dl.acm.org/citation.cfm?id=337196}, author = {Kim,Jung-Min and Porter, Adam and Rothermel,Gregg} } @article {16709, title = {Evaluation of sense disambiguation given hierarchical tag sets}, journal = {Computers and the Humanities}, volume = {34}, year = {2000}, month = {2000///}, author = {Melamed,I.D. and Resnik, Philip} } @conference {16453, title = {Exploiting concurrency in a DBMS implementation for production systems}, booktitle = {Proceedings of the first international symposium on Databases in parallel and distributed systems}, year = {2000}, month = {2000///}, pages = {34 - 45}, author = {Raschid, Louiqa and Sellis,T. and Lin,C. C} } @article {14775, title = {Exploiting fine-grained idle periods in networks of workstations}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {11}, year = {2000}, month = {2000/07//}, pages = {683 - 698}, abstract = {Studies have shown that for a significant fraction of the time, workstations are idle. In this paper, we present a new scheduling policy called Linger-Longer that exploits the fine-grained availability of workstations to run sequential and parallel jobs. We present a two-level workload characterization study and use it to simulate a cluster of workstations running our new policy. We compare two variations of our policy to two previous policies: Immediate-Eviction and Pause-and-Migrate. Our study shows that the Linger-Longer policy can improve the throughput of foreign jobs on a cluster by 60 percent with only a 0.5 percent slowdown of local jobs. For parallel computing, we show that the Linger-Longer policy outperforms reconfiguration strategies when the processor utilization by the local process is 20 percent or less in both synthetic bulk synchronous and real data-parallel applications}, keywords = {cluster of workstations, Computer networks, Concurrent computing, Contracts, Delay, fine-grained availability, Intelligent networks, Linger-Longer, networks of workstations, PARALLEL PROCESSING, Predictive models, Processor scheduling, Resumes, scheduling policy, Throughput, workload characterization, workstation clusters, Workstations}, isbn = {1045-9219}, doi = {10.1109/71.877793}, author = {Kyung Dong Ryu and Hollingsworth, Jeffrey K} } @article {16787, title = {Generating dynamic content at database-backed web servers}, journal = {ACM SIGMOD RecordSIGMOD Rec.}, volume = {29}, year = {2000}, month = {2000/03//}, pages = {26 - 31}, isbn = {01635808}, doi = {10.1145/344788.344794}, url = {http://dl.acm.org/citation.cfm?id=344794}, author = {Labrinidis,Alexandros and Roussopoulos, Nick} } @article {16430, title = {GP+ echo+ subsumption= improved problem solving}, journal = {Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2000)}, year = {2000}, month = {2000///}, pages = {411 - 418}, abstract = {Real-time, adaptive control is a difficult problemthat can be addressed by EC architectures. We are interested in incorporating into an EC architecture some of the features that Holland{\textquoteright}s Echo architecture presents. Echo has been used to model everything from cultures to financial markets. However, the typical application of Echo is a simulation to observe the dynamics of the modeled elements such as found in control problems. We show in this paper that some aspects of Echo can be incorporated into Genetic Programming to solve control problems. The paper discusses EAGP (Echo Augmented Genetic Programming), a modified GP architecture that uses aspects of Echo, and subsumption. We demonstrate the usefulness of EAGP on a robot navigation problem }, author = {Punch,W.F. and Rand, William} } @article {17603, title = {Improved Algorithms via Approximations of Probability Distributions}, journal = {Journal of Computer and System Sciences}, volume = {61}, year = {2000}, month = {2000/08//}, pages = {81 - 107}, abstract = {We present two techniques for constructing sample spaces that approximate probability distributions. The first is a simple method for constructing the small-bias probability spaces introduced by Naor and Naor. We show how to efficiently combine this construction with the method of conditional probabilities to yield improved parallel algorithms for problems such as set discrepancy, finding large cuts in graphs, and finding large acyclic subgraphs. The second is a construction of small probability spaces approximating general independent distributions which are of smaller size than the constructions of Even, Goldreich, Luby, Nisan, and Veli{\v c}kovi{\'c}.}, keywords = {derandomization, discrepancy, explicit constructions, graph coloring, Parallel algorithms, small sample spaces}, isbn = {0022-0000}, doi = {10.1006/jcss.1999.1695}, url = {http://www.sciencedirect.com/science/article/pii/S0022000099916951}, author = {Chari,Suresh and Rohatgi,Pankaj and Srinivasan, Aravind} } @article {16494, title = {Learning response time for websources using query feedback and application in query optimization}, journal = {The VLDB Journal{\textemdash}The International Journal on Very Large Data Bases}, volume = {9}, year = {2000}, month = {2000///}, pages = {18 - 37}, author = {Gruser,J. R and Raschid, Louiqa and Zadorozhny,V. and Zhan,T.} } @article {14626, title = {Ligand-Receptor Pairing Via Tree Comparison}, journal = {Journal of Computational Biology}, volume = {7}, year = {2000}, month = {2000/02//}, pages = {59 - 70}, abstract = {This paper introduces a novel class of tree comparison problems strongly motivated by an important and cost intensive step in drug discovery pipeline viz., mapping cell bound receptors to the ligands they bind to and vice versa. Tree comparison studies motivated by problems such as virus-host tree comparison, gene-species tree comparison and consensus tree problem have been reported. None of these studies are applicable in our context because in all these problems, there is a well-defined mapping of the nodes the trees are built on across the set of trees being compared. A new class of tree comparison problems arises in cases where finding the correspondence among the nodes of the trees being compared is itself the problem. The problem arises while trying to find the interclass correspondence between the members of a pair of coevolving classes, e.g., cell bound receptors and their ligands. Given the evolution of the two classes, the combinatorial problem is to find a mapping among the leaves of the two trees that optimizes a given cost function. In this work we formulate various combinatorial optimization problems motivated by the aforementioned biological problem for the first time. We present hardness results, give an efficient algorithm for a restriction of the problem and demonstrate its applicability.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/10665270050081388}, url = {http://www.liebertonline.com/doi/abs/10.1089/10665270050081388}, author = {Bafna,Vineet and Hannenhalli, Sridhar and Rice,Ken and Vawter,Lisa} } @article {16479, title = {Logic-based query optimization for object databases}, journal = {IEEE Transactions on Knowledge and Data Engineering}, volume = {12}, year = {2000}, month = {2000/08//Jul}, pages = {529 - 547}, abstract = {We present a technique for transferring query optimization techniques, developed for relational databases, into object databases. We demonstrate this technique for ODMG database schemas defined in ODL and object queries expressed in OQL. The object schema is represented using a logical representation (Datalog). Semantic knowledge about the object data model, e.g., class hierarchy information, relationship between objects, etc., as well as semantic knowledge about a particular schema and application domain are expressed as integrity constraints. An OQL object query is represented as a logic query and query optimization is performed in the Datalog representation. We obtain equivalent (optimized) logic queries, and subsequently obtain equivalent (optimized) OQL queries for each equivalent logic query. We present one optimization technique for semantic query optimization (SQO) based on the residue technique of U. Charavarthy et al. (1990; 1986; 1988). We show that our technique generalizes previous research on SQO for object databases. We handle a large class of OQL queries, including queries with constructors and methods. We demonstrate how SQO can be used to eliminate queries which contain contradictions and simplify queries, e.g., by eliminating joins, or by reducing the access scope for evaluating a query to some specific subclass(es). We also demonstrate how the definition of a method or integrity constraints describing the method, can be used in optimizing a query with a method}, keywords = {access scope, application domain, class hierarchy information, Constraint optimization, data integrity, Data models, Datalog, Datalog representation, deductive databases, equivalent logic query, integrity constraints, Lifting equipment, Logic, logic based query optimization, logic programming, logic queries, logic query, logical representation, object data model, object databases, object queries, object schema, object-oriented databases, ODL, ODMG database schemas, optimization technique, optimized OQL queries, OQL object query, query languages, Query optimization, query optimization techniques, Query processing, Relational databases, residue technique, semantic knowledge, semantic query optimization}, isbn = {1041-4347}, doi = {10.1109/69.868906}, author = {Grant,J. and Gryz,J. and Minker, Jack and Raschid, Louiqa} } @conference {16715, title = {Measuring verb similarity}, booktitle = {Proceedings of the Twenty-second Annual Conference of the Cognitive Science Society: August 13-15, 2000, Institute for Research in Cognitive Science, University of Pennsylvania, Philadelphia, PA}, year = {2000}, month = {2000///}, pages = {399 - 399}, author = {Resnik, Philip and Diab,M.} } @conference {14987, title = {MOCHA: a database middleware system featuring automatic deployment of application-specific functionality}, booktitle = {Proceedings of the 2000 ACM SIGMOD International Conference on Management of Data, Dallas, Texas}, year = {2000}, month = {2000///}, author = {Rodr{\i}guez-Martinez,M. and Roussopoulos, Nick and McGann,J. M and Keyley,S. and Katz,V. and Song,Z. and JaJa, Joseph F.} } @conference {16747, title = {MOCHA: a self-extensible database middleware system for distributed data sources}, booktitle = {ACM SIGMOD Record}, volume = {29}, year = {2000}, month = {2000///}, pages = {213 - 224}, author = {Rodr{\'\i}guez-Mart{\'\i}nez,M. and Roussopoulos, Nick} } @article {15370, title = {A model for magnetic aftereffect in the presence of time varying demagnetizing fields}, journal = {Magnetics, IEEE Transactions on}, volume = {36}, year = {2000}, month = {2000/09//}, pages = {3182 - 3184}, abstract = {Preisach models driven by stochastic inputs are employed to model magnetic aftereffect in the presence of demagnetizing fields. As a result of thermal relaxation, the magnetization and, consequently, the demagnetizing field vary in time. The new model generalizes earlier work and self-consistently accounts for the effect of time varying demagnetizing fields on the relaxation process. Three practical numerical techniques are proposed to compute the time variation in the magnetic field and the state of the Preisach plane}, keywords = {aftereffect;, aftereffect;magnetization;numerical, demagnetizing, field;demagnetisation;magnetic, model;magnetic, Preisach, relaxation;time, simulation;thermal, varying}, isbn = {0018-9464}, doi = {10.1109/20.908729}, author = {Korman,C.E. and Adly,A.A. and Mayergoyz, Issak D and Rugkwamsook,P.} } @conference {13614, title = {Off-line Skilled Forgery Detection using Stroke and Substroke Features}, booktitle = {ICPR}, volume = {2}, year = {2000}, month = {2000///}, pages = {355 - 359}, author = {Guo,K. and David Doermann and Rosenfeld, A.} } @conference {17640, title = {Optimal design of signaling networks for Internet telephony}, booktitle = {IEEE INFOCOM 2000. Nineteenth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {2}, year = {2000}, month = {2000///}, pages = {707-716 vol.2 - 707-716 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present an approach for efficient design of a signaling network for a network of software switches supporting Internet telephony. While one may take an integer programming approach to solve this problem, it quickly becomes intractable even for modest-sized networks. Instead, our topology design uses random graphs that we show to be nearly optimal in cost, highly connected, and computationally efficient even for large networks. We then formulate a quadratic assignment problem (QAP) to map the abstract topology into the physical network to achieve optimal load balancing for given demand forecasts, which we solve using randomized heuristics. Numerical results on several example networks illustrate the performance and computational efficiency of our method. A graphical design tool has been developed based on our algorithms}, keywords = {bandwidth allocation, Computational efficiency, Computer networks, Cost function, Demand forecasting, demand forecasts, graph theory, graphical design tool, Internet telephony, Linear programming, Load forecasting, Load management, Network topology, optimal design, optimal load balancing, optimisation, performance, quadratic assignment problem, random graphs, randomised algorithms, randomized heuristics, Signal design, signaling networks, Switches, telecommunication signalling, topology design}, isbn = {0-7803-5880-5}, doi = {10.1109/INFCOM.2000.832245}, author = {Srinivasan, Aravind and Ramakrishnan,K. G and Kumaran,K. and Aravamudan,M. and Naqvi,S.} } @article {16490, title = {Producing Interoperable Queries for Relational and Object-Oriented Databases}, journal = {Journal of Intelligent Information Systems}, volume = {14}, year = {2000}, month = {2000///}, pages = {51 - 75}, author = {Chang,Y. H and Raschid, Louiqa} } @inbook {14801, title = {Resource-aware meta-computing}, booktitle = {Emphasizing Distributed SystemsEmphasizing Distributed Systems}, volume = {Volume 53}, year = {2000}, month = {2000///}, pages = {109 - 169}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {Meta-computing, is an increasingly popular and useful method of obtaining resources to solve large computational problems. However, meta-computer environments pose a number of unique challenges, many of which have yet to be addressed effectively. Among these are dynamicism in both applications and environments, and heterogeneity at several different levels. This chapter discusses current approaches to these problems, and uses them in the Active Harmony system as a running example. Harmony supports an interface that allows applications to export tuning alternatives to the higher-level system. By exposing different parameters that can be changed at runtime, applications can be automatically adapted to changes in their execution environment caused by other programs, the addition or deletion of nodes, or changes in the availability of resources like communication links. Applications expose not only options, but also expected resource utilization with each option and the effect that the option will have on the application{\textquoteright}s performance. We discuss how this flexibility can be used to tune the overall performance of a collection of applications in a system.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245800800054}, author = {Hollingsworth, Jeffrey K and Keleher, Peter J. and Ryu, Kyung D.}, editor = {Marvin V. Zelkowits} } @article {16437, title = {Reverse Engineering and UML: A Case Study of AuctionBot}, volume = {EECS 581}, year = {2000}, month = {2000///}, institution = {University of Michigan}, author = {Bangera,R. and Rand, William} } @article {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 {16162, title = {Simulation based learning environments and the use of learning histories}, booktitle = {CHI {\textquoteright}00 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {2 - 3}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We have developed an application framework for constructing simulation-based learning environments using dynamic simulations and visualizations to represent realistic time-dependent behavior. The development environment is described and many examples are given. In particular we will focus on the learning historian which provides users and learners with a manipulatable recording of their actions which facilitates the exchange of annotated history records among peers and mentors.}, keywords = {education, engineering, History, learning, simulation}, isbn = {1-58113-248-4}, doi = {10.1145/633292.633294}, url = {http://doi.acm.org/10.1145/633292.633294}, author = {Rose,A. and Salter,R. and Keswani,S. and Kositsyna,N. and Plaisant, Catherine and Rubloff,G. and Shneiderman, Ben} } @article {16651, title = {A SIMULATION ENVIRONMENT FOR EVOLVING MULTIAGENT COMMUNICATION}, volume = {UMIACS-TR-2000-64}, year = {2000}, month = {2000/09/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {A simulation environment has been created to support study of emergentcommunication. Multiple agents exist in a two-dimensional world where they must find food and avoid predators. While non-communicating agents may survive, the world is configured so that survival and fitness can be enhanced through the use of inter-agent communication. The goal with this version of the simulator is to determine conditions under which simple communication (signaling) emerges and persists during an evolutionary process. (Also cross-referenced as UMIACS-TR-2000-64) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1101}, author = {Reggia, James A. and Schultz,Reiner and Uriagereka,Juan and Wilkinson,Jerry} } @article {16633, title = {The temporal correlation hypothesis for self-organizing feature maps}, journal = {International Journal of Systems Science}, volume = {31}, year = {2000}, month = {2000///}, pages = {911 - 921}, author = {Chen,Y. and Reggia, James A.} } @conference {16796, title = {Using Hilbert curve in image storing and retrieving}, booktitle = {Proceedings of the 2000 ACM workshops on Multimedia - MULTIMEDIA {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {167 - 170}, address = {Los Angeles, California, United States}, doi = {10.1145/357744.357921}, url = {http://dl.acm.org/citation.cfm?id=357921}, author = {Song,Zhexuan and Roussopoulos, Nick} } @conference {16505, title = {Using quality of data metadata for source selection and ranking}, booktitle = {Proceedings of the Third International Workshop on the Web and Databases, WebDB}, year = {2000}, month = {2000///}, pages = {93 - 98}, author = {Mihaila,G. A and Raschid, Louiqa and Vidal,M. E} } @conference {17501, title = {Visualizing digital library search results with categorical and hierarchical axes}, booktitle = {Proceedings of the fifth ACM conference on Digital libraries}, series = {DL {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {57 - 66}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Digital library search results are usually shown as a textual list, with 10-20 items per page. Viewing several thousand search results at once on a two-dimensional display with continuous variables is a promising alternative. Since these displays can overwhelm some users, we created a simplified two-dimensional display that uses categorical and hierarchical axes, called hieraxes. Users appreciate the meaningful and limited number of terms on each hieraxis. At each grid point of the display we show a cluster of color-coded dots or a bar chart. Users see the entire result set and can then click on labels to move down a level in the hierarchy. Handling broad hierarchies and arranging for imposed hierarchies led to additional design innovations. We applied hieraxes to a digital video library of science topics used by middle school teachers, a legal information system, and a technical library using the ACM Computing Classification System. Feedback from usability testing with 32 subjects revealed strengths and weaknesses.}, keywords = {categorical axes, digital libraries, Graphical user interfaces, hierarchy, hieraxes, Information Visualization}, isbn = {1-58113-231-X}, doi = {10.1145/336597.336637}, url = {http://doi.acm.org/10.1145/336597.336637}, author = {Shneiderman, Ben and Feldman,David and Rose,Anne and Grau,Xavier Ferr{\'e}} } @conference {13482, title = {Visualizing high-dimensional predictive model quality}, booktitle = {Visualization 2000. Proceedings}, year = {2000}, month = {2000///}, pages = {493-496, - 493-496,}, publisher = {IEEE}, organization = {IEEE}, abstract = {Using inductive learning techniques to construct classification models from large, high-dimensional data sets is a useful way to make predictions in complex domains. However, these models can be difficult for users to understand. We have developed a set of visualization methods that help users to understand and analyze the behavior of learned models, including techniques for high-dimensional data space projection, display of probabilistic predictions, variable/class correlation, and instance mapping. We show the results of applying these techniques to models constructed from a benchmark data set of census data, and draw conclusions about the utility of these methods for model understanding.}, isbn = {0-7803-6478-3}, doi = {10.1109/VISUAL.2000.885740}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=885740}, author = {Rheingans,P. and desJardins, Marie} } @conference {16455, title = {Web Query Optimizer}, booktitle = {Data Engineering, International Conference on}, year = {2000}, month = {2000///}, pages = {661 - 661}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {We demonstrate a Web Query Optimizer (WQO) within an architecture of mediators and wrappers, for WebSources of limited capability in a wide area environment. The WQO has several innovative features including a CBR (capability based rewriting) Tool, an enhanced randomized relational optimizer extended to a Web environment, and a WebWrapper cost model that can provide relevant metrics for accessing WebSources. The prototype has been tested against a number of WebSources.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDE.2000.839484}, author = {Zadorozhny,Vladimir and Bright,Laura and Raschid, Louiqa and Urhan,Tolga and Vidal,Maria Esther} } @article {16810, title = {WebView materialization}, journal = {SIGMOD Rec.}, volume = {29}, year = {2000}, month = {2000/05//}, pages = {367 - 378}, abstract = {A WebView is a web page automatically created from base data typically stored in a DBMS. Given the multi-tiered architecture behind database-backed web servers, we have the option of materializing a WebView inside the DBMS, at the web server, or not at all, always computing it on the fly (virtual). Since WebViews must be up to date, materialized WebViews are immediately refreshed with every update on the base data. In this paper we compare the three materialization policies (materialized inside the DBMS, materialized at the web server and virtual) analytically, through a detailed cost model, and quantitatively, through extensive experiments on an implemented system. Our results indicate that materializing at the web server is a more scalable solution and can facilitate an order of magnitude more users than the virtual and materialized inside the DBMS policies, even under high update workloads.}, isbn = {0163-5808}, doi = {10.1145/335191.335430}, url = {http://doi.acm.org/10.1145/335191.335430}, author = {Labrinidis,Alexandros and Roussopoulos, Nick} } @article {16762, title = {The active MultiSync controller of the cubetree storage organization}, journal = {ACM SIGMOD Record}, volume = {28}, year = {1999}, month = {1999///}, pages = {582 - 583}, author = {Roussopoulos, Nick and Kotidis,Y. and Sismanis,Y.} } @article {16659, title = {The Bible as a parallel corpus: Annotating the {\textquoteleft}Book of 2000 Tongues{\textquoteright}}, journal = {Computers and the Humanities}, volume = {33}, year = {1999}, month = {1999///}, pages = {129 - 153}, author = {Resnik, Philip and Olsen,M.B. and Diab,M.} } @conference {18666, title = {Building dependable distributed applications using AQUA}, year = {1999}, month = {1999///}, pages = {189 - 196}, abstract = {Building dependable distributed systems using ad hoc methods is a challenging task. Without proper support, an application programmer must face the daunting requirement of having to provide fault tolerance at the application level, in addition to dealing with the complexities of the distributed application itself. This approach requires a deep knowledge of fault tolerance on the part of the application designer, and has a high implementation cost. What is needed is a systematic approach to providing dependability to distributed applications. Proteus, part of the AQuA architecture, fills this need and provides facilities to make a standard distributed CORBA application dependable, with minimal changes to an application. Furthermore, it permits applications to specify, either directly or via the Quality Objects (QuO) infrastructure, the level of dependability they expect of a remote object, and will attempt to configure the system to achieve the requested dependability level. Our previous papers have focused on the architecture and implementation of Proteus. This paper describes how to construct dependable applications using the AQuA architecture, by describing the interface that a programmer is presented with and the graphical monitoring facilities that it provides}, keywords = {ad hoc methods, application programmer, AQuA, complexities, computational complexity, dependable distributed applications, distributed CORBA application, distributed object management, Fault tolerance, fault tolerant computing, proteus}, doi = {10.1109/HASE.1999.809494}, author = {Ren,J. and Michel Cukier and Rubel,P. and Sanders,W. H. and Bakken,D. E. and Karr,D. A.} } @conference {18639, title = {Building dependable distributed objects with the AQuA architecture}, year = {1999}, month = {1999///}, pages = {17 - 18}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.16.2819\&rep=rep1\&type=pdf}, author = {Michel Cukier and Ren,J. and Rubel,P. and Bakken,D. E. and Karr,D. A.} } @article {18693, title = {A comparative study of the backbone dynamics of two closely related lipid binding proteins: Bovine heart fatty acid binding protein and porcine ileal lipid binding protein}, journal = {Molecular and Cellular Biochemistry}, volume = {192}, year = {1999}, month = {1999///}, pages = {109 - 121}, abstract = {The backbone dynamics of bovine heart fatty acid binding protein (H-FABP) and porcine ileal lipid binding protein (ILBP) were studied by 15N NMR relaxation (T1 and T2) and steady state heteronuclear 15N1H NOE measurements. The microdynamic parameters characterizing the backbone mobility were determined using the {\textquoteleft}model-free{\textquoteright} approach. For H-FABP, the non-terminal backbone amide groups display a rather compact protein structure of low flexibility. In contrast, for ILBP an increased number of backbone amide groups display unusually high internal mobility. Furthermore, the data indicate a higher degree of conformational exchange processes in the {\textmu}sec-msec time range for ILBP compared to H-FABP. These results suggest significant differences in the conformational stability for these two structurally highly homologous members of the fatty acid binding protein family.}, keywords = {Biomedical and Life Sciences}, isbn = {0300-8177}, doi = {10.1023/A:1006834708786}, url = {http://www.springerlink.com/content/w2j255781546j880/abstract/}, author = {L{\"u}cke,Christian and Fushman, David and Ludwig,Christian and Hamilton,James A. and Sacchettini,James C. and R{\"u}terjans,Heinz} } @book {13528, title = {Content-Based Access to Multimedia Information: From Technology Trends to Sate of the Art}, year = {1999}, month = {1999///}, publisher = {Kluwer}, organization = {Kluwer}, author = {Perry,B. and Chang,S-K. and Dinsmore,J. and David Doermann and Rosenfeld, A. and Stevens,S.} } @article {16694, title = {Creating a parallel corpus from the book of 2000 tongues}, journal = {Computers and the Humanities}, volume = {33}, year = {1999}, month = {1999///}, pages = {1 - 2}, author = {Resnik, Philip and Olsen,M.B. and Diab,M.} } @conference {16166, title = {The design of history mechanisms and their use in collaborative educational simulations}, booktitle = {Proceedings of the 1999 conference on Computer support for collaborative learning}, series = {CSCL {\textquoteright}99}, year = {1999}, month = {1999///}, publisher = {International Society of the Learning Sciences}, organization = {International Society of the Learning Sciences}, abstract = {Reviewing past events has been useful in many domains. Videotapes and flight data recorders provide invaluable technological help to sports coaches or aviation engineers. Similarly, providing learners with a readable recording of their actions may help them monitor their behavior, reflect on their progress, and experiment with revisions of their experiences. It may also facilitate active collaboration among dispersed learning communities. Learning histories can help students and professionals make more effective use of digital library searching, word processing tasks, computer-assisted design tools, electronic performance support systems, and web navigation.This paper describes the design space and discusses the challenges of implementing learning histories. It presents guidelines for creating effective implementations, and the design tradeoffs between sparse and dense history records. The paper also presents a first implementation of learning histories for a simulation-based engineering learning environment called SimPLE (Simulated Processes in a Learning Environment) for the case of a semiconductor fabrication module, and reports on early user evaluation of learning histories implemented within SimPLE.}, keywords = {hci, scaffolding, simulation}, url = {http://dl.acm.org/citation.cfm?id=1150240.1150284}, author = {Plaisant, Catherine and Rose,Anne and Rubloff,Gary and Salter,Richard and Shneiderman, Ben} } @conference {13938, title = {Designing PETS: a personal electronic teller of stories}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: the CHI is the limit}, series = {CHI {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {326 - 329}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We have begun the development of a new robotic pet that cansupport children in the storytelling process. Children can build their own pet by snapping together the modular animal parts of the PETS robot. After their pet is built, children can tell stories using the My Pets software. These stories can then be acted out by their robotic pet. This video paper describes the motivation for this research and the design process of our intergenerational design team in building the first PETS prototypes. We will discuss our progress to date and our focus for the future. }, keywords = {children, cooperative inquiry, design techniques, educational applications, intergenerational design team, PETS, ROBOTICS}, isbn = {0-201-48559-1}, doi = {10.1145/302979.303103}, url = {http://doi.acm.org/10.1145/302979.303103}, author = {Druin, Allison and Montemayor,Jamie and Hendler,Jim and McAlister,Britt and Boltman,Angela and Fiterman,Eric and Plaisant,Aurelie and Kruskal,Alex and Olsen,Hanne and Revett,Isabella and Schwenn,Thomas Plaisant and Sumida,Lauren and Wagner,Rebecca} } @article {16658, title = {Distinguishing systems and distinguishing senses: New evaluation methods for word sense disambiguation}, journal = {Natural language engineering}, volume = {5}, year = {1999}, month = {1999///}, pages = {113 - 133}, author = {Resnik, Philip and Yarowsky,D.} } @conference {16732, title = {DynaMat: a dynamic view management system for data warehouses}, booktitle = {Proceedings of the 1999 ACM SIGMOD international conference on Management of data}, year = {1999}, month = {1999///}, pages = {371 - 382}, author = {Kotidis,Y. and Roussopoulos, Nick} } @article {16565, title = {Interhemispheric effects on map organization following simulated cortical lesions}, journal = {Artificial intelligence in medicine}, volume = {17}, year = {1999}, month = {1999///}, pages = {59 - 85}, author = {Levitan,S. and Reggia, James A.} } @inbook {15765, title = {Latent Semantic Indexing via a Semi-Discrete Matrix Decomposition}, booktitle = {The Mathematics of Information Coding, Extraction and DistributionThe Mathematics of Information Coding, Extraction and Distribution}, year = {1999}, month = {1999///}, pages = {73 - 80}, publisher = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, organization = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, address = {New York}, abstract = {With the electronic storage of documents comes the possibility of building search engines that can automatically choose documents relevant to a given set of topics. In information retrieval, we wish to match queries with relevant documents. Documents can be represented by the terms that appear within them, but literal matching of terms does not necessarily retrieve all relevant documents. There are a number of information retrieval systems based on inexact matches. Latent Semantic Indexing represents documents by approximations and tends to cluster documents on similar topics even if their term profiles are somewhat different. This approximate representation is usually accomplished using a low-rank singular value decomposition (SVD) approximation. In this paper, we use an alternate decomposition, the semi-discrete decomposition (SDD). For equal query times, the SDD does as well as the SVD and uses less than one-tenth the storage for the MEDLINE test set.}, author = {Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P.}, editor = {Cybenko,George and O{\textquoteright}Leary, Dianne P. and Rissanen,Jorma} } @conference {16520, title = {Lesion effects in a bihemispheric letter-identification model}, booktitle = {Neural Networks, 1999. IJCNN{\textquoteright}99. International Joint Conference on}, volume = {1}, year = {1999}, month = {1999///}, pages = {215 - 218}, author = {Shevtsova,N. and Reggia, James A.} } @conference {16678, title = {Mining the web for bilingual text}, booktitle = {Proceedings of the 37th annual meeting of the Association for Computational Linguistics on Computational Linguistics}, year = {1999}, month = {1999///}, pages = {527 - 534}, author = {Resnik, Philip} } @conference {16579, title = {A model of lateralization and asymmetries in cortical maps}, booktitle = {Neural Networks, 1999. IJCNN{\textquoteright}99. International Joint Conference on}, volume = {1}, year = {1999}, month = {1999///}, pages = {121 - 124}, author = {Levitan,S. and Stoica,I. and Reggia, James A.} } @article {15853, title = {Multilingual Information Discovery and AccesS (MIDAS): A Joint ACM DL{\textquoteright}99/ ACM SIGIR{\textquoteright}99 Workshop.}, journal = {D-Lib MagazineD-Lib Magazine}, volume = {5}, year = {1999}, month = {1999///}, pages = {1 - 12}, abstract = {Discusses a multidisciplinary workshop that addressed issues concerning internationally distributed information networks. Highlights include multilingual information access in media other than character-coded text; cross-language information retrieval and multilingual metadata; and evaluation of multilingual systems. (LRW)}, keywords = {Distributed computing, Electronic Media}, isbn = {ISSN-1082-9873}, url = {http://www.eric.ed.gov/ERICWebPortal/detail?accno=EJ601937}, author = {Oard, Douglas and Peters,Carol and Ruiz,Miguel and Frederking,Robert and Klavans,Judith and Sheridan,Paraic} } @article {16634, title = {A neural network model of lateralization during letter identification}, journal = {Journal of Cognitive Neuroscience}, volume = {11}, year = {1999}, month = {1999///}, pages = {167 - 181}, author = {Shevtsova,N. and Reggia, James A.} } @conference {17631, title = {New algorithmic aspects of the Local Lemma with applications to routing and partitioning}, booktitle = {Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {643 - 652}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, isbn = {0-89871-434-6}, url = {http://dl.acm.org/citation.cfm?id=314500.314886}, author = {Leighton,Tom and Rao,Satish and Srinivasan, Aravind} } @article {16557, title = {Pathogenic mechanisms in ischemic damage: a computational study}, journal = {Computers in biology and medicine}, volume = {29}, year = {1999}, month = {1999///}, pages = {39 - 59}, author = {Ruppin,E. and Ofer,E. and Reggia, James A. and Revett,K.} } @article {16526, title = {Penumbral tissue damage following acute stroke: a computational investigation}, journal = {Progress in brain research}, volume = {121}, year = {1999}, month = {1999///}, pages = {243 - 260}, author = {Ruppin,E. and Revett,K. and Ofer,E. and Goodall,S. and Reggia, James A.} } @conference {18689, title = {Proteus: a flexible infrastructure to implement adaptive fault tolerance in AQuA}, year = {1999}, month = {1999/11//}, pages = {149 - 168}, abstract = {Building dependable distributed systems from commercial off-the-shelf components is of growing practical importance. For both cost and production reasons, there is interest in approaches and architectures that facilitate building such systems. The AQuA architecture is one such approach; its goal is to provide adaptive fault tolerance to CORBA applications by replicating objects, providing a high-level method for applications to specify their desired dependability, and providing a dependability manager that attempts to reconfigure a system at runtime so that dependability requests are satisfied. This paper describes how dependability is provided in AQuA. In particular it describes Proteus, the part of AQuA that dynamically manages replicated distributed objects to make them dependable. Given a dependability request, Proteus chooses a fault tolerance approach and reconfigures the system to try to meet the request. The infrastructure of Proteus is described in this paper, along with its use in implementing active replication and a simple dependability policy}, keywords = {adaptive fault tolerance, AQuA, commercial off-the-shelf components, CORBA applications, cost, dependable distributed systems, distributed object management, object replication, proteus, reconfigurable architectures, Runtime, Software architecture, software fault tolerance}, doi = {10.1109/DCFTS.1999.814294}, author = {Sabnis,C. and Michel Cukier and Ren,J. and Rubel,P. and Sanders,W. H. and Bakken,D. E. and Karr,D.} } @article {13349, title = {A Study of the Structure of the Web}, journal = {University of California, Berkeley}, year = {1999}, month = {1999///}, abstract = {The World Wide Web is a huge, growing repository of information on a wide range of topics. It is alsobecoming important, commercially and sociologically, as a place of human interaction within different communities. In this paper we present an experimental study of the structure of the Web. We analyze link topologies of various communities, and patterns of mirroring of content, on 1997 and 1999 snapshots of the Web. Our results give insight into patterns of interaction within communities and how they evolve, as well as patterns of data replication. We also describe the techniques we have developed for performing complex processing on this large data set, and our experiences in doing so. We present new algorithms for finding partial and complete mirrors in URL hierarchies; these are also of independent interest for search and redirection. In order to study and visualize link topologies of different communities, we have developed techniques to compact these large link graphs without much information loss. }, author = {Deshpande, Amol and Huang,R. and Raman,V. and Riggs,T. and Song,D. and Subramanian,L.} } @article {16711, title = {Support for interactive document selection in cross-language information retrieval}, journal = {Information Processing \& Management}, volume = {35}, year = {1999}, month = {1999/05//}, pages = {363 - 379}, abstract = {As digital libraries grow to global scale, the provision of interactive access to content in many languages will become increasingly important. In systems that support query-based searching, the presence of multilingual content will affect both the search technology itself and the user interface components that support query formulation, document selection and query refinement. This article describes the interactions among these components and presents a practical way of evaluating the adequacy of the selection interface. A categorization-based model for the user{\textquoteright}s selection process is presented and an experimental methodology suitable for obtaining process centered results in this context is developed. The methodology is applied to assess the adequacy of a selection interface in which multiple candidate translations for a term can be simultaneously presented. The results indicate that the modeled selection process is somewhat less effective when users are presented with multi-translation glosses from Japanese to English rather than materials generated originally in English, but that users with access to the gloss translations substantially outperform a Naive Bayes classification algorithm.}, isbn = {0306-4573}, doi = {10.1016/S0306-4573(98)00066-1}, url = {http://www.sciencedirect.com/science/article/pii/S0306457398000661}, author = {Oard, Douglas and Resnik, Philip} } @conference {13480, title = {Visualization of high-dimensional model characteristics}, booktitle = {Proceedings of the 1999 workshop on new paradigms in information visualization and manipulation in conjunction with the eighth ACM internation conference on Information and knowledge management}, series = {NPIVM {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {6 - 8}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Using inductive learning techniques to construct explanatory models for large, high-dimensional data sets is a useful way to discover useful information. However, these models can be difficult for users to understand. We have developed a set of visualization methods that enable a user to evaluate the quality of learned models, to compare alternative models, and identify ways in which a model might be improved We describe the visualization techniques we have explored, including methods for high-dimensional data space projection, variable/class correlation, instance mapping, and model sampling We show the results of applying these techniques to several models built from a benchmark data set of census data.}, keywords = {data mining and knowledge discovery, multidimensional information spaces, Visualization}, isbn = {1-58113-254-9}, doi = {10.1145/331770.331774}, url = {http://doi.acm.org/10.1145/331770.331774}, author = {desJardins, Marie and Rheingans,Penny} } @conference {16803, title = {An alternative storage organization for ROLAP aggregate views based on cubetrees}, booktitle = {ACM Sigmod Record}, volume = {27}, year = {1998}, month = {1998///}, pages = {249 - 258}, author = {Kotidis,Y. and Roussopoulos, Nick} } @conference {18662, title = {AQuA: an adaptive architecture that provides dependable distributed objects}, booktitle = {Seventeenth IEEE Symposium on Reliable Distributed Systems}, year = {1998}, month = {1998/10//}, pages = {245 - 253}, abstract = {Dependable distributed systems are difficult to build. This is particularly true if they have dependability requirements that change during the execution of an application, and are built with commercial off-the-shelf hardware. In that case, fault tolerance must be achieved using middleware software, and mechanisms must be provided to communicate the dependability requirements of a distributed application to the system and to adapt the system{\textquoteright}s configuration to try to achieve the desired dependability. The AQuA architecture allows distributed applications to request a desired level of availability using the Quality Objects (QuO) framework and includes a dependability manager that attempts to meet requested availability levels by configuring the system in response to outside requests and changes in system resources due to faults. The AQuA architecture uses the QuO runtime to process and invoke availability requests, the Proteus dependability manager to configure the system in response to faults and availability requests, and the Ensemble protocol stack to provide group communication services. Furthermore, a CORBA interface is provided to application objects using the AQuA gateway. The gateway provides a mechanism to translate between process-level communication, as supported by Ensemble, and IIOP messages, understood by Object Request Brokers. Both active and passive replication are supported, and the replication type to use is chosen based on the performance and dependability requirements of particular distributed applications}, keywords = {adaptive architecture, AQuA, availability requests, client-server systems, commercial off-the-shelf hardware, CORBA, dependability manager, dependability requirements, dependable distributed objects, distributed object management, Ensemble protocol stack, Fault tolerance, group communication services, middleware software, Object Request Brokers, process-level communication, proteus, Quality Objects, replication, software fault tolerance, Software quality}, doi = {10.1109/RELDIS.1998.740506}, author = {Cukier, Michel and Ren,J. and Sabnis,C. and Henke,D. and Pistole,J. and Sanders,W. H. and Bakken,D. E. and Berman,M.E. and Karr,D. A. and Schantz,R.E.} } @article {16718, title = {The Bible, Truth, and Multilingual OCR Evaluation}, year = {1998}, month = {1998/12//}, institution = {University of Maryland, College Park}, abstract = {Multilingual OCR has emerged as an important information technology, thanks to the increasing need for cross-language information access. While many research groups and companies have developed OCR algorithms for various languages, it is difficult to compare the performance of these OCR algorithms across languages. This difficulty arises because most evaluation methodologies rely on the use of a document image dataset in each of the languages and it is difficult to find document datasets in different languages that are similar in content and layout. In this paper we propose to use the Bible as a dataset for comparing OCR accuracy across languages. Besides being available in a wide range of languages, Bible translation are closely parallel in content, carefully translated, surprisingly relevant with respect to modern-day language, and quite inexpensive. A project at the University of Maryland is currently implementing this idea. We have created a scanned image dataset with groundtruth from an Arabic Bible. We have also used image degradation models to create synthetically degraded images of a French Bible. We hope to generate similar Bible datasets for other languages, and we are exploring alternative corpora such as the Koran and the Bhagavad Gita that have similar properties. Quantitative OCR evaluation based on the Arabic Bible dataset is currently in progress.}, keywords = {*BIBLE, *CORPUS, *DATASETS, *GROUNDTRUTH, *OPTICAL CHARACTER RECOGNITION, *TEST SETS, *TRANSLATIONS, accuracy, algorithms, CYBERNETICS, DOCUMENT IMAGES, DOCUMENTS, IMAGES, INFORMATION SCIENCE, LANGUAGE, linguistics, MULTILINGUAL OCR(OPTICAL CHARACTER RECOGNITION), SYMPOSIA, TEST AND EVALUATION}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458666}, author = {Kanungo,Tapas and Resnik, Philip} } @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} } @article {16570, title = {Cellular automata models of self-replicating systems}, journal = {Advances in Computers}, volume = {47}, year = {1998}, month = {1998///}, pages = {141 - 183}, author = {Reggia, James A. and Chou,H. H. and Lohn,J. D} } @conference {14842, title = {Clustering appearances of 3D objects}, booktitle = {Computer Vision and Pattern Recognition, 1998. Proceedings. 1998 IEEE Computer Society Conference on}, year = {1998}, month = {1998/06//}, pages = {414 - 420}, abstract = {We introduce a method for unsupervised clustering of images of 3D objects. Our method examines the space of all images and partitions the images into sets that form smooth and parallel surfaces in this space. It further uses sequences of images to obtain more reliable clustering. Finally, since our method relies on a non-Euclidean similarity measure we introduce algebraic techniques for estimating local properties of these surfaces without first embedding the images in a Euclidean space. We demonstrate our method by applying it to a large database of images}, keywords = {3D, clustering;image, clustering;sequences, images;unsupervised, objects;local, of, properties;reliable, recognition;, sequences;object}, doi = {10.1109/CVPR.1998.698639}, author = {Basri,R. and Roth,D. and Jacobs, David W.} } @article {16574, title = {Computational Models for the Formation of Protocell Structures}, journal = {Artificial Life}, volume = {4}, year = {1998}, month = {1998///}, pages = {61 - 77}, author = {Peng,L. E.Y and Reggia, James A.} } @article {16544, title = {Computational studies of lateralization of phoneme sequence generation}, journal = {Neural Computation}, volume = {10}, year = {1998}, month = {1998///}, pages = {1277 - 1297}, author = {Reggia, James A. and Goodall,S. and Shkuro,Y.} } @conference {16763, title = {The Cubetree Storage Organization}, booktitle = {VLDB}, year = {1998}, month = {1998///}, pages = {700 - 700}, author = {Roussopoulos, Nick and Kotidis,Y.} } @inbook {16255, title = {De-amortization of Algorithms}, booktitle = {Computing and CombinatoricsComputing and Combinatorics}, series = {Lecture Notes in Computer Science}, volume = {1449}, year = {1998}, month = {1998///}, pages = {4 - 14}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {De-amortization aims to convert algorithms with excellent overall speed, f ( n ) for performing n operations, into algorithms that take no more than O ( f ( n )/ n ) steps for each operation. The paper reviews several existing techniques for de-amortization of algorithms.}, isbn = {978-3-540-64824-6}, url = {http://dx.doi.org/10.1007/3-540-68535-9_4}, author = {Rao Kosaraju,S. and Pop, Mihai}, editor = {Hsu,Wen-Lian and Kao,Ming-Yang} } @inbook {16258, title = {Drawing of Two-Dimensional Irregular Meshes}, booktitle = {Graph DrawingGraph Drawing}, series = {Lecture Notes in Computer Science}, volume = {1547}, year = {1998}, month = {1998///}, pages = {1 - 14}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present a method for transforming two-dimensional irregular meshes into square meshes with only a constant blow up in area. We also explore context invariant transformations of irregular meshes into square meshes and provide a lower bound for the transformation of down-staircases.}, isbn = {978-3-540-65473-5}, url = {http://dx.doi.org/10.1007/3-540-37623-2_1}, author = {Aggarwal,Alok and Rao Kosaraju,S. and Pop, Mihai}, editor = {Whitesides,Sue} } @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 {16181, title = {Exploring LifeLines to Visualize Patient Records}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {LifeLines provide a general visualization environment for personalhistories. We explored its use for medical patient records. A one screen overview of the record using timelines provides direct access to the data. Problems, hospitalization and medications can be represented as horizontal lines, while icons represent discrete events such as physician consultations (and progress notes) or tests. Line color and thickness can illustrate relationships or significance. Techniques are described to display large records. Rescaling tools and filters allow users to focus on part of the information, revealing more details. Computerized medical records pose tremendous problems to system developers. Infrastructure and privacy issues need to be resolved before physicians can even start using the records. Non-intrusive hardware is required for physicians to do their work (i.e. interview patients) away from their desk and cumbersome workstations. But all the efforts to solve those problems will only succeed if appropriate attention is also given to the user interface design [1][8]. Long lists to scroll, clumsy search, endless menus and lengthy dialogs will lead to user rejection. But techniques are being developed to summarize, filter and present large amount of information, leading us to believe that rapid access to needed data is possible with careful design. While more attention is now put on developing standards for gathering medical records we found that very little effort had been made to design appropriate visualization and navigation techniques to present and explore personal history records. An intuitive approach to visualizing histories is to use graphical time series. The consistent, linear time scale allows comparisons and relations between the quantities displayed. Data can be graphed on the timeline to show time series of quantitative data. Highly interactive interfaces turn the display into a meaningfully structured menu with direct access to the data needed to review a problem or conduct the diagnosis. Also cross-referenced as CAR-TR-819 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/455}, author = {Plaisant, Catherine and Rose,Anne} } @article {18832, title = {Feature Recognition for Interactive Applications: Exploiting Distributed Resources}, volume = {UMIACS-TR-94-126.1}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The availability of low-cost computational power is a drivingforce behind the growing sophistication of CAD software. Tools designed to reduce time-consuming build-test-redesign iterations are essential for increasing engineering quality and productivity. However, automation of the design process poses many difficult computational problems. As more downstream engineering activities are being considered during the design phase, guaranteeing reasonable response times within design systems becomes problematic. Design is an interactive process and speed is a critical factor in systems that enable designers to explore and experiment with alternative ideas during the design phase. Achieving interactivity requires an increasingly sophisticated allocation of computational resources in order to perform realistic design analyses and generate feedback in real time. This paper presents our initial efforts to develop techniques to apply distributed algorithms to the problem of recognizing machining features from solid models. Existing work on recognition of features has focused exclusively on serial computer architectures. Our objective is to show that distributed algorithms can be employed on realistic parts with large numbers of features and many geometric and topological entities to obtain significant improvements in computation time using existing hardware and software tools. Migrating solid modeling applications toward a distributed computing framework enables interconnection of many of the autonomous and geographically diverse software tools used in the modern manufacturing enterprise. (Also cross-referenced as UMIACS-TR-94-126.1) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/675}, author = {Regli,William C. and Gupta, Satyandra K. and Nau, Dana S.} } @article {13672, title = {The function of documents}, journal = {Image and Vision Computing}, volume = {16}, year = {1998}, month = {1998/08/01/}, pages = {799 - 814}, abstract = {The purpose of a document is to facilitate the transfer of information from its author to its readers. It is the author{\textquoteright}s job to design the document so that the information it contains can be interpreted accurately and efficiently. To do this, the author can make use of a set of stylistic tools. In this paper, we introduce the concept of document functionality, which attempts to describe the roles of documents and their components in the process of transferring information. A functional description of a document provides insight into the type of the document, into its intended uses, and into strategies for automatic document interpretation and retrieval.To demonstrate these ideas, we define a taxonomy of functional document components and show how functional descriptions can be used to reverse-engineer the intentions of the author, to navigate in document space, and to provide important contextual information to aid in interpretation. }, keywords = {Document functionality, Information transfer}, isbn = {0262-8856}, doi = {10.1016/S0262-8856(98)00068-7}, url = {http://www.sciencedirect.com/science/article/pii/S0262885698000687}, author = {David Doermann and Rivlin,Ehud and Rosenfeld,Azriel} } @article {18849, title = {IMACS: a case study in real-world planning}, journal = {Intelligent Systems and their Applications, IEEE}, volume = {13}, year = {1998}, month = {1998/06//may}, pages = {49 - 60}, abstract = {This article discusses the complexities of real-world planning and how to create planning systems to address them. IMACS (Interactive Manufacturability Analysis and Critiquing System), an automated designer{\textquoteright}s aid, evaluates machined parts and suggests design modifications to improve their manufacturability, offering advantages over the planning techniques used in classical planning systems}, keywords = {automated designer{\textquoteright}s aid, CAD/CAM, case study, computer aided analysis, computer aided production planning, design modifications, IMACS, intelligent design assistants, Interactive Manufacturability Analysis and Critiquing System, interactive systems, machined parts evaluation, machining, manufacturability, planning (artificial intelligence), planning systems}, isbn = {1094-7167}, doi = {10.1109/5254.683210}, author = {Gupta,S.K. and Nau, Dana S. and Regli,W. C.} } @conference {17609, title = {Improved bounds and algorithms for hypergraph two-coloring}, booktitle = {39th Annual Symposium on Foundations of Computer Science, 1998. Proceedings}, year = {1998}, month = {1998/11/08/11}, pages = {684 - 693}, publisher = {IEEE}, organization = {IEEE}, abstract = {We show that for all large n, every n-uniform hypergraph with at most 0.7√(n/lnn){\texttimes}2n edges can be two-colored. We, in fact, present fast algorithms that output a proper two-coloring with high probability for such hypergraphs. We also derandomize and parallelize these algorithms, to derive NC1 versions of these results. This makes progress on a problem of Erdos (1963), improving the previous-best bound of n1/3-0(1){\texttimes}2n due to Beck (1978). We further generalize this to a {\textquotedblleft}local{\textquotedblright} version, improving on one of the first applications of the Lovasz Local Lemma}, keywords = {algorithms, Application software, Approximation algorithms, bounds, computational geometry, Computer science, Contracts, Erbium, graph colouring, History, hypergraph two-coloring, Lab-on-a-chip, MATHEMATICS, n-uniform hypergraph, Parallel algorithms, Polynomials, probability}, isbn = {0-8186-9172-7}, doi = {10.1109/SFCS.1998.743519}, author = {Radhakrishnan,J. and Srinivasan, Aravind} } @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 {16180, title = {Life cycle of user interface techniques: The DJJ information system design Process}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {To take advantage of todays technology, many organizations are migrating fromtheir legacy systems. With help from the Human-Computer Interaction Laboratory (HCIL) and Cognetics Corporation, the Maryland Department of Juvenile Justice (DJJ) is currently undergoing an effort to redesign their information system to take advantage of graphical user interfaces. As a research lab, HCIL identifies interesting research problems and then prototypes solutions. As a project matures, the exploratory prototypes are adapted to suit the end product requirements. This case study describes the life cycle of three DJJ prototypes: (1) LifeLines, which uses time lines to display an overview of a youth in one screen, (2) the DJJ Navigator, which helps manage individual workloads by displaying different user views, and (3) the ProgramFinder, a tool for selecting the best program for a youth. (Also cross-referenced as CAR-TR-826) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/458}, author = {Rose,Anne and Ellis,Jason and Plaisant, Catherine and Greene,Stephan} } @conference {14815, title = {Linger longer: Fine-grain cycle stealing for networks of workstations}, booktitle = {Proceedings of the 1998 ACM/IEEE Conference on Supercomputing (CDROM)}, year = {1998}, month = {1998///}, pages = {1 - 12}, author = {Ryu, K. D and Hollingsworth, Jeffrey K} } @article {15519, title = {Logic knowledge bases with two default rules}, journal = {Annals of Mathematics and Artificial Intelligence}, volume = {22}, year = {1998}, month = {1998///}, pages = {333 - 361}, author = {Ruiz,C. and Minker, Jack} } @article {15227, title = {Low Degree Spanning Trees of Small Weight}, volume = {UMIACS-TR-94-1}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Given n points in the plane, the degree-K spanning tree problemasks for a spanning tree of minimum weight in which the degree of each vertex is at most K. This paper addresses the problem of computing low-weight degree-K spanning trees for K>2. It is shown that for an arbitrary collection of n points in the plane, there exists a spanning tree of degree three whose weight is at most 1.5 times the weight of a minimum spanning tree. It is shown that there exists a spanning tree of degree four whose weight is at most 1.25 times the weight of a minimum spanning tree. These results solve open problems posed by Papadimitriou and Vazirani. Moreover, if a minimum spanning tree is given as part of the input, the trees can be computed in O(n) time. The results are generalized to points in higher dimensions. It is shown that for any d [greater than or equal to] 3, an arbitrary collection of points in DimD contains a spanning tree of degree three, whose weight is at most 5/3 times the weight of a minimum spanning tree. This is the first paper that achieves factors better than two for these problems. (Also cross-referenced as UMIACS-TR-94-1) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/611}, author = {Khuller, Samir and Raghavachari,Balaji and Young,Neal} } @article {16767, title = {Materialized views and data warehouses}, journal = {ACM SIGMOD RecordSIGMOD Rec.}, volume = {27}, year = {1998}, month = {1998/03//}, pages = {21 - 26}, isbn = {01635808}, doi = {10.1145/273244.273253}, url = {http://dl.acm.org/citation.cfm?id=273244.273253}, author = {Roussopoulos, Nick} } @conference {16478, title = {A Meta-Wrapper for Scaling up to Multiple Autonomous Distributed Information Sources}, booktitle = {Cooperative Information Systems, IFCIS International Conference on}, year = {1998}, month = {1998///}, pages = {148 - 148}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Abstract Current mediator and wrapper architectures do not have the flexibility to scale to multiple wrapped sources, where some sources may be redundant, and some sources may provide incomplete answers to a query. We propose a meta-wrapper component which is capable of handling multiple wrapped sources, in a particular domain, where the multiple sources provide related information. The meta-wrapper makes these sources transparent to the mediator, and provides a single meta-wrapper interface for all these sources. Source descriptions specify the content and query capability of the sources. These are used to determine the meta-wrapper interface and to decide which queries from a mediator can be accepted. Sources are partitioned into equivalence classes, based on their descriptions. These equivalence classes are partially ordered, and the lattices that correspond to these orderings are used to identify the relevant sources for a query submitted by the mediator. If there is redundancy of the sources, the meta-wrapper identifies alternate sources for the query. A meta-wrapper cost model is then used to select among alternate relevant sources and choose the best plan.}, keywords = {information resource discovery, integration and interoperability, metadata use and management, wrappers and mediators}, isbn = {0-8186-8380-5}, doi = {http://doi.ieeecomputersociety.org/10.1109/COOPIS.1998.706193}, author = {Vidal,Maria Esther and Raschid, Louiqa and Gruser,Jean Robert} } @article {14804, title = {Modeling and evaluating design alternatives for an on-line instrumentation system: a case study}, journal = {IEEE Transactions on Software Engineering}, volume = {24}, year = {1998}, month = {1998/06//}, pages = {451 - 470}, abstract = {This paper demonstrates the use of a model-based evaluation approach for instrumentation systems (ISs). The overall objective of this study is to provide early feedback to tool developers regarding IS overhead and performance; such feedback helps developers make appropriate design decisions about alternative system configurations and task scheduling policies. We consider three types of system architectures: network of workstations (NOW), symmetric multiprocessors (SMP), and massively parallel processing (MPP) systems. We develop a Resource OCCupancy (ROCC) model for an on-line IS for an existing tool and parameterize it for an IBM SP-2 platform. This model is simulated to answer several {\textquotedblleft}what if{\textquotedblright} questions regarding two policies to schedule instrumentation data forwarding: collect-and-forward (CF) and batch-and-forward (BF). In addition, this study investigates two alternatives for forwarding the instrumentation data: direct and binary tree forwarding for an MPP system. Simulation results indicate that the BF policy can significantly reduce the overhead and that the tree forwarding configuration exhibits desirable scalability characteristics for MPP systems. Initial measurement-based testing results indicate more than 60 percent reduction in the direct IS overhead when the BF policy was added to Paradyn parallel performance measurement tool}, keywords = {alternative system configurations, Application software, batch-and-forward, collect-and-forward, Computer aided software engineering, design alternatives, design decisions, Feedback, IBM SP-2 platform, Instruments, massively parallel processing, model-based evaluation approach, Monitoring, multiprocessing programs, on-line instrumentation system, Paradyn parallel performance measurement tool, PARALLEL PROCESSING, Real time systems, scalability characteristics, software metrics, software tools, Space technology, symmetric multiprocessors, system architectures, system monitoring, System testing, task scheduling policies, tool developers, tree forwarding configuration, Workstations}, isbn = {0098-5589}, doi = {10.1109/32.689402}, author = {Waheed, A. and Rover, D. T and Hollingsworth, Jeffrey K} } @conference {17627, title = {Multicommodity flow and circuit switching}, booktitle = {, Proceedings of the Thirty-First Hawaii International Conference on System Sciences, 1998}, volume = {7}, year = {1998}, month = {1998/01/06/9}, pages = {459-465 vol.7 - 459-465 vol.7}, publisher = {IEEE}, organization = {IEEE}, abstract = {Given a set of request pairs in a network, the problem of routing virtual circuits with low congestion is to connect each pair by a path so that few paths use the same link in the network. We build on an earlier multicommodity flow based approach of Leighton and Rao (1996) to show that short flow paths lead to path selections with low congestion. This shows that such good path selections exist for constant-degree expanders with strong expansion, generalizing a result of (Broder et al., 1994). We also show, for infinitely many n, n-vertex undirected graphs Gn along with a set T of connection requests, such that: T is fractionally realizable using flow-paths that impose a (fractional) congestion of at most 1; but any rounding of such a flow to the given set of flow-paths, leads to a congestion of Ω(log n/log log n). This is progress on a long-standing open problem}, keywords = {Application software, Bandwidth, circuit switching, Computer science, constant-degree expanders, graph theory, High speed integrated circuits, Integrated circuit technology, Laboratories, low congestion, MATHEMATICS, multicommodity flow, National electric code, network routing, path selections, Routing, short flow paths, Switching circuits, switching theory, undirected graphs, virtual circuit routing}, isbn = {0-8186-8255-8}, doi = {10.1109/HICSS.1998.649241}, author = {Leighton,T. and Rao,S. and Srinivasan, Aravind} } @conference {16450, title = {Optimization of wrappers and mediators for web accessible data sources (websources)}, booktitle = {Workshop Web Inf. Data Management (WIDM), Washington DC}, year = {1998}, month = {1998///}, author = {Bright,L. and Raschid, Louiqa and Vidal,M. E} } @article {16712, title = {Parallel strands: A preliminary investigation into mining the web for bilingual text}, journal = {Machine Translation and the Information Soup}, year = {1998}, month = {1998///}, pages = {72 - 82}, author = {Resnik, Philip} } @article {13013, title = {Phylogenetic relationships of platyhelminthes based on 18S ribosomal gene sequences}, journal = {Mol Phylogenet Evol}, volume = {10}, year = {1998}, month = {1998/08//}, pages = {1 - 10}, abstract = {Nucleotide sequences of 18S ribosomal RNA from 71 species of Platyhelminthes, the flatworms, were analyzed using maximum likelihood, and the resulting phylogenetic trees were compared with previous phylogenetic hypotheses. Analyses including 15 outgroup species belonging to eight other phyla show that Platyhelminthes are monophyletic with the exception of a sequence putatively from Acoela sp., Lecithoepitheliata, Polycladida, Tricladida, Trematoda (Aspidobothrii + Digenea), Monogenea, and Cestoda (Gyrocotylidea + Amphilinidea + Eucestoda) are monophyletic groups. Catenulids form the sister group to the rest of platyhelminths, whereas a complex clade formed by Acoela, Tricladida, "Dalyellioida", and perhaps "Typhloplanoida" is sister to Neodermata. "Typhloplanoida" does not appear to be monophyletic; Fecampiida does not appear to belong within "Dalyellioida," nor Kalyptorhynchia within "Typhloplanoida." Trematoda is the sister group to the rest of Neodermata, and Monogenea is sister group to Cestoda. Within Trematoda, Aspidobothrii is the sister group of Digenea and Heronimidae is the most basal family in Digenea. Our trees support the hypothesis that parasitism evolved at least twice in Platyhelminthes, once in the ancestor to Neodermata and again in the ancestor of Fecampiida, independently to the ancestor of putatively parasitic "Dalyellioida."}, doi = {10.1006/mpev.1997.0483}, author = {Campos,A. and Cummings, Michael P. and Reyes,J. L and Laclette,J. P} } @article {16609, title = {Problem solving during artificial selection of self-replicating loops* 1}, journal = {Physica D: Nonlinear Phenomena}, volume = {115}, year = {1998}, month = {1998///}, pages = {293 - 312}, author = {Chou,H. H. and Reggia, James A.} } @article {16627, title = {Self-replicating structures: evolution, emergence, and computation}, journal = {Artificial Life}, volume = {4}, year = {1998}, month = {1998///}, pages = {283 - 302}, author = {Reggia, James A. and Lohn,J. D and Chou,H. H.} } @article {15521, title = {Semantics for Disjunctive and Normal Disjunctive Logic Programs}, journal = {Handbook of logic in artificial intelligence and logic programming}, volume = {5}, year = {1998}, month = {1998///}, pages = {325 - 325}, author = {Lobo,J. and Minker, Jack and Rajasekar,A.} } @article {18714, title = {Solution structure and dynamics of the bioactive retroviral M domain from rous sarcoma virus}, journal = {Journal of Molecular Biology}, volume = {279}, year = {1998}, month = {1998/06/19/}, pages = {921 - 928}, abstract = {A biologically active construct of the retroviral M domain from the avian Rous sarcoma virus is defined and its solution structure described. This M domain is fully active in budding and infectivity without myristylation. In spite of a sequence homology level that suggests no relationship among M domains and the family of matrix proteins in mammalian retroviruses, the conserved structural elements of a central core allow an M domain sequence motif to be described for all retroviruses. The surface of the M domain has a highly clustered positive patch comprised of sequentially distant residues. An analysis of the backbone dynamics, incorporating rotational anisotropy, is used to estimate the thermodynamics of proposed domain oligomerization.}, keywords = {heteronuclear NMR spectroscopy, protein dynamics, RSV matrix protein, sequence homology, three-dimensional structure}, isbn = {0022-2836}, doi = {10.1006/jmbi.1998.1788}, url = {http://www.sciencedirect.com/science/article/pii/S0022283698917880}, author = {McDonnell,James M and Fushman, David and Cahill,Sean M. and Zhou,Wenjun and Wolven,Amy and Wilson,Carol B and Nelle,Timothy D and Resh,Marilyn D and Wills,John and Cowburn,David} } @article {16337, title = {Specification-based Testing of Reactive Software: A Case Study in Technology Transfer}, journal = {Journal of Systems and Software}, volume = {40}, year = {1998}, month = {1998///}, pages = {249 - 262}, author = {Jategaonkar Jagadeesan,L. and Porter, Adam and Puchol,C. and Ramming,J. C and Votta,L. G.} } @article {16572, title = {Spreading depression in focal ischemia: A computational study}, journal = {Journal of Cerebral Blood Flow \& Metabolism}, volume = {18}, year = {1998}, month = {1998///}, pages = {998 - 1007}, author = {Revett,K. and Ruppin,E. and Goodall,S. and Reggia, James A.} } @article {16769, title = {Techniques for update handling in the enhanced client-server DBMS}, journal = {IEEE Transactions on Knowledge and Data Engineering}, volume = {10}, year = {1998}, month = {1998/06//May}, pages = {458 - 476}, abstract = {The Client-Server computing paradigm has significantly influenced the way modern Database Management Systems are designed and built. In such systems, clients maintain data pages in their main-memory caches, originating from the server{\textquoteright}s database. The Enhanced Client-Server architecture takes advantage of all the available client resources, including their long-term memory. Clients can cache server data into their own disk units if these data are part of their operational spaces. However, when updates occur at the server, a number of clients may need to not only be notified about these changes, but also obtain portions of the updates as well. In this paper, we examine the problem of managing server imposed updates that affect data cached on client disk managers. We propose a number of server update propagation techniques in the context of the Enhanced Client-Server DBMS architecture, and examine the performance of these strategies through detailed simulation experiments. In addition, we study how the various settings of the network affect the performance of these policies}, keywords = {client disk managers, client resources, client-server computing paradigm, client-server systems, Computational modeling, Computer architecture, concurrency control, data pages, Database systems, distributed databases, enhanced client-server DBMS, Hardware, Local area networks, long-term memory, main-memory caches, Network servers, operational spaces, Personal communication networks, server update propagation techniques, Transaction databases, update handling, Workstations, Yarn}, isbn = {1041-4347}, doi = {10.1109/69.687978}, author = {Delis,A. and Roussopoulos, Nick} } @article {17741, title = {Time-Domain Extraction of Broad-Band Sources by Tikhonov-Phillips Regularization of Triangular Toeplitz Kernels*}, volume = {UMIACS-TR-95-87}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Single receiver source deconvolution in a shallow waterenvironment is an ill-posed problem whose difficulty is compounded by the multipath nature of the propagation operator. If only sources that are quiescent prior to some initial time to are considered, the result of discretizatizing the problem in the time domain is an ill-conditioned triangular Toeplitz system. In this paper we show how an algorithm of Elden can be used to implement Tikhonov-Phillips regularization for this system. Unlike the multichannel deconvolution techniques used in underwater acoustics, this method can extract source signatures using the outputs of a single sensor. In addition, when the propagation is multipath and source signature extraction is performed as part of an optimization procedure for environmental inversion, we can work with shorter time windows so that the process becomes computationally more efficient than frequency domain deconvolution. A number of examples of the use of the Tikhonov-Philips regularization method for source series extraction are provided. (Also cross-referenced as UMIACS-TR-95-87) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/755}, author = {Roginsky,Jacob and Stewart, G.W.} } @book {13028, title = {Trends in the Early Careers of Life Scientists}, year = {1998}, month = {1998///}, publisher = {National Academy Press}, organization = {National Academy Press}, address = {Washington, DC}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @article {13029, title = {Trends in the early careers of life scientists - Preface and executive summary}, journal = {Mol Biol Cell}, volume = {9}, year = {1998}, month = {1998/11//}, pages = {3007 - 3015}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @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} } @article {16177, title = {User Interface Reengineering: A Diagnostic Approach}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {User interface technology has advanced rapidly in recent years.Incorporating new developments in existing systems could result in substantial improvements in usability, thereby improving performance and user satisfaction, while shortening training an d reducing error rates. Our focus is on low-effort high-payoff improvements to aspects such as data display and entry, consistency, messages, documentation, and system access. This paper provides guidelines for managers and designers responsible for use r interface reengineering, based on the experience we gained from six projects, and compiles our observations, recommendations and outcomes. (Also cross-referenced as CAR-TR-767) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/430}, author = {Vanniamparampil,Ajit J and Shneiderman, Ben and Plaisant, Catherine and Rose,Anne} } @article {16192, title = {Viewing personal history records: A comparison of tabular format and graphical presentation using LifeLines}, journal = {Behaviour \& Information Technology}, volume = {17}, year = {1998}, month = {1998///}, pages = {249 - 262}, abstract = {Thirty-six participants used a static version of either LifeLines, a graphical interface, or a tabular representation to answer questions about a database of temporal personal history information. Results suggest that overall the LifeLines representation led to much faster response times, primarily for questions which involved interval comparisons and making intercategorical connections. A {\textquoteright}first impression{\textquoteright} test showed that LifeLines can reduce some of the biases of the tabular record summary. A post-experimental memory test led to significantly (p< 0.004) higher recall for LifeLines. Finally, simple interaction techniques are proposed to compensate for the problems of the static LifeLines display{\textquoteright}s ability to deal with precise dates, attribute coding and overlaps.Thirty-six participants used a static version of either LifeLines, a graphical interface, or a tabular representation to answer questions about a database of temporal personal history information. Results suggest that overall the LifeLines representation led to much faster response times, primarily for questions which involved interval comparisons and making intercategorical connections. A {\textquoteright}first impression{\textquoteright} test showed that LifeLines can reduce some of the biases of the tabular record summary. A post-experimental memory test led to significantly (p< 0.004) higher recall for LifeLines. Finally, simple interaction techniques are proposed to compensate for the problems of the static LifeLines display{\textquoteright}s ability to deal with precise dates, attribute coding and overlaps. }, isbn = {0144-929X}, doi = {10.1080/014492998119328}, url = {http://www.tandfonline.com/doi/abs/10.1080/014492998119328}, author = {Alonso,Diane Lindwarm and Rose,Anne and Plaisant, Catherine and Norman,Kent L} } @conference {13921, title = {When Two Hands Are Better Than One: Enhancing Collaboration Using Single Display Groupware. CHI{\textquoteright}98}, booktitle = {Extended Abstracts}, year = {1998}, month = {1998///}, pages = {287 - 288}, author = {Stewart,J. and Raybourn,E. and Bederson, Benjamin B. and Druin, Allison} } @article {16661, title = {WordNet and class-based probabilities}, journal = {WordNet: An electronic lexical database}, year = {1998}, month = {1998///}, pages = {239 - 263}, author = {Resnik, Philip} } @conference {16499, title = {Wrapper generation for Web accessible data sources}, booktitle = {3rd IFCIS International Conference on Cooperative Information Systems, 1998. Proceedings}, year = {1998}, month = {1998/08/22/22}, pages = {14 - 23}, publisher = {IEEE}, organization = {IEEE}, abstract = {There is an increase in the number of data sources that can be queried across the WWW. Such sources typically support HTML forms-based interfaces and search engines query collections of suitably indexed data. The data is displayed via a browser: One drawback to these sources is that there is no standard programming interface suitable for applications to submit queries. Second, the output (answer to a query) is not well structured. Structured objects have to be extracted from the HTML documents which contain irrelevant data and which may be volatile. Third, domain knowledge about the data source is also embedded in HTML documents and must be extracted. To solve these problems, we present technology to define and (automatically) generate wrappers for Web accessible sources. Our contributions are as follows: (1) Defining a wrapper interface to specify the capability of Web accessible data sources. (2) Developing a wrapper generation toolkit of graphical interfaces and specification languages to specify the capability of sources and the functionality of the wrapper (3) Developing the technology to automatically generate a wrapper appropriate to the Web accessible source, from the specifications.}, keywords = {application program interfaces, data mining, Databases, Educational institutions, Electrical capacitance tomography, HTML, HTML documents, Internet, Query processing, Read only memory, Search engines, Specification languages, Uniform resource locators, World Wide Web, wrapper generation toolkit, WWW}, isbn = {0-8186-8380-5}, doi = {10.1109/COOPIS.1998.706180}, author = {Gruser,J. and Raschid, Louiqa and Vidal,M. E and Bright,L.} } @article {18817, title = {Automated manufacturability analysis: A survey}, journal = {Research in Engineering Design}, volume = {9}, year = {1997}, month = {1997///}, pages = {168 - 190}, abstract = {In the market-place of the 21st century, there is no place for traditional {\textquoteleft}over-the-wall{\textquoteright} communications between design and manufacturing. In order to {\textquoteleft}design it right the very first time{\textquoteright}, designers must ensure that their products are both functional and easy to manufacture. Software tools have had some successes in reducing the barriers between design and manufacturing. Manufacturability analysis systems are emerging as one such tool {\textemdash} enabling identification of potential manufacturing problems during the design phase and providing suggestions to designers on how to eliminate them.}, keywords = {engineering}, isbn = {0934-9839}, doi = {10.1007/BF01596601}, url = {http://www.springerlink.com/content/p8p5516251023777/abstract/}, author = {Gupta, Satyandra K. and Regli,William C. and Das,Diganta and Nau, Dana S.} } @article {16584, title = {Automatic discovery of self-replicating structures in cellular automata}, journal = {Evolutionary Computation, IEEE Transactions on}, volume = {1}, year = {1997}, month = {1997///}, pages = {165 - 178}, author = {Lohn,J. D and Reggia, James A.} } @article {15525, title = {Combining Closed World Assumptions with Stable Negation}, journal = {Fundamenta Informaticae}, volume = {32}, year = {1997}, month = {1997/01/01/}, pages = {163 - 181}, abstract = {We study the semantics of disjunctive logic programs that simultaneously contain multiple kinds of default negations. We introduce operators notG, notW, and notSTB in the language of logic programs to represent the Generalized Closed World Assumption, the Weak Generalized Closed World Assumption, and the stable negation, respectively. The notion of stratification involving different kinds of negations is defined and the meaning of stratified programs with multiple negations is described. The class of stratified programs is extended to the class of quasi-stratified programs and the semantics of the latest class is studied.}, doi = {10.3233/FI-1997-32205}, url = {http://dx.doi.org/10.3233/FI-1997-32205}, author = {Ruiz,Carolina and Minker, Jack} } @article {16549, title = {A computational model of acute focal cortical lesions}, journal = {Stroke}, volume = {28}, year = {1997}, month = {1997///}, pages = {101 - 101}, author = {Goodall,S. and Reggia, James A. and Chen,Y. and Ruppin,E. and Whitney,C.} } @article {16538, title = {Computer models: A new approach to the investigation of disease}, journal = {MD Computing}, volume = {14}, year = {1997}, month = {1997///}, pages = {160 - 168}, author = {Reggia, James A. and Ruppin,E. and Berndt,R. S} } @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 {16569, title = {Emergence of self-replicating structures in cellular automata space}, journal = {Physica D}, volume = {110}, year = {1997}, month = {1997///}, pages = {252 - 276}, author = {Reggia, James A. and Chou,H. H.} } @article {16701, title = {Evaluating multilingual gisting of Web pages}, volume = {SS-97-02}, year = {1997}, month = {1997///}, institution = {Association for the Advancement of Artificial Intelligence}, author = {Resnik, Philip} } @conference {13673, title = {The Function of Documents}, booktitle = {ICDAR}, year = {1997}, month = {1997///}, pages = {1077 - 1081}, abstract = {The purpose of a document is to facilitate the transfer of information from its author to its readers. It is the author{\textquoteright}s job to design the document so that the information it contains can be interpreted accurately and efficiently. To do this, the author can make use of a set of stylistic tools. In this paper we introduce the concept of document functionality, which attempts to describe the roles of documents and their components in the process of transferring information. A functional description of a document provides insight into the type of the document, into its intended uses, and into strategies for automatic document interpretation and retrieval. To demonstrate these ideas, we define a taxonomy of functional document components and show how functional descriptions can be used to reverse-engineer the intentions of the author, to navigate in document space, and to provide important contextual information to aid in interpretation.}, author = {David Doermann and Rosenfeld, A. and Rivlin,E.} } @conference {13573, title = {Image Indexing with Minimum Adaptive Spatial Segmentation}, booktitle = {Proceedings of VISUAL 1997}, year = {1997}, month = {1997///}, author = {Zhong,S. and David Doermann and Rosenfeld, A.} } @article {16706, title = {Implicit object constructions and the (in) transitivity continuum}, journal = {33rd Proceedings of the Chicago Linguistic Society}, year = {1997}, month = {1997///}, pages = {327 - 336}, author = {Olsen,M.B. and Resnik, Philip} } @conference {16348, title = {Iteration space slicing and its application to communication optimization}, booktitle = {Proceedings of the 11th international conference on Supercomputing}, year = {1997}, month = {1997///}, pages = {221 - 228}, author = {Pugh, William and Rosser,E.} } @article {16698, title = {A Language Identification Application Built on the Java Client/Server Platform}, journal = {From Research to Commercial Applications: Making NLP Work in Practice}, year = {1997}, month = {1997///}, pages = {43 - 47}, author = {Adams,G. and Resnik, Philip} } @conference {13584, title = {Local correspondence for detecting random forgeries}, booktitle = {Document Analysis and Recognition, 1997., Proceedings of the Fourth International Conference on}, volume = {1}, year = {1997}, month = {1997/08//}, pages = {319 -323 vol.1 - 319 -323 vol.1}, abstract = {Progress on the problem of signature verification has advanced more rapidly in online applications than offline applications, in part because information which can easily be recorded in online environments, such as pen position and velocity, is lost in static offline data. In offline applications, valuable information which can be used to discriminate between genuine and forged signatures is embedded at the stroke level. We present an approach to segmenting strokes into stylistically meaningful segments and establish a local correspondence between a questioned signature and a reference signature to enable the analysis and comparison of stroke features. Questioned signatures which do not conform to the reference signature are identified as random forgeries. Most simple forgeries can also be identified, as they do not conform to the reference signature{\textquoteright}s invariant properties such as connections between letters. Since we have access to both local and global information, our approach also shows promise for extension to the identification of skilled forgeries}, keywords = {applications;online, applications;questioned, correspondence;offline, detection;reference, extraction;handwriting, features;stroke, forged, forgeries;random, forgeries;stroke, Forgery, level;stroke, meaningful, processing;, properties;local, recognition;image, segmentation;stylistically, segmentation;word, segments;feature, signature;random, signature;signature, signatures;invariant, verification;skilled}, doi = {10.1109/ICDAR.1997.619864}, author = {Guo,J. K and David Doermann and Rosenfeld, A.} } @article {17283, title = {Low-effort, high-payoff user interface reengineering}, journal = {IEEE Software}, volume = {14}, year = {1997}, month = {1997/08//Jul}, pages = {66 - 72}, abstract = {Although increasingly sophisticated design methodologies for developing new user interfaces exist, low-effort, high-payoff user interface reengineering represents a new direction-and opportunity. Yet reengineering a working system is complex and risky because of the potential disruption to users and managers, their justifiable fear of change, and the lack of guarantees that such changes will be for the better. Our largely positive experiences with the projects described here lead us to believe that user interface reengineering is a viable and important process. Low effort, high-payoff improvement recommendations can probably be made for most existing systems. Nevertheless, a narrowly focused user interface reengineering plan may be inappropriate when the major problems lie outside the scope of the user interface, such as inadequate functionalities, frequent crashes, and network problems. Attempts at improving less severe problems while ignoring deeper ones may be perceived as insensitive by the users. In such cases it is important to consider either making similar short-term improvements for other parts of the systems or postponing short-term user interface reengineering in favour of a more complete system reengineering. Similarly, the need for interface stability might outweigh the benefits of the short-term improvements if a complete reengineering is planned for the near future. But most likely these proposed diagnostic strategies and opportunities for improvement are only a prelude to the much larger task of business reengineering, which implies extensive user interface reengineering}, keywords = {Business process re-engineering, complete system reengineering, Design methodology, Error analysis, Hardware, inadequate functionalities, interface stability, iterative methods, low-effort high-payoff user interface reengineering, short-term improvements, short-term user interface reengineering, software engineering, Software testing, System analysis and design, System testing, systems re-engineering, User centered design, user centred design, User interfaces}, isbn = {0740-7459}, doi = {10.1109/52.595958}, author = {Plaisant, Catherine and Rose,A. and Shneiderman, Ben and Vanniamparampil,A. J} } @article {15523, title = {Model generation and state generation for disjunctive logic programs}, journal = {The Journal of Logic Programming}, volume = {32}, year = {1997}, month = {1997/07//}, pages = {49 - 69}, abstract = {This paper investigates two fixpoint approaches for minimal model reasoning with disjunctive logic programs P. The first one, called model generation, is based on an operator TPINT defined on sets of Herbrand interpretations whose least fixpoint is logically equivalent to the set of minimal Herbrand models of the program. The second approach, called state generation, uses a fixpoint operation TPs based on hyperresolution. It operates on disjunctive Herbrand states, and its least fixpoint is the set of logical consequences of P, the so-called minimal model state of the program. We establish a useful relationship between hyperresolution by PPs and model generation by TPINT. Then we investigate the problem of continuity of the two operators TPs and TPINT. It is known that the operator TPs is continuous, and so it reaches its least fixpoint in at most ω iterations. On the other hand, the question of whether TPINT is continuous has been open. We show by a counterexample that TPINT is not continuous. Nevertheless, we prove that it converges towards its least fixpoint in at most ω iterations, too, as follows from the relationship that we show exists between hyperresolution and model generation. We define an iterative version of TPINT that computes the perfect model semantics of stratified disjunctive logic programs. On each stratum of the program, this operator converges in at most ω iterations. Model generations for the stable semantics and the partial stable semantics are respectively achieved by using this iterative operator together with the evidential transformation and the 3-S transformation.}, isbn = {0743-1066}, doi = {10.1016/S0743-1066(96)00116-1}, url = {http://www.sciencedirect.com/science/article/pii/S0743106696001161}, author = {Seipel,Dietmar and Minker, Jack and Ruiz,Carolina} } @article {17954, title = {Multiresolution surface modeling}, journal = {SIGGRAPH 1997 Course Notes}, year = {1997}, month = {1997///}, author = {Heckbert,P. and Rossignac,J. and Hoppe,H. and Schroeder,W. and Soucy,M. and Varshney, Amitabh} } @article {15223, title = {A Network-Flow Technique for Finding Low-Weight Bounded-Degree Spanning Trees}, journal = {Journal of Algorithms}, volume = {24}, year = {1997}, month = {1997/08//}, pages = {310 - 324}, abstract = {Given a graph with edge weights satisfying the triangle inequality, and a degree bound for each vertex, the problem of computing a low-weight spanning tree such that the degree of each vertex is at most its specified bound is considered. In particular, modifying a given spanning treeTusingadoptionsto meet the degree constraints is considered. A novel network-flow-based algorithm for finding a good sequence of adoptions is introduced. The method yields a better performance guarantee than any previous algorithm. If the degree constraintd(v) for eachvis at least 2, the algorithm is guaranteed to find a tree whose weight is at most the weight of the given tree times 2\&$\#$xa0;-\&$\#$xa0;min{(d(v)\&$\#$xa0;-\&$\#$xa0;2)/(degT(v)\&$\#$xa0;-\&$\#$xa0;2)\&$\#$xa0;:\&$\#$xa0;degT(v)\&$\#$xa0;\>\&$\#$xa0;2}, where degT(v) is the initial degree ofv. Equally importantly, it takes this approach to the limit in the following sense: if any performance guarantee that is solely a function of the topology and edge weights of a given tree holds foranyalgorithm at all, then it also holds for the given algorithm. Examples are provided in which no lighter tree meeting the degree constraint exists. Linear-time algorithms are provided with the same worst-case performance guarantee. ChoosingTto be a minimum spanning tree yields approximation algorithms with factors less than 2 for the general problem on geometric graphs with distances induced by variousLpnorms. Finally, examples of Euclidean graphs are provided in which the ratio of the lengths of an optimal Traveling Salesman path and a minimum spanning tree can be arbitrarily close to 2.}, isbn = {0196-6774}, doi = {10.1006/jagm.1997.0862}, url = {http://www.sciencedirect.com/science/article/pii/S0196677497908622}, author = {Fekete,S{\'a}ndor P and Khuller, Samir and Klemmstein,Monika and Raghavachari,Balaji and Young,Neal} } @conference {16663, title = {A perspective on word sense disambiguation methods and their evaluation}, booktitle = {Proceedings of the ACL SIGLEX workshop on tagging text with lexical semantics: Why, what, and how}, volume = {86}, year = {1997}, month = {1997///}, author = {Resnik, Philip and Yarowsky,D.} } @conference {15625, title = {A practical approximation algorithm for the LMS line estimator}, booktitle = {Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {473 - 482}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, keywords = {Approximation algorithms, least median-of-squares regression, line arrangements, line fitting, randomized algorithms, robust estimation}, isbn = {0-89871-390-0}, url = {http://dl.acm.org/citation.cfm?id=314161.314349}, author = {Mount, Dave and Netanyahu,Nathan S. and Romanik,Kathleen and Silverman,Ruth and Wu,Angela Y.} } @conference {16714, title = {Selectional preference and sense disambiguation}, booktitle = {Proceedings of the ACL SIGLEX Workshop on Tagging Text with Lexical Semantics: Why, What, and How}, year = {1997}, month = {1997///}, pages = {52 - 57}, author = {Resnik, Philip} } @conference {16464, title = {Semantic query optimization for object databases}, booktitle = {Data Engineering, 1997. Proceedings. 13th International Conference on}, year = {1997}, month = {1997///}, pages = {444 - 453}, author = {Grant,J. and Gryz,J. and Minker, Jack and Raschid, Louiqa} } @conference {15524, title = {Semantic query optimization for object databases}, booktitle = {Data Engineering, 1997. Proceedings. 13th International Conference on}, year = {1997}, month = {1997/04//}, pages = {444 - 453}, abstract = {Presents a technique for semantic query optimization (SQO) for object databases. We use the ODMG-93 (Object Data Management Group) standard ODL (Object Database Language) and OQL (Object Query Language) languages. The ODL object schema and the OQL object query are translated into a DATALOG representation. Semantic knowledge about the object model and the particular application is expressed as integrity constraints. This is an extension of the ODMG-93 standard. SQO is performed in the DATALOG representation, and an equivalent logic query and (subsequently) an equivalent OQL object query are obtained. SQO is based on the residue technique of Chakravarthy et al. (1990). We show that our technique generalizes previous research on SQO for object databases. It can be applied to queries with structure constructors and method application. It utilizes integrity constraints about keys, methods and knowledge of access support relations, to produce equivalent queries, which may have more efficient evaluation plans}, keywords = {application;object, constraints;keys;method, constructors;DATALOG;data, databases;object-oriented, databases;query, Datalog, Evaluation, integrity;data, languages;query, Logic, object, optimization;structure, plans;residue, processing;software, query, query;access, query;integrity, relations;equivalent, representation;ODL, schema;ODMG-93, standard;OQL, standards;, structures;object-oriented, Support, technique;semantic}, doi = {10.1109/ICDE.1997.581983}, author = {Grant,J. and Gryz,J. and Minker, Jack and Raschid, Louiqa} } @conference {16666, title = {Semi-automatic acquisition of domain-specific translation lexicons}, booktitle = {Proceedings of the fifth conference on Applied natural language processing}, year = {1997}, month = {1997///}, pages = {340 - 347}, author = {Resnik, Philip and Melamed,I.D.} } @conference {16336, title = {Specification-based Testing of Reactive Software: Tools and Experiments}, booktitle = {Software Engineering, International Conference on}, year = {1997}, month = {1997///}, pages = {525 - 525}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Testing commercial software is expensive and time consuming. Automated testing methods promise to save a great deal of time and money throughout the software industry. One approach that is well-suited for the reactive systems found in telephone switching systems is specification-based testing.We have built a set of tools to automatically test softmare applications for violations of safety properties expressed in temporal logic. Our testing system automatically constructs finite state machine oracles corresponding to safety properties, builds test harnesses, and integrates them with the application. The test harness then generates inputs automatically to test the application.We describe a study examining the feasibility of this approach for testing industrial applications. To conduct this study we formally modeled an Automatic Protection Switching system (APS), which is an application common to many telephony systems. We then asked a number of computer science graduate students to develop several versions of the APS and use our tools to test them. We found that the tools are very effective, save significant amounts of human effort (at the expense of machine resources), and are easy to use. We also discuss improvements that are needed before we can use the tools with professional developers building commercial products.}, keywords = {empirical studies, reactive systems, specification-based testing, temporal logic}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICSE.1997.610373}, author = {Jagadeesan,Lalita Jategaonkar and Porter, Adam and Puchol,Carlos and Ramming,J. Christopher and Votta,Lawrence G.} } @article {13655, title = {Symbolic Compression and Processing of Document Images}, volume = {LAMP-TR-004,CFAR-TR-849,CS-TR-3734}, year = {1997}, month = {1997/01//}, institution = {University of Maryland, College Park}, abstract = {In this paper we describe a compression and representation scheme which exploits the component-level redundancy found within a document image. The approach identifies patterns which appear repeatedly, represents similar patterns with a single prototype, stores the location of pattern instances and codes the residuals between the prototypes and the pattern instances. Using a novel encoding scheme, we provide a representation which facilitates scalable lossy compression and progressive transmission, and supports document image analysis in the compressed domain. We motivate the approach, provide details of the encoding procedures, report compression results and describe a class of document image understanding tasks which operate on the compressed representation.}, author = {Kia,Omid and David Doermann and Rosenfeld,Azriel and Chellapa, Rama} } @article {15562, title = {Testing simple polygons}, journal = {Computational Geometry}, volume = {8}, year = {1997}, month = {1997/07//}, pages = {97 - 114}, abstract = {We consider the problem of verifying a simple polygon in the plane using {\textquotedblleft}test points{\textquotedblright}. A test point is a geometric probe that takes as input a point in Euclidean space, and returns {\textquotedblleft}+{\textquotedblright} if the point is inside the object being probed or {\textquotedblleft}-{\textquotedblright} if it is outside. A verification procedure takes as input a description of a target object, including its location and orientation, and it produces a set of test points that are used to verify whether a test object matches the description. We give a procedure for verifying an n-sided, non-degenerate, simple target polygon using 5n test points. This testing strategy works even if the test polygon has n + 1 vertices, and we show a lower bound of 3n + 1 test points for this case. We also give algorithms using O(n) test points for simple polygons that may be degenerate and for test polygons that may have up to n + 2 vertices. All of these algorithms work for polygons with holes. We also discuss extensions of our results to higher dimensions.}, keywords = {probing, Testing, Verifying}, isbn = {0925-7721}, doi = {10.1016/S0925-7721(96)00015-6}, url = {http://www.sciencedirect.com/science/article/pii/S0925772196000156}, author = {Arkin,Esther M. and Belleville,Patrice and Mitchell,Joseph S.B. and Mount, Dave and Romanik,Kathleen and Salzberg,Steven and Souvaine,Diane} } @article {18868, title = {Towards multiprocessor feature recognition}, journal = {Computer-Aided Design}, volume = {29}, year = {1997}, month = {1997/01//}, pages = {37 - 51}, abstract = {The availability of low-cost computational power is enabling the development of increasingly sophisticated cad software. Automation of design and manufacturing activities poses many difficult computational problems{\textemdash}significant among them is how to develop interactive systems that enable designers to explore and experiment with alternative ideas. As more downstream manufacturing activities are considered during the design phase, computational costs become problematic. Creating working software-based solutions requires a sophisticated allocation of computational resources in order to perform realistic design analyses and generate feedback. This paper presents our initial efforts to employ multiprocessor algorithms to recognize machining features from solid models of parts with large numbers of features and many geometric and topological entities. Our goal is to outline how improvements in computation time can be obtained by migrating existing software tools to multiprocessor architectures. An implementation of our approach is discussed.}, keywords = {Distributed computing, feature recognition, feature-based modelling, multiprocessor solid modelling}, isbn = {0010-4485}, doi = {10.1016/S0010-4485(96)00047-4}, url = {http://www.sciencedirect.com/science/article/pii/S0010448596000474}, author = {Regli,William C. and Gupta, Satyandra K. and Nau, Dana S.} } @article {16197, title = {User Interface Reengineering: Low-Effort, High-Payoff Strategies}, journal = {IEEE Software}, volume = {14}, year = {1997}, month = {1997///}, pages = {66 - 72}, abstract = {User interface technology has advanced rapidly in recent years. Incorporating new developments in existing systems could result in substantial improvements in usability, thereby improving performance and user satisfaction, while shortening training and reducing error rates. We describe low-effort, high-payoff strategies that focus attention on improvements to data display and entry, consistency, messages, documentation, system access and additional functionality. We report on experience from six projects, describing observations, recommendations and outcomes. We close with guidance for managers and designers who are responsible for user interface reengineering.}, author = {Plaisant, Catherine and Rose,A. and Shneiderman, Ben and Vanniamparampil,A. J} } @article {12177, title = {A zooming web browser}, journal = {Human Factors in Web Development}, year = {1997}, month = {1997///}, author = {Bederson, Benjamin B. and Hollan,J.D. and Stewart,J. and Rogers,D. and Druin, Allison and Vick,D. and Ring,L. and Grose,E. and Forsythe,C.} } @article {16562, title = {Alignment of coexisting cortical maps in a motor control model}, journal = {Neural computation}, volume = {8}, year = {1996}, month = {1996///}, pages = {731 - 755}, author = {Chen,Y. and Reggia, James A.} } @conference {16460, title = {Answering queries using OQL view expressions}, booktitle = {In Workshop on Materialized Views, in cooperation with ACM SIGMOD}, year = {1996}, month = {1996///}, author = {Florescu,D. and Raschid, Louiqa and Valduriez,P.} } @article {13499, title = {Applying algebraic and differential invariants for logo recognition}, journal = {Machine Vision and Applications}, volume = {9}, year = {1996}, month = {1996///}, pages = {73 - 86}, abstract = {The problem of logo recognition is of great interest in the document domain, especially for document databases. By recognizing the logo we obtain semantic information about the document which may be useful in deciding whether or not to analyze the textual components. Given a logo block candidate from a document image and alogo database, we would like to determine whether the region corresponds to a logo in the database. Similarly, if we are given a logo block candidate and adocumentdatabase, we wish to determine whether there are any documents in the database of similar origin. Both problems require indexing into a possibly large model space.In this contribution, we present a novel application of algebraic and differential invariants to the problem of logo recognition. By using invariants we have shape descriptors for matching that are unique and independent of the point of view. The algebraic invariants handle cases in which the whole shape of the logo is given and it is easy to describe. The differential invariants cover complex arbitrary logo shape and handle situations in which only part of the logo is recovered. We outline a hierarchical approach to logo recognition and define methods for page segmentation, feature extraction, and indexing. We demonstrate our approach and present results on a database of approximately 100 logos. }, author = {David Doermann and Rivlin,E. and Weiss, I.} } @book {16719, title = {The Balancing Act: Combining Symbolic and Statistical Approaches to Language}, year = {1996}, month = {1996/12/06/}, publisher = {MIT Press}, organization = {MIT Press}, abstract = {Symbolic and statistical approaches to language have historically been at odds{\textemdash}the former viewed as difficult to test and therefore perhaps impossible to define, and the latter as descriptive but possibly inadequate. At the heart of the debate are fundamental questions concerning the nature of language, the role of data in building a model or theory, and the impact of the competence-performance distinction on the field of computational linguistics. Currently, there is an increasing realization in both camps that the two approaches have something to offer in achieving common goals.The eight contributions in this book explore the inevitable "balancing act" that must take place when symbolic and statistical approaches are brought together{\textemdash}including basic choices about what knowledge will be represented symbolically and how it will be obtained, what assumptions underlie the statistical model, what principles motivate the symbolic model, and what the researcher gains by combining approaches.The topics covered include an examination of the relationship between traditional linguistics and statistical methods, qualitative and quantitative methods of speech translation, study and implementation of combined techniques for automatic extraction of terminology, comparative analysis of the contributions of linguistic cues to a statistical word grouping system, automatic construction of a symbolic parser via statistical techniques, combining linguistic with statistical methods in automatic speech understanding, exploring the nature of transformation-based learning, and a hybrid symbolic/statistical approach to recovering from parser failures.}, keywords = {computational linguistics, Computational linguistics - Congresses, Computational linguistics/ Congresses, Computers / Intelligence (AI) \& Semantics, Foreign Language Study / General, Language Arts \& Disciplines / Linguistics / General, linguistics, Linguistics - Statistical methods - Congresses, Linguistics/ Statistical methods/ Congresses, Social Science / General}, isbn = {9780262611220}, author = {Klavans,Judith L. and Resnik, Philip} } @article {15038, title = {The block distributed memory model}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {7}, year = {1996}, month = {1996/08//}, pages = {830 - 840}, abstract = {We introduce a computation model for developing and analyzing parallel algorithms on distributed memory machines. The model allows the design of algorithms using a single address space and does not assume any particular interconnection topology. We capture performance by incorporating a cost measure for interprocessor communication induced by remote memory accesses. The cost measure includes parameters reflecting memory latency, communication bandwidth, and spatial locality. Our model allows the initial placement of the input data and pipelined prefetching. We use our model to develop parallel algorithms for various data rearrangement problems, load balancing, sorting, FFT, and matrix multiplication. We show that most of these algorithms achieve optimal or near optimal communication complexity while simultaneously guaranteeing an optimal speed-up in computational complexity. Ongoing experimental work in testing and evaluating these algorithms has thus far shown very promising results}, keywords = {accesses;single, address, algorithms;performance, algorithms;performance;remote, allocation;sorting;, balancing;matrix, bandwidth;communication, communication;load, complexity;computation, complexity;computational, complexity;cost, complexity;distributed, distributed, evaluation;resource, FFT;block, Fourier, latency;parallel, locality;communication, machines;interconnection, measure;data, memory, model;communication, model;computational, multiplication;memory, multiplication;parallel, problems;distributed, rearrangement, space;sorting;spatial, systems;fast, topology;interprocessor, transforms;matrix}, isbn = {1045-9219}, doi = {10.1109/71.532114}, author = {JaJa, Joseph F. and Ryu,Kwan Woo} } @article {13524, title = {Compressed Video Segmentation}, volume = {LAMP-TR-001,CFAR-TR-839,CS-TR-3688}, year = {1996}, month = {1996/09//}, institution = {University of Maryland, College Park}, abstract = {Segmentation of video into shots and scenes in the compressed domain allows rapid, real-time analysis of video content using standard hardware. This paper presents robust techniques for parsing MPEG-compressed video sequences into shots based on their physical structure and further into scenes based on their semantic structure by identifying changes in content and camera motion. The analysis is performed in the compressed domain using available macroblock and motion vector information, and if necessary, DCT information. Motion vector analysis yields a qualitative description of the camera motion and is used to subdivide shots into subshots. Key frames for the shots and scenes can be used for browsing, indexing, and retrieval.}, author = {Kobla,Vikrant and David Doermann and Rosenfeld,Azriel} } @article {16615, title = {Computational studies of synaptic alterations in Alzheimer{\textquoteright}s disease}, journal = {Neural modeling of brain and cognitive disorders}, year = {1996}, month = {1996///}, pages = {63 - 87}, author = {Ruppin,E. and Horn,D. and Levy,N. and Reggia, James A.} } @conference {13671, title = {The Development of a General Framework for Intelligent Document Image Retrieval}, booktitle = {Proceedings in the International Workshop on Document Analysis Systems}, year = {1996}, month = {1996///}, pages = {605 - 632}, author = {David Doermann and Sauvola,J. and Kauniskangas,H. and Shin,C. and Pietikainen,M. and Rosenfeld, A.} } @article {16546, title = {Effects of varying parameters on properties of self-organizing feature maps}, journal = {Neural Processing Letters}, volume = {4}, year = {1996}, month = {1996///}, pages = {53 - 59}, author = {Cho,S. and Jang,M. and Reggia, James A.} } @article {16656, title = {Feature discovery and classification of Doppler umbilical artery blood flow velocity waveforms}, journal = {Computers in Biology and Medicine}, volume = {26}, year = {1996}, month = {1996/11//}, pages = {451 - 462}, abstract = {Doppler umbilical artery blood flow velocity waveform measurements are used in perinatal surveillance for the evaluation of fetal condition. There is an ongoing debate on the predictive value of Doppler measurements concerning the critical effect of the selection of parameters for the interpretation of Doppler waveforms. In this paper, we describe how neural network methods can be used both to discover relevant classification features and subsequently to classify Doppler umbilical artery blood flow velocity waveforms. Results obtained from 199 normal and high risk patients{\textquoteright} umbilical artery waveforms highlighted a classification concordance varying from 90 to 98\% accuracy.}, keywords = {Doppler umbilical artery blood flow velocity waveforms, Feature extraction, IMAGE PROCESSING, Pattern classification}, isbn = {0010-4825}, doi = {10.1016/S0010-4825(96)00018-2}, url = {http://www.sciencedirect.com/science/article/pii/S0010482596000182}, author = {Baykal,Nazife and Reogia,James A. and Yalabik,Nese and Erkmen,Aydan and Beksac,M.Sinan} } @article {13674, title = {The Function of Documents}, volume = {LAMP-TR-002,CFAR-TR-841,CS-TR-3697}, year = {1996}, month = {1996/10//}, institution = {University of Maryland, College Park}, abstract = {The purpose of a document is to facilitate the transfer of information from its author to its readers. It is the author{\textquoteright}s job to design the document so that the information it contains can be interpreted accurately and efficiently. To do this, the author can make use of a set of stylistic tools. In this paper we introduce the concept of document functionality, which attempts to describe the roles of documents and their components in the process of transferring information. A functional description of a document provides insight into the type of the document, into its intended uses, and into strategies for automatic document interpretation and retrieval. To demonstrate these ideas, we define a taxonomy of functional document components and show how functional descriptions can be used to reverse-engineer the intentions of the author, to navigate in document space, and to provide important contextual information to aid in interpretation.}, author = {David Doermann and Rivlin,Ehud and Rosenfeld,Azriel} } @article {15220, title = {Graph and network algorithms}, journal = {ACM Computing Surveys}, volume = {28}, year = {1996}, month = {1996/03//}, pages = {43 - 45}, isbn = {0360-0300}, doi = {10.1145/234313.234334}, url = {http://doi.acm.org/10.1145/234313.234334}, author = {Khuller, Samir and Raghavachari,Balaji} } @article {16206, title = {Hybrid network management (communication systems)}, journal = {16th AIAA International Communications Satellite Systems Conference}, year = {1996}, month = {1996///}, abstract = {We describe our collaborative efforts towards the design and implementation of a next-generation integrated network management system for hybrid networks (INMS/HN). We describe the overall software architecture of the system at its current stage of development. This NMS is specifically designed to address issues relevant to complex heterogeneous networks consisting of seamlessly interoperable terrestrial and satellite networks. NMSs are a key element for interoperability in such networks. We describe the integration of configuration management and performance management. The next step in this integration is fault management. In particular, we describe the object model, issues concerning the graphical user interface, browsing tools, performance data graphical widget displays, and management information database organization issues.}, author = {Baras,J. S and Ball,M. and Karne,R. K and Kelley,S. and Jang,K.D. and Plaisant, Catherine and Roussopoulos, Nick and Stathatos,K. and Vakhutinsky,A. and Valluri,J.} } @article {16202, title = {Integrated network management of hybrid networks}, journal = {AIP Conference Proceedings}, volume = {361}, year = {1996}, month = {1996/03/01/}, pages = {345 - 350}, abstract = {We describe our collaborative efforts towards the design and implementation of a next generation integrated network management system for hybrid networks (INMS/HN). We describe the overall software architecture of the system at its current stage of development. This network management system is specifically designed to address issues relevant for complex heterogeneous networks consisting of seamlessly interoperable terrestrial and satellite networks. Network management systems are a key element for interoperability in such networks. We describe the integration of configuration management and performance management. The next step in this integration is fault management. In particular we describe the object model, issues of the Graphical User Interface (GUI), browsing tools and performance data graphical widget displays, management information database (MIB) organization issues. Several components of the system are being commercialized by Hughes Network Systems. {\textcopyright} 1996 American Institute of Physics.}, isbn = {0094243X}, doi = {doi:10.1063/1.50028}, url = {http://proceedings.aip.org/resource/2/apcpcs/361/1/345_1?isAuthorized=no}, author = {Baras,John S and Ball,Mike and Karne,Ramesh K and Kelley,Steve and Jang,Kap D and Plaisant, Catherine and Roussopoulos, Nick and Stathatos,Kostas and Vakhutinsky,Andrew and Jaibharat,Valluri and Whitefield,David} } @article {15222, title = {Landmarks in graphs}, journal = {Discrete Applied Mathematics}, volume = {70}, year = {1996}, month = {1996/10/08/}, pages = {217 - 229}, abstract = {Navigation can be studied in a graph-structured framework in which the navigating agent (which we shall assume to be a point robot) moves from node to node of a {\textquotedblleft}graph space{\textquotedblright}. The robot can locate itself by the presence of distinctively labeled {\textquotedblleft}landmark{\textquotedblright} nodes in the graph space. For a robot navigating in Euclidean space, visual detection of a distinctive landmark provides information about the direction to the landmark, and allows the robot to determine its position by triangulation. On a graph, however, there is neither the concept of direction nor that of visibility. Instead, we shall assume that a robot navigating on a graph can sense the distances to a set of landmarks.Evidently, if the robot knows its distances to a sufficiently large set of landmarks, its position on the graph is uniquely determined. This suggests the following problem: given a graph, what are the fewest number of landmarks needed, and where should they be located, so that the distances to the landmarks uniquely determine the robot{\textquoteright}s position on the graph? This is actually a classical problem about metric spaces. A minimum set of landmarks which uniquely determine the robot{\textquoteright}s position is called a {\textquotedblleft}metric basis{\textquotedblright}, and the minimum number of landmarks is called the {\textquotedblleft}metric dimension{\textquotedblright} of the graph. In this paper we present some results about this problem. Our main new results are that the metric dimension of a graph with n nodes can be approximated in polynomial time within a factor of O(log n), and some properties of graphs with metric dimension two. }, isbn = {0166-218X}, doi = {10.1016/0166-218X(95)00106-2}, url = {http://www.sciencedirect.com/science/article/pii/0166218X95001062}, author = {Khuller, Samir and Raghavachari,Balaji and Rosenfeld,Azriel} } @conference {16551, title = {Learning activation rules for associative networks}, booktitle = {Neural Networks, 1996., IEEE International Conference on}, volume = {1}, year = {1996}, month = {1996///}, pages = {365 - 370}, author = {Reggia, James A. and Grundstrom,E. and Berndt,R. S} } @article {16625, title = {Learning Activation Rules Rather Than Connection Weights}, journal = {International journal of neural systems}, volume = {7}, year = {1996}, month = {1996///}, pages = {129 - 148}, author = {Grundstrom,E. L and Reggia, James A.} } @conference {16203, title = {LifeLines: visualizing personal histories}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: common ground}, series = {CHI {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {221 - 227}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {History, justice, medical record, overview, personal record, screen design, screen management, timeline, Visualization}, isbn = {0-89791-777-4}, doi = {10.1145/238386.238493}, url = {http://doi.acm.org/10.1145/238386.238493}, author = {Plaisant, Catherine and Milash,Brett and Rose,Anne and Widoff,Seth and Shneiderman, Ben} } @conference {13924, title = {Local tools: an alternative to tool palettes}, booktitle = {Proceedings of the 9th annual ACM symposium on User interface software and technology}, year = {1996}, month = {1996///}, pages = {169 - 170}, author = {Bederson, Benjamin B. and Hollan,J.D. and Druin, Allison and Stewart,J. and Rogers,D. and Proft,D.} } @article {16452, title = {A methodology for query reformulation in CIS using semantic knowledge}, journal = {International Journal of Cooperative Information Systems}, volume = {5}, year = {1996}, month = {1996///}, pages = {431 - 468}, author = {Florescu,D. and Raschid, Louiqa and Valduriez,P.} } @conference {15530, title = {Mixing a default rule with stable negation}, booktitle = {Proceedings of the Fourth International Symposium on Artificial Intelligence and Mathematics}, year = {1996}, month = {1996///}, pages = {122 - 125}, abstract = {Logic programs containing only at most one form ofdefault negation have been studied in the literature. We describe a class of logic programs containing multi- ple forms of default negation. We de ne a meaning for these programs based on the well{founded semantics and the stable semantics. We investigate properties of the new combined semantics and calculate the com- putational complexity of determining the existence of models, and of skeptical and credulous reasoning. An e ective procedure to construct the collection of mod- els characterizing the semantics of a program is given. Applications to knowledge representation and knowl- edge base merging are presented. }, author = {Minker, Jack and Ruiz,C.} } @conference {14787, title = {Modeling, Evaluation, and Testing of Paradyn Instrumentation System}, booktitle = {Proceedings of the 1996 ACM/IEEE Conference on Supercomputing, 1996}, year = {1996}, month = {1996///}, pages = {18 - 18}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a case study of modeling, evaluating, and testing the data collection services (called an instrumentation system) of the Paradyn parallel performance measurement tool using well-known performance evaluation and experiment design techniques. The overall objective of the study is to use modeling- and simulation-based evaluation to provide feedback to the tool developers to help them choose system configurations and task scheduling policies that can significantly reduce the data collection overheads. We develop and parameterize a resource occupancy model for the Paradyn instrumentation system (IS) for an IBM SP-2 platform. This model is parameterized with a measurement-based workload characterization and subsequently used to answer several "what if" questions regarding configuration options and two policies to schedule instrumentation system tasks: collect-and-forward (CF) and batch-and-forward (BF) policies. Simulation results indicate that the BF policy can significantly reduce the overheads. Based on this feedback, the BF policy was implemented in the Paradyn IS as an option to manage the data collection. Measurement-based testing results obtained from this enhanced version of the Paradyn IS are reported in this paper and indicate more than 60\% reduction in the direct IS overheads when the BF policy is used.}, keywords = {Distributed control, Feedback, High performance computing, Instruments, Monitoring, Real time systems, Software measurement, Software systems, Software testing, System testing}, isbn = {0-89791-854-1}, doi = {10.1109/SUPERC.1996.183524}, author = {Waheed, A. and Rover, D. T and Hollingsworth, Jeffrey K} } @article {16548, title = {A neural model of positive schizophrenic symptoms}, journal = {Schizophrenia Bulletin}, volume = {22}, year = {1996}, month = {1996///}, pages = {105 - 123}, author = {Ruppin,E. and Reggia, James A. and Horn,D.} } @article {14947, title = {An optimal randomized parallel algorithm for the single function coarsest partition problem}, journal = {PPL-Parallel Processing Letters}, volume = {6}, year = {1996}, month = {1996///}, pages = {187 - 194}, abstract = {We describe a randomized parallel algorithm to solve the single function coarsest partition problem. The algorithm runs in O(log n) time using O(n) operations with high probability on the Priority CRCW PRAM. The previous best known algorithms run in O(log2 n) time using O(n log2 n) operations on the CREW PRAM and O(log n) time using O(n log log n) operations on the Arbitrary CRCW PRAM. The technique presented can be used to generate the Euler tour of a rooted tree optimally from the parent representation.}, doi = {10.1142/S0129626496000182}, author = {JaJa, Joseph F. and Ryu,K. W.} } @article {16564, title = {Pathogenesis of schizophrenic delusions and hallucinations: a neural model}, journal = {Schizophrenia bulletin}, volume = {22}, year = {1996}, month = {1996///}, pages = {105 - 105}, author = {Ruppin,E. and Reggia, James A. and Horn,D.} } @conference {17872, title = {Runtime coupling of data-parallel programs}, booktitle = {Proceedings of the 10th international conference on Supercomputing}, year = {1996}, month = {1996///}, pages = {229 - 236}, author = {Ranganathan,M. and Acharya, A. and Edjlali,G. and Sussman, Alan and Saltz, J.} } @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.} } @article {16672, title = {Selectional constraints: an information-theoretic model and its computational realization}, journal = {Cognition}, volume = {61}, year = {1996}, month = {1996///}, pages = {127 - 159}, abstract = {A new, information-theoretic model of selectional constraints is proposed. The strategy adopted here is a minimalist one: how far can one get making as few assumptions as possible? In keeping with that strategy, the proposed model consists of only two components: first, a fairly generic taxonomic representation of concepts, and, second, a probabilistic formalization of selectional constraints defined in terms of that taxonomy, computed on the basis of simple, observable frequencies of co-occurrence between predicates and their arguments. Unlike traditional selection restrictions, the information-theoretic approach avoids empirical problems associated with definitional theories of word meaning, accommodates the observation that semantic anomaly often appears to be a matter of degree, and provides an account of how selectional constraints can be learned. A computational implementation of the model {\textquotedblleft}learns{\textquotedblright} selectional constraints from collections of naturally occurring text; the predictions of the implemented model are evaluated against judgments elicited from adult subjects, and used to explore the way that arguments are syntactically realized for a class of English verbs. The paper concludes with a discussion of the role of selectional constraints in the acquisition of verb meaning.}, isbn = {0010-0277}, doi = {10.1016/S0010-0277(96)00722-6}, url = {http://www.sciencedirect.com/science/article/pii/S0010027796007226}, author = {Resnik, Philip} } @mastersthesis {15528, title = {Semantics of knowledge-based systems with multiple forms of negation}, year = {1996}, month = {1996///}, school = {University of Maryland at College Park}, author = {Ruiz,C. and Minker, Jack} } @conference {17371, title = {Social impact statements: engaging public participation in information technology design}, booktitle = {Proceedings of the symposium on Computers and the quality of life}, series = {CQL {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {90 - 96}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-827-4}, doi = {10.1145/238339.238378}, url = {http://doi.acm.org/10.1145/238339.238378}, author = {Shneiderman, Ben and Rose,Anne} } @article {15025, title = {Sorting strings and constructing digital search trees in parallel}, journal = {Theoretical Computer Science}, volume = {154}, year = {1996}, month = {1996/02/05/}, pages = {225 - 245}, abstract = {We describe two simple optimal-work parallel algorithms for sorting a list L= (X1, X2, {\textellipsis}, Xm) of m strings over an arbitrary alphabet Σ, where ∑i = 1m{\textbrokenbar}Xi{\textbrokenbar} = n and two elements of Σ can be compared in unit time using a single processor. The first algorithm is a deterministic algorithm that runs in O(log2m/log log m) time and the second is a randomized algorithm that runs in O(logm) time. Both algorithms use O(m log m + n) operations. Compared to the best-known parallel algorithms for sorting strings, our algorithms offer the following improvements. 1.1. The total number of operations used by our algorithms is optimal while all previous parallel algorithms use a nonoptimal number of operations. 2. 2. We make no assumption about the alphabet while the previous algorithms assume that the alphabet is restricted to {1, 2, {\textellipsis}, no(1)}. 3. 3. The computation model assumed by our algorithms is the Common CRCW PRAM unlike the known algorithms that assume the Arbitrary CRCW PRAM. 4. 4. Our algorithms use O(m log m + n) space, while the previous parallel algorithms use O(n1 + ε) space, where ε is a positive constant. We also present optimal-work parallel algorithms to construct a digital search tree for a given set of strings and to search for a string in a sorted list of strings. We use our parallel sorting algorithms to solve the problem of determining a minimal starting point of a circular string with respect to lexicographic ordering. Our solution improves upon the previous best-known result to solve this problem. }, isbn = {0304-3975}, doi = {10.1016/0304-3975(94)00263-0}, url = {http://www.sciencedirect.com/science/article/pii/0304397594002630}, author = {JaJa, Joseph F. and Ryu,Kwan Woo and Vishkin, Uzi} } @article {15221, title = {On strongly connected digraphs with bounded cycle length}, journal = {Discrete Applied Mathematics}, volume = {69}, year = {1996}, month = {1996/08/27/}, pages = {281 - 289}, abstract = {Given a directed graph G = (V, E), a natural problem is to choose a minimum number of the edges in E such that, for any two vertices u and v, if there is a path from u to v in E, then there is a path from u to v among the chosen edges. We show that in graphs having no directed cycle with more than three edges, this problem is equivalent to Maximum Bipartite Matching. This leads to a small improvement in the performance guarantee of the previous best approximation algorithm for the general problem.}, isbn = {0166-218X}, doi = {10.1016/0166-218X(95)00105-Z}, url = {http://www.sciencedirect.com/science/article/pii/0166218X9500105Z}, author = {Khuller, Samir and Raghavachari,Balaji and Young,Neal} } @conference {13504, title = {A Theory of Document Functionality}, booktitle = {Proceedings in FLAIRS}, year = {1996}, month = {1996///}, pages = {429 - 433}, author = {Rivlin,E. and Doermann, David and Rosenfeld, A.} } @article {16349, title = {Transitive closure of infinite graphs and its applications}, journal = {Languages and Compilers for Parallel Computing}, year = {1996}, month = {1996///}, pages = {126 - 140}, author = {Kelly,W. and Pugh, William and Rosser,E. and Shpeisman,T.} } @conference {16205, title = {Where is information visualization technology going?}, booktitle = {Proceedings of the 9th annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {75 - 77}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-798-7}, doi = {10.1145/237091.237101}, url = {http://doi.acm.org/10.1145/237091.237101}, author = {Hasco{\"e}t-Zizi,Mountaz and Ahlberg,Chris and Korfhage,Robert and Plaisant, Catherine and Chalmers,Matthew and Rao,Ramana} } @conference {16211, title = {An applied ethnographic method for redesigning user interfaces}, booktitle = {Proceedings of the 1st conference on Designing interactive systems: processes, practices, methods, \& techniques}, series = {DIS {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {115 - 122}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-673-5}, doi = {10.1145/225434.225447}, url = {http://doi.acm.org/10.1145/225434.225447}, author = {Rose,Anne and Shneiderman, Ben and Plaisant, Catherine} } @article {15216, title = {Approximating the minimum equivalent digraph}, journal = {SIAM Journal on Computing (SICOMP)}, volume = {24}, year = {1995}, month = {1995///}, pages = {859 - 872}, author = {Khuller, Samir and Raghavachari,B. and Young,N.} } @article {18818, title = {Automated Manufacturability Analysis: A Survey}, volume = {ISR; TR 1995-14}, year = {1995}, month = {1995///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {In the marketplace of the 21st century, there is no place for traditional {\textquoteleft}{\textquoteleft}over-the-wall{\textquoteright}{\textquoteright} communications between design and manufacturing. In order to {\textquoteleft}{\textquoteleft}design it right the very first time,{\textquoteright}{\textquoteright} designers must ensure that their products are both functional and easy to manufacture. Software tools have had some successes in reducing the barriers between design and manufacturing. Manufacturability analysis systems are emerging as one such tool---enabling identification of potential manufacturing problems during the design phase and providing suggestions to designers on how to eliminate them.

In this paper, we provide a survey of current state of the art in automated manufacturability analysis. We present the historical context in which this area has emerged and outline characteristics to compare and classify various systems. We describe the two dominant approaches to automated manufacturability analysis and overview representative systems based on their application domain. We describe support tools that enhance the effectiveness of manufacturability analysis systems. Finally, we attempt to expose some of the existing research challenges and future directions.

}, keywords = {manufacturability, Manufacturing, Solid modeling, Systems Integration Methodology}, url = {http://drum.lib.umd.edu//handle/1903/5609}, author = {Das,Diganta and Gupta, Satyandra K. and Regli,W. C. and Nau, Dana S.} } @article {15217, title = {Balancing minimum spanning trees and shortest-path trees}, journal = {Algorithmica}, volume = {14}, year = {1995}, month = {1995///}, pages = {305 - 321}, abstract = {We give a simple algorithm to find a spanning tree that simultaneously approximates a shortest-path tree and a minimum spanning tree. The algorithm provides a continuous tradeoff: given the two trees and agamma>0, the algorithm returns a spanning tree in which the distance between any vertex and the root of the shortest-path tree is at most 1+radic2gamma times the shortest-path distance, and yet the total weight of the tree is at most 1+radic2/gamma times the weight of a minimum spanning tree. Our algorithm runs in linear time and obtains the best-possible tradeoff. It can be implemented on a CREW PRAM to run a logarithmic time using one processor per vertex.}, doi = {10.1007/BF01294129}, author = {Khuller, Samir and Raghavachari,B. and Young,N.} } @conference {16363, title = {Code generation for multiple mappings}, booktitle = {Frontiers of Massively Parallel Computation, 1995. Proceedings. Frontiers {\textquoteright}95., Fifth Symposium on the}, year = {1995}, month = {1995/02/06/9}, pages = {332 - 341}, publisher = {IEEE}, organization = {IEEE}, abstract = {There has been a great amount of recent work toward unifying iteration reordering transformations. Many of these approaches represent transformations as affine mappings from the original iteration space to a new iteration space. These approaches show a great deal of promise, but they all rely on the ability to generate code that iterates over the points in these new iteration spaces in the appropriate order. This problem has been fairly well-studied in the case where all statements use the same mapping. We have developed an algorithm for the less well-studied case where each statement uses a potentially different mapping. Unlike many other approaches, our algorithm can also generate code from mappings corresponding to loop blocking. We address the important trade-off between reducing control overhead and duplicating code}, keywords = {code generation, Computer science, Concurrent computing, control overhead, Educational institutions, iteration reordering transformations, Law, Legal factors, loop blocking, multiple mappings, optimisation, optimising compilers, Optimizing compilers, PARALLEL PROCESSING, Performance analysis, program compilers}, isbn = {0-8186-6965-9}, doi = {10.1109/FMPC.1995.380437}, author = {Kelly,W. and Pugh, William and Rosser,E.} } @article {15536, title = {Computing stable and partial stable models of extended disjunctive logic programs}, journal = {Non-Monotonic Extensions of Logic Programming}, year = {1995}, month = {1995///}, pages = {205 - 229}, abstract = {n [Prz91], Przymusinski introduced the partial (or 3-valued) stable model semantics which extends the (2-valued) stable model semantics defined originally by Gelfond and Lifschitz [GL88]. In this paper we describe a procedure to compute the collection of all partial stable models of an extended disjunctive logic program. This procedure consists in transforming an extended disjunctive logic program into a constrained disjunctive program free of negation-by-default whose set of 2-valued minimal models corresponds to the set of partial stable models of the original program.}, doi = {10.1007/BFb0030666}, author = {Ruiz,C. and Minker, Jack} } @article {18824, title = {Current Trends and Future Challenges in Automated Manufacturability Analysis}, volume = {ISR; TR 1995-16}, year = {1995}, month = {1995///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {In the marketplace of the 21st century, there is no place for traditional communications between design and manufacturing. In order to {\textquoteleft}{\textquoteleft}design it right the first time,{\textquoteright}{\textquoteright} designers must ensure that their products are both functional and easy to manufacture. Software tools have had some successes in reducing the barriers between design and manufacturing. Manufacturability analysis systems are emerging as one such tool---enabling identification of potential manufacturing problems during the design phase and providing suggestions to designers on how to eliminate them.

In this paper, we survey of current state of the art in automated manufacturability analysis. We describe the two dominant approaches to automated manufacturability analysis and overview representative systems based on their application domain. Finally, we attempt to expose some of the existing research challenges and future directions.}, keywords = {computer integrated manufacturing, manufacturability, Manufacturing, Solid modeling, Systems Integration Methodology}, url = {http://drum.lib.umd.edu//handle/1903/5611}, author = {Gupta, Satyandra K. and Das,Diganta and Regli,W. C. and Nau, Dana S.} } @conference {17052, title = {Dealing with complexity: uniting agents and direct manipulation (panel session)}, booktitle = {Conference companion on Human factors in computing systems}, series = {CHI {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {191 - 192}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-755-3}, doi = {10.1145/223355.223504}, url = {http://doi.acm.org/10.1145/223355.223504}, author = {Riecken,Doug and Maes,Pattie and Shneiderman, Ben and Smith,David Canfield} } @conference {17944, title = {Defining, Computing, and Visualizing Molecular Interfaces}, booktitle = {Proceedings of the 6th conference on Visualization {\textquoteright}95}, series = {VIS {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {36{\textendash} - 36{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {A parallel, analytic approach for defining and computing the inter- and intra-molecular interfaces in three dimensions is described. The "molecular interface surfaces" are derived from approximations to the power-diagrams over the participating molecular units. For a given molecular interface our approach can generate a family of interface surfaces parametrized by alpha and beta, where alpha is the radius of the solvent molecule (also known as the probe-radius) and beta is the interface radius that defines the size of the molecular interface. Molecular interface surfaces provide biochemists with a powerful tool to study surface complementarity and to efficiently characterize the interactions during a protein-substrate docking. The complexity of our algorithm for molecular environments is O(n k \log^2{k}), where n is the number of atoms in the participating molecular units and k is the average number of neighboring atoms -- a constant, given alpha and beta.}, keywords = {Computational Biochemistry Algorithms Molecular Graphics, Connolly Surfaces, Molecular Interfaces, Molecular Surfaces, Protein-Protein Recognition}, isbn = {0-8186-7187-4}, url = {http://dl.acm.org/citation.cfm?id=832271.833834}, author = {Varshney, Amitabh and Brooks Jr,Frederick P. and Manocha,Dinesh and Wright,William V. and Richardson,David C.} } @conference {16713, title = {Disambiguating noun groupings with respect to WordNet senses}, booktitle = {Proceedings of the Third Workshop on Very Large Corpora}, year = {1995}, month = {1995///}, pages = {54 - 68}, author = {Resnik, Philip} } @conference {16619, title = {Discovery of self-replicating structures using a genetic algorithm}, booktitle = {Evolutionary Computation, 1995., IEEE International Conference on}, volume = {2}, year = {1995}, month = {1995///}, pages = {678 - 683}, author = {Lohn,J. D and Reggia, James A.} } @article {18831, title = {Extracting alternative machining features: An algorithmic approach}, journal = {Research in Engineering Design}, volume = {7}, year = {1995}, month = {1995///}, pages = {173 - 192}, abstract = {Automated recognition of features from CAD models has been attempted for a wide range of application domains. In this article we address the problem of representing and recognizing a complete class of features in alternative interpretation for a given design.}, keywords = {engineering}, isbn = {0934-9839}, doi = {10.1007/BF01638098}, url = {http://www.springerlink.com/content/t271m7t670m36484/abstract/}, author = {Regli,William C. and Gupta, Satyandra K. and Nau, Dana S.} } @article {15218, title = {Graphbots: Mobility in discrete spaces}, journal = {Automata, Languages and Programming}, year = {1995}, month = {1995///}, pages = {593 - 604}, abstract = {Most previous theoretical work on motion planning has addressed the problem of path planning for geometrically simple robots in geometrically simple regions of Euclidean space (e.g., a planar region containing polygonal obstacles). In this paper we define a natural version of the motion planning problem in a graph theoretic setting. We establish conditions under which a ldquorobotrdquo or team of robots having a particular graph structure can move from any start location to any goal destination in a graph-structured space.}, doi = {10.1007/3-540-60084-1_108}, author = {Khuller, Samir and Rivlin,E. and Rosenfeld, A.} } @book {17211, title = {Human-Computer Interaction Laboratory 1995 Video Reports}, year = {1995}, month = {1995///}, publisher = {University of Maryland at College Park, Human/Computer Interaction Laboratory}, organization = {University of Maryland at College Park, Human/Computer Interaction Laboratory}, author = {Plaisant, Catherine and Morrison,S. and Skokowski,C. and Reesch,J. and Shneiderman, Ben and Laboratory,University of Maryland at College Park. Human/Computer Interaction and Channel,F.} } @conference {15219, title = {Improved approximation algorithms for uniform connectivity problems}, booktitle = {Proceedings of the twenty-seventh annual ACM symposium on Theory of computing}, series = {STOC {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {1 - 10}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-718-9}, doi = {10.1145/225058.225066}, url = {http://doi.acm.org/10.1145/225058.225066}, author = {Khuller, Samir and Raghavachari,Balaji} } @conference {18750, title = {Interactive feature recognition using multi-processor methods}, year = {1995}, month = {1995///}, author = {Regli,W. C. and Gupta,S.K. and Nau, Dana S.} } @article {16457, title = {Interoperable query processing from object to relational schemas based on a parameterized canonical representation}, journal = {Int. J. Cooperative Inf. Syst.}, volume = {4}, year = {1995}, month = {1995///}, pages = {81 - 120}, author = {Raschid, Louiqa and Chang,Y.} } @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.} } @conference {18858, title = {Manufacturing feature instances: which ones to recognize?}, series = {SMA {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {141 - 152}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-672-7}, doi = {10.1145/218013.218052}, url = {http://doi.acm.org/10.1145/218013.218052}, author = {Gupta, Satyandra K. and Regli,William C. and Nau, Dana S.} } @article {16607, title = {A modified cellular automata model of nucleotide interactions and non-enzymatic transcription of DNA}, journal = {inbs}, year = {1995}, month = {1995///}, pages = {136 - 136}, author = {Hilke,J. and Reggia, James A. and Navarro-Gonzalez,R. and Lohn,J.} } @article {16524, title = {A neural model of delusions and hallucinations in schizophrenia}, journal = {Advances in Neural Information Processing Systems}, year = {1995}, month = {1995///}, pages = {149 - 156}, author = {Ruppin,E. and Reggia, James A. and Horn,D.} } @article {16630, title = {A neural model of memory impairment in diffuse cerebral atrophy}, journal = {The British Journal of Psychiatry}, volume = {166}, year = {1995}, month = {1995///}, pages = {19 - 19}, author = {Ruppin,E. 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} } @conference {18046, title = {Parallel algorithms for database operations and a database operation for parallel algorithms}, booktitle = {Parallel Processing Symposium, 1995. Proceedings., 9th International}, year = {1995}, month = {1995///}, pages = {173 - 179}, author = {Raman,R. and Vishkin, Uzi} } @article {16586, title = {Patterns of functional damage in neural network models of associative memory}, journal = {Neural computation}, volume = {7}, year = {1995}, month = {1995///}, pages = {1105 - 1127}, author = {Ruppin,E. and Reggia, James A.} } @article {17648, title = {Randomness-Optimal Unique Element Isolation with Applications to Perfect Matching and Related Problems}, journal = {SIAM Journal on Computing}, volume = {24}, year = {1995}, month = {1995///}, pages = {1036 - 1036}, abstract = {In this paper, we precisely characterize the randomness complexity of the unique element isolation problem, a crucial step in the $RNC$ algorithm for perfect matching by Mulmuley, Vazirani, and Vazirani [Combinatorica, 7 (1987), pp. 105{\textendash}113] and in several other applications. Given a set $S$ and an unknown family $\mathcal{F} \subseteq 2^{S}$ with $|\mathcal{F}| \leq Z$, we present a scheme for assigning polynomially bounded weights to the elements of $S$ using only $O(\log Z + \log |S|)$ random bits, such that the minimum weight set in $\mathcal{F}$ is unique with high probability. This generalizes the solution of Mulmuley, Vazirani, and Vazirani, who use $O(S \log S)$ bits, independent of $Z$. We also provide a matching lower bound for the randomness complexity of this problem. The new weight assignment scheme yields a randomness-efficient $RNC^{2}$ algorithm for perfect matching which uses $O(\log Z + \log n)$ random bits, where $Z$ is any given upper bound on the number of perfect matchings in the input graph. This generalizes the result of Grigoriev and Karpinski [Proc. IEEE Symposium on Foundations of computer Science, 1987, pp. 166{\textendash}172], who presentan $NC^{3}$ algorithm when $Z$ is polynomial and improves the running time in this case. The worst-case randomness complexity of our algorithm is $O(n \log (m/n))$ random bits improving on the previous bound of $O(m \log n)$. Our scheme also gives randomness-efficient solutions for several problems where unique element isolation is used, such as $RNC$ algorithms for variants of matching and basic problems on linear matroids. We obtain a randomness-efficient random reduction from SAT to USAT, the language of uniquely satisfiable formulas, which can be derandomized in the case of languages in Few $P$ to yield new proofs of the results Few $P \subseteq \oplus P$ and Few $P \subseteq C_{=} P$.}, isbn = {00975397}, doi = {10.1137/S0097539793250330}, url = {http://link.aip.org/link/SMJCAT/v24/i5/p1036/s1\&Agg=doi}, author = {Chari,Suresh and Rohatgi,Pankaj and Srinivasan, Aravind} } @article {13679, title = {The representation of document structure: A generic object-process approach}, volume = {CAR-TR-785}, year = {1995}, month = {1995///}, institution = {University of Maryland, College Park}, author = {Dori,D. and David Doermann and Shin,C. and Haralick,R. and Phillips,I. and Buchman,M. and Ross,D.} } @article {14255, title = {Seeing and understanding: representing the visual world}, journal = {ACM Comput. Surv.}, volume = {27}, year = {1995}, month = {1995/09//}, pages = {307 - 309}, isbn = {0360-0300}, doi = {10.1145/212094.212101}, url = {http://doi.acm.org/10.1145/212094.212101}, author = {Aloimonos, J. and Ferm{\"u}ller, Cornelia and Rosenfeld, A.} } @article {16507, title = {Symmetries of natural and artificial neural networks}, journal = {Symmetry: Culture and Science}, volume = {6}, year = {1995}, month = {1995///}, pages = {446 - 449}, author = {Reggia, James A.} } @article {16697, title = {Using information content to evaluate semantic similarity in a taxonomy}, journal = {Arxiv preprint cmp-lg/9511007}, year = {1995}, month = {1995///}, author = {Resnik, Philip} } @article {13413, title = {AAAI 1994 Spring Symposium Series Reports}, journal = {AI Magazine}, volume = {15}, year = {1994}, month = {1994/09/15/}, pages = {22 - 22}, isbn = {0738-4602}, doi = {10.1609/aimag.v15i3.1101}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1101}, author = {Woods,William and Uckun,Sendar and Kohane,Isaac and Bates,Joseph and Hulthage,Ingemar and Gasser,Les and Hanks,Steve and Gini,Maria and Ram,Ashwin and desJardins, Marie and Johnson,Peter and Etzioni,Oren and Coombs,David and Whitehead,Steven} } @article {16643, title = {Adaptation of noncompetitive and competitive neural networks to focal lesions}, journal = {Journal of Artificial Neural Networks}, volume = {1}, year = {1994}, month = {1994///}, pages = {51 - 60}, author = {Weinrich,M. and Sutton,G. G and Reggia, James A. and D{\textquoteright}Autrechy,C. L} } @article {18813, title = {An Application of Distributed Solid Modeling: Feature Recognition}, volume = {ISR; TR 1994-82}, year = {1994}, month = {1994///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The availability of low-cost computational power is a driving force behind the growing sophistication of CAD software. Tools designed to reduce time-consuming build-test-redesign iterations are essential for increasing engineering quality and productivity. However, automation of the design process poses many difficult computational problems. As more downstream engineering activities are being considered during the design phase, guaranteeing reasonable response times within design systems becomes problematic. Design is an interactive process and speed is a critical factor in systems that enable designers to explore and experiment with alternative ideas during the design phase. Achieving interactivity requires an increasingly sophisticated allocation of computational resources in order to perform realistic design analyses and generate feedback in real time.

This paper presents our initial efforts to develop techniques to apply distributed algorithms to the problem of recognizing machining features from solid models. Existing work on recognition of features has focused exclusively on serial computer architectures. Our objective is to show that distributed algorithms can be employed on realistic parts with large numbers of features and many geometric and topological entities to obtain significant improvements in computation time using existing hardware and software tools. Migrating solid modeling applications toward a distributed computing frame-work enables interconnection of many of the autonomous and geographically diverse software tools used in the modern manufacturing enterprise.

This has been implemented on a network of SUN workstations using the ACIS solid modeler and the NIH C++ class library; inter-processor communication is handled with TCP/IP- based network communication tools.}, keywords = {Distributed computing, feature recognition, feature- based modeling, multiprocessor solid modeling, Systems Integration Methodology}, url = {http://drum.lib.umd.edu//handle/1903/5552}, author = {Regli,W. C. and Gupta, Satyandra K. and Nau, Dana S.} } @conference {15039, title = {The block distributed memory model for shared memory multiprocessors}, booktitle = {Parallel Processing Symposium, 1994. Proceedings., Eighth International}, year = {1994}, month = {1994/04//}, pages = {752 - 756}, abstract = {Introduces a computation model for developing and analyzing parallel algorithms on distributed memory machines. The model allows the design of algorithms using a single address space and does not assume any particular interconnection topology. We capture performance by incorporating a cost measure for interprocessor communication induced by remote memory accesses. The cost measure includes parameters reflecting memory latency, communication bandwidth, and spatial locality. Our model allows the initial placement of the input data and pipelined prefetching. We use our model to develop parallel algorithms for various data rearrangement problems, load balancing, sorting, FFT, and matrix multiplication. We show that most of these algorithms achieve optimal or near optimal communication complexity while simultaneously guaranteeing an optimal speed-up in computational complexity}, keywords = {accesses;shared, address, algebra;parallel, algorithms;performance, algorithms;performance;pipelined, allocation;shared, balancing;matrix, bandwidth;computation, block, Communication, communication;load, complexity;computational, complexity;cost, complexity;distributed, complexity;optimal, data, distributed, evaluation;resource, Fourier, latency;optimal, locality;communication, measure;data, memory, model;communication, model;computational, multiplication;memory, multiprocessors;single, placement;interprocessor, prefetching;remote, problems;fast, rearrangement, space;sorting;spatial, speedup;parallel, systems;fast, systems;sorting;, transforms;input, transforms;matrix}, doi = {10.1109/IPPS.1994.288220}, author = {JaJa, Joseph F. and Ryu,Kwan Woo} } @article {18821, title = {Building MRSEV models for CAM applications}, journal = {Advances in Engineering Software}, volume = {20}, year = {1994}, month = {1994///}, pages = {121 - 139}, abstract = {In integrating CAD and CAM applications, one major problem is how to interpret CAD information in a manner that makes sense for CAM. The goal is to develop a general approach that can be used with a variety of CAD and CAM applications for the manufacture of machined parts.In particular, a methodology is presented for taking a CAD model, extracting alternative interpretations of the model as collections of MRSEVs (material removal shape element volumes, a STEP-based library of machining features), and evaluating these interpretations to determine which one is optimal. The evaluation criteria may be defined by the user, in order to select the best interpretation for the particular application at hand. }, keywords = {CAD/CAM integration, design critiquing, feature recognition}, isbn = {0965-9978}, doi = {10.1016/0965-9978(94)90054-X}, url = {http://www.sciencedirect.com/science/article/pii/096599789490054X}, author = {Gupta, Satyandra K. and Kramer,Thomas R. and Nau, Dana S. and Regli,William C. and Zhang,Guangming} } @article {15732, title = {Confidence Intervals for Discrete Approximations to Ill-Posed Problems}, journal = {The Journal of Computational and Graphical Statistics}, volume = {3}, year = {1994}, month = {1994///}, pages = {67 - 96}, author = {Rust,Bert W. and O{\textquoteright}Leary, Dianne P.} } @article {16621, title = {Cortical map reorganization as a competitive process}, journal = {Neural Computation}, volume = {6}, year = {1994}, month = {1994///}, pages = {1 - 13}, author = {Sutton III,G. G. and Reggia, James A. and Armentrout,S. L and D{\textquoteright}Autrechy,C. L} } @article {16553, title = {Effects of normalization constraints on competitive learning}, journal = {Neural Networks, IEEE Transactions on}, volume = {5}, year = {1994}, month = {1994///}, pages = {502 - 504}, author = {Sutton,G. G and Reggia, James A.} } @article {14940, title = {An efficient parallel algorithm for the single function coarsest partition problem}, journal = {Theoretical computer science}, volume = {129}, year = {1994}, month = {1994///}, pages = {293 - 307}, abstract = {We describe an efficient parallel algorithm to solve the single function coarsest partition problem. The algorithm runs in O(log n) time using O(n log log n) operations on the arbitrary CRCW PRAM. The previous best-known algorithms run in O(log2 n) time using O(n log2 n) operations on the CREW PRAM, and O(log n) time using O(n log n) operations on the arbitrary CRCW PRAM. Our solution is based on efficient algorithms for solving several subproblems that are of independent interest. In particular, we present efficient parallel algorithms to find a minimal starting point of a circular string with respect to lexicographic ordering and to sort lexicographically a list of strings of different lengths}, author = {JaJa, Joseph F. and Ryu,K. W.} } @article {16595, title = {An extended cellular space method for simulating autocatalytic oligonucleotides}, journal = {Computers \& chemistry}, volume = {18}, year = {1994}, month = {1994///}, pages = {33 - 43}, author = {Chou,H. H. and Reggia, James A. and Navarro-Gonzalez,R. and Wu,J.} } @article {18833, title = {Feature Recognition for Manufacturability Analysis}, volume = {ISR; TR 1994-10}, year = {1994}, month = {1994///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {While automated recognition of features has been attempted for a wide range of applications, no single existing approach possesses the functionality required to perform manufacturability analysis. In this paper, we present a methodology for taking a CAD model and extracting a set of machinable features suitable for generating all alternative interpretations of the model as collections of MRSEVs (Material Removal Shape Element Volumes, a STEP-based library of machining, features). This set of MRSEVs is to be employed for manufacturability analysis. The algorithm handles a variety of features including those describing holes, pockets, slots, and chamfering and filleting operations. In addition, it considers elementary accessibility constraints for these features and is provably complete over a, significant class of machinable parts the features describe. Further, the approach has low-order polynomial-time worst-case complexity.}, keywords = {algorithms, Automation, COMPUTER AIDED DESIGN, computer aided manufacturing, computer integrated manufacturing, Feature extraction, manufacturability, Manufacturing, Solid modeling, Systems Integration}, url = {http://drum.lib.umd.edu//handle/1903/5490}, author = {Regli,W. C. and Gupta, Satyandra K. and Nau, Dana S.} } @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 {13577, title = {Instrument Grasp: AModel and its Effects on Handwritten Strokes}, journal = {Pattern Recognition}, volume = {27}, year = {1994}, month = {1994///}, pages = {233 - 245}, author = {David Doermann and Varma,V. and Rosenfeld, A.} } @article {18853, title = {Integrating DFM with CAD through Design Critiquing}, journal = {Concurrent EngineeringConcurrent Engineering}, volume = {2}, year = {1994}, month = {1994/06/01/}, pages = {85 - 95}, abstract = {The increasing focus on design for manufacturability (DFM) in research in concurrent engineering and engineering design is expanding the scope of traditional design activities in order to identify and eliminate manufacturing problems during the design stage. Manufacturing a product generally involves many different kinds of manufacturing activities, each having different characteristics. A design that is good for one kind of activity may not be good for another; for example, a design that is easy to assemble may not be easy to machine. One obstacle to DFM is the difficulty involved in building a single system that can handle the various manufacturing domains relevant to a design.}, keywords = {design critiquing, design for manufacturability, feature-based modeling, manufacturability analysis, multi-agent coordination.}, isbn = {1063-293X, 1531-2003}, doi = {10.1177/1063293X9400200202}, url = {http://cer.sagepub.com/content/2/2/85}, author = {Gupta, Satyandra K. and Regli,William C. and Nau, Dana S.} } @conference {16629, title = {Interpretation of Doppler blood flow velocity waveforms using neural networks.}, booktitle = {Proceedings of the Annual Symposium on Computer Application in Medical Care}, year = {1994}, month = {1994///}, pages = {865 - 865}, author = {Baykal,N. and Reggia, James A. and Yalabik,N. and Erkmen,A. and Beksac,M. S.} } @article {16594, title = {Map formation in proprioceptive cortex.}, journal = {International journal of neural systems}, volume = {5}, year = {1994}, month = {1994///}, pages = {87 - 87}, author = {Cho,S. and Reggia, James A.} } @conference {16559, title = {Modeling brain adaptation to focal damage.}, booktitle = {Proceedings of the Annual Symposium on Computer Application in Medical Care}, year = {1994}, month = {1994///}, pages = {860 - 860}, author = {Goodall,S. and Reggia, James A. and Cho,S.} } @article {16649, title = {A modified cellular automata model of nucleotide interactions and DNA replication}, year = {1994}, month = {1994///}, institution = {University of Maryland at College Park}, address = {College Park, MD, USA}, author = {Hilke,James and Lohn,Jason and Reggia, James A. and Navarro,Rafael} } @article {17305, title = {Navigating in hyperspace: designing a structure-based toolbox}, journal = {Communications of the ACM}, volume = {37}, year = {1994}, month = {1994/02//}, pages = {87 - 96}, isbn = {0001-0782}, doi = {10.1145/175235.175242}, url = {http://doi.acm.org/10.1145/175235.175242}, author = {Rivlin,Ehud and Botafogo,Rodrigo and Shneiderman, Ben} } @article {16508, title = {A neural model of cortical map reorganization following a focal lesion}, journal = {Artificial Intelligence in Medicine}, volume = {6}, year = {1994}, month = {1994///}, pages = {383 - 400}, author = {Armentrout,S. L and Reggia, James A. and Weinrich,M.} } @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} } @conference {18053, title = {Optimal randomized parallel algorithms for computing the row maxima of a totally monotone matrix}, booktitle = {Proceedings of the fifth annual ACM-SIAM symposium on Discrete algorithms}, year = {1994}, month = {1994///}, pages = {613 - 621}, author = {Raman,R. and Vishkin, Uzi} } @article {18984, title = {P element-mediated in vivo deletion analysis of white-apricot: deletions between direct repeats are strongly favored.}, journal = {GeneticsGenetics}, volume = {136}, year = {1994}, month = {1994/03/01/}, pages = {1001 - 1011}, abstract = {We have isolated and characterized deletions arising within a P transposon, P[hswa], in the presence of P transposase. P[hswa] carries white-apricot (wa) sequences, including a complete copia element, under the control of an hsp70 promoter, and resembles the original wa allele in eye color phenotype. In the presence of P transposase, P[hswa] shows a high overall rate (approximately 3\%) of germline mutations that result in increased eye pigmentation. Of 234 derivatives of P[hswa] with greatly increased eye pigmentation, at least 205 carried deletions within copia. Of these, 201 were precise deletions between the directly repeated 276-nucleotide copia long terminal repeats (LTRs), and four were unique deletions. High rates of transposase-induced precise deletion were observed within another P transposon carrying unrelated 599 nucleotide repeats (yeast 2 mu FLP; recombinase target sites) separated by 5.7 kb. Our observation that P element-mediated deletion formation occurs preferentially between direct repeats suggests general methods for controlling deletion formation.}, isbn = {0016-6731, 1943-2631}, url = {http://www.genetics.org/content/136/3/1001}, author = {Kurkulos,M. and Weinberg,J. M. and Roy,D. and Mount, Stephen M.} } @conference {11947, title = {Principles of computer vision}, booktitle = {Handbook of pattern recognition and image processing (vol. 2)}, year = {1994}, month = {1994///}, pages = {1 - 15}, author = {Aloimonos, J. and Rosenfeld, A.} } @article {13845, title = {Query transformation techniques for interoperable query processing in cooperative information systems}, journal = {Proceedings of the Second International Conference on Cooperative Information Systems (CoopIS94), May}, year = {1994}, month = {1994///}, pages = {17 - 20}, author = {Raschid, Louiqa and Chang,Y. and Dorr, Bonnie J} } @article {17337, title = {QUEST{\textemdash}Query Environment for Science Teaching}, journal = {Digital Libraries{\textquoteright} 94}, year = {1994}, month = {1994///}, abstract = {QUery Environment for Science Teaching (QUEST) is a proposed digital library implementation consisting of a set of research projects dealing with data capture and organization, content analysis, information seeking and visual interfaces.The QUEST team includes a large number of renown technical collaborators and prominent source collaborators, as well as a significant number of contributors in the University of Maryland, the central, co-ordinating agency.A large collection of multidisciplinary materials in visual and textual formats, made accessible to us by our source collaborators, will be organized to allow integrated access by users from the science education community, that is elementary school through college level teachers. QUEST will be structured so as to provide seamless access to widespread resources on disparate subjects. We intend to provide first-rate subject analysis and representation in order to provide ready access. QUEST will be accessible nationally by means of Mosaic. We propose to provide highly sophisticated querying, browsing and information investigation facilities which will handle integrated textual and visual materials without difficulty. They will be augmented by online reference and referral services, immediately accessible by the user. QUEST will provide a comprehensive information resource for science education accessible through a dynamic, visual user interface. }, author = {Shneiderman, Ben and Rosenfeld, A. and Marchioni,G. and Holliday,W. and Ricart, G. and Faloutsos,С. and Dick,J.} } @article {13631, title = {Recovery of Temporal Information from Static Images of Handwriting}, journal = {International Journal of Computer Vision}, volume = {52}, year = {1994}, month = {1994///}, pages = {143 - 164}, abstract = {The problem of off-line handwritten character recognition has eluded a satisfactory solution for several decades. Researchers working in the area of on-line recognition have had greater success, but the possibility of extracting on-line information from static images has not been fully explored. The experience of forensic document examiners assures us that in many cases, such information can be successfully recovered.We outline the design of a system for the recovery of temporal information from static handwritten images. We provide a taxonomy of local, regional and global temporal clues which are often found in hand-written samples, and describe methods for recovering these clues from the image. We show how this system can benefit from obtaining a comprehensive understanding of the handwriting signal and a detailed analysis of stroke and sub-stroke properties. We suggest that the recovery task requires that we break away from traditional thresholding and thinning techniques, and we provide a framework for such analysis. We demonstrate how isolated temporal clues can reliably be extracted from this framework and propose a control structure for integrating the partial information. We show how many seemingly ambiguous situations can be resolved by the derived clues and our knowledge of the writing process, and provide several examples to illustrate our approach. The support of this research by the Ricoh Corporation is gratefully acknowledged. }, author = {David Doermann and Rosenfeld, A.} } @conference {16688, title = {A rule-based approach to prepositional phrase attachment disambiguation}, booktitle = {Proceedings of the 15th conference on Computational linguistics-Volume 2}, year = {1994}, month = {1994///}, pages = {1198 - 1204}, author = {Brill,E. and Resnik, Philip} } @article {16465, title = {A Semantics for a class of non-deterministic and causal production system programs}, journal = {Journal of Automated Reasoning}, volume = {12}, year = {1994}, month = {1994///}, pages = {305 - 349}, author = {Raschid, Louiqa and Lobo,J.} } @article {16476, title = {A simulation-based study on the concurrent execution of rules in a database environment}, journal = {Journal of Parallel and Distributed computing}, volume = {20}, year = {1994}, month = {1994///}, pages = {20 - 42}, author = {Raschid, Louiqa and Sellis,T. and Delis,A.} } @article {19003, title = {Suppressor U1 snRNAs in Drosophila.}, journal = {GeneticsGenetics}, volume = {138}, year = {1994}, month = {1994/10/01/}, pages = {365 - 378}, abstract = {Although the role of U1 small nuclear RNAs (snRNAs) in 5{\textquoteright} splice site recognition is well established, suppressor U1 snRNAs active in intact multicellular animals have been lacking. Here we describe suppression of a 5{\textquoteright} splice site mutation in the Drosophila melanogaster white gene (w(DR18)) by compensatory changes in U1 snRNA. Mutation of positions -1 and +6 of the 5{\textquoteright} splice site of the second intron (ACG|GTGACT to ACC|GTGAGC) results in the accumulation of RNA retaining this 74-nucleotide intron in both transfected cells and transgenic flies. U1-3G, a suppressor U1 snRNA which restores basepairing at position +6 of the mutant intron, increases the ratio of spliced to unspliced w(DR18) RNA up to fivefold in transfected Schneider cells and increases eye pigmentation in w(DR18) flies. U1-9G, which targets position -1, suppresses w(DR18) in transfected cells less well. U1-3G,9G has the same effect as U1-3G although it accumulates to lower levels. Suppression of w(DR18) has revealed that the U1b embryonic variant (G134 to U) is active in Schneider cells and pupal eye discs. However, the combination of 9G with 134U leads to reduced accumulation of both U1b-9G and U1b-3G,9G, possibly because nucleotides 9 and 134 both participate in a potential long-range intramolecular base-pairing interaction. High levels of functional U1-3G suppressor reduce both viability and fertility in transformed flies. These results show that, despite the difficulties inherent in stably altering splice site selection in multicellular organisms, it is possible to obtain suppressor U1 snRNAs in flies.}, isbn = {0016-6731, 1943-2631}, url = {http://www.genetics.org/content/138/2/365}, author = {Lo,P. C. and Roy,D. and Mount, Stephen M.} } @inbook {13879, title = {Transforming queries from a relational schema to an object schema: A prototype based on F-logic}, booktitle = {Methodologies for Intelligent SystemsMethodologies for Intelligent Systems}, series = {Lecture Notes in Computer Science}, volume = {869}, year = {1994}, month = {1994///}, pages = {154 - 163}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, isbn = {978-3-540-58495-7}, url = {http://dx.doi.org/10.1007/3-540-58495-1_16}, author = {Chang,Yahui and Raschid, Louiqa and Dorr, Bonnie J}, editor = {Ras,Zbigniew and Zemankova,Maria} } @conference {17497, title = {Visualization in the information highway}, booktitle = {Proceedings of the conference on Visualization {\textquoteright}94}, series = {VIS {\textquoteright}94}, year = {1994}, month = {1994///}, pages = {4 - 7}, publisher = {IEEE Computer Society Press}, organization = {IEEE Computer Society Press}, address = {Los Alamitos, CA, USA}, isbn = {0-7803-2521-4}, url = {http://dl.acm.org/citation.cfm?id=951087.951091}, author = {Gershon,Nahum and Card,Stuart K. and Roth,Steven F. and Shneiderman, Ben} } @article {16740, title = {ADMS: a testbed for incremental access methods}, journal = {IEEE Transactions on Knowledge and Data Engineering}, volume = {5}, year = {1993}, month = {1993/10//}, pages = {762 - 774}, abstract = {ADMS is an advanced database management system developed-to experiment with incremental access methods for large and distributed databases. It has been developed over the past eight years at the University of Maryland. The paper provides an overview of ADMS, and describes its capabilities and the performance attained by its incremental access methods. This paper also describes an enhanced client-server architecture that allows an incremental gateway access to multiple heterogeneous commercial database management systems}, keywords = {Add-drop multiplexers, ADMS, advanced database management system, client-server architecture, commercial database management systems, Computational modeling, Database systems, distributed databases, heterogeneous DBMS, incremental access methods, incremental gateway, Information retrieval, interoperability, join index, large databases, Navigation, network operating systems, Object oriented databases, Object oriented modeling, Query processing, System testing, very large databases, view index, Workstations}, isbn = {1041-4347}, doi = {10.1109/69.243508}, author = {Roussopoulos, Nick and Economou,N. and Stamenas,A.} } @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.} } @article {16440, title = {Coupling production systems and database systems: A homogeneous approach}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {5}, year = {1993}, month = {1993///}, pages = {240 - 256}, author = {Sellis,T. and Lin,C. C and Raschid, Louiqa} } @article {18743, title = {Development of machining alternatives, based on MRSEVs}, journal = {Computers in Engineering}, year = {1993}, month = {1993///}, pages = {47 - 47}, abstract = {One missing link between CAD and CAM is the lack ofa systematic methodology for generating and evaluating al- ternative ways to manufacture a proposed design. To ad- dress this problem, we are developing a systematic approach for generating and evaluating alternative ways to manufac- ture machined parts, in order to provide information to the designer about the manufacturability of the proposed de- sign, and information to the process engineer about how best to machine the part. This paper describes our overall approach, and how MRSEVs (Material Removal Shape El- ement Volumes, a STEP library of machining features) can be used to support it. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.37.6348\&rep=rep1\&type=pdf}, author = {Nau, Dana S. and Gupta,S.K. and Kramer,T. R. and Regli,W. C. and Zhang, G.} } @article {16471, title = {An Experimental Study of Three Dataflow Paradigms in Multithreaded Database Transitive Closure Algorithms on Shared Memory Multiprocessors}, journal = {Journal of Parallel and Distributed Computing}, volume = {18}, year = {1993}, month = {1993/07//}, pages = {371 - 389}, abstract = {This paper describes an experimental study of three dataflow paradigms, namely, no dataflow, pipelined dataflow, and network dataflow, in multithreaded database transitive closure algorithms on shared memory multiprocessors. This study shows that dataflow paradigm directly influences performance parameters such as the amount of interthread communication, how data are partitioned among the threads, whether access to each page of data is exclusive or shared, whether locks are needed for concurrency control, and how calculation termination is detected. The algorithm designed with no dataflow outperforms the algorithms with dataflow. Approximately linear speedup is achieved by the no dataflow algorithm with sufficient workload and primary memory. An exclusive access working set model and a shared access working set model describe the interactions between two or more threads' working sets when access to each page of data is exclusive or shared among the threads, respectively. These models are experimentally verified.}, isbn = {0743-7315}, doi = {10.1006/jpdc.1993.1071}, url = {http://www.sciencedirect.com/science/article/pii/S0743731583710713}, author = {Youngmyers,H. and Raschid, Louiqa} } @book {13793, title = {Information mediation techniques for problem solving with multiple knowledge servers}, year = {1993}, month = {1993///}, publisher = {University of Maryland}, organization = {University of Maryland}, abstract = {This paper describes two important information mediation prob-lems that arise when multiple knowledge and data servers are accessed for problem solving. The rst problem is building an intelligent interface be- tween a knowledge server (KS) and a processor (KP) so that queries may be answered intelligently and completely. The second problem is to provide interoperability among multiple KP/KS pairs so that a query may be an- swered using information from multiple sources. We present example scenar- ios which highlight each of these problems and then outline techniques and tasks that are applied towards obtaining a solution. These techniques draw upon disciplines such as query and transaction processing with knowledge bases and machine understanding and translation of natural language. The techniques for solving the information mediation problems described involve parameterized canonical representations (CR) for the KP/KS pairs. The CR will represent possible mappings between a query and the knowledge model and will be used during query transformation to produce a query which will provide more complete and correct answers. Parameterization will help in merging CRs to support interoperability for distributed problem solving. }, author = {Dorr, Bonnie J and Raschid, Louiqa} } @conference {13800, title = {Interoperable query processing with multiple heterogeneous knowledge servers}, booktitle = {Proceedings of the second international conference on Information and knowledge management}, series = {CIKM {\textquoteright}93}, year = {1993}, month = {1993///}, pages = {461 - 470}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-626-3}, doi = {10.1145/170088.170395}, url = {http://doi.acm.org/10.1145/170088.170395}, author = {Raschid, Louiqa and Chang,Yahui and Dorr, Bonnie J} } @conference {13677, title = {The Interpretation and Recognition of Interfering Strokes}, booktitle = {IWFHR}, year = {1993}, month = {1993///}, pages = {41 - 50}, author = {David Doermann and Rosenfeld, A.} } @article {17267, title = {Investigating touchscreen typing: the effect of keyboard size on typing speed}, journal = {Behaviour \& Information Technology}, volume = {12}, year = {1993}, month = {1993///}, pages = {17 - 22}, abstract = {Abstract Two studies investigated the effect keyboard size has on typing speed and error rates for touchscreen keyboards using the lift-off strategy. A cursor appeared when users touched the screen and a key was selected when they lifted their finger from the screen. Four keyboard sizes were investigated ranging from 24.6 cm to 6.8 cm wide. Results indicate that novices can type approximately 10 words per minute (WPM) on the smallest keyboard and 20 WPM on the largest. Experienced users improved to 21 WPM on the smallest keyboard and 32 WPM on the largest. These results indicate that, although slower, small touchscreen keyboards can be used for limited data entry when the presence of a regular keyboard is not practical. Applications include portable pocket-sized or palmtop computers, messaging systems, and personal information resources. Results also suggest the increased importance of experience on these smaller keyboards. Research directions are suggested.Abstract Two studies investigated the effect keyboard size has on typing speed and error rates for touchscreen keyboards using the lift-off strategy. A cursor appeared when users touched the screen and a key was selected when they lifted their finger from the screen. Four keyboard sizes were investigated ranging from 24.6 cm to 6.8 cm wide. Results indicate that novices can type approximately 10 words per minute (WPM) on the smallest keyboard and 20 WPM on the largest. Experienced users improved to 21 WPM on the smallest keyboard and 32 WPM on the largest. These results indicate that, although slower, small touchscreen keyboards can be used for limited data entry when the presence of a regular keyboard is not practical. Applications include portable pocket-sized or palmtop computers, messaging systems, and personal information resources. Results also suggest the increased importance of experience on these smaller keyboards. Research directions are suggested. }, isbn = {0144-929X}, doi = {10.1080/01449299308924362}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449299308924362}, author = {Sears,Andrew and REVIS,DOREEN and SWATSKI,JANET and CRITTENDEN,ROB and Shneiderman, Ben} } @article {16571, title = {Learning competition and cooperation}, journal = {Neural computation}, volume = {5}, year = {1993}, month = {1993///}, pages = {242 - 259}, author = {Cho,S. and Reggia, James A.} } @article {16556, title = {Local conditions for phase transitions in neural networks with variable connection strengths}, journal = {Neural networks}, volume = {6}, year = {1993}, month = {1993///}, pages = {667 - 676}, author = {McFadden,F. E and Peng,Y. and Reggia, James A.} } @article {13589, title = {Logo Recognition}, volume = {CS-TR-3145}, year = {1993}, month = {1993///}, institution = {University of Maryland, College Park}, address = {College Park, MD}, author = {David Doermann and Rivlin,E. and Weiss, I.} } @conference {13590, title = {Logo Recognition using Geomentric Invariants}, booktitle = {ICDAR}, year = {1993}, month = {1993///}, pages = {894 - 897}, author = {David Doermann and Rivlin,E. and Weiss, I.} } @article {16735, title = {MANDATE: managing networks using database technology}, journal = {IEEE Journal on Selected Areas in Communications}, volume = {11}, year = {1993}, month = {1993/12//}, pages = {1360 - 1372}, abstract = {There has been a growing demand for the development of tools to manage enterprise communication networks. A management information database is the heart of a network management system-it provides the interface between all functions of the network management system and, therefore, has to provide sophisticated functionality allied with high performance. The authors introduce the design of MANDATE (MAnaging Networks using DAtabase TEchnology), a proposed database system for effectively supporting the management of large enterprise networks. The MANDATE design makes a conscious attempt to take advantage of the special characteristics of network data and transactions, and of advances in database technology, to efficiently derive some of the required management functionality}, keywords = {Communication networks, database management systems, enterprise communication networks, Heart, Information management, interface, internetworking, Local area networks, management functionality, management information database, managing networks using database technology, MANDATE, Manufacturing, network operating systems, open systems, Optical fiber cables, Research and development management, Technology management, telecommunication network management, Transaction databases, wide area networks}, isbn = {0733-8716}, doi = {10.1109/49.257929}, author = {Haritsa,J. R and Ball,M. O and Roussopoulos, Nick and Datta,A. and Baras,J. S} } @article {16541, title = {Multiple disorder diagnosis with adaptive competitive neural networks}, journal = {Artificial intelligence in medicine}, volume = {5}, year = {1993}, month = {1993///}, pages = {469 - 487}, author = {Cho,S. and Reggia, James A.} } @article {16644, title = {Neural computation in medicine}, journal = {Artificial Intelligence in Medicine}, volume = {5}, year = {1993}, month = {1993///}, pages = {143 - 157}, author = {Reggia, James A.} } @article {15000, title = {Optimal algorithms on the pipelined hypercube and related networks}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {4}, year = {1993}, month = {1993/05//}, pages = {582 - 591}, abstract = {Parallel algorithms for several important combinatorial problems such as the all nearest smaller values problem, triangulating a monotone polygon, and line packing are presented. These algorithms achieve linear speedups on the pipelined hypercube, and provably optimal speedups on the shuffle-exchange and the cube-connected-cycles for any number p of processors satisfying 1 les;p les;n/((log3n)(loglog n)2), where n is the input size. The lower bound results are established under no restriction on how the input is mapped into the local memories of the different processors}, keywords = {algorithms;pipeline, algorithms;pipelined, combinatorial, geometry;parallel, hypercube;shuffle-exchange;combinatorial, mathematics;computational, packing;monotone, polygon;parallel, problems;cube-connected-cycles;line, processing;}, isbn = {1045-9219}, doi = {10.1109/71.224210}, author = {JaJa, Joseph F. and Ryu,K. W.} } @article {16795, title = {Performance comparison of three modern DBMS architectures}, journal = {IEEE Transactions on Software Engineering}, volume = {19}, year = {1993}, month = {1993/02//}, pages = {120 - 138}, abstract = {The introduction of powerful workstations connected through local area networks (LANs) inspired new database management system (DBMS) architectures that offer high performance characteristics. The authors examine three such software architecture configurations: client-server (CS), the RAD-UNIFY type of DBMS (RU), and enhanced client-server (ECS). Their specific functional components and design rationales are discussed. Three simulation models are used to provide a performance comparison under different job workloads. Simulation results show that the RU almost always performs slightly better than the CS, especially under light workloads, and that ECS offers significant performance improvement over both CS and RU. Under reasonable update rates, the ECS over CS (or RU) performance ratio is almost proportional to the number of participating clients (for less than 32 clients). The authors also examine the impact of certain key parameters on the performance of the three architectures and show that ECS is more scalable that the other two}, keywords = {client-server, Computational modeling, Computer architecture, database management systems, DBMS architectures, design rationales, functional components, Indexes, Local area networks, Military computing, Packaging, Performance analysis, performance evaluation, RAD-UNIFY type, simulation models, simulation results, Software architecture, software architecture configurations, software engineering, Throughput, Workstations}, isbn = {0098-5589}, doi = {10.1109/32.214830}, author = {Delis,A. and Roussopoulos, Nick} } @conference {13678, title = {The processing of form documents}, booktitle = {Document Analysis and Recognition, 1993., Proceedings of the Second International Conference on}, year = {1993}, month = {1993/10//}, pages = {497 - 501}, abstract = {An overview of an approach to the generic modeling and processing of known forms is presented. The system provides a methodology by which models are generated from regions in the document based on their usage. Automatic extraction of an optimal set of features to be used for registration is proposed, and it is shown how specialized detectors can be designed for each feature based on their position, orientation and width properties. Registration of the form with the model is accomplished using probing to establish correspondence. Form components which are corrupted by markings are detected and isolated, the intersections are interpreted and the properties of the non-form markings are used to reconstruct the strokes through the intersections. The feasibility of these ideas is demonstrated through an implementation of key components of the system}, keywords = {AUTOMATIC, business, detectors;, document, documents;, extraction;, feature, form, forms;, generation;, generic, handling;, known, markings;, model, modeling;, non-form, optimal, properties;, reconstruction;, set;, specialized, stroke, width}, doi = {10.1109/ICDAR.1993.395687}, author = {David Doermann and Rosenfeld, A.} } @article {13844, title = {Query mapping and transformation techniques for problem solving with multiple knowledge servers}, journal = {Proceedings of the Second International Conference on Information and Knowledge Management (CIKM-93)}, year = {1993}, month = {1993///}, abstract = {This paper describes a technique for infor-mation mediation when multiple heterogeneous knowl- edge and data servers are to be accessed during query processing. One problem is building an intelligent in- terface between each knowledge server (KS) and its processor (KP); and the second is to provide interoper- ability among multiple KP/KS so that a query may be answered using information from multiple sources. We present example scenarios which highlight these prob- lems and then outline query mapping and transforma- tion techniques that are applicable. The techniques for solving the interoperability problems involve rep- resentations in some canonical form. This includes a canonical representation (CR) corresponding to each KP/KS pair and a merged CR (MCR) to represent the mapping among the CRs. The MCR and CRs include relevant information obtained from a source query, and heterogeneous mapping (het-map) information, for all possible mappings among the multiple servers. The knowledge in the canonical form must be represented so that it can be easily accessed during query transfor- mation. We use an example of translating queries from an object schema to a relational schema to illustrate typical knowledge that must be represented in some canonical form. We use a high level logical language, F-logic, to represent the heterogeneous mapping (het- map) and query transformation information as a set of declarative rules, in the canonical form. }, author = {Raschid, Louiqa and Chang,Y. and Dorr, Bonnie J} } @conference {16695, title = {Semantic classes and syntactic ambiguity}, booktitle = {Proceedings of the workshop on Human Language Technology}, year = {1993}, month = {1993///}, pages = {278 - 283}, author = {Resnik, Philip} } @article {16513, title = {Simple systems that exhibit template-directed replication}, journal = {Science}, volume = {259}, year = {1993}, month = {1993///}, pages = {1282 - 1287}, author = {Reggia, James A. and Armentrout,S. L and Chou,H. H. and Peng,Y.} } @conference {16710, title = {Structural ambiguity and conceptual relations}, booktitle = {Proceedings of the Workshop on Very Large Corpora: Academic and Industrial Perspectives}, year = {1993}, month = {1993///}, pages = {58 - 64}, author = {Resnik, Philip and Hearst,M.} } @conference {16491, title = {Transitive closure: an experimental case study of three multithreaded database algorithms on a shared memory multiprocessor}, booktitle = {Parallel and Distributed Information Systems, 1993., Proceedings of the Second International Conference on}, year = {1993}, month = {1993///}, pages = {255 - 259}, author = {Young-Myers,H. and Raschid, Louiqa} } @article {16782, title = {Using differential technlques to efficiently support transaction time}, journal = {The VLDB JournalVLDB Journal}, volume = {2}, year = {1993}, month = {1993/01//}, pages = {75 - 111}, isbn = {1066-8888}, doi = {10.1007/BF01231799}, url = {http://dl.acm.org/citation.cfm?id=615162}, author = {Jensen,Christian S. and Mark,Leo and Roussopoulos, Nick and Sells,Timos} } @conference {18779, title = {Using MRSEVs to develop machining alternatives}, year = {1993}, month = {1993///}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.47.4870\&rep=rep1\&type=pdf}, author = {Nau, Dana S. and Gupta,S.K. and Kramer,T. R. and Regli,W. C. and Zhang, G.} } @article {14199, title = {Behavioral Visual Motion Analysis,"}, journal = {Proceedings, DARPA Image Understanding Workshop}, year = {1992}, month = {1992///}, pages = {521 - 541}, author = {Aloimonos, J. and Duri{\c c},Z. and Ferm{\"u}ller, Cornelia and Huang, L. and Rivlin,E. and Sharma, R.} } @conference {16700, title = {A class-based approach to lexical discovery}, booktitle = {Proceedings of the 30th annual meeting on Association for Computational Linguistics}, year = {1992}, month = {1992///}, pages = {327 - 329}, author = {Resnik, Philip} } @article {16567, title = {A competitive distribution theory of neocortical dynamics}, journal = {Neural Computation}, volume = {4}, year = {1992}, month = {1992///}, pages = {287 - 317}, author = {Reggia, James A. and D{\textquoteright}Autrechy,C. L and Sutton III,G. G. and Weinrich,M.} } @article {16596, title = {A connectionist approach to vertex covering problems}, journal = {Int{\textquoteright}l J. Neural Systems}, volume = {3}, year = {1992}, month = {1992///}, pages = {43 - 56}, author = {Peng,Y. and Reggia, James A. and Li,T.} } @article {12987, title = {copia-like retrotransposons are ubiquitous among plants}, journal = {Proc Natl Acad Sci USA}, volume = {89}, year = {1992}, month = {1992/08//}, pages = {7124 - 7128}, abstract = {Transposable genetic elements are assumed to be a feature of all eukaryotic genomes. Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny. We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences. copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri. The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms. DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes.}, author = {Voytas,D. F and Cummings, Michael P. and Koniczny,A. and Ausubel,F. M and Rodermel,S. R} } @conference {16502, title = {Experiments on the concurrent rule execution in database systems}, booktitle = {Tools with Artificial Intelligence, 1992. TAI{\textquoteright}92, Proceedings., Fourth International Conference on}, year = {1992}, month = {1992///}, pages = {405 - 412}, author = {Delis,A. and Raschid, Louiqa and Sellis,T.} } @article {16727, title = {Incrementally maintained network{\textrightarrow}relational database mapping}, journal = {Software: Practice and Experience}, volume = {22}, year = {1992}, month = {1992/12/01/}, pages = {1099 - 1131}, abstract = {An incrementally maintained mapping from a network to a relational database is presented. This mapping may be established either to support the efficient retrieval of data from a network database through a relational interface, or as the first step in a gradual conversion of data and applications from a network to a relational database system. After the mapping has been established, the only data mapped from the network to the relational database are the increments resulting from updates on the network database. The mapping is therefore an efficient alternative to mappings that repeatedly map the results of retrievals through the relational interface from the network database to the relational database. This is in particular the case when the two databases reside on different hosts. Applications on the network database may, under certain restrictions, gradually be moved to the relational database, while the mapping incrementally maintains the relational database for the applications that remain on the network database.}, keywords = {Database conversion, Database gateway, Database mapping, Incremental database mapping}, isbn = {1097-024X}, doi = {10.1002/spe.4380221205}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.4380221205/abstract}, author = {Mark,Leo and Roussopoulos, Nick and Newsome,Tina and Laohapipattana,Piriya} } @article {13576, title = {Instrument Grasp: AModel and its Effects on Handwritten Strokes}, volume = {CAR-TR-614}, year = {1992}, month = {1992///}, institution = {University of Maryland, College Park}, author = {David Doermann and Varma,V. and Rosenfeld, A.} } @conference {16654, title = {Lateral cortical inhibition without lateral inhibitory connections}, booktitle = {Neural Networks, 1992. IJCNN., International Joint Conference on}, volume = {3}, year = {1992}, month = {1992/06//}, pages = {415 -420 vol.3 - 415 -420 vol.3}, abstract = {The authors consider how a set of neurons forming a cortical column, none of which individually can competitively distribute its activity, can function collectively to produce competitive distribution of activation. To address this issue, they describe a model cortical column composed of three populations of excitatory neurons that collectively distribute their activity competitively. The idea of competitive distribution and the neural circuitry that could bring it about are described. Computer simulation results, implications, and testable predictions of the theory are presented}, keywords = {brain models, competitive distribution of activation, digital simulation, excitatory neurons, lateral cortical inhibition, neural circuitry, neurophysiology, physiological models}, doi = {10.1109/IJCNN.1992.227139}, author = {Reggia, James A. and Sutton,G. and D{\textquoteright}Autrechy,C. L and Weinrich,M.} } @conference {16588, title = {Learning visual coordinate transformations with competition}, booktitle = {Neural Networks, 1992. IJCNN., International Joint Conference on}, volume = {4}, year = {1992}, month = {1992///}, pages = {49 - 54}, author = {Cho,S. and Reggia, James A.} } @conference {16716, title = {Left-corner parsing and psychological plausibility}, booktitle = {Proceedings of the 14th conference on Computational linguistics-Volume 1}, year = {1992}, month = {1992///}, pages = {191 - 197}, author = {Resnik, Philip} } @article {14983, title = {Load balancing and routing on the hypercube and related networks}, journal = {Journal of Parallel and Distributed Computing}, volume = {14}, year = {1992}, month = {1992/04//}, pages = {431 - 435}, abstract = {Several results related to the load balancing problem on the hypercube, the shuffle-exchange, the cube-connected cycles, and the butterfly are shown. Implications of these results for routing algorithms are also discussed. Our results include the following: {\textbullet}⊎ Efficient load balancing algorithms are found for the hypercube, the shuffle-exchange, the cube-connected cycles, and the butterfly. {\textbullet} ⊎ Load balancing is shown to require more time on a p-processor shuffle-exchange, cube-connected cycle or butterfly than on a p-processor weak hypercube. {\textbullet} ⊎ Routing n packets on a p-processor hypercube can be done optimally whenever n = p1+1/k, for any fixed k \> 0. }, isbn = {0743-7315}, doi = {10.1016/0743-7315(92)90081-W}, url = {http://www.sciencedirect.com/science/article/pii/074373159290081W}, author = {JaJa, Joseph F. and Ryu,Kwan Woo} } @article {16441, title = {A parallel pipelined strategy for evaluating linear recursive predicates in a multiprocessor environment.}, journal = {J. Parallel Distrib. Comput.}, volume = {14}, year = {1992}, month = {1992///}, pages = {146 - 162}, author = {Raschid, Louiqa and Su,S. Y.W} } @conference {16660, title = {Probabilistic tree-adjoining grammar as a framework for statistical natural language processing}, booktitle = {Proceedings of the 14th conference on Computational linguistics-Volume 2}, year = {1992}, month = {1992///}, pages = {418 - 424}, author = {Resnik, Philip} } @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} } @conference {13629, title = {Recovery of temporal information from static images of handwriting}, booktitle = {Proceedings in the IEEE CVPR}, year = {1992}, month = {1992/06//}, pages = {162 - 168}, abstract = {The problem of off-line handwritten character recognition has eluded a satisfactory solution for several decades. Researchers working in the area of on-line recognition have had greater success, but the possibility of extracting on-line information from static images has not been fully explored. The experience of forensic document examiners assures us that in many cases, such information can be successfully recovered.We outline the design of a system for the recovery of temporal information from static handwritten images. We provide a taxonomy of local, regional and global temporal clues which are often found in hand-written samples, and describe methods for recovering these clues from the image. We show how this system can benefit from obtaining a comprehensive understanding of the handwriting signal and a detailed analysis of stroke and sub-stroke properties. We suggest that the recovery task requires that we break away from traditional thresholding and thinning techniques, and we provide a framework for such analysis. We demonstrate how isolated temporal clues can reliably be extracted from this framework and propose a control structure for integrating the partial information. We show how many seemingly ambiguous situations can be resolved by the derived clues and our knowledge of the writing process, and provide several examples to illustrate our approach. The support of this research by the Ricoh Corporation is gratefully acknowledged. }, author = {David Doermann and Rosenfeld, A.} } @conference {16481, title = {Semantics for Rule-based Programs that Express Non-determinism, Causality and Exception Handling Behavior}, booktitle = {Workshop on Deductive Databases, JICSLP}, year = {1992}, month = {1992///}, pages = {163 - 174}, author = {Raschid, Louiqa} } @article {16650, title = {Simple systems exhibiting self-directed replication: annex of transition functions and software documentation}, year = {1992}, month = {1992///}, institution = {University of Maryland at College Park}, address = {College Park, MD, USA}, author = {Reggia, James A. and Chou,Hui-Hsien and Armentrout,Steven L. and Peng,Yun} } @article {17971, title = {Six Generations of Building Walkthrough: Final Technical Report to the National Science Foundation}, year = {1992}, month = {1992///}, institution = {University of North Carolina at Chapel Hill}, address = {Chapel Hill, NC, USA}, author = {Brooks,Frederick P. and Airey,John and Alspaugh,John and Bell,Andrew and Brown,Randolph and Hill,Curtis and Nimscheck,Uwe and Rheingans,Penny and Rohlf,John and Smith,Dana and Turner,Douglass and Varshney, Amitabh and Wang,Yulan and Weber,Hans and Yuan,Xialin} } @article {16545, title = {Software approaches to segmentation analysis}, journal = {Computer Science Technical Report Series; Vol. CS-TR-2991}, year = {1992}, month = {1992///}, pages = {24 - 24}, author = {D{\textquoteright}Autrechy,C. L and Reggia, James A. and Berndt,R. S} } @article {17382, title = {Structural analysis of hypertexts: identifying hierarchies and useful metrics}, journal = {ACM Transactions on Information Systems}, volume = {10}, year = {1992}, month = {1992/04//}, pages = {142 - 180}, abstract = {Hypertext users often suffer from the {\textquotedblleft}lost in hyperspace{\textquotedblright} problem: disorientation from too many jumps while traversing a complex network. One solution to this problem is improved authoring to create more comprehensible structures. This paper proposes several authoring tools, based on hypertext structure analysis.In many hypertext systems authors are encouraged to create hierarchical structures, but when writing, the hierarchy is lost because of the inclusion of cross-reference links. The first part of this paper looks at ways of recovering lost hierarchies and finding new ones, offering authors different views of the same hypertext. The second part helps authors by identifying properties of the hypertext document. Multiple metrics are developed including compactness and stratum. Compactness indicates the intrinsic connectedness of the hypertext, and stratum reveals to what degree the hypertext is organized so that some nodes must be read before others. Several existing hypertexts are used to illustrate the benefits of each technique. The collection of techniques provides a multifaceted view of the hypertext, which should allow authors to reduce undesired structural complexity and create documents that readers can traverse more easily. }, keywords = {graph theory, hierarchies, hypertext, metrics, structural analysis}, isbn = {1046-8188}, doi = {10.1145/146802.146826}, url = {http://doi.acm.org/10.1145/146802.146826}, author = {Botafogo,Rodrigo A. and Rivlin,Ehud and Shneiderman, Ben} } @conference {13660, title = {Temporal clues in handwriting}, booktitle = {Pattern Recognition, 1992. Vol.II. Conference B: Pattern Recognition Methodology and Systems, Proceedings., 11th IAPR International Conference on}, year = {1992}, month = {1992/09/03/aug}, pages = {317 - 320}, abstract = {Handwritten character recognition is typically classified as online or offline depending on the nature of the input data. Online data consists of a temporal sequence of instrument positions while offline data is in the form of a 2D image of the writing sample. Online recognition techniques have been relatively successful but have the disadvantage of requiring the data to be gathered during the writing process. This paper presents work on the extraction of temporal information from static images of handwriting and its implications for character recognition}, keywords = {character, extraction;, feature, handwriting, information, offline, online, recognition;, techniques;, temporal}, doi = {10.1109/ICPR.1992.201781}, author = {David Doermann and Rosenfeld, A.} } @conference {16686, title = {Wordnet and distributional analysis: A class-based approach to lexical discovery}, booktitle = {AAAI workshop on statistically-based natural language processing techniques}, year = {1992}, month = {1992///}, pages = {56 - 64}, author = {Resnik, Philip} } @conference {16781, title = {An algebra and calculus for relational multidatabase systems}, booktitle = {, First International Workshop on Interoperability in Multidatabase Systems, 1991. IMS {\textquoteright}91. Proceedings}, year = {1991}, month = {1991/04//}, pages = {118 - 124}, publisher = {IEEE}, organization = {IEEE}, abstract = {With the existence of many autonomous databases widely accessible through computer networks, users will require the capability to jointly manipulate data in different databases. A multidatabase system provides such a capability through a multidatabase manipulation language. The authors propose a theoretical foundation for such languages by presenting a multirelational algebra and calculus based on the relational algebra and calculus. The proposal is illustrated by various queries on an example multidatabase}, keywords = {Algebra, autonomous databases, Calculus, Computer networks, Computer science, Data models, Data structures, Database systems, database theory, distributed databases, Military computing, multidatabase manipulation language, multidatabase system, multirelational algebra, query languages, relational algebra, Relational databases, Spatial databases, theoretical foundation}, isbn = {0-8186-2205-9}, doi = {10.1109/IMS.1991.153694}, author = {Grant,J. and Litwin,W. and Roussopoulos, Nick and Sellis,T.} } @article {16622, title = {Competitive activation mechanisms in connectionist models}, journal = {Advances in control networks and large-scale parallel distributed processing models}, volume = {1}, year = {1991}, month = {1991///}, pages = {119 - 119}, author = {Reggia, James A. and Sutton,G. and Cho,S.} } @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 {17634, title = {On finding the minimum bandwidth of interval graphs}, journal = {Information and Computation}, volume = {95}, year = {1991}, month = {1991/12//}, pages = {218 - 224}, abstract = {Let G = (V, E) be an interval graph, with |V| = n, and |E| = m. An O(n2 log n) algorithm was proposed in Kratsch (Inform Comput. 74, 140{\textendash}158 (1987)) to find the bandwidth of G. We show that this algorithm is wrong, and provide a corrected version of the same. Also, it was observed in [4] that the bandwidth of a proper interval graph can be computed in O(n log n + m) time. We show how this idea can be modified slightly to yield an O(n = m) algorithm.}, isbn = {0890-5401}, doi = {10.1016/0890-5401(91)90045-4}, url = {http://www.sciencedirect.com/science/article/pii/0890540191900454}, author = {Mahesh,R. and Rangan,C.Pandu and Srinivasan, Aravind} } @article {16764, title = {Incremental implementation model for relational databases with transaction time}, journal = {IEEE Transactions on Knowledge and Data Engineering}, volume = {3}, year = {1991}, month = {1991/12//}, pages = {461 - 473}, abstract = {An implementation model for the standard relational data model extended with transaction time is presented. The implementation model integrates techniques of view materialization, differential computation, and deferred update into a coherent whole. It is capable of storing any view (reflecting past or present states) and subsequently using stored views as outsets for incremental and decremental computations of requested views, making it more flexible than previously proposed partitioned storage models. The working and the expressiveness of the model are demonstrated by sample queries that show how historical data are retrieved}, keywords = {Computational modeling, Computer science, Data models, data retrieval, Database languages, Database systems, database theory, decremental computations, deferred update, Degradation, differential computation, historical data, History, incremental computations, Information retrieval, partitioned storage models, queries, relational data model, Relational databases, stored views, Transaction databases, transaction time, view materialization}, isbn = {1041-4347}, doi = {10.1109/69.109107}, author = {Jensen,C. S and Mark,L. and Roussopoulos, Nick} } @article {16749, title = {Modern client-server DBMS architectures}, journal = {ACM SIGMOD RecordSIGMOD Rec.}, volume = {20}, year = {1991}, month = {1991/09//}, pages = {52 - 61}, isbn = {01635808}, doi = {10.1145/126482.126489}, url = {http://dl.acm.org/citation.cfm?doid=126482.126489}, author = {Roussopoulos, Nick and Delis,Alexis} } @article {16768, title = {A pipeline N-way join algorithm based on the 2-way semijoin program}, journal = {IEEE Transactions on Knowledge and Data Engineering}, volume = {3}, year = {1991}, month = {1991/12//}, pages = {486 - 495}, abstract = {The semijoin has been used as an effective operator in reducing data transmission and processing over a network that allows forward size reduction of relations and intermediate results generated during the processing of a distributed query. The authors propose a relational operator, two-way semijoin, which enhanced the semijoin with backward size reduction capability for more cost-effective query processing. A pipeline N-way join algorithm for joining the reduced relations residing on N sites is introduced. The main advantage of this algorithm is that it eliminates the need for transferring and storing intermediate results among the sites. A set of experiments showing that the proposed algorithm outperforms all known conventional join algorithms that generate intermediate results is included}, keywords = {2-way semijoin program, backward size reduction, Bandwidth, Computer networks, Costs, Data communication, data transmission, Database systems, database theory, Delay, distributed databases, distributed query, forward size reduction, intermediate results, Local area networks, network, Parallel algorithms, pipeline N-way join algorithm, pipeline processing, Pipelines, programming theory, Query processing, Relational databases, relational operator, SITES, Workstations}, isbn = {1041-4347}, doi = {10.1109/69.109109}, author = {Roussopoulos, Nick and Kang,H.} } @article {15575, title = {Pyramid computation of neighbor distance statistics in dot patterns}, journal = {CVGIP: Graphical Models and Image Processing}, volume = {53}, year = {1991}, month = {1991/07//}, pages = {373 - 381}, abstract = {This paper describes an algorithm for computing statistics of Voronoi neighbor distances in a dot pattern, using a cellular pyramid computer, in a logarithmic number of computational steps. Given a set of dots in a square region of the digital plane, the algorithm determines with high probability the Voronoi neighbors of the dots in the interior of the region and then computes statistics of the neighbor distances. An algorithm of this type may account for the ability of humans to perceive at a glance whether the dots in a pattern are randomly or regularly spaced, i.e., their neighbor distances have high or low variance.}, isbn = {1049-9652}, doi = {10.1016/1049-9652(91)90040-Q}, url = {http://www.sciencedirect.com/science/article/pii/104996529190040Q}, author = {Banerjee,Saibal and Mount, Dave and Rosenfeld,Azriel} } @article {16514, title = {Recent applications of competitive activation mechanisms}, journal = {Neural Networks: Advances and Applications}, year = {1991}, month = {1991///}, pages = {33 - 62}, author = {Reggia, James A. and Peng,Y. and Bourret,P.} } @article {13630, title = {Recovery of Temporal Information from Static Images of Handwriting}, volume = {CAR-TR-595}, year = {1991}, month = {1991///}, institution = {Center for Automation Research, University of Maryland}, address = {College Park, Maryland}, abstract = {The problem of off-line handwritten character recognition has eluded a satisfactory solution for several decades. Researchers working in the area of on-line recognition have had greater success, but the possibility of extracting on-line information from static images has not been fully explored. The experience of forensic document examiners assures us that in many cases, such information can be successfully recovered.We outline the design of a system for the recovery of temporal information from static handwritten images. We provide a taxonomy of local, regional and global temporal clues which are often found in hand-written samples, and describe methods for recovering these clues from the image. We show how this system can benefit from obtaining a comprehensive understanding of the handwriting signal and a detailed analysis of stroke and sub-stroke properties. We suggest that the recovery task requires that we break away from traditional thresholding and thinning techniques, and we provide a framework for such analysis. We demonstrate how isolated temporal clues can reliably be extracted from this framework and propose a control structure for integrating the partial information. We show how many seemingly ambiguous situations can be resolved by the derived clues and our knowledge of the writing process, and provide several examples to illustrate our approach. The support of this research by the Ricoh Corporation is gratefully acknowledged. }, author = {David Doermann and Rosenfeld, A.} } @conference {16501, title = {Semantics for update rule programs and implementation in a relational database management system}, booktitle = {ACM Transactions on Database Systems}, year = {1991}, month = {1991///}, author = {Raschid, Louiqa and Lobo,J.} } @article {16743, title = {Trie hashing with controlled load}, journal = {IEEE Transactions on Software Engineering}, volume = {17}, year = {1991}, month = {1991/07//}, pages = {678 - 691}, abstract = {Trie hashing (TH), a primary key access method for storing and accessing records of dynamic files, is discussed. The key address is computed through a trie. A key search usually requires only one disk access when the trie is in core and two disk accesses for very large files when the trie must be on disk. A refinement to trie hashing, trie hashing with controlled load (THCL), is presented. It is designed to control the load factor of a TH file as tightly as that of a B-tree file, allows high load factor of up to 100\% for ordered insertions, and increases the load factor for random insertions from 70\% to over 85\%. It is shown that these properties make trie hashing preferable to a B-tree}, keywords = {B-tree file, Computer science, controlled load, Databases, disk access, dynamic files, file organisation, high load factor, information retrieval systems, key search, load factor, Military computing, ordered insertions, Predictive models, primary key access method, Protocols, random insertions, TH file, THCL, Tree data structures, trees (mathematics), trie hashing}, isbn = {0098-5589}, doi = {10.1109/32.83904}, author = {Litwin,W. A and Roussopoulos, Nick and Levy,G. and Hong,W.} } @book {11977, title = {Visual recovery}, year = {1991}, month = {1991///}, publisher = {University of Maryland, Center for Automation Research, Computer Vision Laboratory}, organization = {University of Maryland, Center for Automation Research, Computer Vision Laboratory}, author = {Aloimonos, J. and Rosenfeld, A.} } @book {16577, title = {Abductive Inference Models for Diagnostic Problem-Solving}, year = {1990}, month = {1990///}, publisher = {Springer-Verlag, New York}, organization = {Springer-Verlag, New York}, author = {Yun,P. and Reggia, James A.} } @conference {16568, title = {Competitive learning using competitive activation rules}, booktitle = {Neural Networks, 1990., 1990 IJCNN International Joint Conference on}, year = {1990}, month = {1990///}, pages = {285 - 291}, author = {Sutton III,G. G. and Reggia, James A. and Maisog,J. M} } @article {16639, title = {Connectionist models and information retrieval}, journal = {Annual review of information science and technology}, volume = {25}, year = {1990}, month = {1990///}, pages = {209 - 262}, author = {Doszkocs,T. E and Reggia, James A. and others} } @conference {16542, title = {Diagnostic reasoning at multiple levels of abstraction}, booktitle = {AI Systems in Government Conference, 1990. Proceedings., Fifth Annual}, year = {1990}, month = {1990///}, pages = {168 - 175}, author = {Chu,B. T.B and Reggia, James A.} } @article {14957, title = {Efficient algorithms for list ranking and for solving graph problems on the hypercube}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {1}, year = {1990}, month = {1990/01//}, pages = {83 - 90}, abstract = {A hypercube algorithm to solve the list ranking problem is presented. Let n be the length of the list, and let p be the number of processors of the hypercube. The algorithm described runs in time O(n/p) when n= Omega;(p 1+ epsi;) for any constant epsi; gt;0, and in time O(n log n/p+log3 p) otherwise. This clearly attains a linear speedup when n= Omega;(p 1+ epsi;). Efficient balancing and routing schemes had to be used to achieve the linear speedup. The authors use these techniques to obtain efficient hypercube algorithms for many basic graph problems such as tree expression evaluation, connected and biconnected components, ear decomposition, and st-numbering. These problems are also addressed in the restricted model of one-port communication}, keywords = {algorithm;hypercube, algorithms;graph, algorithms;linear, algorithms;sorting;, balancing;one-port, basic, communication;sorting;st-numbering;tree, complexity;graph, components;ear, decomposition;graph, evaluation;computational, Expression, graph, problems;biconnected, problems;hypercube, ranking;load, speedup;list, theory;parallel}, isbn = {1045-9219}, doi = {10.1109/71.80127}, author = {Ryu,K. W. and JaJa, Joseph F.} } @article {16805, title = {Efficient compilation of large rule bases using logical access paths}, journal = {Information Systems}, volume = {15}, year = {1990}, month = {1990///}, pages = {73 - 84}, abstract = {This paper presents an efficient way to compile and store large deductive databases. Deductive rules are modeled through logical access paths and then integrated into a global structure, the Rule-base Access Path Schema (RAP Schema). The RAP Schema stores information on the interrelationships that exist among the computations required for rule executions. Ground data as well as data derived through some rule executions and cached for later reuse are also modeled in the RAP Schema. Some of the advantages of using this rule base organization scheme include the automatic detection of shared computations, the inclusion of cached results of rule executions and query results in the knowledge base. The details of the compilation and query processing phases are the focus of the paper.}, isbn = {0306-4379}, doi = {16/0306-4379(90)90017-J}, url = {http://www.sciencedirect.com/science/article/pii/030643799090017J}, author = {Sellis,Timos K. and Roussopoulos, Nick and Ng,Raymond T.} } @book {16563, title = {Inductive inference model for diagnostic problem-solving}, year = {1990}, month = {1990///}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, author = {Peng,Y. and Reggia, James A.} } @article {16730, title = {Information interchange between self-describing databases}, journal = {Information Systems}, volume = {15}, year = {1990}, month = {1990///}, pages = {393 - 400}, abstract = {Within the framework of a self-describing database system we describe a set of data management tools and a data dictionary supporting information interchange. The concepts are based on our experience from a project on standardized information interchange in NASA.}, isbn = {0306-4379}, doi = {16/0306-4379(90)90043-O}, url = {http://www.sciencedirect.com/science/article/pii/030643799090043O}, author = {Mark,Leo and Roussopoulos, Nick} } @article {16783, title = {Interoperability of multiple autonomous databases}, journal = {ACM Computing SurveysACM Comput. Surv.}, volume = {22}, year = {1990}, month = {1990/09//}, pages = {267 - 293}, isbn = {03600300}, doi = {10.1145/96602.96608}, url = {http://dl.acm.org/citation.cfm?id=96608}, author = {Litwin,Witold and Mark,Leo and Roussopoulos, Nick} } @conference {14984, title = {Load balancing on the hypercube and related networks}, booktitle = {Proceedings of 1990 International Conference on Parallel Processing}, volume = {1}, year = {1990}, month = {1990///}, pages = {203 - 210}, author = {JaJa, Joseph F. and Ryu,K. W.} } @conference {13594, title = {Mailpiece Preprocessing: The population of Character Parts}, booktitle = {ATC}, year = {1990}, month = {1990///}, pages = {961 - 972}, author = {David Doermann and Rosenfeld, A.} } @conference {16442, title = {Maintaining consistency in a stratified production system program}, booktitle = {Proceedings of the AAAI National Conference on Artificial Intelligence}, year = {1990}, month = {1990///}, pages = {284 - 289}, author = {Raschid, Louiqa} } @conference {16652, title = {Modeling diagnostic problem-solving at multiple levels of abstraction}, booktitle = {Artificial Intelligence Applications, 1990., Sixth Conference on}, year = {1990}, month = {1990/05//}, pages = {55 -61 vol.1 - 55 -61 vol.1}, abstract = {A precise domain-independent computational model for diagnostic problem-solving at multiple levels of abstraction is presented. The knowledge representation framework allows causal knowledge to be represented in a precise yet natural way that reflects a human diagnostician{\textquoteright}s experience in guiding diagnostic reasoning at multiple levels of abstraction. The inference mechanism clearly defines how to form plausible diagnostic hypotheses guided by explicit causal links and the principle of parsimonious covering. It permits the efficient formation of high-level diagnostic hypotheses while at the same time ensuring that all plausible diagnostic alternatives will be considered if one wishes to reason at sufficiently detailed levels. A prototype implementation is described to demonstrate that the proposed inference model is natural for capturing a small but representative fragment of medical causal knowledge, and, with the addition of reasonable heuristics, that the inference mechanism exhibits desirable problem-solving behavior}, keywords = {causal knowledge, diagnostic problem-solving, diagnostic reasoning, domain-independent computational model, explicit causal links, heuristic programming, heuristics, inference mechanism, inference mechanisms, knowledge capture, knowledge representation, knowledge representation framework, medical knowledge, multiple abstraction levels, parsimonious covering, plausible diagnostic hypotheses, problem solving}, doi = {10.1109/CAIA.1990.89171}, author = {Chu,B.-T.B. and Reggia, James A.} } @conference {16680, title = {Multiple underlying systems: Translating user requests into programs to produce answers}, booktitle = {Proceedings of the 28th annual meeting on Association for Computational Linguistics}, year = {1990}, month = {1990///}, pages = {227 - 234}, author = {Bobrow,R.J. and Resnik, Philip and Weischedel,R.M.} } @article {16800, title = {Optimal view caching}, journal = {Information Systems}, volume = {15}, year = {1990}, month = {1990///}, pages = {169 - 171}, abstract = {A view in a database is a subset of records selected from several files to satisfy some condition, e.g. the join of two relations.It has been shown that it is more efficient to store pointers to the satisfying records of the base relations rather than the complete records of the view. We are interested in efficient caching of such pointers (in effect constructing the view) when the database lies in secondary storage and only a limited number of buffers exists in memory. A view caching is optimal if it is done with the minimum number of reads from secondary storage. We prove that optimal view caching is NP -complete. }, isbn = {0306-4379}, doi = {16/0306-4379(90)90032-K}, url = {http://www.sciencedirect.com/science/article/pii/030643799090032K}, author = {Amir,Amihood and Roussopoulos, Nick} } @inbook {16511, title = {Parsimonious covering theory in cognitive diagnosis and adaptive instruction}, booktitle = {Diagnostic Monitoring of Skill and Knowledge AcquisitionDiagnostic Monitoring of Skill and Knowledge Acquisition}, year = {1990}, month = {1990///}, pages = {510 - 510}, publisher = {Psychology Press}, organization = {Psychology Press}, isbn = {089859992X, 9780898599923}, author = {Reggia, James A. and D{\textquoteright}Autrechy,C. L} } @article {16533, title = {Phase transitions in connectionist models having rapidly varying connection strengths}, journal = {Neural Computation}, volume = {2}, year = {1990}, month = {1990///}, pages = {523 - 535}, author = {Reggia, James A. and Edwards,M.} } @conference {16575, title = {Supervised and reinforced competitive learning}, booktitle = {Neural Networks, 1990., 1990 IJCNN International Joint Conference on}, year = {1990}, month = {1990///}, pages = {563 - 567}, author = {Sutton III,G. G. and Reggia, James A. and Maisog,J. M} } @article {16550, title = {A comfort measure for diagnostic problem solving}, journal = {Information Sciences}, volume = {47}, year = {1989}, month = {1989/03//}, pages = {149 - 184}, abstract = {In order to apply Bayes{\textquoteright} theorem for diagnostic problem solving when multiple disorders can occur simultaneously, several previous proposals have suggested using the ratio of posterior probabilities to rank diagnostic hypotheses. Approaches using such relative likelihoods lose the measure of absolute strengths of hypotheses, and thus are incapable of evaluating the {\textquotedblleft}quality{\textquotedblright} of a problem solution. In this paper, we propose to impose a quantity called a {\textquotedblleft}comfort measure{\textquotedblright} on the solution: a solution of a diagnostic problem is a minimal-size set of hypotheses such that the sum of their posterior probabilities exceeds a given comfort measure. Based on a probabilistic causal model developed previously, a problem-solving strategy is presented which does not require the manifestation independence assumption required with direct Bayesian classification, and which is applicable to multimembership classification problems. This strategy selectively generates diagnostic hypotheses and calculates both their relative likelihood and the lower and upper bounds of their posterior probabilities. These bounds are successively refined as more hypotheses are generated. Using these bounds, not the real posterior probabilities, the problem-solving strategy identifies a solution satisfying the given comfort measure, usually after only a small portion of all possible hypotheses have been generated.}, isbn = {0020-0255}, doi = {10.1016/0020-0255(89)90011-X}, url = {http://www.sciencedirect.com/science/article/pii/002002558990011X}, author = {Peng,Yun and Reggia, James A.} } @article {16529, title = {A connectionist model for diagnostic problem solving}, journal = {Systems, Man and Cybernetics, IEEE Transactions on}, volume = {19}, year = {1989}, month = {1989///}, pages = {285 - 298}, author = {Peng,Y. and Reggia, James A.} } @article {16587, title = {A connectionist model for dynamic control}, journal = {Telematics and Informatics}, volume = {6}, year = {1989}, month = {1989///}, pages = {375 - 390}, author = {Whitfield,K. C and Goodall,S. M and Reggia, James A.} } @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 {11932, title = {Dynamic bin packing problem}, journal = {SIAM Journal on Computing}, volume = {12}, year = {1989}, month = {1989///}, pages = {227 - 258}, abstract = {In a previous work we have defined a general architecture model for autonomous systems, which can be mapped easily to describe the functions of any automated system (SDAG-86-01). In this note, we use the model to describe the problem of thermal management in space stations. First we briefly review the architecture, then we present the environment of our application, and finally we detail the specific function for each functional block of the architecture for that environment.}, author = {Dikshit,Piyush and Guimaraes,Katia and Ramamurthy,Maya and Agrawala, Ashok K. and Larsen,Ronald L} } @book {14962, title = {Efficient Techniques for Routing and for Solving Graph Problems on the Hypercube}, year = {1989}, month = {1989///}, publisher = {University of Maryland}, organization = {University of Maryland}, author = {JaJa, Joseph F. and Ryu,K. W.} } @article {16648, title = {Functional and psychosocial effects of multimodality limb-sparing therapy in patients with soft tissue sarcomas}, journal = {Journal of Clinical Oncology}, volume = {7}, year = {1989}, month = {1989///}, pages = {1217 - 1217}, author = {Chang,A. E and Steinberg,S. M and Culnane,M. and Lampert,M. H and Reggia, James A. and Simpson,C. G and Hicks,J. E and White,D. E and Yang,J. J and Glatstein,E.} } @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 {17278, title = {Lessons learned from the ACM hypertext on hypertext project}, booktitle = {Proceedings of the second annual ACM conference on Hypertext}, series = {HYPERTEXT {\textquoteright}89}, year = {1989}, month = {1989///}, pages = {385 - 386}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-339-6}, doi = {10.1145/74224.74255}, url = {http://doi.acm.org/10.1145/74224.74255}, author = {Rous,B. and Shneiderman, Ben and Yankelovich,N. and Yoder,E.} } @conference {14982, title = {List ranking on the Hypercube}, booktitle = {Proceedings of the 1989 International Conference on Parallel Processing}, volume = {3}, year = {1989}, month = {1989///}, pages = {20 - 23}, author = {Ryu,K. W. and JaJa, Joseph F.} } @conference {16602, title = {A method for interactive satellite failure diagnosis: Towards a connectionist solution}, booktitle = {NASA. Goddard Space Flight Center, The 1989 Goddard Conference on Space Applications of Artificial Intelligence p 143-152(SEE N 89-26578 20-63)}, year = {1989}, month = {1989///}, author = {Bourret,P. and Reggia, James A.} } @conference {16653, title = {Methods for deriving competitive activation mechanisms}, booktitle = {Neural Networks, 1989. IJCNN., International Joint Conference on}, year = {1989}, month = {1989//00/0}, pages = {357 -363 vol.1 - 357 -363 vol.1}, abstract = {Inhibitory interactions in connectionist models have traditionally been implemented using inhibitory connections. Recently, an alternative approach based on competitive activation mechanisms has been proposed. To make this alternative approach practical in large and complex models, it is necessary to formulate general methods for creating task-specific competitive activation mechanisms. The author presents two such methods that have been applied successfully: heuristic computer-assisted search and decomposition of global optimization criteria. The usefulness of these two methods is demonstrated through simulations that establish the effectiveness of the competitive activation mechanisms so produced.<>}, keywords = {connectionist models, decomposition, global optimization criteria, heuristic computer-assisted search, neural nets, optimisation, search problems, task-specific competitive activation mechanisms, virtual machines}, doi = {10.1109/IJCNN.1989.118609}, author = {Reggia, James A.} } @article {15003, title = {Optimal parallel algorithms for one-layer routing}, year = {1989}, month = {1989///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, author = {Chang,S. C. and JaJa, Joseph F. and Ryu,K. W.} } @article {16539, title = {Parallel plan execution with self-processing networks}, journal = {Telematics and Informatics}, volume = {6}, year = {1989}, month = {1989///}, pages = {145 - 157}, author = {D{\textquoteright}Autrechy,C. L and Reggia, James A.} } @article {16510, title = {Parsimonious covering as a method for natural language interfaces to expert systems* 1}, journal = {Artificial Intelligence in Medicine}, volume = {1}, year = {1989}, month = {1989///}, pages = {49 - 60}, author = {Dasigi,V. R and Reggia, James A.} } @article {16537, title = {Analysis of competition-based spreading activation in connectionist models}, journal = {International journal of man-machine studies}, volume = {28}, year = {1988}, month = {1988///}, pages = {77 - 97}, author = {Wang,P. Y and Seidman,S. B and Reggia, James A.} } @article {16599, title = {Artificial neural systems in medical science and practice.}, journal = {MD computing: computers in medical practice}, volume = {5}, year = {1988}, month = {1988///}, pages = {4 - 4}, author = {Reggia, James A.} } @article {16517, title = {Competitive dynamics in a dual-route connectionist model of print-to-sound transformation}, journal = {Complex Systems}, volume = {2}, year = {1988}, month = {1988///}, pages = {509 - 547}, author = {Reggia, James A. and Marsland,P. M and Berndt,R. S} } @article {15653, title = {The decomposition of a rectangle into rectangles of minimal perimeter}, journal = {SIAM Journal on Computing}, volume = {17}, year = {1988}, month = {1988///}, pages = {1215 - 1215}, abstract = {This paper solves the problem of subdividing a unit square into p rectangles of area 1/p in such a way that the maximal perimeter of a rectangle is as small as possible. The correctness of the solution is proved using the well-known theorems of Menger and Dilworth.}, author = {Kong,T.Y and Mount, Dave and Roscoe,AW} } @conference {16777, title = {Deep compilation of large rule bases}, booktitle = {Proceedings 2nd International Conference on Expert Database Systems}, year = {1988}, month = {1988///}, author = {Sellis,T. and Roussopoulos, Nick} } @conference {18089, title = {Efficient parallel triconnectivity in logarithmic time}, booktitle = {VLSI Algorithms and Architectures}, year = {1988}, month = {1988///}, pages = {33 - 42}, author = {Ramachandran,V. and Vishkin, Uzi} } @article {16791, title = {An efficient pictorial database system for PSQL}, journal = {IEEE Transactions on Software Engineering}, volume = {14}, year = {1988}, month = {1988/05//}, pages = {639 - 650}, abstract = {Pictorial databases require efficient and direct spatial search based on the analog form of spatial objects and relationships instead of search based on some cumbersome alphanumeric encodings of the pictures. A description is given of PSQL, a query language that allows pictorial domains to be presented to the user in their analog form and allows him or her to do direct manipulation on the objects found on those domains. Direct spatial search and computation on the pictures is done using efficient data structures, R- and R+-trees (multidimensional B-trees), which are excellent devices for searching spatial objects and relationships found on pictures}, keywords = {alphanumeric encodings, Computer science, Data structures, Database languages, database management systems, Database systems, Encoding, Image coding, Image databases, multidimensional B-trees, Object oriented databases, pictorial database system, PSQL, query language, query languages, R+-trees, Relational databases, Spatial databases, spatial objects, spatial search, User interfaces}, isbn = {0098-5589}, doi = {10.1109/32.6141}, author = {Roussopoulos, Nick and Faloutsos,C. and Sellis,T.} } @article {16745, title = {Expert database systems: Efficient support for engineering environments}, journal = {Data \& Knowledge Engineering}, volume = {3}, year = {1988}, month = {1988/09//}, pages = {71 - 85}, abstract = {Manufacturing and Engineering processes use both large scale data and knowledge bases, and the use of expert systems in such environments has become a necessity. Expert Database Systems have evolved from conventional database systems to meet the requirements of current Artificial Intelligence applications. However, future Expert Database Systems will contain knowledge bases of significant size which makes main memory insufficient and the use of a database system a necessity. We propose an effective way of building High Performance Expert Database Systems to support manufacturing and engineering environments. These systems are based on Incremental Computation Models; such models utilize results of previous computations by merging them with newly derived results of computations on small increments representing changes in the database. Our system will be able to support very large knowledge bases by utilizing novel structures and access methods and by using a very sophisticated inference engine based on incremental computation models.}, keywords = {engineering databases, Expert database systems, high performance systems, incremental computation models}, isbn = {0169-023X}, doi = {16/0169-023X(88)90007-9}, url = {http://www.sciencedirect.com/science/article/pii/0169023X88900079}, author = {Sellis,T. and Roussopoulos, Nick and Mark,L. and Faloutsos,C.} } @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 {16640, title = {A general-purpose simulation environment for developing connectionist models}, journal = {Simulation}, volume = {51}, year = {1988}, month = {1988///}, pages = {5 - 5}, author = {D{\textquoteright}Autrechy,C. L and Reggia, James A. and Sutton,G. G and Goodall,S. M} } @conference {12010, title = {The Maryland approach to image understanding}, booktitle = {Science Applications International Corp, Proceedings: Image Understanding Workshop,}, volume = {1}, year = {1988}, month = {1988///}, author = {Aloimonos, J. and Davis, Larry S. and Rosenfeld, A.} } @conference {16655, title = {Parallel set covering algorithms}, booktitle = {Artificial Intelligence Applications, 1988., Proceedings of the Fourth Conference on}, year = {1988}, month = {1988/03//}, pages = {274 - 279}, abstract = {The authors develop some parallel algorithms for set covering. A brief introduction is given into the parsimonious set covering theory, and algorithms using one type of parsimony called irredundancy are developed. They also discuss several machine-independent parallel constructs that are used to express the parallel algorithms. The algorithms were tested on the Butterfly parallel processor system. The authors present some of the tests conducted and their analyses. Finally, the merits and limitations of the algorithms that were identified during the tests are presented}, keywords = {Butterfly parallel processor system, irredundancy, Parallel algorithms, parsimonious set covering theory, set covering, set theory}, doi = {10.1109/CAIA.1988.196115}, author = {Sekar,S. and Reggia, James A.} } @article {18985, title = {Partial Revertants of the Transposable Element-Associated Suppressible Allele White-Apricot in Drosophila Melanogaster: Structures and Responsiveness to Genetic Modifiers}, journal = {GeneticsGenetics}, volume = {118}, year = {1988}, month = {1988/02//}, pages = {221 - 234}, abstract = {The eye color phenotype of white-apricot (w(a)), a mutant allele of the white locus caused by the insertion of the transposable element copia into a small intron, is suppressed by the extragenic suppressor suppressor-of-white-apricot (su(w(a))) and enhanced by the extragenic enhancers suppressor-of-forked su(f)) and Enhancer-of-white-apricot (E(w(a))). Derivatives of w(a) have been analyzed molecularly and genetically in order to correlate the structure of these derivatives with their response to modifiers. Derivatives in which the copia element is replaced precisely by a solo long terminal repeat (sLTR) were generated in vitro and returned to the germline by P-element mediated transformation; flies carrying this allele within a P transposon show a nearly wild-type phenotype and no response to either su(f) or su(w(a)). In addition, eleven partial phenotypic revertants of w(a) were analyzed. Of these, one appears to be a duplication of a large region which includes w(a), three are new alleles of su(w(a)), two are sLTR derivatives whose properties confirm results obtained using transformation, and five are secondary insertions into the copia element within w(a). One of these, w(aR84h), differs from w(a) by the insertion of the most 3{\textquoteright} 83 nucleotides of the I factor. The five insertion derivatives show a variety of phenotypes and modes of interaction with su((f) and su(w(a)). The eye pigmentation of w(aR84h) is affected by su(f) and E(w(a)), but not su(w(a)). These results demonstrate that copia (as opposed to the interruption of white sequences) is essential for the w(a) phenotype and its response to genetic modifiers, and that there are multiple mechanisms for the alteration of the w(a) phenotype by modifiers.}, isbn = {0016-6731}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203276/}, author = {Mount, Stephen M. and Green,M. M. and Rubin,G. M.} } @article {16561, title = {Self-processing networks and their biomedical implications}, journal = {Proceedings of the IEEE}, volume = {76}, year = {1988}, month = {1988///}, pages = {680 - 692}, author = {Reggia, James A. and Sutton III,G. G.} } @article {16757, title = {Analysis of object oriented spatial access methods}, journal = {ACM SIGMOD Record}, volume = {16}, year = {1987}, month = {1987///}, pages = {426 - 439}, author = {Faloutsos,C. and Sellis,T. and Roussopoulos, Nick} } @article {16809, title = {On Cost-effectiveness of a Semijoin in Distributed Query Processing.}, volume = {ISR-TR-1987-38}, year = {1987}, month = {1987///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The cost-effective reduction of relations by semijoins is the basis of the heuristic approach to distributed query processing. The cost-effectiveness of a semijoin was simply determined in the literature assuming that the local processing cost is negligible compared to the data transmission cost in distributed query processing. However, recently questions have been raised about the validity of the assumption, and some experimental works revealed that the local processing cost is also significant in distributed query processing. In this paper, we are concerned with the cost-effectiveness of a semijoin considering the local processing cost as well as the data transmission cost. To measure the effectiveness of a semijoin in terms of the local processing cost, we introduce the join sequence in which the relations are joined at the result site to answer the query. A dynamic programming algorithm is developed to generate the optimal join sequence for a given query. A simple heuristic algorithm is also developed to generate a join sequence for a given query.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/4547}, author = {Kang,Hyunmo and Roussopoulos, Nick} } @article {16581, title = {Diagnostic problem-solving with causal chaining}, journal = {International Journal of Intelligent Systems}, volume = {2}, year = {1987}, month = {1987///}, pages = {265 - 302}, author = {Peng,Y. and Reggia, James A.} } @inbook {15755, title = {Fine and Medium Grained Parallel Algorithms for Matrix QR Factorization}, booktitle = {Algorithms and Applications on Vector and Parallel ComputersAlgorithms and Applications on Vector and Parallel Computers}, year = {1987}, month = {1987///}, pages = {347 - 349}, publisher = {Elsevier Science Publishers B.V. (North Holland)}, organization = {Elsevier Science Publishers B.V. (North Holland)}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Riele,H.J.J. te and Dekker,Th.J. and Vorst,H.A. van der} } @article {16811, title = {Meta-Data Management.}, volume = {ISR-TR-1987-31}, year = {1987}, month = {1987///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {A database system should support a rich variety of meta-data describing and controlling the management and use of data. Few present database systems provide even rudimentary integrated meta-data management facilities.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/4540}, author = {Mark,Leo and Roussopoulos, Nick} } @article {16632, title = {Modeling diagnostic reasoning: a summary of parsimonious covering theory}, journal = {Computer methods and programs in biomedicine}, volume = {25}, year = {1987}, month = {1987///}, pages = {125 - 134}, author = {Reggia, James A. and Peng,Y.} } @article {16611, title = {A probabilistic causal model for diagnostic problem solving (parts 1 and 2)}, journal = {IEEE Transactions on Systems, Man and Cybernetics}, year = {1987}, month = {1987///}, pages = {146 - 162}, author = {Peng,Y. and Reggia, James A.} } @conference {16603, title = {Properties of a competition-based activation mechanism in neuromimetic network models}, booktitle = {Proceedings of the First International Conference on Neural Networks}, year = {1987}, month = {1987///}, author = {Reggia, James A.} } @article {16726, title = {The R+-tree: A dynamic index for multi-dimensional data}, journal = {Proceedings of VLDB 1987}, year = {1987}, month = {1987///}, pages = {507 - 518}, author = {Sellis,T. and Roussopoulos, Nick and Faloutsos,C.} } @book {12064, title = {Structure from Motion from Line Correspondencies: New Results}, year = {1987}, month = {1987///}, author = {Science, University of Maryland at College Park. Dept. of Computer and Spetsakis, M. E and Aloimonos, J. and Research, University of Maryland at College Park. Center for Automation} } @article {16808, title = {Using 2-way Semijoins in Distributed Query Processing.}, volume = {ISR-TR-1987-35}, year = {1987}, month = {1987///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {In distributed query processing, the semijoin has been used as an effective operator in reducing relations referenced in the query to reduce the total amount of data transmission. In this paper, we propose a new relational algebra operator, 2-way semijoin, which is an extended version of the semijoin, for more cost- effective distributed query processing. The 2-way semijoin is compared to the semijoin in terms of the reduction power and the propagation of reduction effects. We show that the 2-way semijoin has more reduction power than the semijoin and that the propagation of reduction effects by the 2-way semijoin is further than by the semijoin.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/4544}, author = {Kang,Hyunmo and Roussopoulos, Nick} } @article {17268, title = {Is Bigger Better?: The Effects of Display Size on Program Reading}, journal = {Tech Report HCIL-86-08}, year = {1986}, month = {1986///}, abstract = {An experiment was conducted in which four window sizes (10, 22, 60 and 120 lines) were compared for their effectiveness for program reading. The largest window, in which the entire program could be seen at one time, was found significantly better, in both time to complete the reading task and the number of correct answers in the reading task. Subjects also preferred the larger windows to the smaller windows.}, author = {Reisel,J.F. and Shneiderman, Ben} } @article {16628, title = {A comparative analysis of methods for expert systems}, journal = {International journal of man-machine studies}, volume = {24}, year = {1986}, month = {1986///}, pages = {475 - 499}, author = {Ramsey,C. L and Reggia, James A. and Nau, Dana S. and Ferrentino,A.} } @article {15733, title = {Confidence Intervals for Inequality-Constrained Least Squares Problems, with Applications to Ill-Posed Problems}, journal = {SIAM Journal on Scientific and Statistical Computing}, volume = {7}, year = {1986}, month = {1986///}, pages = {473 - 489}, abstract = {Computing confidence intervals for functions b(x) wT"x,where Kx y + e and e is a normallydistributed error vector, is a standard problem in multivariate statistics. In this work, we develop an algorithm for solving this problem if additional information, x->0, is given. Applications to estimating solutions to integral equations of the first kind are given. }, author = {O{\textquoteright}Leary, Dianne P. and Rust,B. W.} } @conference {16728, title = {Engineering Information Systems: Builders and Designers Perspective}, booktitle = {SIGMOD Conference}, year = {1986}, month = {1986///}, pages = {1 - 3}, author = {Roussopoulos, Nick} } @article {16638, title = {Modelling reading aloud and its relevance to acquired dyslexia}, journal = {Computer methods and programs in biomedicine}, volume = {22}, year = {1986}, month = {1986///}, pages = {13 - 19}, author = {Reggia, James A. and Berndt,R. S} } @conference {16456, title = {A parallel processing strategy for evaluating recursive queries}, booktitle = {Proceedings of the 12th International Conference on Very Large Data Bases}, year = {1986}, month = {1986///}, pages = {412 - 419}, author = {Raschid, Louiqa and Su,S. Y.W} } @article {16626, title = {The parsimonious covering model for inexact abductive reasoning in diagnostic systems}, journal = {Recent Developments in the Theory and Applications of Fuzzy Sets. Proceedings of NAFIPS}, year = {1986}, month = {1986///}, pages = {86 - 1986}, author = {Ahuja,S. B and Reggia, James A.} } @article {16744, title = {Principles and techniques in the design of ADMS+((advanced data-base management system))}, journal = {Computer}, volume = {19}, year = {1986}, month = {1986///}, pages = {19 - 23}, author = {Roussopoulos, Nick and Kang,H.} } @conference {16598, title = {Relationships between deductive and abductive inference in knowledge-based diagnostic problem solving}, booktitle = {Expert Database Systems: Proceedings of the First International Workshop. New York: Benjamin Cummings}, year = {1986}, month = {1986///}, author = {Nau, Dana S. and Reggia, James A.} } @article {16445, title = {A Special-Function Unit for Sorting and Sort-Based Database Operations}, journal = {IEEE Transactions on Computers}, volume = {C-35}, year = {1986}, month = {1986/12//}, pages = {1071 - 1077}, abstract = {Achieving efficiency in database management functions is a fundamental problem underlying many computer applications. Efficiency is difficult to achieve using the traditional general-purpose von Neumann processors. Recent advances in microelectronic technologies have prompted many new research activities in the design, implementation, and application of database machines which are tailored for processing database management functions. To build an efficient system, the software algorithms designed for this type of system need to be tailored to take advantage of the hardware characteristics of these machines. Furthermore, special hardware units should be used, if they are cost- effective, to execute or to assist the execution of these software algorithms.}, keywords = {Application software, Computer applications, Database machines, Hardware, hardware sorter, Microelectronics, Software algorithms, Software design, Software systems, sort-based algorithms for database operations, sorting, special-function processor, Technology management}, isbn = {0018-9340}, doi = {10.1109/TC.1986.1676715}, author = {Raschid, Louiqa and Fei,T. and Lam,H. and Su,S. Y.W} } @conference {16509, title = {Using abductive inferencing to derive complex error classifications for discrete sequential processes}, booktitle = {Proceedings of the 19th annual symposium on Simulation}, year = {1986}, month = {1986///}, pages = {207 - 225}, author = {Ahuja,S. B and Reggia, James A.} } @conference {16531, title = {Abductive inference}, booktitle = {Proceedigns of the Expert Systems in Government Symposium}, year = {1985}, month = {1985///}, pages = {484 - 489}, author = {Reggia, James A.} } @article {16580, title = {Answer justification in abductive expert systems for diagnostic problem solving}, journal = {IEEE Transactions on Biomedical Engineering}, year = {1985}, month = {1985///}, author = {Reggia, James A. and Perricone,B. and Nau, Dana S. and Peng,Y.} } @article {16624, title = {Answer Justification in Diagnostic Expert Systems-Part II: Supporting Plausible Justifications}, journal = {Biomedical Engineering, IEEE Transactions on}, year = {1985}, month = {1985///}, pages = {268 - 272}, author = {Reggia, James A. and Perricone,B. T. and Nau, Dana S. and Peng,Y.} } @article {18970, title = {Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins.}, journal = {Molecular and Cellular BiologyMol. Cell. Biol.}, volume = {5}, year = {1985}, month = {1985/07/01/}, pages = {1630 - 1638}, abstract = {We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.}, isbn = {0270-7306, 1098-5549}, doi = {10.1128/MCB.5.7.1630}, url = {http://mcb.asm.org/content/5/7/1630}, author = {Mount, Stephen M. and Rubin,G. M.} } @conference {16773, title = {Direct spatial search on pictorial databases using packed R-trees}, booktitle = {ACM SIGMOD Record}, volume = {14}, year = {1985}, month = {1985///}, pages = {17 - 31}, author = {Roussopoulos, Nick and Leifker,D.} } @article {16614, title = {DS Nau, and PY Wang. A formal model of diagnostic inference}, journal = {Information Sciences}, volume = {37}, year = {1985}, month = {1985///}, pages = {227 - 285}, author = {Reggia, James A.} } @article {16804, title = {Dynamic access control for relational views.}, journal = {INFO. SYST.}, volume = {10}, year = {1985}, month = {1985///}, pages = {361 - 369}, author = {Roussopoulos, Nick and Bader,C.} } @conference {16576, title = {Evaluation of Medical Expert Systems: A Case Study in Performance Analysis}, booktitle = {Proceedings of the Ninth Annual Symposium on Computer Applications in Medical Care}, year = {1985}, month = {1985///}, pages = {287 - 291}, author = {Reggia, James A.} } @article {16636, title = {A formal model of abductive inference}, journal = {Information Sciences}, volume = {37}, year = {1985}, month = {1985///}, pages = {227 - 285}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. and Peng,Y.} } @article {16612, title = {A formal model of diagnostic inference, II. Algorithmic solution and application}, journal = {Information Sciences}, volume = {37}, year = {1985}, month = {1985///}, pages = {257 - 285}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. Y and Peng,Y.} } @article {16752, title = {Schema manipulation in self-describing and self-documenting data models}, journal = {International Journal of Parallel Programming}, volume = {14}, year = {1985}, month = {1985///}, pages = {1 - 28}, author = {Roussopoulos, Nick and Mark,L.} } @article {16751, title = {SEES{\textemdash}A Software testing Environment Support System}, journal = {IEEE Transactions on Software Engineering}, volume = {SE-11}, year = {1985}, month = {1985/04//}, pages = {355 - 366}, abstract = {SEES is a database system to support program testing. The program database is automatically created during the compilation of the program by a compiler built using the YACC compiler-compiler.}, keywords = {Computer architecture, Database systems, Error correction, Program processors, Programming profession, Relational databases, Software testing, software tools, Workstations, Writing}, isbn = {0098-5589}, doi = {10.1109/TSE.1985.232225}, author = {Roussopoulos, Nick and Yeh,R. T} } @article {16786, title = {SELF-DESCRIBING AND SELF-DOCUMENTING DATABASE SYSTEMS}, journal = {Languages for automation}, year = {1985}, month = {1985///}, pages = {275 - 275}, author = {Roussopoulos, Nick and Mark,L.} } @book {16535, title = {A theoretical foundation for abductive expert systems}, year = {1985}, month = {1985///}, publisher = {North-Holland, New York}, organization = {North-Holland, New York}, author = {Reggia, James A. and Nau, Dana S. and Peng,Y. and Perricone,B.} } @conference {16755, title = {A timed petri net methodolgoy for specifying real-time system timing requirements}, booktitle = {International Workshop on Timed Petri Nets}, year = {1985}, month = {1985///}, pages = {24 - 31}, author = {Coolahan Jr,J. E and Roussopoulos, Nick} } @conference {16519, title = {An abductive non-monotonic logic}, booktitle = {Workshop on Nonmonotonic Reasoning}, year = {1984}, month = {1984///}, author = {Reggia, James A. and Nau, Dana S.} } @article {16610, title = {Computer-aided assessment of transient ischemic attacks. A clinical evaluation.}, journal = {Archives of neurology}, volume = {41}, year = {1984}, month = {1984///}, pages = {1248 - 1248}, author = {Reggia, James A. and Tabb,D. R. and Price,T. R. and Banko,M. and Hebel,R.} } @conference {16733, title = {A framework for self-describing and self-documenting database systems}, booktitle = {NBS Trends and Application Conference}, year = {1984}, month = {1984///}, author = {Roussopoulos, Nick and Mark,L.} } @article {16750, title = {GDDT--A graphical design and documentation tool for software development}, journal = {Computers \& Graphics}, volume = {8}, year = {1984}, month = {1984///}, pages = {309 - 323}, abstract = {This paper describes "The Graphical Design and Documentation Tool" (GDDT), a general purpose support system for design and documentation. Self documentation and ease of use are presented as important criteria for such tools. Interactive graphics is introduced as a methodology for creating and maintaining hierarchical representations. The graphical representations of various requirements specification techniques and design tools are supported by an extended network model which supports hierarchical decomposition of structures. GDDT is proposed as a general purpose design tool which supports the most common logical constructions of both requirements specification and design methodologies and yet has a high level human interface which makes it easy to learn and use.}, isbn = {0097-8493}, doi = {16/0097-8493(84)90013-X}, url = {http://www.sciencedirect.com/science/article/pii/009784938490013X}, author = {Roussopoulos, Nick and Kelley,Stephen} } @conference {16801, title = {An introduction to PSQL: A pictorial structured query language}, booktitle = {Proc. IEEE Workshop on Visual Languages}, year = {1984}, month = {1984///}, pages = {77 - 87}, author = {Roussopoulos, Nick and Leifker,D.} } @article {18405, title = {Monitoring an Ada software development}, journal = {ACM SIG Ada Letters}, volume = {IV}, year = {1984}, month = {1984/07//}, pages = {32 - 39}, isbn = {1094-3641}, doi = {10.1145/998401.998402}, url = {http://doi.acm.org/10.1145/998401.998402}, author = {Basili, Victor R. and Chang,Shih and Gannon,John and Katz,Elizabeth and Panlilio-Yap,N. Monina and Ramsey,Connie Loggia and Zelkowitz, Marvin V and Bailey,John and Kruesi,Elizabeth and Sheppard,Sylvia} } @conference {16813, title = {A Programming Environment Framework Based on Reusability}, booktitle = {Proceedings of the First International Conference on Data Engineering}, year = {1984}, month = {1984///}, pages = {277 - 280}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, isbn = {0-8186-0533-2}, url = {http://dl.acm.org/citation.cfm?id=645470.655219}, author = {Yeh,Raymond T. and Mittermeir,Roland and Roussopoulos, Nick and Reed,Joylyn} } @conference {16589, title = {Simulation of phonemic errors using artificial intelligence symbol processing techniques}, booktitle = {Proceedings of the 17th annual symposium on Simulation}, year = {1984}, month = {1984///}, pages = {49 - 64}, author = {Reggia, James A. and Ahuja,S. B} } @article {16582, title = {SLIPS}, journal = {Journal of Medical Systems}, volume = {8}, year = {1984}, month = {1984///}, pages = {197 - 204}, author = {Morris,M. S and Reggia, James A. and Ahuja,S. B and Hart,J. and Watson,V.} } @book {19123, title = {Achievements and Prospects with Regard to Energy Recycling in Textile Finishing Shops}, year = {1983}, month = {1983}, publisher = {UN}, organization = {UN}, author = {Pop, Mihai and Romas, D. and Romania} } @conference {16555, title = {The case for artificial intelligence in medicine}, booktitle = {Computer Applications in Medical Care, 1983. Proceedings. The Seventh Annual Symposium on}, year = {1983}, month = {1983///}, pages = {4 - 7}, author = {Reggia, James A.} } @article {16616, title = {Diagnostic expert systems based on a set covering model}, journal = {International Journal of Man-Machine Studies}, volume = {19}, year = {1983}, month = {1983///}, pages = {437 - 460}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. Y} } @article {17141, title = {Evaluating multiple coordinated windows for programming workstations}, journal = {NASA. Goddard Space Flight Center Proc. of the Eighth Ann. Software Eng. Workshop 11 p(SEE N 84-23137 13-61)}, year = {1983}, month = {1983///}, abstract = {Programmers might benefit from larger screens with multiple windows or multiple screens, especially if convenient coordination among screens are arranged. Uses for multiple coordinated displays in a programmers workstation are explored. Initial efforts focus on the potential applications, a command language for coordinating the displays, and the psychological basis for effective utilization so as to avoid information overload. Subsequent efforts will be devoted to implementing the concepts and performing controlled psychologically oriented experiments to validate the hypotheses.}, author = {Shneiderman, Ben and GRANTHAM,C. and Norman,K. and ROGERS,J. and Roussopoulos, Nick} } @article {16528, title = {Expert systems based on set covering model}, journal = {International Journal on Man-Machine Studies}, volume = {19}, year = {1983}, month = {1983///}, pages = {443 - 460}, author = {Reggia, James A. and Dana,S. N. and Pearl,Y. W.} } @article {15772, title = {Multi-resolution relaxation}, journal = {Pattern Recognition}, volume = {16}, year = {1983}, month = {1983///}, pages = {223 - 230}, abstract = {Several types of iterative methods can be used to segment the pixels in an image into light and dark regions; these include {\textquotedblleft}relaxation{\textquotedblright} methods of probability adjustment and steepest-descent methods of cost function minimization. Conventionally, these methods operate on the image at a single resolution. This paper investigates the possibility of using these approaches at two (or more) resolutions in order to reduce their computational cost{\textemdash}e.g. first obtain an approximate solution by iterating at low resolution, then refine the solution using a few iterations at high resolution.}, keywords = {Multigrid methods, Pyramids, Relaxation, segmentation}, isbn = {0031-3203}, doi = {10.1016/0031-3203(83)90026-2}, url = {http://www.sciencedirect.com/science/article/pii/0031320383900262}, author = {Narayanan,K. A. and O{\textquoteright}Leary, Dianne P. and Rosenfeld,Azriel} } @conference {16605, title = {A New Inference Method for Frame-based Expert System}, booktitle = {Proceedings of the National Conference on Artificial Intelligence}, year = {1983}, month = {1983///}, pages = {333 - 337}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. Y} } @conference {16771, title = {A Relational Database to Support Graphical Design and Documentation}, booktitle = {Databases for Business and Office Applications, Database Week}, year = {1983}, month = {1983///}, pages = {135 - 149}, author = {Roussopoulos, Nick and Kelley,S.} } @article {16641, title = {The Role of Spatial Knowledge in Expert Systems}, journal = {Representation and Processing of Spatial Knowledge, TR-1275. Dept. of Comp. sci {\quotedblbase}Univ. of Maryland, May}, year = {1983}, month = {1983///}, pages = {3 - 8}, author = {Reggia, James A.} } @article {16547, title = {S., Wang. PY, Diagnostic Expert Systems Based on a Set Covering Model}, journal = {International Journal on Man-Machine studies}, volume = {19}, year = {1983}, month = {1983///}, pages = {437{\textendash}46O - 437{\textendash}46O}, author = {Reggia, James A. and Nau, Dana S.} } @conference {16723, title = {A self-describing meta-schema for the RM/T data model}, booktitle = {IEEE Workshop On Languages for Automation, IEEE Computer Society Press}, year = {1983}, month = {1983///}, author = {Roussopoulos, Nick and Mark,L.} } @article {18996, title = {Small Ribonucleoproteins from Eukaryotes: Structures and Roles in RNA Biogenesis}, journal = {Cold Spring Harbor Symposia on Quantitative BiologyCold Spring Harb Symp Quant Biol}, volume = {47}, year = {1983}, month = {1983/01/01/}, pages = {893 - 900}, abstract = {Detailed reviews describing work presented at the annual Cold Spring Harbor Symposia on Quantitative Biology}, isbn = {0091-7451, 1943-4456}, doi = {10.1101/SQB.1983.047.01.103}, url = {http://symposium.cshlp.org/content/47/893}, author = {Steitz,J. A. and Wolin,S. L. and Rinke,J. and Pettersson,I. and Mount, Stephen M. and Lerner,E. A. and Hinterberger,M. and Gottlieb,E.} } @article {16788, title = {Timing Requirements for Time-Driven Systems Using Augmented Petri Nets}, journal = {IEEE Transactions on Software Engineering}, volume = {SE-9}, year = {1983}, month = {1983/09//}, pages = {603 - 616}, abstract = {A methodology for the statement of timing requirements is presented for a class of embedded computer systems. The notion of a "time-driven" system is introduced which is formalized using a Petri net model augmented with timing information. Several subclasses of time-driven systems are defined with increasing levels of complexity. By deriving the conditions under which the Petri net model can be proven to be safe in the presence of time, timing requirements for modules in the system can be obtained. Analytical techniques are developed for proving safeness in the presence of time for the net constructions used in the defined subclasses of time-driven systems.}, keywords = {Application software, Concurrent computing, Control systems, Embedded computing, Embedded system, Helium, Modeling methodology, performance specifications, Petri nets, Power system modeling, Real time systems, real-time systems, Timing, timing requirements}, isbn = {0098-5589}, doi = {10.1109/TSE.1983.235261}, author = {Coolahan,J. E. and Roussopoulos, Nick} } @article {16540, title = {Transferability of medical decision support systems based on Bayesian classification}, journal = {Medical Decision Making}, volume = {3}, year = {1983}, month = {1983///}, pages = {501 - 501}, author = {Zagoria,R. J and Reggia, James A.} } @article {15759, title = {Image Smoothing and Segmentation by Cost Minimization}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {SMC-12}, year = {1982}, month = {1982///}, pages = {91 - 96}, author = {Narayanan,K. A. and O{\textquoteright}Leary, Dianne P. and Rosenfeld,Azriel} } @article {16554, title = {KMS reference manual}, journal = {Dep. Comput. Sci., Univ. Maryland, College Park, Tech. Rep. TR-1136}, year = {1982}, month = {1982///}, author = {Reggia, James A. and Perricone,B.} } @article {16737, title = {The Logical Access Path Schema of a Database}, journal = {IEEE Transactions on Software Engineering}, volume = {SE-8}, year = {1982}, month = {1982/11//}, pages = {563 - 573}, abstract = {A new schema which models the usage of the logical access paths of the database is proposed. The schema models all database activities (i.e., retrievals and updates), and integrates their logical access paths by recognizing common subpaths and increasing the "weight" of the shared subpaths. The logical access path schema provides a comprehensive picture of the logical access paths, and the cumulative usage of the shared subpaths and/or intermediate results. The schema serves a dual purpose. Firstly, it is used as a model of the access requirements during the database design, and secondly, as the basis for optimization during the operation of the database.}, keywords = {Aggregation hierarchy, Calculus, Computer science, Data structures, Databases, Design optimization, external logical subschema, generalization hierarchy, Information retrieval, Joining processes, logical access path, propositional calculus, views}, isbn = {0098-5589}, doi = {10.1109/TSE.1982.235886}, author = {Roussopoulos, Nick} } @article {15714, title = {An Optimization Approach to Edge Reinforcement}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {SMC-12}, year = {1982}, month = {1982///}, pages = {551 - 553}, abstract = {The present investigation is concerned with an optimization approach to edge reinforcement which does not involve probabilistic concepts. A cost function is defined, based on the local pattern of edge responses, which is low for sharp, strong edges, and a steepest descent method is used to adjust the edge magnitudes so as to reduce the value of this cost function. The edge reinforcement results obtained in this way appear to be better than those obtained by relaxation methods, whether based on conditional probability or on optimization. The results of an application of the considered procedure to a portion of a Landsat scene are shown, taking into account the input image, the results of 10 iterations of the steepest descent procedure, results produced by means of the relaxation process reported by Schachter et al. (1977), and results obtained with the aid of the optimization relaxation process considered by Faugeras and Berthod (1979).}, author = {Narayanan,K. A. and O{\textquoteright}Leary, Dianne P. and Rosenfeld,Azriel} } @article {16748, title = {View indexing in relational databases}, journal = {ACM Transactions on Database SystemsACM Trans. Database Syst.}, volume = {7}, year = {1982}, month = {1982/06//}, pages = {258 - 290}, isbn = {03625915}, doi = {10.1145/319702.319729}, url = {http://dl.acm.org/citation.cfm?id=319702.319729}, author = {Roussopoulos, Nick} } @conference {16635, title = {Bayesian classification in medicine: The transferability question}, booktitle = {Proceedings of the Fifth Annual Symposium on Computer Applications in Medical Care}, year = {1981}, month = {1981///}, pages = {250 - 252}, author = {Zagoria,R. and Reggia, James A. and Price,T. and Banko,M.} } @article {16573, title = {Computer-assisted medical decision making: a critical review}, journal = {Annals of biomedical engineering}, volume = {9}, year = {1981}, month = {1981///}, pages = {605 - 619}, author = {Reggia, James A.} } @conference {16618, title = {Knowledge-based decision support systems: Development through high-level languages}, booktitle = {Proc. 20th Ann. Tech. Meeting of Wash. DC ACM}, year = {1981}, month = {1981///}, author = {Reggia, James A. and Perricone,B. T.} } @article {11935, title = {An Algorithm for Mutual Exclusion in Computer Networks.}, year = {1980}, month = {1980///}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {An algorithm is proposed which creates mutual exclusion in a computer network whose nodes can communicate only by messages and do not share memory. The algorithm sends only 2*(N-1) Messages, where N is the number of nodes in the network, per critical section invocation. This number of messages is a minimum if parallel, distributed, symmetric control is used; hence, the algorithm is optimal in this minimal under some general assumptions. Like Lamport{\textquoteright}s {\textquoteright}bakery algorithm,{\textquoteright} unbounded sequence numbers are used to provide first-come first-served priority into the critical section. It is shown that the number can be contained in a fixed amount of memory by storing it as the residue of a modulus. The number of messages required to implement the exclusion can be reduced by using sequential node-by-node processing, by using broadcast message techniques or by sending information through timing channels. The readers and writers problem is solved by a simple modification of the algorithm. The modifications necessary to make the algorithm robust are described.}, author = {Agrawala, Ashok K. and Ricart, G.} } @article {16775, title = {Approximate pattern matching in a pattern database system}, journal = {Information Systems}, volume = {5}, year = {1980}, month = {1980///}, pages = {107 - 119}, abstract = {This work is concerned with the organization of a large database of binary pictures (normalized for size, rotation and position) and with the efficient "inexact match" of an input pattern against the whole database. Current techniques in pattern analysis use matching algorithms without any regard to the global organization of the storage representations of the models they are to match. Consequently, the algorithms are only practical for small databases. This paper discusses the design of a pattern database system and the economy that it provides for the matching problem. The database organization is based on the quad-tree representation of binary patterns. Given an arbitrary decomposition D (or partition) of a pattern P and an arbitrary function f on the pattern, we repeatedly apply f on D(P), D(D(P))P, ... to obtain higher and higher levels of abstraction f(D)(P)), f(D(D(P))), ... of the pattern. The computed values obtained after the jth application of f are used to label the ith level of the pyramid. The specific representation used in this paper is called the sum-quad-tree, in which each level of the tree stores the sum of the labels of its sons. The lowest level of the sum-quad-tree corresponds to the individual pixels and is the nth level (i.e. node m at level n implies v(m) = 0 or v(m) = 1). Nodes at the jth level of the sum-quad-tree correspond to sums of 2n-j {\texttimes} 2n-j picture points, so that the 0th level contains the number of 1{\textquoteright}s in the pattern. The pyramid representation is used as a hierarchical (n-level) indexing scheme of the database. The advantage of this organization is that the matching algorithms presented reject most of the patterns in the database by utilizing the relatively small in size index tables and thus avoid the overhead of unnecessary CPU time and operation between main memory and secondary storage.}, isbn = {0306-4379}, doi = {16/0306-4379(80)90002-2}, url = {http://www.sciencedirect.com/science/article/pii/0306437980900022}, author = {Davis, Larry S. and Roussopoulos, Nick} } @article {11936, title = {The Effect of the Future in Work Distribution.}, year = {1980}, month = {1980///}, institution = {COMPUTER SCIENCE CENTER, UNIVERSITY OF MARYLAND COLLEGE PARK}, abstract = {A controller is considered which routes arrivals among several servers of different speeds. A decision which sends work to the server which will complete it soonest does not optimize the average completion time (mean flow time) because it doesn{\textquoteright}t take into account the impact of the decision on future arrivals. This impact on future arrivals, the {\textquoteright}future effect{\textquoteright}, can be significant at high arrival rates. An estimate of the size of the future effect is derived and controllers which take it into account in routing decisions can reduce the average completion time to near optimum. The effect is most pronounced when the service requirements for arrivals are nearly constant, server speeds are markedly different, and the arrival rate is close to the system{\textquoteright}s capacity. A controller considering the future effect will more heavily weigh a potential server{\textquoteright}s backlog than the arrival{\textquoteright}s service time when making a routing decision}, author = {Agrawala, Ashok K. and Ricart, G.} } @conference {16770, title = {Systematic Derivation of Software Requirements}, booktitle = {Proceedings of the 1st International Conference on the Entity-Relationship Approach to Systems Analysis and Design}, year = {1980}, month = {1980///}, pages = {403 - 404}, author = {Yeh,R. Y and Roussopoulos, Nick and Chang,P.} } @book {11941, title = {Foundations of microprogramming: architecture, software, and applications}, year = {1976}, month = {1976///}, publisher = {Academic Press}, organization = {Academic Press}, author = {Agrawala, Ashok K. and Rauscher,T. G} } @inbook {15701, title = {A Generalized Conjugate Gradient Method for the Numerical Solution of Elliptic Partial Differential Equations}, booktitle = {Sparse Matrix ComputationsSparse Matrix Computations}, year = {1976}, month = {1976///}, pages = {309 - 332}, publisher = {Academic Press}, organization = {Academic Press}, address = {New York}, abstract = {We consider a generalized conjugate gradient method for solvingsparse, symmetric, positive-definite systems of linear equations, principally those arising from the discretization of boundary value problems for elliptic partial differential equations. The method is based on splitting off from the original coefficient matrix a symmetric, positive-definiteonethat corresponds to a more easily solvable system of equations, and then accelerating the associated iteration using conjugate gradients. Optimality and convergence properties are presented, and the relation to other methods is discussed. Several splittings for which the method seems particularly effective are also discussed, and for some, numerical examples are given }, author = {Concus,Paul and Golub, Gene H. and O{\textquoteright}Leary, Dianne P.}, editor = {Bunch,James R. and Rose,Donald J.} } @article {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.} } @conference {16776, title = {Using semantic networks for data base management}, booktitle = {Proceedings of the 1st International Conference on Very Large Data Bases}, year = {1975}, month = {1975///}, pages = {144 - 172}, author = {Roussopoulos, Nick and Mylopoulos,J.} } @article {16798, title = {A max {m, n} algorithm for determining the graph H from its line graph G}, journal = {Information Processing Letters}, volume = {2}, year = {1973}, month = {1973///}, pages = {108 - 112}, author = {Roussopoulos, Nick} }