@article {19691, title = {Discovering Pronoun Categories using Discourse Information}, journal = {Proceedings of the 35th Annual Conference of the Cognitive Science Society}, year = {Submitted}, abstract = {Abstract Interpretation of a pronoun is driven by properties of syntactic distribution. Consequently, acquiring the meaning and the distribution are intertwined. In order to learn that a pronoun is reflexive, learners need to know which entity the pronoun refers to in a ...}, url = {http://ling.umd.edu/~naho/orita_cogsci2013.pdf}, author = {McKeown, R and Feldman, N H and Lidz, J and Jordan Boyd-Graber} } @article {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 {20295, title = {Biofilms Comprise a Component of the Annual Cycle of Vibrio cholerae in the Bay of Bengal Estuary}, journal = {mBio}, year = {2018}, month = {Feb-05-2018}, pages = {e00483-18}, abstract = {Vibrio cholerae, an estuarine bacterium, is the causative agent of cholera, a severe diarrheal disease that demonstrates seasonal incidence in Bangladesh. In an extensive study of V. cholerae occurrence in a natural aquatic environment, water and plankton samples were collected biweekly between December 2005 and November 2006 from Mathbaria, an estuarine village of Bangladesh near the mangrove forests of the Sundarbans. Toxigenic V. cholerae exhibited two seasonal growth peaks, one in spring (March to May) and another in autumn (September to November), corresponding to the two annual seasonal outbreaks of cholera in this region. The total numbers of bacteria determined by heterotrophic plate count (HPC), representing culturable bacteria, accounted for 1\% to 2.7\% of the total numbers obtained using acridine orange direct counting (AODC). The highest bacterial culture counts, including toxigenic V. cholerae, were recorded in the spring. The direct fluorescent antibody (DFA) assay was used to detect V. cholerae O1 cells throughout the year, as free-living cells, within clusters, or in association with plankton. V. cholerae O1 varied significantly in morphology, appearing as distinctly rod-shaped cells in the spring months, while small coccoid cells within thick clusters of biofilm were observed during interepidemic periods of the year, notably during the winter months. Toxigenic V. cholerae O1 was culturable in natural water during the spring when the temperature rose sharply. The results of this study confirmed biofilms to be a means of persistence for bacteria and an integral component of the annual life cycle of toxigenic V. cholerae in the estuarine environment of Bangladesh.}, doi = {10.1128/mBio.00483-18}, url = {https://mbio.asm.org/content/9/2/e00483-18}, author = {Sultana, Marzia and Nusrin, Suraia and Hasan, Nur A. and Sadique, Abdus and Ahmed, Kabir U. and Islam, Atiqul and Hossain, Anwar and Longini, Ira and Nizam, Azhar and Huq, Anwar and Siddique, Abul K. and Sack, David A. and Sack, Richard B. and Rita R Colwell and Alam, Munirul}, editor = {Vidaver, Anne K.} } @article {20288, title = {Characterization of the Microbiome at the World{\textquoteright}s Largest Potable Water Reuse Facility}, journal = {Frontiers in Microbiology}, year = {2018}, month = {Feb-10-2020}, abstract = {Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 {\texttimes} 106 copies in source, unchlorinated wastewater feed to 5.49 {\texttimes} 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature. Keywords: water reuse, pathogens, water purification, metatranscriptomics, metagenomics}, doi = {10.3389/fmicb.2018.02435}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2018.02435/full}, author = {Stamps, Blake W. and Leddy, Menu B. and Plumlee, Megan H. and Hasan, Nur A. and Rita R Colwell and Spear, John R.} } @article {20293, title = {Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments}, journal = {Frontiers in Microbiology}, year = {2018}, month = {Jan-06-2020}, doi = {10.3389/fmicb.2018.01361}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.01361/full}, author = {Hourigan, Suchitra K. and Subramanian, Poorani and Hasan, Nur A. and Ta, Allison and Klein, Elisabeth and Chettout, Nassim and Huddleston, Kathi and Deopujari, Varsha and Levy, Shira and Baveja, R and Clemency, Nicole C. and Baker, Robin L. and Niederhuber, John E. and Rita R Colwell} } @article {20300, title = {High-Throughput DNA Sequencing To Profile Microbial Water Quality Of Potable Reuse}, year = {2018}, url = {https://www.wateronline.com/doc/high-throughput-dna-sequencing-to-profile-microbial-water-quality-of-potable-reuse-0001}, author = {Menu B. Leddy and Megan H. Plumlee and Rose S. Kantor and Kara L. Nelson and Scott E. Miller and Lauren C. Kennedy and Blake W. Stamps and John R. Spear and Nur A. Hasan and Rita R Colwell} } @article {20307, title = {Characterization of Microbial Signatures From Advanced Treated Wastewater Biofilms}, journal = {Journal - American Water Works Association}, volume = {109}, year = {2017}, month = {Jan-11-2017}, pages = {E503 - E512}, abstract = {Next-generation sequencing (NGS) and metagenomics were used to identify microbial communities in biofilms of microfiltration (MF) and reverse osmosis (RO) membranes in an advanced water purification facility (AWPF) that treats municipal wastewater to produce potable quality water. Secondary treated wastewater effluent is the source of influent to the AWPF treatment train and was also characterized by NGS. Results show low bacterial diversity in biofilms obtained from the feed-side surfaces of MF and RO membranes. Microbial communities and antibiotic resistance genes (ARGs) in the RO biofilm were compared with those of the MF and influent, revealing lower abundance of bacterial species and ARGs in the RO biofilm than in the other samples. Opportunistic pathogens were detected in all samples; however, indicator bacteria, viruses, and bacteriophages were not detected in the RO biofilm. It is concluded that NGS has great potential for improved detection and characterization of microbial communities in biofilms that form on AWPF MF and RO membranes.}, doi = {10.5942/jawwa.2017.109.0116}, url = {http://doi.wiley.com/10.5942/jawwa.2017.109.0116}, author = {Leddy, Menu B. and Hasan, Nur A. and Subramanian, Poorani and Heberling, Colin and Cotruvo, Joseph and Rita R Colwell} } @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 {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 {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 {20341, title = {Building Infectious Disease Research Programs to Promote Security and Enhance Collaborations with Countries of the Former Soviet Union}, journal = {Frontiers in Public Health}, volume = {35361632}, year = {2015}, month = {Feb-11-2017}, doi = {10.3389/fpubh.2015.00271}, url = {http://journal.frontiersin.org/Article/10.3389/fpubh.2015.00271/abstract}, author = {Bartholomew, James C. and Pearson, Andrew D. and Stenseth, Nils C. and LeDuc, James W. and Hirschberg, David L. and Rita R Colwell} } @article {20348, title = {Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species}, journal = {Proceedings of the National Academy of Sciences}, year = {2015}, month = {Feb-05-2017}, pages = {E2813 - E2819}, abstract = {Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea.}, issn = {0027-8424}, doi = {10.1073/pnas.1503928112}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1503928112}, author = {Hasan, Nur A. and Grim, Christopher J. and Lipp, Erin K. and Rivera, Irma N. G. and Chun, Jongsik and Haley, Bradd J. and Taviani, Elisa and Choi, Seon Young and Hoq, Mozammel and Munk, A. Christine and Brettin, Thomas S. and Bruce, David and Challacombe, Jean F. and Detter, J. Chris and Han, Cliff S. and Eisen, Jonathan A. and Huq, Anwar and Rita R Colwell} } @article {20347, title = {Hybrid Vibrio~cholerae El Tor Lacking SXT Identified as the Cause of a Cholera Outbreak in the Philippines}, journal = {mBio}, year = {2015}, month = {Jan-05-2015}, abstract = {Cholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died. Vibrio cholerae O1 was confirmed as the etiological agent. Source attribution is critical in cholera outbreaks for proper management of the disease, as well as to control spread. In this study, three V. cholerae O1 isolates from a Philippines cholera outbreak were sequenced and their genomes analyzed to determine phylogenetic relatedness to V. cholerae O1 isolates from recent outbreaks of cholera elsewhere. The Philippines V. cholerae O1 isolates were determined to be V. cholerae O1 hybrid El Tor belonging to the seventh-pandemic clade. They clustered tightly, forming a monophyletic clade closely related to V. cholerae O1 hybrid El Tor from Asia and Africa. The isolates possess a unique multilocus variable-number tandem repeat analysis (MLVA) genotype (12-7-9-18-25 and 12-7-10-14-21) and lack SXT. In addition, they possess a novel 15-kb genomic island (GI-119) containing a predicted type I restriction-modification system. The CTXΦ-RS1 array of the Philippines isolates was similar to that of V. cholerae O1 MG116926, a hybrid El Tor strain isolated in Bangladesh in 1991. Overall, the data indicate that the Philippines V. cholerae O1 isolates are unique, differing from recent V. cholerae O1 isolates from Asia, Africa, and Haiti. Furthermore, the results of this study support the hypothesis that the Philippines isolates of V. cholerae O1 are indigenous and exist locally in the aquatic ecosystem of the Philippines.}, doi = {10.1128/mBio.00047-15}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00047-15}, author = {Klinzing, David C. and Choi, Seon Young and Hasan, Nur A. and Matias, Ronald R. and Tayag, Enrique and Geronimo, Josefina and Skowronski, Evan and Rashed, Shah M. and Kawashima, Kent and Rosenzweig, C. Nicole and Gibbons, Henry S. and Torres, Brian C. and Liles, Veni and Alfon, Alicia C. and Juan, Maria Luisa and Natividad, Filipinas F. and Cebula, Thomas A. and Rita R Colwell} } @article {20319, title = {Occurrence and Diversity of Clinically Important Vibrio Species in the Aquatic Environment of Georgia}, journal = {Frontiers in Public Health}, year = {2015}, month = {10/2015}, doi = {10.3389/fpubh.2015.00232}, url = {http://journal.frontiersin.org/Article/10.3389/fpubh.2015.00232/}, author = {Kokashvili, Tamar and Whitehouse, Chris A. and Tskhvediani, Ana and Grim, Christopher J. and Elbakidze, Tinatin and Mitaishvili, Nino and Janelidze, Nino and Jaiani, Ekaterine and Haley, Bradd J. and Lashkhi, Nino and Huq, Anwar and Rita R Colwell and Tediashvili, Marina} } @inbook {19631, title = {Can Optimally-Fair Coin Tossing Be Based on One-Way Functions?}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2014}, month = {2014/01/01/}, pages = {217 - 239}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Coin tossing is a basic cryptographic task that allows two distrustful parties to obtain an unbiased random bit in a way that neither party can bias the output by deviating from the protocol or halting the execution. Cleve [STOC{\textquoteright}86] showed that in any r round coin tossing protocol one of the parties can bias the output by Ω(1/r) through a {\textquotedblleft}fail-stop{\textquotedblright} attack; namely, they simply execute the protocol honestly and halt at some chosen point. In addition, relying on an earlier work of Blum [COMPCON{\textquoteright}82], Cleve presented an r-round protocol based on one-way functions that was resilient to bias at most O(1/r√)O(1/\sqrt r) . Cleve{\textquoteright}s work left open whether {\textquotedblright}{\textquoteleft}optimally-fair{\textquoteright}{\textquotedblright} coin tossing (i.e. achieving bias O(1/r) in r rounds) is possible. Recently Moran, Naor, and Segev [TCC{\textquoteright}09] showed how to construct optimally-fair coin tossing based on oblivious transfer, however, it was left open to find the minimal assumptions necessary for optimally-fair coin tossing. The work of Dachman-Soled et al. [TCC{\textquoteright}11] took a step toward answering this question by showing that any black-box construction of optimally-fair coin tossing based on a one-way functions with n-bit input and output needs Ω(n/logn) rounds. In this work we take another step towards understanding the complexity of optimally-fair coin-tossing by showing that this task (with an arbitrary number of rounds) cannot be based on one-way functions in a black-box way, as long as the protocol is {\textquotedblright}{\textquoteleft}oblivious{\textquoteright}{\textquotedblright} to the implementation of the one-way function. Namely, we consider a natural class of black-box constructions based on one-way functions, called function oblivious, in which the output of the protocol does not depend on the specific implementation of the one-way function and only depends on the randomness of the parties. Other than being a natural notion on its own, the known coin tossing protocols of Blum and Cleve (both based on one-way functions) are indeed function oblivious. Thus, we believe our lower bound for function-oblivious constructions is a meaningful step towards resolving the fundamental open question of the complexity of optimally-fair coin tossing.}, keywords = {Algorithm Analysis and Problem Complexity, black-box separations, Coin-Tossing, Computation by Abstract Devices, Data Encryption, Discrete Mathematics in Computer Science, One-Way Functions, Systems and Data Security}, isbn = {978-3-642-54241-1, 978-3-642-54242-8}, url = {http://link.springer.com/chapter/10.1007/978-3-642-54242-8_10}, author = {Dana Dachman-Soled and Mahmoody, Mohammad and Malkin, Tal}, editor = {Lindell, Yehuda} } @article {20361, title = {Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing}, journal = {PLoS ONE}, year = {2014}, month = {Aug-05-2015}, pages = {e97699}, abstract = {Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90\% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.}, doi = {10.1371/journal.pone.0097699}, url = {https://dx.plos.org/10.1371/journal.pone.0097699}, author = {Hasan, Nur A. and Young, Brian A. and Minard-Smith, Angela T. and Saeed, Kelly and Li, Huai and Heizer, Esley M. and McMillan, Nancy J. and Isom, Richard and Abdullah, Abdul Shakur and Bornman, Daniel M. and Faith, Seth A. and Choi, Seon Young and Dickens, Michael L. and Cebula, Thomas A. and Rita R Colwell}, editor = {Ahmed, Niyaz} } @article {20334, title = {Occurrence in Mexico, 1998{\textendash}2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage}, journal = {Proceedings of the National Academy of Sciences}, volume = {111}, year = {2014}, month = {Aug-07-2014}, pages = {9917 - 9922}, issn = {0027-8424}, doi = {10.1073/pnas.1323408111}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1323408111}, author = {Alam, Munirul and Rashed, Shah M and Mannan, Shahnewaj Bin and Islam, Tarequl and Lizarraga-Partida, Marcial L. and Delgado, Gabriela and Morales-Espinosa, Rosario and Mendez, Jose Luis and Navarro, Armando and Watanabe, Haruo and Ohnishi, Makoto and Hasan, Nur A. and Huq, Anwar and Sack, R. Bradley and Rita R Colwell and Cravioto, Alejandro} } @conference {19215, title = {Combining Crowdsourcing and Google Street View to Identify Street-level Accessibility Problems}, booktitle = {CHI 2013 To Appear}, year = {2013}, month = {2013}, abstract = {Poorly maintained sidewalks, missing curb ramps, and other obstacles pose considerable accessibility challenges; however, there are currently few if any, mechanisms to determine accessible areas of a city a priori. In this paper, we investigate the feasibility of using untrained crowd workers from Amazon Mechanical Turk (turkers) to find, label, and assess sidewalk accessibility problems in Google Street View imagery. We report on two studies: Study 1 examines the feasibility of this labeling task with six dedicated labelers including three wheelchair users; Study 2 investigates the comparative performance of turkers. In all, we collected 13,379 labels and 19,189 verification labels from a total of 402 turkers We show that turkers are capable of determining the presence of an accessibility problem with 81\% accuracy. With simple quality control methods, this number increases to 93\%. Our work demonstrates a promising new, highly scalable method for acquiring knowledge about sidewalk accessibility. }, author = {Hara, K. and Le, V. and Jon Froehlich} } @article {20363, title = {Engaging Actively with Issues in the Responsible Conduct of Science: Lessons from International Efforts Are Relevant for Undergraduate Education in the United States}, journal = {CBE{\textemdash}Life Sciences Education}, year = {2013}, month = {Jan-12-2013}, pages = {596 - 603}, abstract = {Numerous studies are demonstrating that engaging undergraduate students in original research can improve their achievement in the science, technology, engineering, and mathematics (STEM) fields and increase the likelihood that some of them will decide to pursue careers in these disciplines. Associated with this increased prominence of research in the undergraduate curriculum are greater expectations from funders, colleges, and universities that faculty mentors will help those students, along with their graduate students and postdoctoral fellows, develop an understanding and sense of personal and collective obligation for responsible conduct of science (RCS). This Feature describes an ongoing National Research Council (NRC) project and a recent report about educating faculty members in culturally diverse settings (Middle East/North Africa and Asia) to employ active-learning strategies to engage their students and colleagues deeply in issues related to RCS. The NRC report describes the first phase of this project, which took place in Aqaba and Amman, Jordan, in September 2012 and April 2013, respectively. Here we highlight the findings from that report and our subsequent experience with a similar interactive institute in Kuala Lumpur, Malaysia. Our work provides insights and perspectives for faculty members in the United States as they engage undergraduate and graduate students, as well as postdoctoral fellows, to help them better understand the intricacies of and connections among various components of RCS. Further, our experiences can provide insights for those who may wish to establish {\textquotedblleft}train-the-trainer{\textquotedblright} programs at their home institutions.}, doi = {10.1187/cbe.13-09-0184}, url = {https://www.lifescied.org/doi/10.1187/cbe.13-09-0184}, author = {Clements, John D. and Connell, Nancy D. and Dirks, Clarissa and El-Faham, Mohamed and Hay, Alastair and Heitman, Elizabeth and Stith, James H. and Bond, Enriqueta C. and Rita R Colwell and Anestidou, Lida and Husbands, Jo L. and Labov, Jay B.} } @article {19705, title = {Exploring Early Solutions for Automatically Identifying Inaccessible Sidewalks in the Physical World Using Google Street View}, journal = {HCIC 2013}, year = {2013}, month = {2013/00/01}, abstract = {Abstract Poorly maintained sidewalks , missing curb ramps, and other obstacles pose considerable accessibility challenges. Although pedestrian-and bicycle-oriented maps and associated routing algorithms continue to improve, there has been a lack of work focusing ...}, url = {http://www.cs.umd.edu/~jonf/publications/Hara_ExploringEarlySolutionsForAutomaticallyIdentifyingInaccessibleSidewalksInThePhysicalWorldUsingGoogleStreetView_HCIC2013.pdf}, author = {Hara, K and Le, V and Sun, J and Jacobs, D and Jon Froehlich} } @article {19700, title = {Improving public transit accessibility for blind riders by crowdsourcing bus stop landmark locations with Google street view}, journal = {The 15th International ACM SIGACCESS Conference}, year = {2013}, month = {2013/00/21}, pages = {16 - 8}, publisher = {SIGACCESS, ACM Special Interest Group on Accessible ComputingACM}, address = {New York, New York, USA}, abstract = {Abstract Low-vision and blind bus riders often rely on known physical landmarks to help locate and verify bus stop locations (eg., by searching for a shelter, bench, newspaper bin). However, there are currently few, if any, methods to determine this information a priori via ...}, isbn = {9781450324052}, doi = {10.1145/2513383.2513448}, url = {http://dl.acm.org/citation.cfm?doid=2513383.2513448}, author = {Hara, Kotaro and Azenkot, Shiri and Campbell, Megan and Bennett, Cynthia L and Le, Vicki and Pannella, Sean and Moore, Robert and Minckler, Kelly and Ng, Rochelle H and Jon Froehlich} } @article {20371, title = {A new integrative conjugative element detected in Haitian isolates of Vibrio cholerae non-O1/non-O139}, journal = {Research in Microbiology}, volume = {164}, year = {2013}, month = {Jan-11-2013}, pages = {891 - 893}, abstract = {The presence of SXT/R391-related integrating conjugative elements (ICEs) in Vibrio cholerae O1 and non-O1/non-O139 isolated from clinical and environmental samples in Haiti in 2010 was studied. The main finding of this work was the identification of the novel ICEVchHai2 among closely related V. cholerae non-O1/non-O139 clinical strains. The mosaic structure of this element confirms the role of ICEs as efficient recombination systems whereby new genetic material can be acquired and exchanged, according V. cholerae strains new accessory functions. }, issn = {09232508}, doi = {10.1016/j.resmic.2013.08.004}, url = {https://linkinghub.elsevier.com/retrieve/pii/S092325081300154X}, author = {Ceccarelli, Daniela and Spagnoletti, Matteo and Hasan, Nur A. and Lansing, Stephanie and Huq, Anwar and Rita R Colwell} } @article {19590, title = {Optimizing Abstract Abstract Machines}, journal = {arXiv:1211.3722 [cs]}, year = {2013}, note = {Comment: Proceedings of the International Conference on Functional Programming 2013 (ICFP 2013). Boston, Massachusetts. September, 2013}, month = {2013///}, abstract = {The technique of abstracting abstract machines (AAM) provides a systematic approach for deriving computable approximations of evaluators that are easily proved sound. This article contributes a complementary step-by-step process for subsequently going from a naive analyzer derived under the AAM approach, to an efficient and correct implementation. The end result of the process is a two to three order-of-magnitude improvement over the systematically derived analyzer, making it competitive with hand-optimized implementations that compute fundamentally less precise results.}, keywords = {Computer Science - Programming Languages, F.3.2}, url = {http://arxiv.org/abs/1211.3722}, author = {Johnson, J. Ian and Labich, Nicholas and Might, Matthew and David Van Horn} } @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 {20369, title = {Quantification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae in French Mediterranean coastal lagoons}, journal = {Research in Microbiology}, volume = {164}, year = {2013}, month = {Jan-10-2013}, pages = {867 - 874}, abstract = {Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae are human pathogens. Little is known about these Vibrio spp. in the coastal lagoons of France. The purpose of this study was to investigate their incidence in water, shellfish and sediment of three French Mediterranean coastal lagoons using the most probable number-polymerase chain reaction (MPN-PCR). In summer, the total number of V. parahaemolyticus in water, sediment, mussels and clams collected from the three lagoons varied from 1 to >1.1 {\texttimes} 103 MPN/l, 0.09 to 1.1 {\texttimes} 103 MPN/ml, 9 to 210 MPN/g and 1.5 to 2.1 MPN/g, respectively. In winter, all samples except mussels contained V. parahaemolyticus, but at very low concentrations. Pathogenic (tdh- or trh2-positive) V. parahaemolyticus were present in water, sediment and shellfish samples collected from these lagoons. The number of V. vulnificus in water, sediment and shellfish samples ranged from 1 to 1.1 {\texttimes} 103 MPN/l, 0.07 to 110 MPN/ml and 0.04 to 15 MPN/g, respectively, during summer. V. vulnificus was not detected during winter. V. cholerae was rarely detected in water and sediment during summer. In summary, results of this study highlight the finding that the three human pathogenic Vibrio spp. are present in the lagoons and constitute a potential public health hazard.}, issn = {09232508}, doi = {10.1016/j.resmic.2013.06.005}, url = {https://linkinghub.elsevier.com/retrieve/pii/S092325081300106X}, author = {Cantet, Franck and Hervio-Heath, Dominique and Caro, Audrey and Le Mennec, C{\'e}cile and Monteil, Caroline and Qu{\'e}m{\'e}r{\'e}, Catherine and Jolivet-Gougeon, Anne and Rita R Colwell and Monfort, Patrick} } @article {20064, title = {Understanding the impact of image quality on segmentation accuracy}, journal = {SPIE Newsroom}, year = {2013}, month = {2013}, author = {Li-Baboud, Ya-Shian and Cardone, Antonio and Chalfoun, Joe and Bajcsy, Peter and Elliott, John} } @inbook {19646, title = {Why {\textquotedblleft}Fiat-Shamir for Proofs{\textquotedblright} Lacks a Proof}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2013}, month = {2013/01/01/}, pages = {182 - 201}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {The Fiat-Shamir heuristic [CRYPTO {\textquoteright}86] is used to convert any 3-message public-coin proof or argument system into a non-interactive argument, by hashing the prover{\textquoteright}s first message to select the verifier{\textquoteright}s challenge. It is known that this heuristic is sound when the hash function is modeled as a random oracle. On the other hand, the surprising result of Goldwasser and Kalai [FOCS {\textquoteright}03] shows that there exists a computationally sound argument on which the Fiat-Shamir heuristic is never sound, when instantiated with any actual efficient hash function. This leaves us with the following interesting possibility: perhaps we can securely instantiates the Fiat-Shamir heuristic for all 3-message public-coin statistically sound proofs, even if we must fail for some computationally sound arguments. Indeed, this has been conjectured to be the case by Barak, Lindell and Vadhan [FOCS {\textquoteright}03], but we do not have any provably secure instantiation under any {\textquotedblleft}standard assumption{\textquotedblright}. In this work, we give a broad black-box separation result showing that the security of the Fiat-Shamir heuristic for statistically sound proofs cannot be proved under virtually any standard assumption via a black-box reduction. More precisely: {\textendash}If we want to have a {\textquotedblleft}universal{\textquotedblright} instantiation of the Fiat-Shamir heuristic that works for all 3-message public-coin proofs, then we cannot prove its security via a black-box reduction from any assumption that has the format of a {\textquotedblleft}cryptographic game{\textquotedblright}. {\textendash}For many concrete proof systems, if we want to have a {\textquotedblleft}specific{\textquotedblright} instantiation of the Fiat-Shamir heuristic for that proof system, then we cannot prove its security via a black box reduction from any {\textquotedblleft}falsifiable assumption{\textquotedblright} that has the format of a cryptographic game with an efficient challenger.}, keywords = {Algorithm Analysis and Problem Complexity, Computation by Abstract Devices, Data Encryption, Systems and Data Security}, isbn = {978-3-642-36593-5, 978-3-642-36594-2}, url = {http://link.springer.com/chapter/10.1007/978-3-642-36594-2_11}, author = {Bitansky, Nir and Dana Dachman-Soled and Garg, Sanjam and Jain, Abhishek and Kalai, Yael Tauman and L{\'o}pez-Alt, Adriana and Wichs, Daniel}, editor = {Sahai, Amit} } @article {19130, title = {AGORA: Assembly Guided by Optical Restriction Alignment}, journal = {BMC bioinformatics}, volume = {13}, year = {2012}, month = {2012}, abstract = {Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs). Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. However, optical maps have not previously been used within the genome assembly process. Here, we use optical map information within the popular de Bruijn graph assembly paradigm to eliminate paths in the de Bruijn graph which are not consistent with the optical map and help determine the correct reconstruction of the genome.We developed a new algorithm called AGORA: Assembly Guided by Optical Restriction Alignment. AGORA is the first algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. Our simulations on bacterial genomes show that AGORA is effective at producing assemblies closely matching the reference sequences. Additionally, we show that noise in the optical map can have a strong impact on the final assembly quality for some complex genomes, and we also measure how various characteristics of the starting de Bruijn graph may impact the quality of the final assembly. Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly. Our work shows that optical maps can be used effectively to assemble genomes within the de Bruijn graph assembly framework. Our experiments also provide insights into the characteristics of the mapping data that most affect the performance of our algorithm, indicating the potential benefit of more accurate optical mapping technologies, such as nano-coding. }, author = {Lin, H.C. and Goldstein, S. and Mendelowitz, L. and Zhou, S. and Wetzel, J. and Schwartz, D.C. and Pop, Mihai} } @article {19654, title = {BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection}, journal = {Proceedings of the National Academy of Sciences}, volume = {109}, year = {2012}, month = {2012/06/12/}, pages = {9575 - 9580}, abstract = {Cell proteins can restrict the replication of viruses. Here, we identify the cellular BclAF1 protein as a human cytomegalovirus restriction factor and describe two independent mechanisms the virus uses to decrease its steady-state levels. Immediately following infection, the viral pp71 and UL35 proteins, which are delivered to cells within virions, direct the proteasomal degradation of BclAF1. Although BclAF1 reaccumulates through the middle stages of infection, it is subsequently down-regulated at late times by miR-UL112-1, a virus-encoded microRNA. In the absence of BclAF1 neutralization, viral gene expression and replication are inhibited. These data identify two temporally and mechanistically distinct functions used by human cytomegalovirus to down-regulate a cellular antiviral protein.}, keywords = {innate immunity, intrinsic immunity, miRNA, Proteasome, UL82}, isbn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/content/109/24/9575}, author = {Lee, Song Hee and Kalejta, Robert F. and Kerry, Julie and Semmes, Oliver John and O{\textquoteright}Connor, Christine M. and Zia Khan and Garcia, Benjamin A. and Shenk, Thomas and Murphy, Eain} } @article {12980, title = {BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics}, journal = {Systematic BiologySyst Biol}, volume = {61}, year = {2012}, month = {2012/01/01/}, pages = {170 - 173}, abstract = {Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.}, keywords = {Bayesian phylogenetics, gpu, maximum likelihood, parallel computing}, isbn = {1063-5157, 1076-836X}, doi = {10.1093/sysbio/syr100}, url = {http://sysbio.oxfordjournals.org/content/61/1/170}, author = {Ayres,Daniel L and Darling,Aaron and Zwickl,Derrick J and Beerli,Peter and Holder,Mark T and Lewis,Paul O and Huelsenbeck,John P and Ronquist,Fredrik and Swofford,David L and Cummings, Michael P. and Rambaut,Andrew and Suchard,Marc A} } @conference {18541, title = {$\#$bias: Measuring the Tweeting Behavior of Propagandists}, booktitle = {Sixth International AAAI Conference on Weblogs and Social Media}, year = {2012}, month = {2012/05/20/}, abstract = {$\#$bias: Measuring the Tweeting Behavior of Propagandists}, url = {http://www.aaai.org/ocs/index.php/ICWSM/ICWSM12/paper/view/4588}, author = {Lumezanu,Cristian and Feamster, Nick and Klein,Hans} } @article {20063, title = {Biases from model assumptions in texture sub-cellular image segmentation}, journal = {SPIE Newsroom}, volume = {13}, year = {2012}, author = {Cardone, Antonio and Amelot, Julien and Li-Baboud, Ya-Shian and Brady, Mary and Bajcsy, Peter} } @article {15065, title = {Class consistent k-means: Application to face and action recognition}, journal = {Computer Vision and Image Understanding}, volume = {116}, year = {2012}, month = {2012/06//}, pages = {730 - 741}, abstract = {A class-consistent k-means clustering algorithm (CCKM) and its hierarchical extension (Hierarchical CCKM) are presented for generating discriminative visual words for recognition problems. In addition to using the labels of training data themselves, we associate a class label with each cluster center to enforce discriminability in the resulting visual words. Our algorithms encourage data points from the same class to be assigned to the same visual word, and those from different classes to be assigned to different visual words. More specifically, we introduce a class consistency term in the clustering process which penalizes assignment of data points from different classes to the same cluster. The optimization process is efficient and bounded by the complexity of k-means clustering. A very efficient and discriminative tree classifier can be learned for various recognition tasks via the Hierarchical CCKM. The effectiveness of the proposed algorithms is validated on two public face datasets and four benchmark action datasets.}, keywords = {Action recognition, Class consistent k-means, Discriminative tree classifier, face recognition, Supervised clustering}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2012.02.004}, url = {http://www.sciencedirect.com/science/article/pii/S1077314212000367}, author = {Zhuolin Jiang and Zhe Lin and Davis, Larry S.} } @inbook {12400, title = {Collecting Semantic Similarity Ratings to Connect Concepts in Assistive Communication Tools}, booktitle = {Modeling, Learning, and Processing of Text Technological Data StructuresModeling, Learning, and Processing of Text Technological Data Structures}, series = {Studies in Computational Intelligence}, volume = {370}, year = {2012}, month = {2012///}, pages = {81 - 93}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {To compensate for the common inability of people with lexical production impairments to access and express intended concepts, we make use of models of human semantic memory that build on the notion of semantic similarity and relatedness. Such models, constructed on evidence gained from psycholinguistic experiments, form the basis of a large lexical database, WordNet . We augment WordNet with many additional links among words and concepts that are semantically related. Making this densely connected semantic network available to people with anomic aphasia through assistive technologies should enable them to navigate among related words and concepts and retrieve the words that they intend to express.}, isbn = {978-3-642-22612-0}, url = {http://dx.doi.org/10.1007/978-3-642-22613-7_5}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Fellbaum,Christiane}, editor = {Mehler,Alexander and K{\"u}hnberger,Kai-Uwe and Lobin,Henning and L{\"u}ngen,Harald and Storrer,Angelika and Witt,Andreas} } @article {19128, title = {Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease}, journal = {PloS one}, volume = {7}, year = {2012}, month = {2012}, abstract = {The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ~90\%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.}, author = {Liu,B. and Faller, L.L. and Klitgord, N. and Mazumdar, V. and Ghodsi,M. and Sommer, D.D. and Gibbons, T.R. and Treangen, T.J. and Chang, Y.C. and Li,S.} } @conference {19218, title = {The design and evaluation of prototype eco-feedback displays for fixture-level water usage data}, year = {2012}, month = {2012}, pages = {2367 - 2376}, publisher = {ACM}, organization = {ACM}, isbn = {145031015X}, author = {Jon Froehlich and Findlater,L. and Ostergren, M. and Ramanathan, S. and Peterson,J. and Wragg, I. and Larson,E. and Fu, F. and Bai, M. and Patel,S.} } @article {14328, title = {Disaggregated water sensing from a single, pressure-based sensor: An extended analysis of HydroSense using staged experiments}, journal = {Pervasive and Mobile Computing}, volume = {8}, year = {2012}, month = {2012/02//}, pages = {82 - 102}, abstract = {We present an extended analysis of our previous work on the HydroSense technology, which is a low-cost and easily installed single-point sensor of pressure for automatically disaggregating water usage activities in the home (Froehlich et~al., 2009~[53]). We expand upon this work by providing a survey of existing and emerging water disaggregation techniques, a more comprehensive description of the theory of operation behind our approach, and an expanded analysis section that includes hot versus cold water valve usage classification and a comparison between two classification approaches: the template-based matching scheme used in Froehlich et~al. (2009)~[53] and a new stochastic approach using a Hidden Markov Model. We show that both are successful in identifying valve- and fixture-level water events with greater than 90\% accuracies. We conclude with a discussion of the limitations in our experimental methodology and open problems going forward.}, keywords = {Activity sensing, H1.2, H5.2, Infrastructure-mediated sensing, Sensors, Water usage}, isbn = {1574-1192}, doi = {10.1016/j.pmcj.2010.08.008}, url = {http://www.sciencedirect.com/science/article/pii/S1574119210000842}, author = {Larson,Eric and Jon Froehlich and Campbell,Tim and Haggerty,Conor and Atlas,Les and Fogarty,James and Patel,Shwetak N.} } @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.} } @article {20387, title = {Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)}, journal = {Applied and Environmental Microbiology}, year = {2012}, month = {Mar-10-2013}, pages = {7249 - 7257}, abstract = {Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.}, issn = {0099-2240}, doi = {10.1128/AEM.01296-12}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01296-12}, author = {Johnson, Crystal N. and Bowers, John C. and Griffitt, Kimberly J. and Molina, Vanessa and Clostio, Rachel W. and Pei, Shaofeng and Laws, Edward and Paranjpye, Rohinee N. and Strom, Mark S. and Chen, Arlene and Hasan, Nur A. and Huq, Anwar and Noriea, Nicholas F. and Grimes, D. Jay and Rita R Colwell} } @article {19612, title = {Efficient Verification of Web-content Searching Through Authenticated Web Crawlers}, journal = {Proc. VLDB Endow.}, volume = {5}, year = {2012}, month = {2012/06//}, pages = {920 - 931}, abstract = {We consider the problem of verifying the correctness and completeness of the result of a keyword search. We introduce the concept of an authenticated web crawler and present its design and prototype implementation. An authenticated web crawler is a trusted program that computes a specially-crafted signature over the web contents it visits. This signature enables (i) the verification of common Internet queries on web pages, such as conjunctive keyword searches---this guarantees that the output of a conjunctive keyword search is correct and complete; (ii) the verification of the content returned by such Internet queries---this guarantees that web data is authentic and has not been maliciously altered since the computation of the signature by the crawler. In our solution, the search engine returns a cryptographic proof of the query result. Both the proof size and the verification time are proportional only to the sizes of the query description and the query result, but do not depend on the number or sizes of the web pages over which the search is performed. As we experimentally demonstrate, the prototype implementation of our system provides a low communication overhead between the search engine and the user, and fast verification of the returned results by the user.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=2336664.2336666}, author = {Goodrich, Michael T. and Charalampos Papamanthou and Nguyen, Duy and Tamassia, Roberto and Lopes, Cristina Videira and Ohrimenko, Olga and Triandopoulos, Nikos} } @article {14330, title = {Fast track article: Disaggregated water sensing from a single, pressure-based sensor: An extended analysis of HydroSense using staged experiments}, journal = {Pervasive Mob. Comput.}, volume = {8}, year = {2012}, month = {2012/02//}, pages = {82 - 102}, abstract = {We present an extended analysis of our previous work on the HydroSense technology, which is a low-cost and easily installed single-point sensor of pressure for automatically disaggregating water usage activities in the home (Froehlich et al., 2009 [53]). We expand upon this work by providing a survey of existing and emerging water disaggregation techniques, a more comprehensive description of the theory of operation behind our approach, and an expanded analysis section that includes hot versus cold water valve usage classification and a comparison between two classification approaches: the template-based matching scheme used in Froehlich et al. (2009) [53] and a new stochastic approach using a Hidden Markov Model. We show that both are successful in identifying valve- and fixture-level water events with greater than 90\% accuracies. We conclude with a discussion of the limitations in our experimental methodology and open problems going forward.}, keywords = {Activity sensing, H1.2, H5.2, Infrastructure-mediated sensing, Sensors, Water usage}, isbn = {1574-1192}, doi = {10.1016/j.pmcj.2010.08.008}, url = {http://dx.doi.org/10.1016/j.pmcj.2010.08.008}, author = {Larson,Eric and Jon Froehlich and Campbell,Tim and Haggerty,Conor and Atlas,Les and Fogarty,James and Patel,Shwetak N.} } @conference {19217, title = {A feasibility study of crowdsourcing and google street view to determine sidewalk accessibility}, year = {2012}, month = {2012}, pages = {273 - 274}, publisher = {ACM}, organization = {ACM}, isbn = {1450313213}, author = {Hara, K. and Le, V. and Jon Froehlich} } @article {16267, title = {Gene Prediction with Glimmer for Metagenomic Sequences Augmented by Classification and Clustering}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {40}, year = {2012}, month = {2012/01/01/}, pages = {e9-e9 - e9-e9}, abstract = {Environmental shotgun sequencing (or metagenomics) is widely used to survey the communities of microbial organisms that live in many diverse ecosystems, such as the human body. Finding the protein-coding genes within the sequences is an important step for assessing the functional capacity of a metagenome. In this work, we developed a metagenomics gene prediction system Glimmer-MG that achieves significantly greater accuracy than previous systems via novel approaches to a number of important prediction subtasks. First, we introduce the use of phylogenetic classifications of the sequences to model parameterization. We also cluster the sequences, grouping together those that likely originated from the same organism. Analogous to iterative schemes that are useful for whole genomes, we retrain our models within each cluster on the initial gene predictions before making final predictions. Finally, we model both insertion/deletion and substitution sequencing errors using a different approach than previous software, allowing Glimmer-MG to change coding frame or pass through stop codons by predicting an error. In a comparison among multiple gene finding methods, Glimmer-MG makes the most sensitive and precise predictions on simulated and real metagenomes for all read lengths and error rates tested.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkr1067}, url = {http://nar.oxfordjournals.org/content/40/1/e9}, author = {Kelley,David R and Liu,Bo and Delcher,Arthur L. and Pop, Mihai and Salzberg,Steven L.} } @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 {19660, title = {Global secretome analysis identifies novel mediators of bone metastasis}, journal = {Cell Research}, volume = {22}, year = {2012}, month = {2012/09//}, pages = {1339 - 1355}, abstract = {Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis. Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1, CST2, and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1. Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.}, keywords = {bone, cancer, metastasis, proteomics, secretome}, isbn = {1001-0602}, url = {http://www.nature.com/cr/journal/v22/n9/abs/cr201289a.html}, author = {Blanco, Mario Andres and LeRoy, Gary and Zia Khan and Ale{\v c}kovi{\'c}, Ma{\v s}a and Zee, Barry M. and Garcia, Benjamin A. and Kang, Yibin} } @conference {18848, title = {Gripper synthesis for indirect manipulation of cells using Holographic Optical Tweezers}, year = {2012}, month = {2012/05//}, pages = {2749 - 2754}, abstract = {Optical Tweezers (OT) are used for highly accurate manipulations of biological cells. However, the direct exposure of cells to focused laser beam may negatively influence their biological functions. In order to overcome this problem, we generate multiple optical traps to grab and move a 3D ensemble of inert particles such as silica microspheres to act as a reconfigurable gripper for a manipulated cell. The relative positions of the microspheres are important in order for the gripper to be robust against external environmental forces and the exposure of high intensity laser on the cell to be minimized. In this paper, we present results of different gripper configurations, experimentally tested using our OT setup, that provide robust gripping as well as minimize laser intensity experienced by the cell. We developed a computational approach that allowed us to perform preliminary modeling and synthesis of the gripper configurations. The gripper synthesis is cast as a multi-objective optimization problem.}, doi = {10.1109/ICRA.2012.6225153}, author = {Chowdhury,Sagar and Svec,Petr and Wang,Chenlu and Losert,Wolfgang and Gupta, Satyandra K.} } @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 {19216, title = {Individuals among commuters: Building personalised transport information services from fare collection systems}, journal = {Pervasive and Mobile Computing}, year = {2012}, month = {2012}, author = {Lathia,N. and Smith,C. and Jon Froehlich and Capra,L.} } @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 {13829, title = {Modality and Negation in SIMT Use of Modality and Negation in Semantically-Informed Syntactic MT}, journal = {Computational Linguistics}, year = {2012}, month = {2012///}, pages = {1 - 48}, abstract = {This paper describes the resource- and system-building efforts of an eight-week Johns Hopkins University Human Language Technology Center of Excellence Summer Camp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation (SIMT). We describe a new modality/negation (MN) annotation scheme, the creation of a (publicly available) MN lexicon, and two automated MN taggers that we built using the annotation scheme and lexicon. Our annotation scheme isolates three components of modality and negation: a trigger (a word that conveys modality or negation), a target (an action associated with modality or negation) and a holder (an experiencer of modality). We describe how our MN lexicon was semi-automatically produced and we demonstrate that a structure-based MN tagger results in precision around 86\% (depending on genre) for tagging of a standard LDC data set.}, isbn = {0891-2017}, doi = {10.1162/COLI_a_00099}, url = {http://dx.doi.org/10.1162/COLI_a_00099}, author = {Baker,Kathryn and Bloodgood,Michael and Dorr, Bonnie J and Callison-Burch,Chris and Filardo,Nathaniel W. and Piatko,Christine and Levin,Lori and Miller,Scott} } @conference {17641, title = {Optimizing epidemic protection for socially essential workers}, booktitle = {Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium}, series = {IHI {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {31 - 40}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Public-health policy makers have many tools to mitigate an epidemic{\textquoteright}s effects. Most related research focuses on the direct effects on those infected (in terms of health, life, or productivity). Interventions including treatment, prophylaxis, quarantine, and social distancing are well studied in this context. These interventions do not address indirect effects due to the loss of critical services and infrastructures when too many of those responsible for their day-to-day operations fall ill. We examine, both analytically and through simulation, the protection of such essential subpopulations by sequestering them, effectively isolating them into groups during an epidemic. We develop a framework for studying the benefits of sequestering and heuristics for when to sequester. We also prove a key property of sequestering placement which helps partition the subpopulations optimally. Thus we provide a first step toward determining how to allocate resources between the direct protection of a population, and protection of those responsible for critical services.}, keywords = {epidemiology, OPTIMIZATION, public health informatics}, isbn = {978-1-4503-0781-9}, doi = {10.1145/2110363.2110371}, url = {http://doi.acm.org/10.1145/2110363.2110371}, author = {Barrett,Chris and Beckman,Richard and Bisset,Keith and Chen,Jiangzhuo and DuBois,Thomas and Eubank,Stephen and Kumar,V. S. Anil and Lewis,Bryan and Marathe,Madhav V. and Srinivasan, Aravind and Stretz,Paula E.} } @article {14415, title = {Organizing User Search Histories}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {24}, year = {2012}, month = {2012/05//}, pages = {912 - 925}, abstract = {Users are increasingly pursuing complex task-oriented goals on the web, such as making travel arrangements, managing finances, or planning purchases. To this end, they usually break down the tasks into a few codependent steps and issue multiple queries around these steps repeatedly over long periods of time. To better support users in their long-term information quests on the web, search engines keep track of their queries and clicks while searching online. In this paper, we study the problem of organizing a user{\textquoteright}s historical queries into groups in a dynamic and automated fashion. Automatically identifying query groups is helpful for a number of different search engine components and applications, such as query suggestions, result ranking, query alterations, sessionization, and collaborative search. In our approach, we go beyond approaches that rely on textual similarity or time thresholds, and we propose a more robust approach that leverages search query logs. We experimentally study the performance of different techniques, and showcase their potential, especially when combined together.}, keywords = {alteration;query, analysis;user, engines;search, engines;text, goal;textual, group, historical, History, identification;query, information, interfaces;, log;sessionization;task-oriented, organization;query, processing;search, query, query;user, quest;query, ranking;search, search, search;long-term, similarity;time, suggestion;result, threshold;user, Web;collaborative}, isbn = {1041-4347}, doi = {10.1109/TKDE.2010.251}, author = {Hwang,Heasoo and Lauw,H. W and Getoor, Lise and Ntoulas,A.} } @conference {19219, title = {Personal informatics in practice: improving quality of life through data}, year = {2012}, month = {2012}, pages = {2799 - 2802}, publisher = {ACM}, organization = {ACM}, isbn = {1450310168}, author = {Li, I. and Medynskiy, Y. and Jon Froehlich and Larsen, J.} } @article {15067, title = {Recognizing Human Actions by Learning and Matching Shape-Motion Prototype Trees}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {34}, year = {2012}, month = {2012/03//}, pages = {533 - 547}, abstract = {A shape-motion prototype-based approach is introduced for action recognition. The approach represents an action as a sequence of prototypes for efficient and flexible action matching in long video sequences. During training, an action prototype tree is learned in a joint shape and motion space via hierarchical K-means clustering and each training sequence is represented as a labeled prototype sequence; then a look-up table of prototype-to-prototype distances is generated. During testing, based on a joint probability model of the actor location and action prototype, the actor is tracked while a frame-to-prototype correspondence is established by maximizing the joint probability, which is efficiently performed by searching the learned prototype tree; then actions are recognized using dynamic prototype sequence matching. Distance measures used for sequence matching are rapidly obtained by look-up table indexing, which is an order of magnitude faster than brute-force computation of frame-to-frame distances. Our approach enables robust action matching in challenging situations (such as moving cameras, dynamic backgrounds) and allows automatic alignment of action sequences. Experimental results demonstrate that our approach achieves recognition rates of 92.86 percent on a large gesture data set (with dynamic backgrounds), 100 percent on the Weizmann action data set, 95.77 percent on the KTH action data set, 88 percent on the UCF sports data set, and 87.27 percent on the CMU action data set.}, keywords = {action prototype, actor location, brute-force computation, CMU action data set, distance measures, dynamic backgrounds, dynamic prototype sequence matching, flexible action matching, frame-to-frame distances, frame-to-prototype correspondence, hierarchical k-means clustering, human action recognition, Image matching, image recognition, Image sequences, joint probability model, joint shape, KTH action data set, large gesture data set, learning, learning (artificial intelligence), look-up table indexing, motion space, moving cameras, pattern clustering, prototype-to-prototype distances, shape-motion prototype-based approach, table lookup, training sequence, UCF sports data set, Video sequences, video signal processing, Weizmann action data set}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2011.147}, author = {Zhuolin Jiang and Zhe Lin and Davis, Larry S.} } @article {18716, title = {Structural and biochemical studies of the open state of Lys48-linked diubiquitin}, journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research}, year = {2012}, month = {2012///}, abstract = {Ubiquitin (Ub) is a small protein highly conserved among eukaryotes and involved in practically all aspects of eukaryotic cell biology. Polymeric chains assembled from covalently-linked Ub monomers function as molecular signals in the regulation of a host of cellular processes. Our previous studies have shown that the predominant state of Lys48-linked di- and tetra-Ub chains at near-physiological conditions is a closed conformation, in which the Ub{\textendash}Ub interface is formed by the hydrophobic surface residues of the adjacent Ub units. Because these very residues are involved in (poly)Ub interactions with the majority of Ub-binding proteins, their sequestration at the Ub{\textendash}Ub interface renders the closed conformation of polyUb binding incompetent. Thus the existence of open conformation(s) and the interdomain motions opening and closing the Ub{\textendash}Ub interface is critical for the recognition of Lys48-linked polyUb by its receptors. Knowledge of the conformational properties of a polyUb signal is essential for our understanding of its specific recognition by various Ub-receptors. Despite their functional importance, open states of Lys48-linked chains are poorly characterized. Here we report a crystal structure of the open state of Lys48-linked di-Ub. Moreover, using NMR, we examined interactions of the open state of this chain (at pH4.5) with a Lys48-linkage-selective receptor, the UBA2 domain of a shuttle protein hHR23a. Our results show that di-Ub binds UBA2 in the same mode and with comparable affinity as the closed state. Our data suggest a mechanism for polyUb signal recognition, whereby Ub-binding proteins select specific conformations out of the available ensemble of polyUb chain conformations. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics.}, keywords = {Lys48-linked diubiquitin, Lysine-48 linkage selectivity, polyubiquitin, ubiquitin, Ubiquitin-associated domain}, isbn = {0167-4889}, doi = {10.1016/j.bbamcr.2012.04.003}, url = {http://www.sciencedirect.com/science/article/pii/S0167488912000948}, author = {Lai,Ming-Yih and Zhang,Daoning and LaRonde-LeBlanc,Nicole and Fushman, David} } @conference {19374, title = {Sub-cellular feature detection and automated extraction of collocalized actin and myosin regions}, booktitle = {the 2nd ACM SIGHIT symposiumProceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI {\textquoteright}12}, year = {2012}, pages = {399}, publisher = {ACM Press}, organization = {ACM Press}, address = {Miami, Florida, USANew York, New York, USA}, isbn = {9781450307819}, doi = {10.1145/211036310.1145/2110363.2110409}, author = {Martineau, Justin and Mokashi,Ronil and Chapman, David and Grasso, Michael and Brady,Mary and Yesha,Yelena and Yesha,Yaacov and Cardone, Antonio and Dima, Alden} } @article {19220, title = {Systems and Methods for Energy Harvesting in a Contained Fluid Circuit}, year = {2012}, month = {2012}, publisher = {UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION, CAMPBELL, Tim, LARSON, Eric, COHN, Gabriel, ALCAIDE, Ramses, FROEHLICH, Jon, PATEL, Shwetak}, abstract = {Systems and methods for harvesting energy from a closed fluid circuit, such as a water pipe system in a building. An energy harvester can be installed at a point in a water circuit and can generate energy from pressure differentials caused when a valve is opened or closed at any other point in the water circuit that is in fluid communication with the energy harvester. The energy can be used to power, for example, a sensor and/or a transmitter., L{\textquoteright}invention concerne des syst{\`e}mes et des proc{\'e}d{\'e}s de collecte de l{\textquoteright}{\'e}nergie qui provient d{\textquoteright}un circuit de fluide ferm{\'e}, comme un syst{\`e}me de conduites d{\textquoteright}eau dans un immeuble. Un collecteur d{\textquoteright}{\'e}nergie peut {\^e}tre install{\'e} {\`a} un certain point au sein d{\textquoteright}un circuit d{\textquoteright}eau et peut g{\'e}n{\'e}rer de l{\textquoteright}{\'e}nergie {\`a} partir des diff{\'e}rentiels de pression provoqu{\'e}s lorsqu{\textquoteright}une soupape est ouverte ou ferm{\'e}e {\`a} n{\textquoteright}importe quel autre point au sein du circuit d{\textquoteright}eau qui est en communication fluidique avec le collecteur d{\textquoteright}{\'e}nergie. L{\textquoteright}{\'e}nergie peut {\^e}tre utilis{\'e}e pour alimenter, par exemple, un capteur et/ou un {\'e}metteur.}, keywords = {Systems and Methods for Energy Harvesting in a Contained Fluid Circuit}, isbn = {WO/2012/021551}, url = {http://patentscope.wipo.int/search/en/WO2012021551}, author = {Campbell,Tim and Larson,Eric and Cohn, Gabriel and Alcaide,Ramses and Jon Froehlich and Patel,Shwetak} } @article {18605, title = {Towards a cost model for network traffic}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {42}, year = {2012}, month = {2012///}, pages = {54 - 60}, abstract = {We develop a holistic cost model that operators can use to help evaluate the costs of various routing and peering decisions. Using real traffic data from a large carrier network, we show how network operators can use this cost model to significantly reduce the cost of carrying traffic in their networks. We find that adjusting the routing for a small fraction of total flows (and total traffic volume) significantly reduces cost in many cases. We also show how operators can use the cost model both to evaluate potential peering arrangements and for other network operations problems.}, keywords = {cost optimization, traffic cost model}, isbn = {0146-4833}, doi = {10.1145/2096149.2096157}, url = {http://doi.acm.org/10.1145/2096149.2096157}, author = {Motiwala,Murtaza and Dhamdhere,Amogh and Feamster, Nick and Lakhina,Anukool} } @article {19618, title = {Verifying Search Results Over Web Collections}, journal = {arXiv:1204.5446 [cs]}, year = {2012}, month = {2012/04/24/}, abstract = {Searching accounts for one of the most frequently performed computations over the Internet as well as one of the most important applications of outsourced computing, producing results that critically affect users{\textquoteright} decision-making behaviors. As such, verifying the integrity of Internet-based searches over vast amounts of web contents is essential. We provide the first solution to this general security problem. We introduce the concept of an authenticated web crawler and present the design and prototype implementation of this new concept. An authenticated web crawler is a trusted program that computes a special "signature" $s$ of a collection of web contents it visits. Subject to this signature, web searches can be verified to be correct with respect to the integrity of their produced results. This signature also allows the verification of complicated queries on web pages, such as conjunctive keyword searches. In our solution, along with the web pages that satisfy any given search query, the search engine also returns a cryptographic proof. This proof, together with the signature $s$, enables any user to efficiently verify that no legitimate web pages are omitted from the result computed by the search engine, and that no pages that are non-conforming with the query are included in the result. An important property of our solution is that the proof size and the verification time both depend solely on the sizes of the query description and the query result, but not on the number or sizes of the web pages over which the search is performed. Our authentication protocols are based on standard Merkle trees and the more involved bilinear-map accumulators. As we experimentally demonstrate, the prototype implementation of our system gives a low communication overhead between the search engine and the user, and allows for fast verification of the returned results on the user side.}, keywords = {Computer Science - Cryptography and Security}, url = {http://arxiv.org/abs/1204.5446}, author = {Goodrich, Michael T. and Nguyen, Duy and Ohrimenko, Olga and Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikos and Lopes, Cristina Videira} } @article {19717, title = {Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.}, journal = {PLoS Negl Trop Dis}, volume = {6}, year = {2012}, month = {2012}, pages = {e1853}, abstract = {

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

}, keywords = {DNA, Bacterial, Evolution, Molecular, Gene Transfer, Horizontal, Genome, Bacterial, Genomic islands, HUMANS, Leptospira, Molecular Sequence Data, Multigene Family, Prophages, Sequence Analysis, DNA, Virulence factors}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0001853}, author = {Ricaldi, Jessica N and Fouts, Derrick E and Jeremy D Selengut and Harkins, Derek M and Patra, Kailash P and Moreno, Angelo and Lehmann, Jason S and Purushe, Janaki and Sanka, Ravi and Torres, Michael and Webster, Nicholas J and Vinetz, Joseph M and Matthias, Michael A} } @article {16241, title = {Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences}, journal = {BMC Genomics}, volume = {12}, year = {2011}, month = {2011/07/27/}, pages = {S4 - S4}, abstract = {A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-12-S2-S4}, url = {http://www.biomedcentral.com/1471-2164/12/S2/S4}, author = {Liu,Bo and Gibbons,Theodore and Ghodsi,Mohammad and Treangen,Todd and Pop, Mihai} } @article {15158, title = {On Achieving the" Best of Both Worlds" in Secure Multiparty Computation}, journal = {SIAM Journal on Computing}, volume = {40}, year = {2011}, month = {2011///}, pages = {122 - 122}, abstract = {Two settings are traditionally considered for secure multiparty computation, de-pending on whether or not a majority of the parties are assumed to be honest. Existing protocols that assume an honest majority provide {\textquotedblleft}full security{\textquotedblright} (and, in particular, guarantee output delivery and fairness) when this assumption holds, but are completely insecure if this assumption is violated. On the other hand, known protocols tolerating an arbitrary number of corruptions do not guarantee fairness or output delivery even if only a single party is dishonest. It is natural to wonder whether it is possible to achieve the {\textquotedblleft}best of both worlds{\textquotedblright}: namely, a single protocol that simultaneously achieves the best possible security in both the above settings. Here, we rule out this possibility (at least for general functionalities) and show some positive results regarding what can be achieved. }, author = {Ishai,Y. and Katz, Jonathan and Kushilevitz,E. and Lindell,Y. and Petrank,E.} } @conference {16815, title = {Adapting a map query interface for a gesturing touch screen interface}, booktitle = {Proceedings of the 20th international conference companion on World wide web}, series = {WWW {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {257 - 260}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {NewsStand is an example application of a general framework that we are developing to enable searching for information using a map query interface, where the information results from monitoring the output of over 8,000 RSS news sources and is available for retrieval within minutes of publication. The user interface of NewsStand was recently adapted so that NewsStand can execute on mobile and tablet devices with a gesturing touch screen interface such as the iPhone, iPod Touch, and iPad. This action led to a discovery of some shortcomings of current mapping APIs as well as devising some interesting new widgets. These issues are discussed, and the realization can be seen by a demo at http://newsstand.umiacs.umd.edu on any of the above Apple devices as well as other devices that support gestures such as an Android phone.}, keywords = {map query interface, newsstand, touch screen gesturing interface}, isbn = {978-1-4503-0637-9}, doi = {10.1145/1963192.1963303}, url = {http://doi.acm.org/10.1145/1963192.1963303}, author = {Samet, Hanan and Teitler,Benjamin E. and Adelfio,Marco D. and Lieberman,Michael D.} } @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} } @inbook {19640, title = {On the Black-Box Complexity of Optimally-Fair Coin Tossing}, booktitle = {Theory of Cryptography}, series = {Lecture Notes in Computer Science}, year = {2011}, month = {2011/01/01/}, pages = {450 - 467}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {A fair two-party coin tossing protocol is one in which both parties output the same bit that is almost uniformly distributed (i.e., it equals 0 and 1 with probability that is at most negligibly far from one half). It is well known that it is impossible to achieve fair coin tossing even in the presence of fail-stop adversaries (Cleve, FOCS 1986). In fact, Cleve showed that for every coin tossing protocol running for r rounds, an efficient fail-stop adversary can bias the output by Ω(1/r). Since this is the best possible, a protocol that limits the bias of any adversary to O(1/r) is called optimally-fair. The only optimally-fair protocol that is known to exist relies on the existence of oblivious transfer, because it uses general secure computation (Moran, Naor and Segev, TCC 2009). However, it is possible to achieve a bias of O(1/r√)O(1/\sqrt{r}) in r rounds relying only on the assumption that there exist one-way functions. In this paper we show that it is impossible to achieve optimally-fair coin tossing via a black-box construction from one-way functions for r that is less than O(n/logn), where n is the input/output length of the one-way function used. An important corollary of this is that it is impossible to construct an optimally-fair coin tossing protocol via a black-box construction from one-way functions whose round complexity is independent of the security parameter n determining the security of the one-way function being used. Informally speaking, the main ingredient of our proof is to eliminate the random-oracle from {\textquotedblleft}secure{\textquotedblright} protocols with {\textquotedblleft}low round-complexity{\textquotedblright} and simulate the protocol securely against semi-honest adversaries in the plain model. We believe our simulation lemma to be of broader interest.}, keywords = {Algorithm Analysis and Problem Complexity, black-box separations, Coding and Information Theory, coin tossing, Computer Communication Networks, Data Encryption, lower-bound, Math Applications in Computer Science, optimally-fair coin tossing, round-complexity, Systems and Data Security}, isbn = {978-3-642-19570-9, 978-3-642-19571-6}, url = {http://link.springer.com/chapter/10.1007/978-3-642-19571-6_27}, author = {Dana Dachman-Soled and Lindell, Yehuda and Mahmoody, Mohammad and Malkin, Tal}, editor = {Ishai, Yuval} } @conference {18551, title = {Boosting the scalability of botnet detection using adaptive traffic sampling}, booktitle = {Proceedings of the 6th ACM Symposium on Information, Computer and Communications Security}, series = {ASIACCS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {124 - 134}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Botnets pose a serious threat to the health of the Internet. Most current network-based botnet detection systems require deep packet inspection (DPI) to detect bots. Because DPI is a computational costly process, such detection systems cannot handle large volumes of traffic typical of large enterprise and ISP networks. In this paper we propose a system that aims to efficiently and effectively identify a small number of suspicious hosts that are likely bots. Their traffic can then be forwarded to DPI-based botnet detection systems for fine-grained inspection and accurate botnet detection. By using a novel adaptive packet sampling algorithm and a scalable spatial-temporal flow correlation approach, our system is able to substantially reduce the volume of network traffic that goes through DPI, thereby boosting the scalability of existing botnet detection systems. We implemented a proof-of-concept version of our system, and evaluated it using real-world legitimate and botnet-related network traces. Our experimental results are very promising and suggest that our approach can enable the deployment of botnet-detection systems in large, high-speed networks.}, keywords = {adaptive sampling, botnet, intrusion detection, NETWORK SECURITY}, isbn = {978-1-4503-0564-8}, doi = {10.1145/1966913.1966930}, url = {http://doi.acm.org/10.1145/1966913.1966930}, author = {Zhang,Junjie and Luo,Xiapu and Perdisci,Roberto and Gu,Guofei and Lee,Wenke and Feamster, Nick} } @conference {12105, title = {A case study of measuring process risk for early insights into software safety}, booktitle = {Software Engineering (ICSE), 2011 33rd International Conference on}, year = {2011}, month = {2011/05//}, pages = {623 - 632}, abstract = {In this case study, we examine software safety risk in three flight hardware systems in NASA{\textquoteright}s Constellation spaceflight program. We applied our Technical and Process Risk Measurement (TPRM) methodology to the Constellation hazard analysis process to quantify the technical and process risks involving software safety in the early design phase of these projects. We analyzed 154 hazard reports and collected metrics to measure the prevalence of software in hazards and the specificity of descriptions of software causes of hazardous conditions. We found that 49-70\% of 154 hazardous conditions could be caused by software or software was involved in the prevention of the hazardous condition. We also found that 12-17\% of the 2013 hazard causes involved software, and that 23-29\% of all causes had a software control. The application of the TRPM methodology identified process risks in the application of the hazard analysis process itself that may lead to software safety risk.}, keywords = {analysis;software, and, computing;risk, constellation, control;software, Hardware, maintenance;, measurement;aerospace, measurement;software, NASA, process, program;TPRM;flight, risk, safety;technical, spaceflight, systems;process}, doi = {10.1145/1985793.1985881}, author = {Layman,L. and Basili, Victor R. and Zelkowitz, Marvin V and Fisher,K.L.} } @conference {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} } @article {15126, title = {Complete Fairness in Secure Two-Party Computation}, journal = {Journal of the ACM}, volume = {58}, year = {2011}, month = {2011/12//}, pages = {24:1{\textendash}24:37 - 24:1{\textendash}24:37}, abstract = {In the setting of secure two-party computation, two mutually distrusting parties wish to compute some function of their inputs while preserving, to the extent possible, various security properties such as privacy, correctness, and more. One desirable property is fairness which guarantees, informally, that if one party receives its output, then the other party does too. Cleve [1986] showed that complete fairness cannot be achieved in general without an honest majority. Since then, the accepted folklore has been that nothing non-trivial can be computed with complete fairness in the two-party setting. We demonstrate that this folklore belief is false by showing completely fair protocols for various nontrivial functions in the two-party setting based on standard cryptographic assumptions. We first show feasibility of obtaining complete fairness when computing any function over polynomial-size domains that does not contain an {\textquotedblleft}embedded XOR{\textquotedblright}; this class of functions includes boolean AND/OR as well as Yao{\textquoteright}s {\textquotedblleft}millionaires{\textquoteright} problem{\textquotedblright}. We also demonstrate feasibility for certain functions that do contain an embedded XOR, though we prove a lower bound showing that any completely fair protocol for such functions must have round complexity super-logarithmic in the security parameter. Our results demonstrate that the question of completely fair secure computation without an honest majority is far from closed.}, keywords = {cryptography, fairness, secure computation}, isbn = {0004-5411}, doi = {10.1145/2049697.2049698}, url = {http://doi.acm.org/10.1145/2049697.2049698}, author = {Gordon,S. Dov and Hazay,Carmit and Katz, Jonathan and Lindell,Yehuda} } @article {19647, title = {A computational statistics approach for estimating the spatial range of morphogen gradients}, journal = {Development}, volume = {138}, year = {2011}, month = {2011/11/15/}, pages = {4867 - 4874}, abstract = {A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.}, keywords = {Computational Biology, Confidence interval, Dorsal gradient, Drosophila embryo, Morphogen gradient, Statistics}, isbn = {0950-1991, 1477-9129}, url = {http://dev.biologists.org/content/138/22/4867}, author = {Kanodia, Jitendra S. and Kim, Yoosik and Tomer, Raju and Zia Khan and Chung, Kwanghun and Storey, John D. and Lu, Hang and Keller, Philipp J. and Shvartsman, Stanislav Y.} } @article {18558, title = {Countering Botnets: Anomaly-Based Detection, Comprehensive Analysis, and Efficient Mitigation}, year = {2011}, month = {2011/05//}, institution = {GEORGIA TECH RESEARCH CORP ATLANTA}, abstract = {We cover five general areas: (1) botnet detection, (2) botnet analysis, (3) botnet mitigation, (4) add-on tasks to the original contract, including the Conficker Working Group Lessons Learned, Layer-8 Exploration of Botnet Organization, and DREN research, and (5) commercialization in this paper. We have successfully developed new botnet detection and analysis capabilities in this project. These algorithms have been evaluated using real-world data, and have been put into actual, deployed systems. The most significant technical developments include a new dynamic reputation systems for DNS domains, a scalable anomaly detection system for botnet detection in very large network, and a transparent malware analysis system. In addition, on several occasions we have used our botnet data and analysis to help law enforcement agencies arrest botmasters. We also have had great success transitioning technologies to commercial products that are now used by government agencies, ISPs, and major corporations.}, keywords = {*ELECTRONIC SECURITY, *INFORMATION SECURITY, *INTERNET, *INTRUSION DETECTION(COMPUTERS), algorithms, BGP ROUTE INJECTION, BGP(BORDER GATEWAY PROTOCOLS), BOTNET DETECTION, BOTNET TRACEBACK AND ATTRIBUTION, BOTNETS(MALWARE), CLIENT SERVER SYSTEMS, COMMUNICATIONS PROTOCOLS, COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER SYSTEMS MANAGEMENT AND STANDARDS, CYBER ATTACKS, CYBER SECURITY, CYBERNETICS, CYBERTERRORISM, CYBERWARFARE, DATA PROCESSING SECURITY, DNS BASED MONITORING, DNS BASED REDIRECTION, DNS(DOMAIN NAME SYSTEMS), INFORMATION SCIENCE, INTERNET BROWSERS, ISP(INTERNET SERVICE PROVIDERS), MALWARE, MALWARE ANALYSIS, Online Systems, WUAFRLDHS1BOTN}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA543919}, author = {Lee,Wenke and Dagon,David and Giffin,Jon and Feamster, Nick and Ollman,Gunter and Westby,Jody and Wesson,Rick and Vixie,Paul} } @conference {13532, title = {Cross Language Entity Linking}, booktitle = {IJCNLP: International Joint Conference on Natural Language Processing}, year = {2011}, month = {2011///}, abstract = {There has been substantial recent interest in aligning mentions of named entities in unstructured texts to knowledge base descriptors, a task commonly called entity linking. This technology is crucial for applications in knowledge discovery and text data mining. This paper presents experiments in the new problem of cross language entity linking, where documents and named entities are in a different language than that used for the content of the reference knowledge base. We have created a new test collection to evaluate cross-language entity linking performance in twenty-one languages. We present experiments that examine issues such as: the importance of transliteration; the utility of cross-language information retrieval; and, the potential benefit of multilingual named entity recognition. Our best model achieves performance which is 94\% of a strong monolingual baseline.}, author = {McNamee,Paul and Mayfield,James and Lawrie,Dawn and Oard, Douglas and David Doermann} } @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.} } @article {16256, title = {DNACLUST: accurate and efficient clustering of phylogenetic marker genes}, journal = {BMC Bioinformatics}, volume = {12}, year = {2011}, month = {2011/06/30/}, pages = {271 - 271}, abstract = {Clustering is a fundamental operation in the analysis of biological sequence data. New DNA sequencing technologies have dramatically increased the rate at which we can generate data, resulting in datasets that cannot be efficiently analyzed by traditional clustering methods.}, isbn = {1471-2105}, doi = {10.1186/1471-2105-12-271}, url = {http://www.biomedcentral.com/1471-2105/12/271}, author = {Ghodsi,Mohammadreza and Liu,Bo and Pop, Mihai} } @conference {12437, title = {Domain adaptation for object recognition: An unsupervised approach}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {999 - 1006}, publisher = {IEEE}, organization = {IEEE}, abstract = {Adapting the classifier trained on a source domain to recognize instances from a new target domain is an important problem that is receiving recent attention. In this paper, we present one of the first studies on unsupervised domain adaptation in the context of object recognition, where we have labeled data only from the source domain (and therefore do not have correspondences between object categories across domains). Motivated by incremental learning, we create intermediate representations of data between the two domains by viewing the generative subspaces (of same dimension) created from these domains as points on the Grassmann manifold, and sampling points along the geodesic between them to obtain subspaces that provide a meaningful description of the underlying domain shift. We then obtain the projections of labeled source domain data onto these subspaces, from which a discriminative classifier is learnt to classify projected data from the target domain. We discuss extensions of our approach for semi-supervised adaptation, and for cases with multiple source and target domains, and report competitive results on standard datasets.}, keywords = {Data models, data representations, discriminative classifier, Feature extraction, Grassmann manifold, image sampling, incremental learning, labeled source domain, Manifolds, measurement, object category, Object recognition, Principal component analysis, sampling points, semisupervised adaptation, target domain, underlying domain shift, unsupervised approach, unsupervised domain adaptation, Unsupervised learning, vectors}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126344}, author = {Gopalan,R. and Ruonan Li and Chellapa, Rama} } @article {13948, title = {EFFICIENT PARALLEL NON-NEGATIVE LEAST SQUARES ON MULTI-CORE ARCHITECTURES}, journal = {SIAM Journal on Scientific Computing}, volume = {33}, year = {2011}, month = {2011///}, pages = {2848 - 2863}, abstract = {We parallelize a version of the active-set iterative algorithm derived from the originalworks of Lawson and Hanson [Solving Least Squares Problems, Prentice-Hall, 1974] on multicore architectures. This algorithm requires the solution of an unconstrained least squares problem in every step of the iteration for a matrix composed of the passive columns of the original system matrix. To achieve improved performance, we use parallelizable procedures to efficiently update and downdate the QR factorization of the matrix at each iteration, to account for inserted and removed columns. We use a reordering strategy of the columns in the decomposition to reduce computation and memory access costs. We consider graphics processing units (GPUs) as a new mode for efficient parallel computations and compare our implementations to that of multicore CPUs. Both synthetic and nonsynthetic data are used in the experiments. }, author = {Luo,Y. and Duraiswami, Ramani} } @article {16040, title = {Empirical Studies in Information Visualization: Seven Scenarios}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {PP}, year = {2011}, month = {2011///}, pages = {1 - 1}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluating visual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, evaluating visualization algorithms, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios distinguish different study goals and types of research questions and are illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. Scenarios can be used to choose appropriate research questions and goals and the provided examples can be consulted for guidance on how to design one{\textquoteright}s own study.}, isbn = {1077-2626}, doi = {10.1109/TVCG.2011.279}, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @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} } @inbook {12460, title = {Face Tracking and Recognition in Video}, booktitle = {Handbook of Face RecognitionHandbook of Face Recognition}, year = {2011}, month = {2011///}, pages = {323 - 351}, publisher = {Springer London}, organization = {Springer London}, abstract = {In this chapter, we describe the utility of videos in enhancing performance of image-based recognition tasks. We discuss a joint tracking-recognition framework that allows for using the motion information in a video to better localize and identify the person in the video using still galleries. We discuss how to jointly capture facial appearance and dynamics to obtain a parametric representation for video-to-video recognition. We discuss recognition in multi-camera networks where the probe and gallery both consist of multi-camera videos. Concluding remarks and directions for future research are provided.}, isbn = {978-0-85729-932-1}, url = {http://dx.doi.org/10.1007/978-0-85729-932-1_13}, author = {Chellapa, Rama and Du,Ming and Turaga,Pavan and Zhou,Shaohua Kevin}, editor = {Li,Stan Z. and Jain,Anil K.} } @article {14155, title = {Fast solvers for models of ICEO microfluidic flows}, journal = {International Journal for Numerical Methods in Fluids}, volume = {65}, year = {2011}, month = {2011///}, pages = {383 - 404}, author = {Shuttleworth, R. R and Elman, Howard and Long, K. R and Templeton, J. A} } @article {14613, title = {Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and FailureClinical Perspective}, journal = {Circulation: Cardiovascular GeneticsCirc Cardiovasc Genet}, volume = {4}, year = {2011}, month = {2011/02/01/}, pages = {26 - 35}, abstract = {Background{\textemdash} Network analysis techniques allow a more accurate reflection of underlying systems biology to be realized than traditional unidimensional molecular biology approaches. Using gene coexpression network analysis, we define the gene expression network topology of cardiac hypertrophy and failure and the extent of recapitulation of fetal gene expression programs in failing and hypertrophied adult myocardium.Methods and Results{\textemdash} We assembled all myocardial transcript data in the Gene Expression Omnibus (n=1617). Because hierarchical analysis revealed species had primacy over disease clustering, we focused this analysis on the most complete (murine) dataset (n=478). Using gene coexpression network analysis, we derived functional modules, regulatory mediators, and higher-order topological relationships between genes and identified 50 gene coexpression modules in developing myocardium that were not present in normal adult tissue. We found that known gene expression markers of myocardial adaptation were members of upregulated modules but not hub genes. We identified ZIC2 as a novel transcription factor associated with coexpression modules common to developing and failing myocardium. Of 50 fetal gene coexpression modules, 3 (6\%) were reproduced in hypertrophied myocardium and 7 (14\%) were reproduced in failing myocardium. One fetal module was common to both failing and hypertrophied myocardium. Conclusions{\textemdash} Network modeling allows systems analysis of cardiovascular development and disease. Although we did not find evidence for a global coordinated program of fetal gene expression in adult myocardial adaptation, our analysis revealed specific gene expression modules active during both development and disease and specific candidates for their regulation. }, keywords = {fetal, Gene expression, heart failure, hypertrophy, myocardium}, isbn = {1942-325X, 1942-3268}, doi = {10.1161/CIRCGENETICS.110.941757}, url = {http://circgenetics.ahajournals.org/content/4/1/26}, author = {Dewey,Frederick E and Perez,Marco V and Wheeler,Matthew T and Watt,Clifton and Spin,Joshua and Langfelder,Peter and Horvath,Steve and Hannenhalli, Sridhar and Cappola,Thomas P. and Ashley,Euan A} } @article {18514, title = {How Many Tiers? Pricing in the Internet Transit Market}, journal = {SIGCOMM-Computer Communication Review}, volume = {41}, year = {2011}, month = {2011///}, pages = {194 - 194}, abstract = {ISPs are increasingly selling {\textquotedblleft}tiered{\textquotedblright} contracts, which offer Inter-net connectivity to wholesale customers in bundles, at rates based on the cost of the links that the traffic in the bundle is traversing. Although providers have already begun to implement and deploy tiered pricing contracts, little is known about how to structure them. Although contracts that sell connectivity on finer granularities im- prove market efficiency, they are also more costly for ISPs to im- plement and more difficult for customers to understand. Our goal is to analyze whether current tiered pricing practices in the whole- sale transit market yield optimal profits for ISPs and whether better bundling strategies might exist. In the process, we offer two contri- butions: (1) we develop a novel way of mapping traffic and topol- ogy data to a demand and cost model; and (2) we fit this model on three large real-world networks: an European transit ISP, a content distribution network, and an academic research network, and run counterfactuals to evaluate the effects of different bundling strate- gies. Our results show that the common ISP practice of structuring tiered contracts according to the cost of carrying the traffic flows (e.g., offering a discount for traffic that is local) can be suboptimal and that dividing contracts based on both traffic demand and the cost of carrying it into only three or four tiers yields near-optimal profit for the ISP. }, author = {Valancius,V. and Lumezanu,C. and Feamster, Nick and Johari,R. and Vazirani,V. V} } @article {14868, title = {Illumination Recovery From Image With Cast Shadows Via Sparse Representation}, journal = {Image Processing, IEEE Transactions on}, volume = {20}, year = {2011}, month = {2011/08//}, pages = {2366 - 2377}, abstract = {In this paper, we propose using sparse representation for recovering the illumination of a scene from a single image with cast shadows, given the geometry of the scene. The images with cast shadows can be quite complex and, therefore, cannot be well approximated by low-dimensional linear subspaces. However, it can be shown that the set of images produced by a Lambertian scene with cast shadows can be efficiently represented by a sparse set of images generated by directional light sources. We first model an image with cast shadows composed of a diffusive part (without cast shadows) and a residual part that captures cast shadows. Then, we express the problem in an $\#$x2113;1-regularized least-squares formulation, with nonnegativity constraints (as light has to be non-negative at any point in space). This sparse representation enjoys an effective and fast solution thanks to recent advances in compressive sensing. In experiments on synthetic and real data, our approach performs favorably in comparison with several previously proposed methods.}, keywords = {$\#$x2113;1-regularized, approximations;, coding;image, compression;image, constraints;sparse, formulation;Lambertian, illumination, image, least-square, light, linear, reconstruction;image, recovery;low-dimensional, representation;data, representation;least, scene;cast, sensing;directional, shadows;compressive, sources;image, squares, subspaces;nonnegativity}, isbn = {1057-7149}, doi = {10.1109/TIP.2011.2118222}, author = {Mei,Xue and Ling,Haibin and Jacobs, David W.} } @book {19360, title = {Image Registration for Remote Sensing}, year = {2011}, month = {2011}, pages = {515}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, abstract = {Image registration is a digital image processing discipline that studies how to bring two or more digital images into precise alignment for analysis and comparison. Accurate registration algorithms are essential for creating mosaics of satellite images and tracking changes on the planet{\textquoteright}s surface over time. Bringing together invited contributions from 36 distinguished researchers, the book presents a detailed overview of current research and practice in the application of image registration to remote sensing imagery. Chapters cover the problem definition, theoretical issues in accuracy and efficiency, fundamental algorithms, and real-world case studies of image registration software applied to imagery from operational satellite systems. This book provides a comprehensive and practical overview for Earth and space scientists, presents image processing researchers with a summary of current research, and can be used for specialized graduate courses.}, keywords = {Science / Astronomy, Science / Earth Sciences / General, Technology \& Engineering / Environmental / General, Technology \& Engineering / Remote Sensing \& Geographic Information Systems}, isbn = {9781139494373}, author = {LeMoigne,Jacqueline and Netanyahu,Nathan S. and Eastman,Roger D.} } @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} } @conference {12218, title = {IP geolocation in metropolitan areas}, booktitle = {Proceedings of the ACM SIGMETRICS joint international conference on Measurement and modeling of computer systems}, series = {SIGMETRICS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {155 - 156}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Current IP geoloation techniques can geolocate an IP address to a region approximately 700 square miles, roughly the size of a metropolitan area. We model geolocation as a pattern-recognition problem, and introduce techniques that geolocate addresses to within 5 miles inside a metropolitan area. We propose two complementary algorithms: The first algorithm, Pattern Based Geolocation (PBG), models the distribution of latencies to the target and compares it to those of the reference landmarks to resolve an address to within 5 miles in a metropolitan area. The second approach, Perturbation Augmented PBG (PAPBG), provides higher resolution by sending extra traffic in the network. While sending an aggregate of 600 Kbps extra traffic to 20 nodes for approximately 2 minutes, PAPBG geolocates addresses to within 3 miles.}, keywords = {geolocation, pattern recognition, perturbation}, isbn = {978-1-4503-0814-4}, doi = {10.1145/1993744.1993803}, url = {http://doi.acm.org/10.1145/1993744.1993803}, author = {Singh,Satinder Pal and Baden,Randolph and Lee,Choon and Bhattacharjee, Bobby and La,Richard and Shayman,Mark} } @article {13274, title = {An iterative algorithm for homology computation on simplicial shapes}, journal = {Computer-Aided Design}, volume = {43}, year = {2011}, month = {2011/11//}, pages = {1457 - 1467}, abstract = {We propose a new iterative algorithm for computing the homology of arbitrary shapes discretized through simplicial complexes. We demonstrate how the simplicial homology of a shape can be effectively expressed in terms of the homology of its sub-components. The proposed algorithm retrieves the complete homological information of an input shape including the Betti numbers, the torsion coefficients and the representative homology generators.To the best of our knowledge, this is the first algorithm based on the constructive Mayer{\textendash}Vietoris sequence, which relates the homology of a topological space to the homologies of its sub-spaces, i.e. the sub-components of the input shape and their intersections. We demonstrate the validity of our approach through a specific shape decomposition, based only on topological properties, which minimizes the size of the intersections between the sub-components and increases the efficiency of the algorithm. }, keywords = {Computational topology, Generators, Mayer{\textendash}Vietoris sequence, shape decomposition, simplicial complexes, Z -homology}, isbn = {0010-4485}, doi = {10.1016/j.cad.2011.08.015}, url = {http://www.sciencedirect.com/science/article/pii/S0010448511002144}, author = {Boltcheva,Dobrina and Canino,David and Merino Aceituno,Sara and L{\'e}on,Jean-Claude and De Floriani, Leila and H{\'e}troy,Franck} } @article {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 {15066, title = {Learning a discriminative dictionary for sparse coding via label consistent K-SVD}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {1697 - 1704}, abstract = {A label consistent K-SVD (LC-KSVD) algorithm to learn a discriminative dictionary for sparse coding is presented. In addition to using class labels of training data, we also associate label information with each dictionary item (columns of the dictionary matrix) to enforce discriminability in sparse codes during the dictionary learning process. More specifically, we introduce a new label consistent constraint called {\textquoteleft}discriminative sparse-code error{\textquoteright} and combine it with the reconstruction error and the classification error to form a unified objective function. The optimal solution is efficiently obtained using the K-SVD algorithm. Our algorithm learns a single over-complete dictionary and an optimal linear classifier jointly. It yields dictionaries so that feature points with the same class labels have similar sparse codes. Experimental results demonstrate that our algorithm outperforms many recently proposed sparse coding techniques for face and object category recognition under the same learning conditions.}, keywords = {classification error, Dictionaries, dictionary learning process, discriminative sparse code error, face recognition, image classification, Image coding, K-SVD, label consistent, learning (artificial intelligence), object category recognition, Object recognition, optimal linear classifier, reconstruction error, singular value decomposition, Training data}, doi = {10.1109/CVPR.2011.5995354}, author = {Zhuolin Jiang and Zhe Lin and Davis, Larry S.} } @conference {14702, title = {Lightweight monadic programming in ML}, booktitle = {Proceedings of the 16th ACM SIGPLAN international conference on Functional programming}, series = {ICFP {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {15 - 27}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many useful programming constructions can be expressed as monads. Examples include probabilistic modeling, functional reactive programming, parsing, and information flow tracking, not to mention effectful functionality like state and I/O. In this paper, we present a type-based rewriting algorithm to make programming with arbitrary monads as easy as using ML{\textquoteright}s built-in support for state and I/O. Developers write programs using monadic values of type m τ as if they were of type τ, and our algorithm inserts the necessary binds, units, and monad-to-monad morphisms so that the program type checks. Our algorithm, based on Jones{\textquoteright} qualified types, produces principal types. But principal types are sometimes problematic: the program{\textquoteright}s semantics could depend on the choice of instantiation when more than one instantiation is valid. In such situations we are able to simplify the types to remove any ambiguity but without adversely affecting typability; thus we can accept strictly more programs. Moreover, we have proved that this simplification is efficient (linear in the number of constraints) and coherent: while our algorithm induces a particular rewriting, all related rewritings will have the same semantics. We have implemented our approach for a core functional language and applied it successfully to simple examples from the domains listed above, which are used as illustrations throughout the paper.}, keywords = {coercion, coherence, monad, rewriting, type}, isbn = {978-1-4503-0865-6}, doi = {10.1145/2034773.2034778}, url = {http://doi.acm.org/10.1145/2034773.2034778}, author = {Swamy,Nikhil and Guts,Nataliya and Leijen,Daan and Hicks, Michael W.} } @inbook {19186, title = {A Longitudinal Study of Pressure Sensing to Infer Real-World Water Usage Events in the Home}, booktitle = {Pervasive Computing}, series = {Lecture Notes in Computer Science}, volume = {6696}, year = {2011}, month = {2011}, pages = {50 - 69}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present the first longitudinal study of pressure sensing to infer real-world water usage events in the home (e.g., dishwasher, upstairs bathroom sink, downstairs toilet). In order to study the pressure-based approach out in the wild , we deployed a ground truth sensor network for five weeks in three homes and two apartments that directly monitored valve-level water usage by fixtures and appliances . We use this data to, first, demonstrate the practical challenges in constructing water usage activity inference algorithms and, second, to inform the design of a new probabilistic-based classification approach. Inspired by algorithms in speech recognition, our novel Bayesian approach incorporates template matching, a language model, grammar, and prior probabilities. We show that with a single pressure sensor, our probabilistic algorithm can classify real-world water usage at the fixture level with 90\% accuracy and at the fixturecategory level with 96\% accuracy. With two pressure sensors, these accuracies increase to 94\% and 98\%. Finally, we show how our new approach can be trained with fewer examples than a strict template-matching approach alone.}, isbn = {978-3-642-21725-8}, url = {http://dx.doi.org/10.1007/978-3-642-21726-5_4}, author = {Jon Froehlich and Larson,Eric and Saba,Elliot and Campbell,Tim and Atlas,Les and Fogarty,James and Patel,Shwetak}, editor = {Lyons,Kent and Hightower,Jeffrey and Huang,Elaine} } @inbook {14324, title = {A Longitudinal Study of Pressure Sensing to Infer Real-World Water Usage Events in the Home}, booktitle = {Pervasive ComputingPervasive Computing}, series = {Lecture Notes in Computer Science}, volume = {6696}, year = {2011}, month = {2011///}, pages = {50 - 69}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present the first longitudinal study of pressure sensing to infer real-world water usage events in the home (e.g., dishwasher, upstairs bathroom sink, downstairs toilet). In order to study the pressure-based approach out in the wild , we deployed a ground truth sensor network for five weeks in three homes and two apartments that directly monitored valve-level water usage by fixtures and appliances . We use this data to, first, demonstrate the practical challenges in constructing water usage activity inference algorithms and, second, to inform the design of a new probabilistic-based classification approach. Inspired by algorithms in speech recognition, our novel Bayesian approach incorporates template matching, a language model, grammar, and prior probabilities. We show that with a single pressure sensor, our probabilistic algorithm can classify real-world water usage at the fixture level with 90\% accuracy and at the fixturecategory level with 96\% accuracy. With two pressure sensors, these accuracies increase to 94\% and 98\%. Finally, we show how our new approach can be trained with fewer examples than a strict template-matching approach alone.}, isbn = {978-3-642-21725-8}, url = {http://dx.doi.org/10.1007/978-3-642-21726-5_4}, author = {Jon Froehlich and Larson,Eric and Saba,Elliot and Campbell,Tim and Atlas,Les and Fogarty,James and Patel,Shwetak}, editor = {Lyons,Kent and Hightower,Jeffrey and Huang,Elaine} } @conference {13383, title = {Maximizing Expected Utility for Stochastic Combinatorial Optimization Problems}, booktitle = {2011 IEEE 52nd Annual Symposium on Foundations of Computer Science (FOCS)}, year = {2011}, month = {2011/10/22/25}, pages = {797 - 806}, publisher = {IEEE}, organization = {IEEE}, abstract = {We study the stochastic versions of a broad class of combinatorial problems where the weights of the elements in the input dataset are uncertain. The class of problems that we study includes shortest paths, minimum weight spanning trees, and minimum weight matchings over probabilistic graphs, and other combinatorial problems like knapsack. We observe that the expected value is inadequate in capturing different types of risk averse or risk-prone behaviors, and instead we consider a more general objective which is to maximize the expected utility of the solution for some given utility function, rather than the expected weight (expected weight becomes a special case). We show that we can obtain a polynomial time approximation algorithm with additive error ϵ for any ϵ >; 0, if there is a pseudopolynomial time algorithm for the exact version of the problem (This is true for the problems mentioned above) and the maximum value of the utility function is bounded by a constant. Our result generalizes several prior results on stochastic shortest path, stochastic spanning tree, and stochastic knapsack. Our algorithm for utility maximization makes use of the separability of exponential utility and a technique to decompose a general utility function into exponential utility functions, which may be useful in other stochastic optimization problems.}, keywords = {Approximation algorithms, Approximation methods, combinatorial problems, Fourier series, knapsack problems, optimisation, OPTIMIZATION, polynomial approximation, polynomial time approximation algorithm, Polynomials, Random variables, stochastic combinatorial optimization, stochastic knapsack, stochastic shortest path, stochastic spanning tree, vectors}, isbn = {978-1-4577-1843-4}, doi = {10.1109/FOCS.2011.33}, author = {Li,Jian and Deshpande, Amol} } @article {19117, title = {MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets}, journal = {BMC proceedings}, volume = {5}, year = {2011}, month = {2011}, author = {Liu,B. and Pop, Mihai} } @article {14413, title = {A method for the detection of meaningful and reproducible group signatures from gene expression profiles}, journal = {Journal of Bioinformatics and Computational Biology}, volume = {9}, year = {2011}, month = {2011///}, pages = {431 - 451}, abstract = {Gene expression microarrays are commonly used to detect the biological signature of a disease or to gain a better understanding of the underlying mechanism of how a group of drugs treat a specific disease. The outcome of such experiments, e.g. the signature, is a list of differentially expressed genes. Reproducibility across independent experiments remains a challenge. We are interested in creating a method that can detect the shared signature of a group of expression profiles, e.g. a group of samples from individuals with the same disease or a group of drugs that treat the same therapeutic indication. We have developed a novel Weighted Influence {\textemdash} Rank of Ranks (WIMRR) method, and we demonstrate its ability to produce both meaningful and reproducible group signatures.}, author = {Licamele,L. and Getoor, Lise} } @article {18587, title = {Modeling Tiered Pricing in the Internet Transit Market}, journal = {Arxiv preprint arXiv:1112.3740}, year = {2011}, month = {2011/12/16/}, abstract = {ISPs are increasingly selling "tiered" contracts, which offer Internet connectivity to wholesale customers in bundles, at rates based on the cost of the links that the traffic in the bundle is traversing. Although providers have already begun to implement and deploy tiered pricing contracts, little is known about how such pricing affects ISPs and their customers. While contracts that sell connectivity on finer granularities improve market efficiency, they are also more costly for ISPs to implement and more difficult for customers to understand. In this work we present two contributions: (1) we develop a novel way of mapping traffic and topology data to a demand and cost model; and (2) we fit this model on three large real-world networks: an European transit ISP, a content distribution network, and an academic research network, and run counterfactuals to evaluate the effects of different pricing strategies on both the ISP profit and the consumer surplus. We highlight three core findings. First, ISPs gain most of the profits with only three or four pricing tiers and likely have little incentive to increase granularity of pricing even further. Second, we show that consumer surplus follows closely, if not precisely, the increases in ISP profit with more pricing tiers. Finally, the common ISP practice of structuring tiered contracts according to the cost of carrying the traffic flows (e.g., offering a discount for traffic that is local) can be suboptimal and that dividing contracts based on both traffic demand and the cost of carrying it into only three or four tiers yields near-optimal profit for the ISP.}, keywords = {Computer Science - Networking and Internet Architecture}, url = {http://arxiv.org/abs/1112.3740}, author = {Valancius,Vytautas and Lumezanu,Cristian and Feamster, Nick and Johari,Ramesh and Vazirani,Vijay V.} } @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 {14994, title = {NSF/IEEE-TCPP curriculum initiative on parallel and distributed computing: core topics for undergraduates}, booktitle = {Proceedings of the 42nd ACM technical symposium on Computer science education}, year = {2011}, month = {2011///}, pages = {617 - 618}, author = {Prasad,S. K. and Chtchelkanova,A. and Das,S. and Dehne,F. and Gouda,M. and Gupta,A. and JaJa, Joseph F. and Kant,K. and La Salle,A. and LeBlanc,R. and others} } @inbook {19037, title = {Oblivious RAM with O((logN)^3) Worst-Case Cost}, booktitle = {Advances in Cryptology {\textendash} ASIACRYPT 2011}, series = {Lecture Notes in Computer Science}, volume = {7073}, year = {2011}, month = {2011}, pages = {197 - 214}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Oblivious RAM is a useful primitive that allows a client to hide its data access patterns from an untrusted server in storage outsourcing applications. Until recently, most prior works on Oblivious RAM aim to optimize its amortized cost, while suffering from linear or even higher worst-case cost. Such poor worst-case behavior renders these schemes impractical in realistic settings, since a data access request can occasionally be blocked waiting for an unreasonably large number of operations to complete. This paper proposes novel Oblivious RAM constructions that achieves poly-logarithmic worst-case cost, while consuming constant client-side storage. To achieve the desired worst-case asymptotic performance, we propose a novel technique in which we organize the O-RAM storage into a binary tree over data buckets, while moving data blocks obliviously along tree edges.}, keywords = {Computer science}, isbn = {978-3-642-25384-3}, url = {http://www.springerlink.com/content/2214q8013376rj37/abstract/}, author = {Elaine Shi and Chan, T. and Stefanov, Emil and Li, Mingfei}, editor = {Lee, Dong and Wang, Xiaoyun} } @conference {14902, title = {Odd Leaf Out: Improving Visual Recognition with Games}, booktitle = {Privacy, security, risk and trust (passat), 2011 ieee third international conference on and 2011 ieee third international conference on social computing (socialcom)}, year = {2011}, month = {2011/10//}, pages = {87 - 94}, abstract = {A growing number of projects are solving complex computational and scientific tasks by soliciting human feedback through games. Many games with a purpose focus on generating textual tags for images. In contrast, we introduce a new game, Odd Leaf Out, which provides players with an enjoyable and educational game that serves the purpose of identifying misclassification errors in a large database of labeled leaf images. The game uses a novel mechanism to solicit useful information from players{\textquoteright} incorrect answers. A study of 165 players showed that game data can be used to identify mislabeled leaves much more quickly than would have been possible using a computer vision algorithm alone. Domain novices and experts were equally good at identifying mislabeled images, although domain experts enjoyed the game more. We discuss the successes and challenges of this new game, which can be applied to other domains with labeled image datasets.}, keywords = {algorithm;educational, classification;object, computational, computing;botany;computer, datasets;misclassification, errors;scientific, feedback;labeled, game;human, games;computer, games;image, image, leaf, Odd, Out;complex, recognition;, recognition;biology, tags;visual, tasks;computer, tasks;textual, VISION}, doi = {10.1109/PASSAT/SocialCom.2011.225}, author = {Hansen,D. L and Jacobs, David W. and Lewis,D. and Biswas,A. and Preece,J. and Rotman,D. and Stevens,E.} } @article {19271, title = {Overview of the MPEG Reconfigurable Video Coding Framework}, journal = {Journal of Signal Processing Systems}, volume = {63}, year = {2011}, month = {2011}, pages = {251 - 263}, abstract = {Video coding technology in the last 20 years has evolved producing a variety of different and complex algorithms and coding standards. So far the specification of such standards, and of the algorithms that build them, has been done case by case providing monolithic textual and reference software specifications in different forms and programming languages. However, very little attention has been given to provide a specification formalism that explicitly presents common components between standards, and the incremental modifications of such monolithic standards. The MPEG Reconfigurable Video Coding (RVC) framework is a new ISO standard currently under its final stage of standardization, aiming at providing video codec specifications at the level of library components instead of monolithic algorithms. The new concept is to be able to specify a decoder of an existing standard or a completely new configuration that may better satisfy application-specific constraints by selecting standard components from a library of standard coding algorithms. The possibility of dynamic configuration and reconfiguration of codecs also requires new methodologies and new tools for describing the new bitstream syntaxes and the parsers of such new codecs. The RVC framework is based on the usage of a new actor/ dataflow oriented language called CAL for the specification of the standard library and instantiation of the RVC decoder model. This language has been specifically designed for modeling complex signal processing systems. CAL dataflow models expose the intrinsic concurrency of the algorithms by employing the notions of actor programming and dataflow. The paper gives an overview of the concepts and technologies building the standard RVC framework and the non standard tools supporting the RVC model from the instantiation and simulation of the CAL model to software and/or hardware code synthesis.}, keywords = {CAL actor language, Circuits and Systems, Code synthesis, Computer Imaging, Vision, Pattern Recognition and Graphics, Dataflow programming, Electrical Engineering, Image Processing and Computer Vision, pattern recognition, Reconfigurable Video Coding, Signal, Image and Speech Processing}, isbn = {1939-8018, 1939-8115}, url = {http://link.springer.com/article/10.1007/s11265-009-0399-3}, author = {Bhattacharyya, Shuvra S. and Eker, Johan and Janneck, J{\"o}rn W. and Lucarz, Christophe and Mattavelli, Marco and Raulet, Micka{\"e}l} } @conference {19042, title = {Privacy settings from contextual attributes: A case study using Google Buzz}, year = {2011}, month = {2011}, pages = {257 - 262}, abstract = {Social networks provide users with privacy settings to control what information is shared with connections and other users. In this paper, we analyze factors influencing changes in privacy-related settings in the Google Buzz social network. Specifically, we show statistics on contextual data related to privacy settings that are derived from crawled datasets and analyze the characteristics of users who changed their privacy settings. We also investigate potential neighboring effects among such users.}, keywords = {contextual attributes, data privacy, Google Buzz, privacy settings, social networking (online), social networks, Statistics}, author = {Mashima, D. and Elaine Shi and Chow, R. and Sarkar, P. and Li,C. and Song,D.} } @conference {14471, title = {A probabilistic approach for learning folksonomies from structured data}, booktitle = {Proceedings of the fourth ACM international conference on Web search and data mining}, series = {WSDM {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {555 - 564}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Learning structured representations has emerged as an important problem in many domains, including document and Web data mining, bioinformatics, and image analysis. One approach to learning complex structures is to integrate many smaller, incomplete and noisy structure fragments. In this work, we present an unsupervised probabilistic approach that extends affinity propagation [7] to combine the small ontological fragments into a collection of integrated, consistent, and larger folksonomies. This is a challenging task because the method must aggregate similar structures while avoiding structural inconsistencies and handling noise. We validate the approach on a real-world social media dataset, comprised of shallow personal hierarchies specified by many individual users, collected from the photosharing website Flickr. Our empirical results show that our proposed approach is able to construct deeper and denser structures, compared to an approach using only the standard affinity propagation algorithm. Additionally, the approach yields better overall integration quality than a state-of-the-art approach based on incremental relational clustering.}, keywords = {collective knowledge, data mining, folksonomies, social information processing, social metadata, taxonomies}, isbn = {978-1-4503-0493-1}, doi = {10.1145/1935826.1935905}, url = {http://doi.acm.org/10.1145/1935826.1935905}, author = {Plangprasopchok,Anon and Lerman,Kristina and Getoor, Lise} } @article {14639, title = {Regulation of Lung Endoderm Progenitor Cell Behavior by miR302/367}, journal = {DevelopmentDevelopment}, volume = {138}, year = {2011}, month = {2011/04/01/}, pages = {1235 - 1245}, abstract = {The temporal and spatial control of organ-specific endoderm progenitor development is poorly understood. miRNAs affect cell function by regulating programmatic changes in protein expression levels. We show that the miR302/367 cluster is a target of the transcription factor Gata6 in mouse lung endoderm and regulates multiple aspects of early lung endoderm progenitor development. miR302/367 is expressed at early stages of lung development, but its levels decline rapidly as development proceeds. Gain- and loss-of-function studies show that altering miR302/367 expression disrupts the balance of lung endoderm progenitor proliferation and differentiation, as well as apical-basal polarity. Increased miR302/367 expression results in the formation of an undifferentiated multi-layered lung endoderm, whereas loss of miR302/367 activity results in decreased proliferation and enhanced lung endoderm differentiation. miR302/367 coordinates the balance between proliferation and differentiation, in part, through direct regulation of Rbl2 and Cdkn1a, whereas apical-basal polarity is controlled by regulation of Tiam1 and Lis1. Thus, miR302/367 directs lung endoderm development by coordinating multiple aspects of progenitor cell behavior, including proliferation, differentiation and apical-basal polarity.}, keywords = {Lung, MicroRNA, mouse, Progenitor}, isbn = {0950-1991, 1477-9129}, doi = {10.1242/dev.061762}, url = {http://dev.biologists.org/content/138/7/1235}, author = {Tian,Ying and Zhang,Yuzhen and Hurd,Laura and Hannenhalli, Sridhar and Liu,Feiyan and Lu,Min Min and Morrisey,Edward E.} } @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} } @conference {18273, title = {Seam carving estimation using forensic hash}, booktitle = {Proceedings of the thirteenth ACM multimedia workshop on Multimedia and security}, series = {MM\&$\#$38;Sec {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {9 - 14}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Seam carving is an adaptive multimedia retargeting technique to resize multimedia data for different display sizes. This technique has found promising applications in media consumption on mobile devices such as tablets and smartphones. However, seam carving can also be used to maliciously alter image content and when combined with other tampering operations, makes tampering detection very difficult by traditional multimedia forensic techniques. In this paper, we study the problem of seam carving estimation and tampering localization using very compact side information called forensic hash. The forensic hash technique bridges two related areas, namely robust image hashing and blind multimedia forensics, to answer a broader scope of forensic questions in a more efficient and accurate manner. We show that our recently proposed forensic hash construction can be extended to accurately estimate seam carving and detect local tampering.}, keywords = {forensic hash, seam carving, sift, visual words}, isbn = {978-1-4503-0806-9}, doi = {10.1145/2037252.2037255}, url = {http://doi.acm.org/10.1145/2037252.2037255}, author = {Lu,Wenjun and M. Wu} } @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} } @conference {18276, title = {Secure video processing: Problems and challenges}, booktitle = {Acoustics, Speech and Signal Processing (ICASSP), 2011 IEEE International Conference on}, year = {2011}, month = {2011/05//}, pages = {5856 - 5859}, abstract = {Secure signal processing is an emerging technology to enable signal processing tasks in a secure and privacy-preserving fashion. It has attracted a great amount of research attention due to the increasing demand to enable rich functionalities for private data stored online. Desirable functionalities may include search, analysis, clustering, etc. In this paper, we discuss the research issues and challenges in secure video processing with focus on the application of secure online video management. Video is different from text due to its large data volume and rich content diversity. To be practical, secure video processing requires efficient solutions that may involve a trade-off between security and complexity. We look at three representative video processing tasks and review existing techniques that can be applied. Many of the tasks do not have efficient solutions yet, and we discuss the challenges and research questions that need to be addressed.}, keywords = {data;video, fashion;secure, management;secure, of, online, privacy-preserving, processing;, processing;security, signal, video}, doi = {10.1109/ICASSP.2011.5947693}, author = {Lu,Wenjun and Varna,A. and M. Wu} } @conference {13403, title = {Sensitivity analysis and explanations for robust query evaluation in probabilistic databases}, booktitle = {Proceedings of the 2011 international conference on Management of data}, year = {2011}, month = {2011///}, pages = {841 - 852}, abstract = {Probabilistic database systems have successfully established them-selves as a tool for managing uncertain data. However, much of the research in this area has focused on efficient query evaluation and has largely ignored two key issues that commonly arise in uncer- tain data management: First, how to provide explanations for query results, e.g., {\textquotedblleft}Why is this tuple in my result?{\textquotedblright} or {\textquotedblleft}Why does this output tuple have such high probability?{\textquotedblright}. Second, the problem of determining the sensitive input tuples for the given query, e.g., users are interested to know the input tuples that can substantially alter the output, when their probabilities are modified (since they may be unsure about the input probability values). Existing systems pro- vide the lineage/provenance of each of the output tuples in addition to the output probabilities, which is a boolean formula indicating the dependence of the output tuple on the input tuples. However, lineage does not immediately provide a quantitative relationship and it is not informative when we have multiple output tuples. In this paper, we propose a unified framework that can handle both the issues mentioned above to facilitate robust query processing. We formally define the notions of influence and explanations and provide algorithms to determine the top-l influential set of variables and the top-l set of explanations for a variety of queries, including conjunctive queries, probabilistic threshold queries, top-k queries and aggregation queries. Further, our framework naturally enables highly efficient incremental evaluation when input probabilities are modified (e.g., if uncertainty is resolved). Our preliminary exper- imental results demonstrate the benefits of our framework for per- forming robust query processing over probabilistic databases. }, author = {Kanagal,B. and Li,J. and Deshpande, Amol} } @article {16041, title = {Seven guiding scenarios for information visualization evaluation}, volume = {2011-992-04}, year = {2011}, month = {2011///}, institution = {Department of Computer Science, University of Calgary}, abstract = {We take a new, scenario based look at evaluation in information visualization. Our seven scenarios, evaluatingvisual data analysis and reasoning, evaluating user performance, evaluating user experience, evaluating environments and work practices, evaluating communication through visualization, automated evaluation of visualizations, and evaluating collaborative data analysis were derived through an extensive literature review of over 800 visualization publications. These scenarios are described through their goals, the types of questions they embody and illustrated through example studies. Through this broad survey and the distillation of these scenarios we make two contributions. One, we encapsulate the current practices in the information visualization research community and, two, we provide a different approach to reaching decisions about what might be the most effective evaluation of a given information visualization. For example, if the research goals or evaluative questions are known they can be used to map to specific scenarios, where practical existing examples can be considered for effective evaluation approaches. }, author = {Lam,H. and Bertini,E. and Isenberg,P. and Plaisant, Catherine and Carpendale,S.} } @article {13072, title = {Smart task-driven video collection}, volume = {11/649,393}, year = {2011}, month = {2011/06/14/}, abstract = {A multi-camera system that collects images and videos of moving objects in dynamic and crowded scenes, subject to task constraints is disclosed. The system constructs {\textquotedblleft}task visibility intervals{\textquotedblright} comprising information about what can be sensed in future time intervals. Methods for constructing these intervals applying prediction of future object motion and including consideration of factors such as object occlusion and camera control parameters are also disclosed. Using a plane-sweep algorithm, these atomic intervals can be combined in a method to form multi-task intervals, during which a single camera can collect videos suitable for multiple tasks simultaneously. Methods for fast camera scheduling that yield solutions within a small constant factor of an optimal solution are also disclosed.}, url = {http://www.google.com/patents?id=pgPnAQAAEBAJ}, author = {Lim,Ser-Nam and Mittal,Anurag and Davis, Larry S.}, editor = {Siemens Corporation} } @inbook {17378, title = {Speeding Up Network Layout and Centrality Measures for Social Computing Goals}, booktitle = {Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction}, series = {Lecture Notes in Computer Science}, volume = {6589}, year = {2011}, month = {2011///}, pages = {244 - 251}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents strategies for speeding up calculation of graph metrics and layout by exploiting the parallel architecture of modern day Graphics Processing Units (GPU), specifically Compute Unified Device Architecture ( CUDA ) by Nvidia . Graph centrality metrics like Eigenvector , Betweenness , Page Rank and layout algorithms like Fruchterman - Rheingold are essential components of Social Network Analysis ( SNA ). With the growth in adoption of SNA in different domains and increasing availability of huge networked datasets for analysis, social network analysts require faster tools that are also scalable. Our results, using NodeXL, show up to 802 times speedup for a Fruchterman-Rheingold graph layout and up to 17,972 times speedup for Eigenvector centrality metric calculations on a 240 core CUDA-capable GPU.}, isbn = {978-3-642-19655-3}, url = {http://dx.doi.org/10.1007/978-3-642-19656-0_35}, author = {Sharma,Puneet and Khurana,Udayan and Shneiderman, Ben and Scharrenbroich,Max and Locke,John}, editor = {Salerno,John and Yang,Shanchieh and Nau, Dana S. and Chai,Sun-Ki} } @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 {13949, title = {Toward improved aeromechanics simulations using recent advancements in scientific computing}, journal = {Proceedings 67th Annual Forum of the American Helicopter Society}, year = {2011}, month = {2011///}, pages = {3 - 5}, author = {Hu,Q. and Syal,M. and Gumerov, Nail A. and Duraiswami, Ramani and Leishman,J.G.} } @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} } @article {13351, title = {A unified approach to ranking in probabilistic databases}, journal = {The VLDB Journal}, volume = {20}, year = {2011}, month = {2011/04//}, pages = {249 - 275}, abstract = {Ranking is a fundamental operation in data analysis and decision support and plays an even more crucial role if the dataset being explored exhibits uncertainty. This has led to much work in understanding how to rank the tuples in a probabilistic dataset in recent years. In this article, we present a unified approach to ranking and top-k query processing in probabilistic databases by viewing it as a multi-criterion optimization problem and by deriving a set of features that capture the key properties of a probabilistic dataset that dictate the ranked result. We contend that a single, specific ranking function may not suffice for probabilistic databases, and we instead propose two parameterized ranking functions, called PRF {\textquestiondown} and PRF e, that generalize or can approximate many of the previously proposed ranking functions. We present novel generating functions-based algorithms for efficiently ranking large datasets according to these ranking functions, even if the datasets exhibit complex correlations modeled using probabilistic and/xor trees or Markov networks. We further propose that the parameters of the ranking function be learned from user preferences, and we develop an approach to learn those parameters. Finally, we present a comprehensive experimental study that illustrates the effectiveness of our parameterized ranking functions, especially PRF e, at approximating other ranking functions and the scalability of our proposed algorithms for exact or approximate ranking.}, keywords = {Approximation techniques, Graphical models, Learning to rank, Probabilistic databases, Ranking}, isbn = {1066-8888}, doi = {10.1007/s00778-011-0220-3}, url = {http://dx.doi.org/10.1007/s00778-011-0220-3}, author = {Li,Jian and Saha,Barna and Deshpande, Amol} } @article {17462, title = {Usability and Accessibility in Consumer Health Informatics: Current Trends and Future Challenges}, journal = {American Journal of Preventive Medicine}, volume = {40}, year = {2011}, month = {2011/05//}, pages = {S187-S197 - S187-S197}, abstract = {It is a truism that, for innovative eHealth systems to have true value and impact, they must first and foremost be usable and accessible by clinicians, consumers, and other stakeholders. In this paper, current trends and future challenges in the usability and accessibility of consumer health informatics will be described. Consumer expectations of their healthcare providers and healthcare records in this new era of consumer-directed care will be explored, and innovative visualizations, assistive technologies, and other ways that healthcare information is currently being provided and/or shared will be described. Challenges for ensuring the usability of current and future systems will also be discussed. An innovative model for conducting systematic, timely, user-centered research on consumer-facing websites at the National Cancer Institute (NCI) and the ongoing efforts at the National Institute of Standards and Technology (NIST) to promote health information technology (HIT) usability standards and evaluation criteria will also be presented.}, isbn = {0749-3797}, doi = {10.1016/j.amepre.2011.01.009}, url = {http://www.sciencedirect.com/science/article/pii/S0749379711000869}, author = {Goldberg,Larry and Lide,Bettijoyce and Lowry,Svetlana and Massett,Holly A. and O{\textquoteright}Connell,Trisha and Preece,Jennifer and Quesenbery,Whitney and Shneiderman, Ben} } @article {17487, title = {Visual Exploration across Biomedical Databases}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, year = {2011}, month = {2011/04//March}, pages = {536 - 550}, abstract = {Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database exploration. A new approach is offered for visualizing and exploring a query-based subset of multiple heterogeneous biomedical databases. Databases are modeled as an entity-relation graph containing nodes (database records) and links (relationships between records). Users specify a keyword search string to retrieve an initial set of nodes, and then explore intra- and interdatabase links. Results are visualized with user-defined semantic substrates to take advantage of the rich set of attributes usually present in biomedical data. Comments from domain experts indicate that this visualization method is potentially advantageous for biomedical knowledge exploration.}, keywords = {Bioinformatics, Biomedical computing, biomedical databases, cross-database exploration, Data exploration and discovery, Data visualization, database management systems, Databases, Factual, DNA, graph theory, Information Storage and Retrieval, information visualization., Keyword search, medical computing, natural language processing, Proteins, semantic networks, semantics, sequences, text mining, User-Computer Interface, user-defined semantics, visual databases}, isbn = {1545-5963}, doi = {10.1109/TCBB.2010.1}, author = {Lieberman,M.D. and Taheri, S. and Guo,Huimin and Mirrashed,F. and Yahav,I. and Aris,A. and Shneiderman, Ben} } @inbook {12503, title = {Aligning Spatio-Temporal Signals on a Special Manifold}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6315}, year = {2010}, month = {2010///}, pages = {547 - 560}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We investigate the spatio-temporal alignment of videos or features/signals extracted from them. Specifically, we formally define an alignment manifold and formulate the alignment problem as an optimization procedure on this non-linear space by exploiting its intrinsic geometry. We focus our attention on semantically meaningful videos or signals, e.g., those describing or capturing human motion or activities, and propose a new formalism for temporal alignment accounting for executing rate variations among realizations of the same video event. By construction, we address this static and deterministic alignment task in a dynamic and stochastic manner: we regard the search for optimal alignment parameters as a recursive state estimation problem for a particular dynamic system evolving on the alignment manifold. Consequently, a Sequential Importance Sampling iteration on the alignment manifold is designed for effective and efficient alignment. We demonstrate the performance on several types of input data that arise in vision problems.}, isbn = {978-3-642-15554-3}, url = {http://dx.doi.org/10.1007/978-3-642-15555-0_40}, author = {Ruonan Li and Chellapa, Rama}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @conference {13422, title = {An animated multivariate visualization for physiological and clinical data in the ICU}, booktitle = {Proceedings of the 1st ACM International Health Informatics Symposium}, series = {IHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {771 - 779}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Current visualizations of electronic medical data in the Intensive Care Unit (ICU) consist of stacked univariate plots of variables over time and a tabular display of the current numeric values for the corresponding variables and occasionally an alarm limit. The value of information is dependent upon knowledge of historic values to determine a change in state. With the ability to acquire more historic information, providers need more sophisticated visualization tools to assist them in analyzing the data in a multivariate fashion over time. We present a multivariate time series visualization that is interactive and animated, and has proven to be as effective as current methods in the ICU for predicting an episode of acute hypotension in terms of accuracy, confidence, and efficiency with only 30-60 minutes of training.}, keywords = {computational physiology, Information Visualization, multivariate, time series}, isbn = {978-1-4503-0030-8}, doi = {10.1145/1882992.1883109}, url = {http://doi.acm.org/10.1145/1882992.1883109}, author = {Ord{\'o}{\~n}ez,Patricia and desJardins, Marie and Lombardi,Michael and Lehmann,Christoph U. and Fackler,Jim} } @article {18536, title = {Autonomous Traffic Engineering using Self-Configuring Link Weights}, volume = {GT-CS-10-16}, year = {2010}, month = {2010///}, institution = {School of Computer Science, Georgia Tech}, abstract = {Network operators use traffic engineering to control the flow of traffic across their networks. Existing TE methods establish static topologies offline, either by setting link weights or by configuring paths a priori. These methods require manual configuration and may not be robust in the face of failures. Some methods also require knowledge about traffic demands and may not be able to handle traffic fluctuations. Even when changes in demand are expected, operators must manually tune network configurations to prepare for them. Because adjusting configurations is difficult to get right, we start from an extreme design point, asking instead whether it is possible to perform traffic engineering online without having to perform any a priori configuration. Our traffic engineering technique, SculpTE, adapts to changing traffic demands by automatically configuring link weights in a stable manner. SculpTE balances load across the network by continually adjusting link weights to expose lightly-loaded paths. We evaluate SculpTE using a simple analytical model and simulations on realistic ISP network topologies. Our results show that SculpTE achieves excellent load balancing, responsiveness, and stability compared to state-of-the-art TE schemes, without requiring network operators to perform any offline configuration.}, url = {http://hdl.handle.net/1853/35011}, author = {Sundaresan,S. and Lumezanu,C. and Feamster, Nick and Fran{\c c}ois,P.} } @article {18549, title = {Autonomous traffic engineering with self-configuring topologies}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2010}, month = {2010/08//}, pages = {{\textendash} - {\textendash}}, abstract = {Network operators use traffic engineering (TE) to control the flow of traffic across their networks. Existing TE methods require manual configuration of link weights or tunnels, which is difficult to get right, or prior knowledge of traffic demands and hence may not be robust to link failures or traffic fluctuations. We present a self-configuring TE scheme, SculpTE, which automatically adapts the network-layer topology to changing traffic demands. SculpTE is responsive, stable, and achieves excellent load balancing.}, keywords = {multi-path routing, online, sculpte, self-configuring, traffic engineering}, isbn = {0146-4833}, url = {http://dl.acm.org/citation.cfm?id=2043164.1851239}, author = {Sundaresan,Srikanth and Lumezanu,Cristian and Feamster, Nick and Francois,Pierre} } @conference {18550, title = {Behavioral clustering of HTTP-based malware and signature generation using malicious network traces}, booktitle = {Proceedings of the 7th USENIX conference on Networked systems design and implementation}, series = {NSDI{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {26 - 26}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {We present a novel network-level behavioral malware clustering system. We focus on analyzing the structural similarities among malicious HTTP traffic traces generated by executing HTTP-based malware. Our work is motivated by the need to provide quality input to algorithms that automatically generate network signatures. Accordingly, we define similarity metrics among HTTP traces and develop our system so that the resulting clusters can yield high-quality malware signatures. We implemented a proof-of-concept version of our network-level malware clustering system and performed experiments with more than 25,000 distinct malware samples. Results from our evaluation, which includes real-world deployment, confirm the effectiveness of the proposed clustering system and show that our approach can aid the process of automatically extracting network signatures for detecting HTTP traffic generated by malware-compromised machines.}, url = {http://dl.acm.org/citation.cfm?id=1855711.1855737}, author = {Perdisci,Roberto and Lee,Wenke and Feamster, Nick} } @conference {13425, title = {Broadening student enthusiasm for computer science with a great insights course}, booktitle = {Proceedings of the 41st ACM technical symposium on Computer science education}, series = {SIGCSE {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {157 - 161}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe the "Great Insights in Computer Science" courses that are taught at Rutgers and UMBC. These courses were designed independently, but have in common a broad, engaging introduction to computing for non-majors. Both courses include a programming component to help the students gain an intuition for computational concepts, but neither is primarily programming focused. We present data to show that these courses attract a diverse group of students; are rated positively; and increase students{\textquoteright} understanding of, and attitudes towards, computing and computational issues.}, keywords = {attitudes towards computing, introductory courses}, isbn = {978-1-4503-0006-3}, doi = {10.1145/1734263.1734317}, url = {http://doi.acm.org/10.1145/1734263.1734317}, author = {desJardins, Marie and Littman,Michael} } @article {18499, title = {Building a dynamic reputation system for DNS}, journal = {19th Usenix Security Symposium}, year = {2010}, month = {2010///}, abstract = {The Domain Name System (DNS) is an essential protocolused by both legitimate Internet applications and cyber at- tacks. For example, botnets rely on DNS to support agile com- mand and control infrastructures. An effective way to disrupt these attacks is to place malicious domains on a {\textquotedblleft}blocklist{\textquotedblright} (or {\textquotedblleft}blacklist{\textquotedblright}) or to add a filtering rule in a firewall or net- work intrusion detection system. To evade such security coun- termeasures, attackers have used DNS agility, e.g., by using new domains daily to evade static blacklists and firewalls. In this paper we propose Notos, a dynamic reputation system for DNS. The premise of this system is that malicious, agile use of DNS has unique characteristics and can be distinguished from legitimate, professionally provisioned DNS services. No- tos uses passive DNS query data and analyzes the network and zone features of domains. It builds models of known legit- imate domains and malicious domains, and uses these models to compute a reputation score for a new domain indicative of whether the domain is malicious or legitimate. We have eval- uated Notos in a large ISP{\textquoteright}s network with DNS traffic from 1.4 million users. Our results show that Notos can identify malicious domains with high accuracy (true positive rate of 96.8\%) and low false positive rate (0.38\%), and can identify these domains weeks or even months before they appear in public blacklists. }, author = {Antonakakis,M. and Perdisci,R. and Dagon,D. and Lee,W. and Feamster, Nick} } @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 {13391, title = {On Computing Compression Trees for Data Collection in Wireless Sensor Networks}, booktitle = {2010 Proceedings IEEE INFOCOM}, year = {2010}, month = {2010/03/14/19}, pages = {1 - 9}, publisher = {IEEE}, organization = {IEEE}, abstract = {We address the problem of efficiently gathering correlated data from a wireless sensor network, with the aim of designing algorithms with provable optimality guarantees, and understanding how close we can get to the known theoretical lower bounds. Our proposed approach is based on finding an optimal or a near-optimal compression tree for a given sensor network: a compression tree is a directed tree over the sensor network nodes such that the value of a node is compressed using the value of its parent. We focus on broadcast communication model in this paper, but our results are more generally applicable to a unicast communication model as well. We draw connections between the data collection problem and a previously studied graph concept called weakly connected dominating sets, and we use this to develop novel approximation algorithms for the problem. We present comparative results on several synthetic and real-world datasets showing that our algorithms construct near-optimal compression trees that yield a significant reduction in the data collection cost.}, keywords = {Approximation algorithms, Base stations, Communications Society, Computer networks, Computer science, computing compression trees, Costs, data collection, Data communication, data compression, designing algorithms, Educational institutions, Entropy, graph concept, Monitoring, Protocols, trees (mathematics), weakly connected dominating sets, Wireless sensor networks}, isbn = {978-1-4244-5836-3}, doi = {10.1109/INFCOM.2010.5462035}, author = {Li,Jian and Deshpande, Amol and Khuller, Samir} } @conference {14449, title = {Constructing folksonomies by integrating structured metadata}, booktitle = {Proceedings of the 19th international conference on World wide web}, series = {WWW {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1165 - 1166}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Aggregating many personal hierarchies into a common taxonomy, also known as a folksonomy, presents several challenges due to its sparseness, ambiguity, noise, and inconsistency. We describe an approach to folksonomy learning based on relational clustering that addresses these challenges by exploiting structured metadata contained in personal hierarchies. Our approach clusters similar hierarchies using their structure and tag statistics, then incrementally weaves them into a deeper, bushier tree. We study folksonomy learning using social metadata extracted from the photo-sharing site Flickr. We evaluate the learned folksonomy quantitatively by automatically comparing it to a reference taxonomy created by the Open Directory Project. Our empirical results suggest that the proposed approach improves upon the state-of-the-art folksonomy learning method.}, keywords = {collective knowledge, data mining, folksonomies}, isbn = {978-1-60558-799-8}, doi = {10.1145/1772690.1772856}, url = {http://doi.acm.org/10.1145/1772690.1772856}, author = {Plangprasopchok,Anon and Lerman,Kristina and Getoor, Lise} } @conference {14502, title = {Constructing Folksonomies by Integrating Structured Metadata with Relational Clustering}, booktitle = {Workshops at the Twenty-Fourth AAAI Conference on Artificial Intelligence}, year = {2010}, month = {2010///}, abstract = {Many social Web sites allow users to annotate the content with descriptive metadata, such as tags, and more recently also to organize content hierarchically. These types of struc- tured metadata provide valuable evidence for learning how a community organizes knowledge. For instance, we can ag- gregate many personal hierarchies into a common taxonomy, also known as a folksonomy, that will aid users in visual- izing and browsing social content, and also to help them in organizing their own content. However, learning from so- cial metadata presents several challenges: sparseness, ambi- guity, noise, and inconsistency. We describe an approach to folksonomy learning based on relational clustering that ad- dresses these challenges by exploiting structured metadata contained in personal hierarchies. Our approach clusters sim- ilar hierarchies using their structure and tag statistics, then incrementally weaves them into a deeper, bushier tree. We study folksonomy learning using social metadata extracted from the photo-sharing site Flickr. We evaluate the learned folksonomy quantitatively by automatically comparing it to a reference taxonomy. Our empirical results suggest that the proposed framework, which addresses the challenges listed above, improves on existing folksonomy learning methods.}, author = {Plangprasopchok,A. and Lerman,K. and Getoor, Lise} } @article {14509, title = {Context-Aware Query Recommendations}, volume = {12/408,726}, year = {2010}, month = {2010/09/23/}, abstract = {Described is a search-related technology in which context information regarding a user{\textquoteright}s prior search actions is used in making query recommendations for a current user action, such as a query or click. To determine whether each set or subset of context information is relevant to the user action, data obtained from a query log is evaluated. More particularly, a query transition (query-query) graph and a query click (query-URL) graph are extracted from the query log; vectors are computed for the current action and each context/sub-context and evaluated against vectors in the graphs to determine current action-to-context similarity. Also described is using similar context to provide the query recommendations, using parameters to control the similarity strictness, and/or whether more recent context information is more relevant than less recent context information, and using context information to distinguish between user sessions.}, url = {http://www.google.com/patents?id=nubWAAAAEBAJ}, author = {Ntoulas,Alexandros and Hwang,Heasoo and Getoor, Lise and Paparizos,Stelios and Lauw,Hady Wirawan}, editor = {Microsoft Corporation} } @conference {17843, title = {Decentralized dynamic scheduling across heterogeneous multi-core desktop grids}, booktitle = {2010 IEEE International Symposium on Parallel \& Distributed Processing, Workshops and Phd Forum (IPDPSW)}, year = {2010}, month = {2010/04/19/23}, pages = {1 - 9}, publisher = {IEEE}, organization = {IEEE}, abstract = {The recent advent of multi-core computing environments increases both the heterogeneity and complexity of managing desktop grid resources, making efficient load balancing challenging even for a centralized manager. Even with good initial job assignments, dynamic scheduling is still needed to adapt to dynamic environments, as well as for applications whose running times are not known a priori. In this paper, we propose new decentralized scheduling schemes that backfill jobs locally and dynamically migrate waiting jobs across nodes to leverage residual resources, while guaranteeing bounded waiting times for all jobs. The methods attempt to maximize total throughput while balancing load across available grid resources. Experimental results via simulation show that our scheduling scheme has performance competitive with an online centralized scheduler.}, keywords = {backfill jobs, bounded waiting time, Computer science, decentralized dynamic scheduling, desktop grid resource management, Dynamic scheduling, Educational institutions, Environmental management, grid computing, heterogeneous multicore desktop grid, job assignment, job migration, load balancing, Load management, multicore computing environment, Peer to peer computing, Processor scheduling, residual resources, resource allocation, Resource management, scheduling, Scheduling algorithm, Throughput}, isbn = {978-1-4244-6533-0}, doi = {10.1109/IPDPSW.2010.5470877}, author = {Jaehwan Lee and Keleher,P. and Sussman, Alan} } @conference {14345, title = {The design of eco-feedback technology}, booktitle = {Proceedings of the 28th international conference on Human factors in computing systems}, series = {CHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1999 - 2008}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {eco-feedback, environmental hci, reflective hci, survey}, isbn = {978-1-60558-929-9}, doi = {10.1145/1753326.1753629}, url = {http://doi.acm.org/10.1145/1753326.1753629}, author = {Jon Froehlich and Findlater,Leah and Landay,James} } @conference {16824, title = {Determining the spatial reader scopes of news sources using local lexicons}, booktitle = {Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {43 - 52}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Information sources on the Internet (e.g., Web versions of newspapers) usually have an implicit spatial reader scope, which is the geographical location for which the content has been primarily produced. Knowledge of the spatial reader scope facilitates the construction of a news search engine that provides readers a set of news sources relevant to the location in which they are interested. In particular, it plays an important role in disambiguating toponyms (e.g., textual specifications of geographical locations) in news articles, as the process of selecting an interpretation for the toponym often reduces to one of selecting an interpretation that seems natural in the context of the spatial reader scope. The key to determining the spatial reader scope of news sources is the notion of local lexicon, which for a location s is a set of concepts such as, but not limited to, names of people, landmarks, and historical events, that are spatially related to s. Techniques to automatically generate the local lexicon of a location by using the link structure of Wikipedia are described and evaluated. A key contribution is the improvement of existing methods used in the semantic relatedness domain to extract concepts spatially related to a given location from the Wikipedia. Results of experiments are presented that indicate that the knowledge of the spatial reader scope significantly improves the disambiguation of textually specified locations in news articles and that using local lexicons is an effective method to determine the spatial reader scopes of news sources.}, keywords = {geotagging, local lexicon, news search engine, spatial reader scope, spatial relatedness}, isbn = {978-1-4503-0428-3}, doi = {10.1145/1869790.1869800}, url = {http://doi.acm.org/10.1145/1869790.1869800}, author = {Quercini,Gianluca and Samet, Hanan and Sankaranarayanan,Jagan and Lieberman,Michael D.} } @article {18828, title = {Developing a Stochastic Dynamic Programming Framework for Optical Tweezer-Based Automated Particle Transport Operations}, journal = {Automation Science and Engineering, IEEE Transactions on}, volume = {7}, year = {2010}, month = {2010/04//}, pages = {218 - 227}, abstract = {Automated particle transport using optical tweezers requires the use of motion planning to move the particle while avoiding collisions with randomly moving obstacles. This paper describes a stochastic dynamic programming based motion planning framework developed by modifying the discrete version of an infinite-horizon partially observable Markov decision process algorithm. Sample trajectories generated by this algorithm are presented to highlight effectiveness in crowded scenes and flexibility. The algorithm is tested using silica beads in a holographic tweezer set-up and data obtained from the physical experiments are reported to validate various aspects of the planning simulation framework. This framework is then used to evaluate the performance of the algorithm under a variety of operating conditions.}, keywords = {holographic tweezer set-up, holography, infinite-horizon partially observable Markov decision process algorithm, Markov processes, motion planning framework, optical tweezer-based automated particle transport operations, optical tweezers, radiation pressure, silica beads, stochastic dynamic programming framework, stochastic programming}, isbn = {1545-5955}, doi = {10.1109/TASE.2009.2026056}, author = {Banerjee,A. G. and Pomerance,A. and Losert,W. and Gupta,S.K.} } @article {12876, title = {Diversity and distribution of cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/08/}, pages = {198 - 207}, abstract = {Non-toxigenic non-O1, non-O139 Vibrio cholerae strains isolated from both environmental and clinical settings carry a suite of virulence factors aside from cholera toxin. Among V. cholerae strains isolated from coastal waters of southern California, this includes cholix toxin, an ADP-ribosylating factor that is capable of halting protein synthesis in eukaryotic cells. The prevalence of the gene encoding cholix toxin, chxA, was assessed among a collection of 155 diverse V. cholerae strains originating from both clinical and environmental settings in Bangladesh and Mexico and other countries around the globe. The chxA gene was present in 47\% of 83 non-O1, non-O139 strains and 16\% of 72 O1/O139 strains screened as part of this study. A total of 86 chxA gene sequences were obtained, and phylogenetic analysis revealed that they fall into two distinct clades. These two clades were also observed in the phylogenies of several housekeeping genes, suggesting that the divergence observed in chxA extends to other regions of the V. cholerae genome, and most likely has arisen from vertical descent rather than horizontal transfer. Our results clearly indicate that ChxA is a major toxin of V. cholerae with a worldwide distribution that is preferentially associated with non-pandemic strains.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2010.00139.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00139.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Purdy,Alexandra E. and Balch,Deborah and Liz{\'a}rraga-Partida,Marcial Leonardo and Islam,Mohammad Sirajul and Martinez-Urtaza,Jaime and Huq,Anwar and Rita R Colwell and Bartlett,Douglas H.} } @article {18539, title = {Don{\textquoteright}t Configure the Network, Program It! Domain-Specific Programming Languages for Network Systems}, volume = {YALEU/DCS/RR-1432}, year = {2010}, month = {2010///}, institution = {Yale University}, abstract = {Network operators must configure networks to accomplish critical, complex, and often conflicting requirements: they must ensure good performance while maintaining security, and satisfy contractual obligations while ensuring profitable use of interdomain connections. Unfortunately, today they have no choice but to implement these high-level goals by configuring hundreds of individual network devices. These interact in complex and unexpected ways, often resulting in misconfigurations or downtime. We propose a new approach: rather than configure individual network devices, operators should program the network holistically, according to high-level policies. Towards this goal, we present Nettle, a system for clearly and concisely expressing network requirements together with mechanisms to control the network accordingly. At the lowest level, we rely on OpenFlow switches for programmable network hardware. On top of this layer, we build an extensible family of embedded domain-specific languages (EDSLs), each aimed at different operational concerns and provide convenient ways to sensibly combine expressions in these languages. We present a case study demonstrating a DSL for networks that provides fine-grained, dynamic access control policies.}, author = {Feamster, Nick and Voellmy,A. and Agarwal,A. and Hudak,P. and Burnett,S. and Launchbury,J.} } @conference {12221, title = {Don{\textquoteright}t love thy nearest neighbor}, booktitle = {Proceedings of the 9th international conference on Peer-to-peer systems}, series = {IPTPS{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {5 - 5}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, url = {http://dl.acm.org/citation.cfm?id=1863145.1863150}, author = {Lumezanu,Cristian and Levin,Dave and Han,Bo and Spring, Neil and Bhattacharjee, Bobby} } @inbook {19300, title = {Dynamic and Multidimensional Dataflow Graphs}, booktitle = {Handbook of Signal Processing Systems}, year = {2010}, month = {2010}, pages = {899 - 930}, publisher = {Springer US}, organization = {Springer US}, abstract = {Much of the work to date on dataflow models for signal processing system design has focused decidable dataflow models that are best suited for onedimensional signal processing. In this chapter, we review more general dataflow modeling techniques that are targeted to applications that include multidimensional signal processing and dynamic dataflow behavior. As dataflow techniques are applied to signal processing systems that are more complex, and demand increasing degrees of agility and flexibility, these classes of more general dataflow models are of correspondingly increasing interest. We begin with a discussion of two dataflow modeling techniques - multi-dimensional synchronous dataflow and windowed dataflow - that are targeted towards multidimensional signal processing applications. We then provide a motivation for dynamic dataflow models of computation, and review a number of specific methods that have emerged in this class of models. Our coverage of dynamic dataflowmodels in this chapter includes Boolean dataflow, the stream-based function model, CAL, parameterized dataflow, and enable-invoke dataflow.}, keywords = {Communications Engineering, Networks, Computer Systems Organization and Communication Networks, Processor Architectures, Signal, Image and Speech Processing}, isbn = {978-1-4419-6344-4, 978-1-4419-6345-1}, url = {http://link.springer.com/chapter/10.1007/978-1-4419-6345-1_32}, author = {Bhattacharyya, Shuvra S. and Deprettere, Ed F. and Keinert, Joachim}, editor = {Bhattacharyya, Shuvra S. and Deprettere, Ed F. and Leupers, Rainer and Takala, Jarmo} } @conference {12222, title = {The effect of packet loss on redundancy elimination in cellular wireless networks}, booktitle = {Proceedings of the 10th annual conference on Internet measurement}, series = {IMC {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {294 - 300}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network-level redundancy elimination (RE) algorithms reduce traffic volume on bandwidth-constrained network paths by avoiding the transmission of repeated byte sequences. Previous work shows that RE can suppress the transmission of 20-50\% bytes when deployed at ISP access links or between routers. In this paper, we focus on the challenges of deploying RE in cellular networks. The potential benefifit is substantial, since cellular networks have a growing subscriber base and network links, including wired backhaul, are often oversubscribed. Using three large traces captured at two North American and one European wireless network providers, we show that RE can reduce the bandwidth consumption of the majority of mobile users by at least 10\%. However, cellular links have much higher packet loss rates than their wired counterparts, which makes applying RE much more difficult. Our experiments also show that the loss of only a few packets can disrupt RE and eliminate the bandwidth savings. We propose informed marking, a lightweight scheme that detects lost packets and prevents RE algorithms from using them for future encodings. We implement RE with informed marking and deploy it in a real-world cellular network. Our results show that with informed marking, more than 60\% of the bandwidth savings of RE are preserved, even when packet loss rates are high.}, keywords = {cellular networks, loss, redundancy elimination}, isbn = {978-1-4503-0483-2}, doi = {10.1145/1879141.1879179}, url = {http://doi.acm.org/10.1145/1879141.1879179}, author = {Lumezanu,Cristian and Guo,Katherine and Spring, Neil and Bhattacharjee, Bobby} } @article {12872, title = {Effect on Human Cells of Environmental Vibrio Parahaemolyticus Strains Carrying Type III Secretion System 2}, journal = {Infection and ImmunityInfect. Immun.}, volume = {78}, year = {2010}, month = {2010/07/01/}, pages = {3280 - 3287}, abstract = {Vibrio parahaemolyticus is an inhabitant of estuarine and marine environments that causes seafood-borne gastroenteritis worldwide. Recently, a type 3 secretion system (T3SS2) able to secrete and translocate virulence factors into the eukaryotic cell has been identified in a pathogenicity island (VP-PAI) located on the smaller chromosome. These virulence-related genes have previously been detected only in clinical strains. Classical virulence genes for this species (tdh, trh) are rarely detected in environmental strains, which are usually considered to lack virulence potential. However, during screening of a collection of environmental V. parahaemolyticus isolates obtained in the North Adriatic Sea in Italy, a number of marine strains carrying virulence-related genes, including genes involved in the T3SS2, were detected. In this study, we investigated the pathogenic potential of these marine V. parahaemolyticus strains by studying their adherence ability, their cytotoxicity, their effect on zonula occludin protein 1 (ZO-1) of the tight junctions, and their effect on transepithelial resistance (TER) in infected Caco-2 cells. By performing a reverse transcription-PCR, we also tested the expression of the T3SS2 genes vopT and vopB2, encoding an effector and a translocon protein, respectively. Our results indicate that, similarly to clinical strains, marine V. parahaemolyticus strains carrying vopT and vopB2 and that other genes included in the VP-PAI are capable of adhering to human cells and of causing cytoskeletal disruption and loss of membrane integrity in infected cells. On the basis of data presented here, environmental V. parahaemolyticus strains should be included in coastal water surveillance plans, as they may represent a risk for human health.}, isbn = {0019-9567, 1098-5522}, doi = {10.1128/IAI.00050-10}, url = {http://iai.asm.org/content/78/7/3280}, author = {Caburlotto,Greta and Lle{\`o},Maria M. and Hilton,Tamara and Huq,Anwar and Rita R Colwell and Kaper,James B.} } @conference {15260, title = {Energy efficient scheduling via partial shutdown}, booktitle = {Proceedings of the Twenty-First Annual ACM-SIAM Symposium on Discrete Algorithms}, series = {SODA {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1360 - 1372}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, abstract = {Motivated by issues of saving energy in data centers we define a collection of new problems referred to as "machine activation" problems. The central framework we introduce considers a collection of m machines (unrelated or related) with each machine i having an activation cost of ai. There is also a collection of n jobs that need to be performed, and pi, j is the processing time of job j on machine i. Standard scheduling models assume that the set of machines is fixed and all machines are available. However, in our setting, we assume that there is an activation cost budget of A - we would like to select a subset S of the machines to activate with total cost a(S) <= A and find a schedule for the n jobs on the machines in S minimizing the makespan (or any other metric). We consider both the unrelated machines setting, as well as the setting of scheduling uniformly related parallel machines, where machine i has activation cost ai and speed si, and the processing time of job j on machine i is pi, j = pjsi, where pj is the processing requirement of job j. For the general unrelated machine activation problem, our main results are that if there is a schedule with makespan T and activation cost A then we can obtain a schedule with makespan (2 + ε)T and activation cost 2(1 + 1/ε)(ln n/OPT + 1)A, for any ε > 0. We also consider assignment costs for jobs as in the generalized assignment problem, and using our framework, provide algorithms that minimize the machine activation and the assignment cost simultaneously. In addition, we present a greedy algorithm which only works for the basic version and yields a makespan of 2T and an activation cost A(1 + ln n). For the uniformly related parallel machine sceduling problem, we develop a polynomial time approximation scheme that outputs a schedule with the property that the activation cost of the subset of machines is at most A and the makespan is at most (1 + ε)T for any ε > 0. For the special case of m identical speed machines, the machine activation problem is trivial, since the cheapest subset of k machines is always the best choice if the optimal solution activates k machines. In addition, we consider the case whem some jobs can be dropped (and are treated as outliers).}, isbn = {978-0-898716-98-6}, url = {http://dl.acm.org/citation.cfm?id=1873601.1873711}, author = {Khuller, Samir and Li,Jian and Saha,Barna} } @article {15882, title = {Evaluation of information retrieval for E-discovery}, journal = {Artificial Intelligence and Law}, volume = {18}, year = {2010}, month = {2010/08/10/}, pages = {347 - 386}, isbn = {0924-8463, 1572-8382}, doi = {10.1007/s10506-010-9093-9}, url = {http://www.springerlink.com/content/m700w2k26n264u01/}, author = {Oard, Douglas and Baron,Jason R. and Hedin,Bruce and Lewis,David D. and Tomlinson,Stephen} } @article {18975, title = {Evolutionary dynamics of U12-type spliceosomal introns}, journal = {BMC Evolutionary Biology}, volume = {10}, year = {2010}, month = {2010/02/17/}, pages = {47 - 47}, abstract = {Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5\%) of introns, referred to as U12-type introns. U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns. A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly.}, isbn = {1471-2148}, doi = {10.1186/1471-2148-10-47}, url = {http://www.biomedcentral.com/1471-2148/10/47/abstract}, author = {Lin,Chiao-Feng and Mount, Stephen M. and Jarmo{\l}owski,Artur and Maka{\l}owski,Wojciech} } @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.} } @conference {12483, title = {Fast directional chamfer matching}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {1696 - 1703}, abstract = {We study the object localization problem in images given a single hand-drawn example or a gallery of shapes as the object model. Although many shape matching algorithms have been proposed for the problem over the decades, chamfer matching remains to be the preferred method when speed and robustness are considered. In this paper, we significantly improve the accuracy of chamfer matching while reducing the computational time from linear to sublinear (shown empirically). Specifically, we incorporate edge orientation information in the matching algorithm such that the resulting cost function is piecewise smooth and the cost variation is tightly bounded. Moreover, we present a sublinear time algorithm for exact computation of the directional chamfer matching score using techniques from 3D distance transforms and directional integral images. In addition, the smooth cost function allows to bound the cost distribution of large neighborhoods and skip the bad hypotheses within. Experiments show that the proposed approach improves the speed of the original chamfer matching upto an order of 45 $\#$x00D7;, and it is much faster than many state of art techniques while the accuracy is comparable.}, keywords = {3D, algorithm;edge, algorithms;single, chamfer, cost, detection;image, directional, distance, distribution;cost, example;smooth, function;sublinear, hand-drawn, images;edge, information;fast, integral, localization, MATCHING, matching;gallery, matching;transforms;, model;piecewise, of, orientation, problem;object, score;directional, shapes;object, smooth;shape, TIME, time;cost, transforms;computational, variation;directional}, doi = {10.1109/CVPR.2010.5539837}, author = {Ming-Yu Liu and Tuzel, O. and Veeraraghavan,A. and Chellapa, Rama} } @article {18217, title = {Forensic hash for multimedia information}, journal = {SPIE Media Forensics and Security}, year = {2010}, month = {2010///}, pages = {7541{\textendash}0Y - 7541{\textendash}0Y}, abstract = {Digital multimedia such as images and videos are prevalent on today{\textquoteright}s internet and cause significantsocial impact, which can be evidenced by the proliferation of social networking sites with user generated contents. Due to the ease of generating and modifying images and videos, it is critical to establish trustworthiness for online multimedia information. In this paper, we propose a new framework to perform multimedia forensics by using compact side information to reconstruct the processing history of a multimedia document. We refer to this framework as FASHION, standing for Forensic hASH for informatION assurance. As a first step in the modular design for FASHION, we propose new algorithms based on Radon transform and scale space theory to effectively estimate the parameters of geometric transforms and detect local tampering that an image may have undergone. The FASHION framework is designed to answer a much broader range of questions regarding the processing history of multimedia data than simple binary decision from robust image hashing, and also offers more efficient and accurate forensic analysis than multimedia forensic techniques that do not use any side information. }, author = {Lu,W. and Varna,A.L. and Wu,M.} } @inbook {19194, title = {GasSense: Appliance-Level, Single-Point Sensing of Gas Activity in the Home}, booktitle = {Pervasive Computing}, series = {Lecture Notes in Computer Science}, volume = {6030}, year = {2010}, month = {2010}, pages = {265 - 282}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents GasSense, a low-cost, single-point sensing solution for automatically identifying gas use down to its source (e.g., water heater, furnace, fireplace). This work adds a complementary sensing solution to the growing body of work in infrastructure-mediated sensing. GasSense analyzes the acoustic response of a home{\textquoteright}s government mandated gas regulator, which provides the unique capability of sensing both the individual appliance at which gas is currently being consumed as well as an estimate of the amount of gas flow. Our approach provides a number of appealing features including the ability to be easily and safely installed without the need of a professional. We deployed our solution in nine different homes and initial results show that GasSense has an average accuracy of 95.2\% in identifying individual appliance usage.}, isbn = {978-3-642-12653-6}, url = {http://dx.doi.org/10.1007/978-3-642-12654-3_16}, author = {Cohn,Gabe and Gupta,Sidhant and Jon Froehlich and Larson,Eric and Patel,Shwetak}, editor = {Flor{\'e}en,Patrik and Kr{\"u}ger,Antonio and Spasojevic,Mirjana} } @conference {13559, title = {GEDI - AGroundtruthing Environment for Document Images}, booktitle = {Ninth IAPRInternational Workshop on Document Analysis Systems (DAS 2010)}, year = {2010}, month = {2010///}, abstract = {In this paper, we describe a freely available highly configurable document image annotation tool called GEDI {\textendash} Groundtruthing Environment for Document Images. Its basic structure involves two types of files, an Image file, and a corresponding .xml file in GEDI format. When users begin ground truthing an image, they can configure the interface to allow the creation of different types of zones, each of which may have a custom set of {\textquotedblleft}attributes{\textquotedblright}. The output is compatible with the UMDDocLib architecture [2] and has been used in numerous funded and unfunded programs to create datasets in multiple languages. GEDI has been developed and released to the community as a comprehensive tool that we hope will ease the burden of document annotation and encourage additional sharing of data.}, author = {David Doermann and Zotkina,Elena and Huiping Li} } @article {12219, title = {A general framework for efficient geographic routing in wireless networks}, journal = {Computer Networks}, volume = {54}, year = {2010}, month = {2010/04/08/}, pages = {844 - 861}, abstract = {We propose a new link metric called normalized advance (NADV) for geographic routing in multihop wireless networks. NADV selects neighbors with the optimal trade-off between proximity and link cost. Coupled with the local next hop decision in geographic routing, NADV enables an adaptive and efficient cost-aware routing strategy. Depending on the objective or message priority, applications can use the NADV framework to minimize various types of link cost.We present efficient methods for link cost estimation and perform detailed experiments in simulated environments. Our results show that NADV outperforms current schemes in many aspects: for example, in high noise environments with frequent packet losses, the use of NADV leads to 81\% higher delivery ratio. When compared to centralized routing under certain settings, geographic routing using NADV finds paths whose cost is close to the optimum. We also conducted experiments in Emulab testbed and the results demonstrate that our proposed approach performs well in practice. }, keywords = {Geographic routing, Link cost estimation, Routing metric, Wireless multihop networks}, isbn = {1389-1286}, doi = {10.1016/j.comnet.2009.09.013}, url = {http://www.sciencedirect.com/science/article/pii/S1389128609002904}, author = {Lee,Seungjoon and Bhattacharjee, Bobby and Banerjee,Suman and Han,Bo} } @article {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} } @article {19094, title = {Genomic characterization of the Yersinia genus}, journal = {Genome biology}, volume = {11}, year = {2010}, month = {2010}, author = {Chen, P.E. and Cook, C. and Stewart, A.C. and Nagarajan,N. and Sommer, D.D. and Pop, Mihai and Thomason, B. and Thomason, M.P.K. and Lentz, S. and Nolan, N. and others} } @conference {16825, title = {Geotagging: using proximity, sibling, and prominence clues to understand comma groups}, booktitle = {Proceedings of the 6th Workshop on Geographic Information Retrieval}, series = {GIR {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {6:1{\textendash}6:8 - 6:1{\textendash}6:8}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Geotagging is the process of recognizing textual references to geographic locations, known as toponyms, and resolving these references by assigning each lat/long values. Typical geotagging algorithms use a variety of heuristic evidence to select the correct interpretation for each toponym. A study is presented of one such heuristic which aids in recognizing and resolving lists of toponyms, referred to as comma groups. Comma groups of toponyms are recognized and resolved by inferring the common threads that bind them together, based on the toponyms{\textquoteright} shared geographic attributes. Three such common threads are proposed and studied --- population-based prominence, distance-based proximity, and sibling relationships in a geographic hierarchy --- and examples of each are noted. In addition, measurements are made of these comma groups{\textquoteright} usage and variety in a large dataset of news articles, indicating that the proposed heuristics, and in particular the proximity and sibling heuristics, are useful for resolving comma group toponyms.}, keywords = {comma groups, geotagging, toponyms}, isbn = {978-1-60558-826-1}, doi = {10.1145/1722080.1722088}, url = {http://doi.acm.org/10.1145/1722080.1722088}, author = {Lieberman,Michael D. and Samet, Hanan and Sankaranayananan,Jagan} } @conference {16819, title = {Geotagging with local lexicons to build indexes for textually-specified spatial data}, booktitle = {Data Engineering (ICDE), 2010 IEEE 26th International Conference on}, year = {2010}, month = {2010/03//}, pages = {201 - 212}, abstract = {The successful execution of location-based and feature-based queries on spatial databases requires the construction of spatial indexes on the spatial attributes. This is not simple when the data is unstructured as is the case when the data is a collection of documents such as news articles, which is the domain of discourse, where the spatial attribute consists of text that can be (but is not required to be) interpreted as the names of locations. In other words, spatial data is specified using text (known as a toponym) instead of geometry, which means that there is some ambiguity involved. The process of identifying and disambiguating references to geographic locations is known as geotagging and involves using a combination of internal document structure and external knowledge, including a document-independent model of the audience{\textquoteright}s vocabulary of geographic locations, termed its spatial lexicon. In contrast to previous work, a new spatial lexicon model is presented that distinguishes between a global lexicon of locations known to all audiences, and an audience-specific local lexicon. Generic methods for inferring audiences{\textquoteright} local lexicons are described. Evaluations of this inference method and the overall geotagging procedure indicate that establishing local lexicons cannot be overlooked, especially given the increasing prevalence of highly local data sources on the Internet, and will enable the construction of more accurate spatial indexes.}, keywords = {data;Internet;data, databases;, databases;spatial, document, indexes;spatial, information, Internet;document-independent, knowledge;feature-based, lexicon, lexicons;location-based, locations;geotagging;inference, method;internal, methods;geographic, mining;geographic, model;external, model;textually-specified, queries;generic, queries;spatial, spatial, structure;local, systems;visual}, doi = {10.1109/ICDE.2010.5447903}, author = {Lieberman,M.D. and Samet, Hanan and Sankaranarayanan,J.} } @conference {12484, title = {Group motion segmentation using a Spatio-Temporal Driving Force Model}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2010 IEEE Conference on}, year = {2010}, month = {2010/06//}, pages = {2038 - 2045}, abstract = {We consider the {\textquoteleft}group motion segmentation{\textquoteright} problem and provide a solution for it. The group motion segmentation problem aims at analyzing motion trajectories of multiple objects in video and finding among them the ones involved in a {\textquoteleft}group motion pattern{\textquoteright}. This problem is motivated by and serves as the basis for the {\textquoteleft}multi-object activity recognition{\textquoteright} problem, which is currently an active research topic in event analysis and activity recognition. Specifically, we learn a Spatio-Temporal Driving Force Model to characterize a group motion pattern and design an approach for segmenting the group motion. We illustrate the approach using videos of American football plays, where we identify the offensive players, who follow an offensive motion pattern, from motions of all players in the field. Experiments using GaTech Football Play Dataset validate the effectiveness of the segmentation algorithm.}, keywords = {activity, American, analysis;image, dataset;group, driving, football, force, model;image, MOTION, pattern;group, play, plays;GaTech, problem;spatiotemporal, recognition, recognition;image, segmentation;, segmentation;motion, trajectories;multiobject}, doi = {10.1109/CVPR.2010.5539880}, author = {Ruonan Li and Chellapa, Rama} } @conference {14446, title = {Growing a tree in the forest: constructing folksonomies by integrating structured metadata}, booktitle = {Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining}, series = {KDD {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {949 - 958}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many social Web sites allow users to annotate the content with descriptive metadata, such as tags, and more recently to organize content hierarchically. These types of structured metadata provide valuable evidence for learning how a community organizes knowledge. For instance, we can aggregate many personal hierarchies into a common taxonomy, also known as a folksonomy, that will aid users in visualizing and browsing social content, and also to help them in organizing their own content. However, learning from social metadata presents several challenges, since it is sparse, shallow, ambiguous, noisy, and inconsistent. We describe an approach to folksonomy learning based on relational clustering, which exploits structured metadata contained in personal hierarchies. Our approach clusters similar hierarchies using their structure and tag statistics, then incrementally weaves them into a deeper, bushier tree. We study folksonomy learning using social metadata extracted from the photo-sharing site Flickr, and demonstrate that the proposed approach addresses the challenges. Moreover, comparing to previous work, the approach produces larger, more accurate folksonomies, and in addition, scales better.}, keywords = {collective knowledge, data mining, folksonomies, relational clustering, social information processing, social metadata, taxonomies}, isbn = {978-1-4503-0055-1}, doi = {10.1145/1835804.1835924}, url = {http://doi.acm.org/10.1145/1835804.1835924}, author = {Plangprasopchok,Anon and Lerman,Kristina and Getoor, Lise} } @article {14622, title = {Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation}, journal = {Developmental Cell}, volume = {19}, year = {2010}, month = {2010/09/14/}, pages = {450 - 459}, abstract = {SummaryRegulation of chromatin structure via histone modification has recently received intense attention. Here,~we demonstrate that the chromatin-modifying enzyme histone deacetylase 2 (Hdac2) functions with a small homeodomain factor, Hopx, to mediate deacetylation of Gata4, which is expressed by cardiac progenitor cells and plays critical roles in the regulation of cardiogenesis. In the absence of Hopx and Hdac2 in mouse embryos, Gata4 hyperacetylation is associated with a marked increase in~cardiac myocyte proliferation, upregulation of Gata4 target genes, and perinatal lethality. Hdac2 physically interacts with Gata4, and this interaction is stabilized by Hopx. The ability of Gata4 to transactivate cell cycle genes is impaired by Hopx/Hdac2-mediated deacetylation, and this effect is abrogated by loss of Hdac2-Gata4 interaction. These results suggest that Gata4 is a nonhistone target of Hdac2-mediated deacetylation and that Hdac2, Hopx, and Gata4 coordinately regulate cardiac myocyte proliferation during embryonic development. }, isbn = {1534-5807}, doi = {10.1016/j.devcel.2010.08.012}, url = {http://www.sciencedirect.com/science/article/pii/S1534580710003874}, author = {Trivedi,Chinmay M. and Zhu,Wenting and Wang,Qiaohong and Jia,Cheng and Kee,Hae Jin and Li,Li and Hannenhalli, Sridhar and Epstein,Jonathan A.} } @article {12875, title = {Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {76}, year = {2010}, month = {2010/03/15/}, pages = {1996 - 2001}, abstract = {The Ibis T5000 is a novel diagnostic platform that couples PCR and mass spectrometry. In this study, we developed an assay that can identify all known pathogenic Vibrio species and field-tested it using natural water samples from both freshwater lakes and the Georgian coastal zone of the Black Sea. Of the 278 total water samples screened, 9 different Vibrio species were detected, 114 (41\%) samples were positive for V. cholerae, and 5 (0.8\%) samples were positive for the cholera toxin A gene (ctxA). All ctxA-positive samples were from two freshwater lakes, and no ctxA-positive samples from any of the Black Sea sites were detected.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01919-09}, url = {http://aem.asm.org/content/76/6/1996}, author = {Whitehouse,Chris A. and Baldwin,Carson and Sampath,Rangarajan and Blyn,Lawrence B. and Melton,Rachael and Li,Feng and Hall,Thomas A. and Harpin,Vanessa and Matthews,Heather and Tediashvili,Marina and Jaiani,Ekaterina and Kokashvili,Tamar and Janelidze,Nino and Grim,Christopher and Rita R Colwell and Huq,Anwar} } @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} } @article {14222, title = {Illusory Lightness Perception Due to Signal Compression and Reconstruction}, journal = {Journal of VisionJ Vis}, volume = {10}, year = {2010}, month = {2010/08/02/}, pages = {426 - 426}, abstract = {We propose a computational model that can account for a large number of lightness illusions, including the seemingly opposing effects of brightness contrast and assimilation. The underlying mathematics is based on the new theory of compressive sensing, which provides an efficient method for sampling and reconstructing a signal that is sparse or compressible. The model states that at the retina the intensity signal is compressed. This process amounts to a random sampling of locally averaged values. In the cortex the intensity values are reconstructed using as input the compressed signal, and combined with the edges. Reconstruction amounts to solving an underdetermined linear equation system using L1 norm minimization. Assuming that the intensity signal is sparse in the Fourier domain, the reconstructed signal, which is a linear combination of a small number of Fourier components, deviates from the original signal. The reconstruction error is consistent with the perception of many well known lightness illusions, including the contrast and the assimilation effect, the articulated enhanced brightness contrast, the checker shadow illusion, and the grating induction. Considering in addition, the space-variant resolution of the human eye, the model also explains illusory patterns with changes in perceived lightness over large ranges, such as the Cornsweet and related illusions. We conducted experiments with new variations of the White and the Dungeon illusion, whose perception changes with the resolution at which the different parts of the patterns appear on the eye, and found that the model predicted well the perception in these stimuli.}, isbn = {, 1534-7362}, doi = {10.1167/10.7.426}, url = {http://www.journalofvision.org/content/10/7/426}, author = {Ferm{\"u}ller, Cornelia and Li,Yi} } @article {14377, title = {Indirect two-sided relative ranking: a robust similarity measure for gene expression data}, journal = {BMC bioinformatics}, volume = {11}, year = {2010}, month = {2010///}, pages = {137 - 137}, abstract = {There is a large amount of gene expression data that exists in the public domain. This data has been generated under a variety of experimental conditions. Unfortunately, these experimental variations have generally prevented researchers from accurately comparing and combining this wealth of data, which still hides many novel insights. Results In this paper we present a new method, which we refer to as indirect two-sided relative ranking, for comparing gene expression profiles that is robust to variations in experimental conditions. This method extends the current best approach, which is based on comparing the correlations of the up and down regulated genes, by introducing a comparison based on the correlations in rankings across the entire database. Because our method is robust to experimental variations, it allows a greater variety of gene expression data to be combined, which, as we show, leads to richer scientific discoveries. Conclusions We demonstrate the benefit of our proposed indirect method on several datasets. We first evaluate the ability of the indirect method to retrieve compounds with similar therapeutic effects across known experimental barriers, namely vehicle and batch effects, on two independent datasets (one private and one public). We show that our indirect method is able to significantly improve upon the previous state-of-the-art method with a substantial improvement in recall at rank 10 of 97.03\% and 49.44\%, on each dataset, respectively. Next, we demonstrate that our indirect method results in improved accuracy for classification in several additional datasets. These datasets demonstrate the use of our indirect method for classifying cancer subtypes, predicting drug sensitivity/resistance, and classifying (related) cell types. Even in the absence of a known (i.e., labeled) experimental barrier, the improvement of the indirect method in each of these datasets is statistically significant.}, author = {Licamele,L. and Getoor, Lise} } @article {14401, title = {Integrating structured metadata with relational affinity propagation}, journal = {In proceedings of AAAI Workshop on Statistical Relational AI}, year = {2010}, month = {2010///}, abstract = {Structured and semi-structured data describing entities, tax- onomies and ontologies appears in many domains. There is a huge interest in integrating structured information from multiple sources; however integrating structured data to in- fer complex common structures is a difficult task because the integration must aggregate similar structures while avoiding structural inconsistencies that may appear when the data is combined. In this work, we study the integration of struc- tured social metadata: shallow personal hierarchies specified by many individual users on the Social Web, and focus on in- ferring a collection of integrated, consistent taxonomies. We frame this task as an optimization problem with structural constraints. We propose a new inference algorithm, which we refer to as Relational Affinity Propagation (RAP) that ex- tends affinity propagation (Frey and Dueck 2007) by intro- ducing structural constraints. We validate the approach on a real-world social media dataset, collected from the photoshar- ing website Flickr. Our empirical results show that our pro- posed approach is able to construct deeper and denser struc- tures compared to an approach using only the standard affin- ity propagation algorithm.}, author = {Plangprasopchok,A. and Lerman,K. and Getoor, Lise} } @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} } @conference {14227, title = {Learning shift-invariant sparse representation of actions}, booktitle = {2010 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)}, year = {2010}, month = {2010/06/13/18}, pages = {2630 - 2637}, publisher = {IEEE}, organization = {IEEE}, abstract = {A central problem in the analysis of motion capture (MoCap) data is how to decompose motion sequences into primitives. Ideally, a description in terms of primitives should facilitate the recognition, synthesis, and characterization of actions. We propose an unsupervised learning algorithm for automatically decomposing joint movements in human motion capture (MoCap) sequences into shift-invariant basis functions. Our formulation models the time series data of joint movements in actions as a sparse linear combination of short basis functions (snippets), which are executed (or {\textquotedblleft}activated{\textquotedblright}) at different positions in time. Given a set of MoCap sequences of different actions, our algorithm finds the decomposition of MoCap sequences in terms of basis functions and their activations in time. Using the tools of L1 minimization, the procedure alternately solves two large convex minimizations: Given the basis functions, a variant of Orthogonal Matching Pursuit solves for the activations, and given the activations, the Split Bregman Algorithm solves for the basis functions. Experiments demonstrate the power of the decomposition in a number of applications, including action recognition, retrieval, MoCap data compression, and as a tool for classification in the diagnosis of Parkinson (a motion disorder disease).}, keywords = {action characterization, Action recognition, action retrieval, action synthesis, Character recognition, data compression, human motion capture, HUMANS, Image matching, Image motion analysis, image representation, Image sequences, Information retrieval, joint movements, large convex minimizations, learning (artificial intelligence), learning shift-invariant sparse representation, Matching pursuit algorithms, minimisation, Minimization methods, MoCap data compression, Motion analysis, motion capture analysis, motion disorder disease, motion sequences, orthogonal matching pursuit, Parkinson diagnosis, Parkinson{\textquoteright}s disease, Pursuit algorithms, shift-invariant basis functions, short basis functions, snippets, sparse linear combination, split Bregman algorithm, time series, time series data, Unsupervised learning, unsupervised learning algorithm}, isbn = {978-1-4244-6984-0}, doi = {10.1109/CVPR.2010.5539977}, author = {Li,Yi and Ferm{\"u}ller, Cornelia and Aloimonos, J. and Hui Ji} } @conference {15310, title = {Learning to efficiently rank}, booktitle = {Proceedings of the 33rd international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {138 - 145}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {It has been shown that learning to rank approaches are capable of learning highly effective ranking functions. However, these approaches have mostly ignored the important issue of efficiency. Given that both efficiency and effectiveness are important for real search engines, models that are optimized for effectiveness may not meet the strict efficiency requirements necessary to deploy in a production environment. In this work, we present a unified framework for jointly optimizing effectiveness and efficiency. We propose new metrics that capture the tradeoff between these two competing forces and devise a strategy for automatically learning models that directly optimize the tradeoff metrics. Experiments indicate that models learned in this way provide a good balance between retrieval effectiveness and efficiency. With specific loss functions, learned models converge to familiar existing ones, which demonstrates the generality of our framework. Finally, we show that our approach naturally leads to a reduction in the variance of query execution times, which is important for query load balancing and user satisfaction.}, keywords = {effectiveness and efficiency tradeoff, Learning to rank, Linear Models}, isbn = {978-1-4503-0153-4}, doi = {10.1145/1835449.1835475}, url = {http://doi.acm.org/10.1145/1835449.1835475}, author = {Wang,Lidan and Jimmy Lin and Metzler,Donald} } @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 {12223, title = {Maranello: practical partial packet recovery for 802.11}, booktitle = {Proceedings of the 7th USENIX conference on Networked systems design and implementation}, series = {NSDI{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {14 - 14}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Partial packet recovery protocols attempt to repair corrupted packets instead of retransmitting them in their entirety. Recent approaches have used physical layer confidence estimates or additional error detection codes embedded in each transmission to identify corrupt bits, or have applied forward error correction to repair without such explicit knowledge. In contrast to these approaches, our goal is a practical design that simultaneously: (a) requires no extra bits in correct packets, (b) reduces recovery latency, except in rare instances, (c) remains compatible with existing 802.11 devices by obeying timing and backoff standards, and (d) can be incrementally deployed on widely available access points and wireless cards. In this paper, we design, implement, and evaluate Maranello, a novel partial packet recovery mechanism for 802.11. In Maranello, the receiver computes checksums over blocks in corrupt packets and bundles these checksums into a negative acknowledgment sent when the sender expects to receive an acknowledgment. The sender then retransmits only those blocks for which the checksum is incorrect, and repeats this partial retransmission until it receives an acknowledgment. Successful transmissions are not burdened by additional bits and the receiver needs not infer which bits were corrupted. We implemented Maranello using OpenFWWF (open source firmware for Broadcom wireless cards) and deployed it in a small testbed. We compare Maranello to alternative recovery protocols using a trace-driven simulation and to 802.11 using a live implementation under various channel conditions. To our knowledge, Maranello is the first partial packet recovery design to be implemented in commonly available firmware.}, url = {http://dl.acm.org/citation.cfm?id=1855711.1855725}, author = {Han,Bo and Schulman,Aaron and Gringoli,Francesco and Spring, Neil and Bhattacharjee, Bobby and Nava,Lorenzo and Ji,Lusheng and Lee,Seungjoon and Miller,Robert} } @conference {16278, title = {MetaPhyler: Taxonomic profiling for metagenomic sequences}, booktitle = {2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)}, year = {2010}, month = {2010/12/18/21}, pages = {95 - 100}, publisher = {IEEE}, organization = {IEEE}, abstract = {A major goal of metagenomics is to characterize the microbial diversity of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the 16S rRNA gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from whole-metagenome sequencing data by matching individual sequences against a database of reference genes. One major limitation of prior methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic profiler MetaPhyler, which uses marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results obtained by applying MetaPhyler to a real metagenomic dataset.}, keywords = {Bioinformatics, CARMA comparison, Databases, Genomics, Linear regression, marker genes, matching length, Megan comparison, metagenomic sequences, metagenomics, MetaPhyler, microbial diversity, microorganisms, molecular biophysics, molecular configurations, Pattern classification, pattern matching, phylogenetic classification, Phylogeny, PhymmBL comparison, reference gene database, Sensitivity, sequence matching, taxonomic classifier, taxonomic level, taxonomic profiling, whole metagenome sequencing data}, isbn = {978-1-4244-8306-8}, doi = {10.1109/BIBM.2010.5706544}, author = {Liu,Bo and Gibbons,T. and Ghodsi,M. and Pop, Mihai} } @conference {19286, title = {Methods for efficient implementation of Model Predictive Control on multiprocessor systems}, booktitle = {2010 IEEE International Conference on Control Applications (CCA)}, year = {2010}, month = {2010}, pages = {1357 - 1362}, abstract = {Model Predictive Control (MPC) has been used in a wide range of application areas including chemical engineering, food processing, automotive engineering, aerospace, and metallurgy. An important limitation on the application of MPC is the difficulty in completing the necessary computations within the sampling interval. Recent trends in computing hardware towards greatly increased parallelism offer a solution to this problem. This paper describes modeling and analysis tools to facilitate implementing the MPC algorithms on parallel computers, thereby greatly reducing the time needed to complete the calculations. The use of these tools is illustrated by an application to a class of MPC problems.}, keywords = {Computational modeling, COMPUTERS, Equations, Hardware, Linear systems, Mathematical model, model predictive control, MPC algorithms, Multiprocessing systems, Multiprocessor systems, parallel computers, predictive control, Program processors}, author = {Gu, Ruirui and Bhattacharyya, Shuvra S. and Levine,W. S} } @conference {14316, title = {Mining Public Transport Usage for Personalised Intelligent Transport Systems}, booktitle = {2010 IEEE 10th International Conference on Data Mining (ICDM)}, year = {2010}, month = {2010}, pages = {887 - 892}, publisher = {IEEE}, organization = {IEEE}, abstract = {Traveller information, route planning, and service updates have become essential components of public transport systems: they help people navigate built environments by providing access to information regarding delays and service disruptions. However, one aspect that these systems lack is a way of tailoring the information they offer in order to provide personalised trip time estimates and relevant notifications to each traveller. Mining each user{\textquoteright}s travel history, collected by automated ticketing systems, has the potential to address this gap. In this work, we analyse one such dataset of travel history on the London underground. We then propose and evaluate methods to (a) predict personalised trip times for the system users and (b) rank stations based on future mobility patterns, in order to identify the subset of stations that are of greatest interest to the user and thus provide useful travel updates.}, keywords = {automated ticketing systems, data mining, Intelligent Transport Systems, London underground, mobility patterns, personalised intelligent transport systems, personalised trip times, Personalization, public administration, public information systems, public transport systems, rapid transit systems, route planning, service disruptions, service updates, traffic information systems, travel history, traveller information}, isbn = {978-1-4244-9131-5}, doi = {10.1109/ICDM.2010.46}, author = {Lathia,N. and Jon Froehlich and Capra,L.} } @inbook {13600, title = {Mobile Visual Aid Tools for Users with Visual Impairments}, booktitle = {Mobile Multimedia ProcessingMobile Multimedia Processing}, year = {2010}, month = {2010///}, pages = {21 - 36}, publisher = {LNSC 5960}, organization = {LNSC 5960}, abstract = {In this chapter we describe {\textquotedblleft}MobileEye{\textquotedblright}, a software suite which converts a camera enabled mobile device into a multi-function vision tool that can assist the visually impaired in their daily activities. MobileEye consists of four subsystems, each customized for a specific type of visual disabilities: A color channel mapper which can tell the visually impaired different colors; a software based magnifier which provides image magnification as well as enhancement; a pattern recognizer which can read currencies; and a document retriever which allows access to printed materials. We developed cutting edge computer vision and image processing technologies, and tackled the challenges of implementing them on mobile devices with limited computational resources and low image quality. The system minimizes keyboard operation for the usability of users with visual impairments. Currently the software suite runs on Symbian and Windows Mobile handsets. In this chapter we provides a high level overview of the system, and then discuss the pattern recognizer in detail. The challenge is how to build a real-time recognition system on mobile devices and we present our detailed solutions.}, author = {Liu,Xu and David Doermann and Huiping Li} } @article {13708, title = {A modality lexicon and its use in automatic tagging}, journal = {Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC{\textquoteright}10)}, year = {2010}, month = {2010///}, pages = {1402 - 1407}, abstract = {This paper describes our resource-building results for an eight-week JHU Human Language Technology Center of Excellence SummerCamp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation. Specifically, we describe the construction of a modality annotation scheme, a modality lexicon, and two automated modality taggers that were built using the lexicon and annotation scheme. Our annotation scheme is based on identifying three components of modality: a trigger, a target and a holder. We describe how our modality lexicon was produced semi-automatically, expanding from an initial hand-selected list of modality trigger words and phrases. The resulting expanded modality lexicon is being made publicly available. We demonstrate that one tagger{\textemdash}a structure-based tagger{\textemdash}results in precision around 86\% (depending on genre) for tagging of a standard LDC data set. In a machine translation application, using the structure-based tagger to annotate English modalities on an English-Urdu training corpus improved the translation quality score for Urdu by 0.3 Bleu points in the face of sparse training data. }, author = {Baker,K. and Bloodgood,M. and Dorr, Bonnie J and Filardo,N.W. and Levin,L. and Piatko,C.} } @article {18252, title = {Multimedia forensic hash based on visual words}, journal = {IEEE Computer Society International Conference on Image Processing}, year = {2010}, month = {2010///}, pages = {989 - 992}, abstract = {In recent years, digital images and videos have become in-creasingly popular over the internet and bring great social im- pact to a wide audience. In the meanwhile, technology ad- vancement allows people to easily alter the content of dig- ital multimedia and brings serious concern on the trustwor- thiness of online multimedia information. Forensic hash is a short signature attached to an image before transmission and acts as side information for analyzing the processing history and trustworthiness of the received image. In this paper, we propose a new construction of forensic hash based on visual words representation. We encode SIFT features into a com- pact visual words representation for robust estimation of geo- metric transformations and propose a hybrid construction us- ing both SIFT and block-based features to detect and localize image tampering. The proposed hash construction achieves more robust and accurate forensic analysis than prior work. }, author = {Lu,W. and Wu,M.} } @article {15300, title = {Natural language annotations for the Semantic Web}, journal = {On the Move to Meaningful Internet Systems 2002: CoopIS, DOA, and ODBASE}, year = {2010}, month = {2010///}, pages = {1317 - 1331}, author = {Katz,B. and Jimmy Lin and Quan,D.} } @conference {18589, title = {Network I/O fairness in virtual machines}, booktitle = {Proceedings of the second ACM SIGCOMM workshop on Virtualized infrastructure systems and architectures}, series = {VISA {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {73 - 80}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a mechanism for achieving network I/O fairness in virtual machines, by applying flexible rate limiting mechanisms directly to virtual network interfaces. Conventional approaches achieve this fairness by implementing rate limiting either in the virtual machine monitor or hypervisor, which generates considerable CPU interrupt and instruction overhead for forwarding packets. In contrast, our design pushes per-VM rate limiting as close as possible to the physical hardware themselves, effectively implementing per-virtual interface rate limiting in hardware. We show that this design reduces CPU overhead (both interrupts and instructions) by an order of magnitude. Our design can be applied either to virtual servers for cloud-based services, or to virtual routers}, keywords = {netfpga, network virtualization, xen}, isbn = {978-1-4503-0199-2}, doi = {10.1145/1851399.1851412}, url = {http://doi.acm.org/10.1145/1851399.1851412}, author = {Anwer,Muhammad Bilal and Nayak,Ankur and Feamster, Nick and Liu,Ling} } @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.} } @conference {12151, title = {Obtaining valid safety data for software safety measurement and process improvement}, booktitle = {Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement}, series = {ESEM {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {46:1{\textendash}46:4 - 46:1{\textendash}46:4}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We report on a preliminary case study to examine software safety risk in the early design phase of the NASA Constellation spaceflight program. Our goal is to provide NASA quality assurance managers with information regarding the ongoing state of software safety across the program. We examined 154 hazard reports created during the preliminary design phase of three major flight hardware systems within the Constellation program. Our purpose was two-fold: 1) to quantify the relative importance of software with respect to system safety; and 2) to identify potential risks due to incorrect application of the safety process, deficiencies in the safety process, or the lack of a defined process. One early outcome of this work was to show that there are structural deficiencies in collecting valid safety data that make software safety different from hardware safety. In our conclusions we present some of these deficiencies.}, keywords = {case study, NASA, risk analysis, safety metrics}, isbn = {978-1-4503-0039-1}, doi = {10.1145/1852786.1852846}, url = {http://doi.acm.org/10.1145/1852786.1852846}, author = {Basili, Victor R. and Zelkowitz, Marvin V and Layman,Lucas and Dangle,Kathleen and Diep,Madeline} } @conference {16826, title = {Ontuition: intuitive data exploration via ontology navigation}, booktitle = {Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {540 - 541}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Ontuition, a system for mapping ontologies, is presented. Transforming data to a usable format for Ontuition involves recognizing and resolving data values corresponding to concepts in multiple ontological domains. In particular, for datasets with a geographic component an attempt is made to identify and extract enough spatio-textual data that specific lat/long values to dataset entries can be assigned. Next, a gazetteer is used to transform the textually-specified locations into lat/long values that can be displayed on a map. Non-spatial ontological concepts are also discovered. This methodology is applied to the National Library of Medicine{\textquoteright}s very popular clinical trials website (http://clinicaltrials.gov/) whose users are generally interested in locating trials near where they live. The trials are specified using XML files. The location data is extracted and coupled with a disease ontology to enable general queries on the data with the result being of use to a very large group of people. The goal is to do this automatically for such ontology datasets with a locational component.}, keywords = {MAPPING, ontology, ontuition, spatio-textual}, isbn = {978-1-4503-0428-3}, doi = {10.1145/1869790.1869887}, url = {http://doi.acm.org/10.1145/1869790.1869887}, author = {Adelfio,Marco D. and Lieberman,Michael D. and Samet, Hanan and Firozvi,Kashif A.} } @article {18708, title = {Perturbing the Ubiquitin Pathway Reveals How Mitosis Is Hijacked to Denucleate and Regulate Cell Proliferation and Differentiation In Vivo}, journal = {PLoS ONEPLoS ONE}, volume = {5}, year = {2010}, month = {2010/10/20/}, pages = {e13331 - e13331}, abstract = {BackgroundThe eye lens presents a unique opportunity to explore roles for specific molecules in cell proliferation, differentiation and development because cells remain in place throughout life and, like red blood cells and keratinocytes, they go through the most extreme differentiation, including removal of nuclei and cessation of protein synthesis. Ubiquitination controls many critical cellular processes, most of which require specific lysines on ubiquitin (Ub). Of the 7 lysines (K) least is known about effects of modification of K6. Methodology and Principal Findings We replaced K6 with tryptophan (W) because K6 is the most readily modified K and W is the most structurally similar residue to biotin. The backbone of K6W-Ub is indistinguishable from that of Wt-Ub. K6W-Ub is effectively conjugated and deconjugated but the conjugates are not degraded via the ubiquitin proteasome pathways (UPP). Expression of K6W-ubiquitin in the lens and lens cells results in accumulation of intracellular aggregates and also slows cell proliferation and the differentiation program, including expression of lens specific proteins, differentiation of epithelial cells into fibers, achieving proper fiber cell morphology, and removal of nuclei. The latter is critical for transparency, but the mechanism by which cell nuclei are removed has remained an age old enigma. This was also solved by expressing K6W-Ub. p27kip, a UPP substrate accumulates in lenses which express K6W-Ub. This precludes phosphorylation of nuclear lamin by the mitotic kinase, a prerequisite for disassembly of the nuclear membrane. Thus the nucleus remains intact and DNAseIIβ neither gains entry to the nucleus nor degrades the DNA. These results could not be obtained using chemical proteasome inhibitors that cannot be directed to specific tissues. Conclusions and Significance K6W-Ub provides a novel, genetic means to study functions of the UPP because it can be targeted to specific cells and tissues. A fully functional UPP is required to execute most stages of lens differentiation, specifically removal of cell nuclei. In the absence of a functional UPP, small aggregate prone, cataractous lenses are formed. }, doi = {10.1371/journal.pone.0013331}, url = {http://dx.doi.org/10.1371/journal.pone.0013331}, author = {Caceres,Andrea and Shang,Fu and Wawrousek,Eric and Liu,Qing and Avidan,Orna and Cvekl,Ales and Yang,Ying and Haririnia,Aydin and Storaska,Andrew and Fushman, David and Kuszak,Jer and Dudek,Edward and Smith,Donald and Taylor,Allen} } @conference {12486, title = {Pose estimation in heavy clutter using a multi-flash camera}, booktitle = {Robotics and Automation (ICRA), 2010 IEEE International Conference on}, year = {2010}, month = {2010/05//}, pages = {2028 - 2035}, abstract = {We propose a novel solution to object detection, localization and pose estimation with applications in robot vision. The proposed method is especially applicable when the objects of interest may not be richly textured and are immersed in heavy clutter. We show that a multi-flash camera (MFC) provides accurate separation of depth edges and texture edges in such scenes. Then, we reformulate the problem, as one of finding matches between the depth edges obtained in one or more MFC images to the rendered depth edges that are computed offline using 3D CAD model of the objects. In order to facilitate accurate matching of these binary depth edge maps, we introduce a novel cost function that respects both the position and the local orientation of each edge pixel. This cost function is significantly superior to traditional Chamfer cost and leads to accurate matching even in heavily cluttered scenes where traditional methods are unreliable. We present a sub-linear time algorithm to compute the cost function using techniques from 3D distance transforms and integral images. Finally, we also propose a multi-view based pose-refinement algorithm to improve the estimated pose. We implemented the algorithm on an industrial robot arm and obtained location and angular estimation accuracy of the order of 1 mm and 2 $\#$x00B0; respectively for a variety of parts with minimal texture.}, keywords = {3D, algorithm;object, based, camera;multiview, depth, detection;object, detection;pose, distance, edge, edges;cameras;image, edges;integral, estimation;binary, estimation;multiflash, estimation;robot, function;depth, images;location, localization;pose, maps, matching;cost, matching;image, pose-refinement, texture;object, transforms;angular, vision;texture, vision;transforms;}, doi = {10.1109/ROBOT.2010.5509897}, author = {Ming-Yu Liu and Tuzel, O. and Veeraraghavan,A. and Chellapa, Rama and Agrawal,A. and Okuda, H.} } @conference {13843, title = {Putting the user in the loop: interactive Maximal Marginal Relevance for query-focused summarization}, booktitle = {Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, series = {HLT {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {305 - 308}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This work represents an initial attempt to move beyond "single-shot" summarization to interactive summarization. We present an extension to the classic Maximal Marginal Relevance (MMR) algorithm that places a user "in the loop" to assist in candidate selection. Experiments in the complex interactive Question Answering (ciQA) task at TREC 2007 show that interactively-constructed responses are significantly higher in quality than automatically-generated ones. This novel algorithm provides a starting point for future work on interactive summarization.}, isbn = {1-932432-65-5}, url = {http://dl.acm.org/citation.cfm?id=1857999.1858040}, author = {Jimmy Lin and Madnani,Nitin and Dorr, Bonnie J} } @article {13398, title = {Ranking continuous probabilistic datasets}, journal = {Proc. VLDB Endow.}, volume = {3}, year = {2010}, month = {2010/09//}, pages = {638 - 649}, abstract = {Ranking is a fundamental operation in data analysis and decision support, and plays an even more crucial role if the dataset being explored exhibits uncertainty. This has led to much work in understanding how to rank uncertain datasets in recent years. In this paper, we address the problem of ranking when the tuple scores are uncertain, and the uncertainty is captured using continuous probability distributions (e.g. Gaussian distributions). We present a comprehensive solution to compute the values of a parameterized ranking function (PRF) [18] for arbitrary continuous probability distributions (and thus rank the uncertain dataset); PRF can be used to simulate or approximate many other ranking functions proposed in prior work. We develop exact polynomial time algorithms for some continuous probability distribution classes, and efficient approximation schemes with provable guarantees for arbitrary probability distributions. Our algorithms can also be used for exact or approximate evaluation of k-nearest neighbor queries over uncertain objects, whose positions are modeled using continuous probability distributions. Our experimental evaluation over several datasets illustrates the effectiveness of our approach at efficiently ranking uncertain datasets with continuous attribute uncertainty.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=1920841.1920923}, author = {Li,Jian and Deshpande, Amol} } @conference {15302, title = {Ranking under temporal constraints}, booktitle = {Proceedings of the 19th ACM international conference on Information and knowledge management}, series = {CIKM {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {79 - 88}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper introduces the notion of temporally constrained ranked retrieval, which, given a query and a time constraint, produces the best possible ranked list within the specified time limit. Naturally, more time should translate into better results, but the ranking algorithm should always produce some results. This property is desirable from a number of perspectives: to cope with diverse users and information needs, as well as to better manage system load and variance in query execution times. We propose two temporally constrained ranking algorithms based on a class of probabilistic prediction models that can naturally incorporate efficiency constraints: one that makes independent feature selection decisions, and the other that makes joint feature selection decisions. Experiments on three different test collections show that both ranking algorithms are able to satisfy imposed time constraints, although the joint model outperforms the independent model in being able to deliver more effective results, especially under tight time constraints, due to its ability to capture feature dependencies.}, keywords = {efficiency, Learning to rank, Linear Models}, isbn = {978-1-4503-0099-5}, doi = {10.1145/1871437.1871452}, url = {http://doi.acm.org/10.1145/1871437.1871452}, author = {Wang,Lidan and Metzler,Donald and Jimmy Lin} } @conference {12473, title = {Recognizing offensive strategies from football videos}, booktitle = {Image Processing (ICIP), 2010 17th IEEE International Conference on}, year = {2010}, month = {2010/09//}, pages = {4585 - 4588}, abstract = {We address the problem of recognizing offensive play strategies from American football play videos. Specifically, we propose a probabilistic model which describes the generative process of an observed football play and takes into account practical issues in real football videos, such as difficulty in identifying offensive players, view changes, and tracking errors. In particular, we exploit the geometric properties of nonlinear spaces of involved variables and design statistical models on these manifolds. Then recognition is performed via {\textquoteright}analysis-by-synthesis{\textquoteright} technique. Experiments on a newly established dataset of American football videos demonstrate the effectiveness of the approach.}, keywords = {American, analysis;video, changes;image, errors;variables, football, identification;tracking, models;geometric, models;view, play, players, processing;, properties;nonlinear, recognition;offensive, recognition;statistical, signal, spaces;offensive, statistical, strategies, technique;design, videos;analysis-by-synthesis}, doi = {10.1109/ICIP.2010.5652192}, author = {Ruonan Li and Chellapa, Rama} } @inbook {14638, title = {Regulating the Regulators: Modulators of Transcription Factor Activity}, booktitle = {Computational Biology of Transcription Factor BindingComputational Biology of Transcription Factor Binding}, series = {Methods in Molecular Biology}, volume = {674}, year = {2010}, month = {2010///}, pages = {297 - 312}, publisher = {Humana Press}, organization = {Humana Press}, abstract = {Gene transcription is largely regulated by DNA-binding transcription factors ( TFs ). However, the TF activity itself is modulated via, among other things, post-translational modifications ( PTMs ) by specific modification enzymes in response to cellular stimuli. TF-PTMs thus serve as {\textquotedblleft}molecular switchboards{\textquotedblright} that map upstream signaling events to the downstream transcriptional events. An important long-term goal is to obtain a genome-wide map of {\textquotedblleft}regulatory triplets{\textquotedblright} consisting of a TF, target gene, and a modulator gene that specifically modulates the regulation of the target gene by the TF. A variety of genome-wide data sets can be exploited by computational methods to obtain a rough map of regulatory triplets, which can guide directed experiments. However, a prerequisite to developing such computational tools is a systematic catalog of known instances of regulatory triplets. We first describe PTM-Switchboard, a recent database that stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on one or more PTMs catalyzed by a third gene, the modifying enzyme. We also review current computational approaches to infer regulatory triplets from genome-wide data sets and conclude with a discussion of potential future research. PTM-Switchboard is accessible at http://cagr.pcbi.upenn.edu/PTMswitchboard /}, isbn = {978-1-60761-854-6}, url = {http://dx.doi.org/10.1007/978-1-60761-854-6_19}, author = {Everett,Logan and Hansen,Matthew and Hannenhalli, Sridhar}, editor = {Ladunga,Istvan} } @article {18711, title = {Reversible Post-Translational Carboxylation Modulates the Enzymatic Activity of N-Acetyl-l-ornithine Transcarbamylase}, journal = {Biochemistry}, volume = {49}, year = {2010}, month = {2010///}, pages = {6887 - 6895}, abstract = {N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis.N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using 13C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue Nδ-(phosphonoacetyl)-Nα-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis. }, isbn = {0006-2960}, doi = {10.1021/bi1007386}, url = {http://dx.doi.org/10.1021/bi1007386}, author = {Li,Yongdong and Yu,Xiaolin and Ho,Jeremy and Fushman, David and Allewell,Norma M. and Tuchman,Mendel and Shi,Dashuang} } @conference {15283, title = {Scaling Populations of a Genetic Algorithm for Job Shop Scheduling Problems Using MapReduce}, booktitle = {Cloud Computing Technology and Science (CloudCom), 2010 IEEE Second International Conference on}, year = {2010}, month = {2010///}, pages = {780 - 785}, abstract = {Inspired by Darwinian evolution, a genetic algorithm (GA) approach is one popular heuristic method for solving hard problems such as the Job Shop Scheduling Problem (JSSP), which is one of the hardest problems lacking efficient exact solutions today. It is intuitive that the population size of a GA may greatly affect the quality of the solution, but it is unclear what are the effects of having population sizes that are significantly greater than typical experiments. The emergence of MapReduce, a framework running on a cluster of computers that aims to provide large-scale data processing, offers great opportunities to investigate this issue. In this paper, a GA is implemented to scale the population using MapReduce. Experiments are conducted on a large cluster, and population sizes up to 107 are inspected. It is shown that larger population sizes not only tend to yield better solutions, but also require fewer generations. Therefore, it is clear that when dealing with a hard problem such as JSSP, an existing GA can be improved by massively scaling up populations with MapReduce, so that the solution can be parallelized and completed in reasonable time.}, keywords = {algorithm;job, algorithms;job, computing;genetic, data, large-scale, MapReduce;cloud, problems;parallel, processing;, processing;cloud, scheduling, scheduling;parallel, shop}, doi = {10.1109/CloudCom.2010.18}, author = {Di-Wei Huang and Jimmy Lin} } @article {18277, title = {Security analysis for privacy preserving search of multimedia}, journal = {Image Processing (ICIP)}, year = {2010}, month = {2010///}, pages = {26 - 29}, abstract = {With the increasing popularity of digital multimedia such asimages and videos and the advent of the cloud computing paradigm, a fast growing amount of private and sensitive mul- timedia data are being stored and managed over the network cloud. To provide enhanced security and privacy protection beyond traditional access control techniques, privacy preserv- ing multimedia retrieval techniques have been proposed re- cently to allow content-based multimedia retrieval directly over encrypted databases and achieve accurate retrieval com- parable to conventional retrieval schemes. In this paper, we introduce a security definition for the privacy preserving re- trieval scenario and show that the recently proposed schemes are secure under the proposed security definition. }, author = {Lu,W. and Varna,A.L. and Wu,M.} } @article {19205, title = {Sensing Events Affecting Liquid Flow in a Liquid Distribution System}, year = {2010}, month = {2010}, publisher = {University of Washington}, abstract = {By monitoring pressure transients in a liquid within a liquid distribution system using only a single sensor, events such as the opening and closing of valves at specific fixtures are readily detected. The sensor, which can readily be coupled to a faucet bib, transmits an output signal to a computing device. Each such event can be identified by the device based by comparing characteristic features of the pressure transient waveform with previously observed characteristic features for events in the system. These characteristic features, which can include the varying pressure, derivative, and real Cepstrum of the pressure transient waveform, can be used to select a specific fixture where a valve open or close event has occurred. Flow to each fixture and leaks in the system can also be determined from the pressure transient signal. A second sensor disposed at a point disparate from the first sensor provides further event information.}, url = {http://www.google.com/patents?id=2JXnAAAAEBAJ}, author = {Patel,Shwetak N. and Fogarty,James A. and Jon Froehlich and Larson,Eric C.} } @article {12878, title = {Serodiversity and ecological distribution of Vibrio parahaemolyticus in the Venetian Lagoon, Northeast Italy}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/01/}, pages = {151 - 157}, abstract = {Vibrio parahaemolyticus is a natural inhabitant of estuarine and marine environments constituting part of the autochthonous microflora. This species is associated with human gastroenteritis caused by ingestion of contaminated water and undercooked seafood. During the past several years, the number of V. parahaemolyticus gastroenteritis cases have increased worldwide, causing over half of all food-poisoning outbreaks of bacterial origin. Vibrio populations in water are known to be influenced by environmental factors. Notably, it has been shown that in different parts of the world the distribution of V. parahaemolyticus in the marine environment is related to the water temperature. In this study, we identified environmental determinants affecting distribution of V. parahaemolyticus in the Venetian Lagoon, in the Italian North Adriatic Sea. Data obtained revealed that sea surface temperature constitutes the key factor influencing occurrence of V. parahaemolyticus, but salinity and chlorophyll concentration are also important. Serotyping of a collection of V. parahaemolyticus environmental isolates revealed high serodiversity, with serotypes O3:KUT and O1:KUT, belonging to the {\textquoteleft}pandemic group{\textquoteright}, occurring with higher frequency. From our results, we conclude that there is no correlation between serotype and specific geographic site or season of the year. However, certain serotypes were isolated in the Lagoon during the entire 18 months of the study, strongly suggesting persistence in this environment.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2009.00123.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2009.00123.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Caburlotto,Greta and Haley,Bradd J. and Lle{\`o},Maria M. and Huq,Anwar and Rita R Colwell} } @article {13089, title = {Shape analysis and its applications in image understanding}, journal = {IEEE transactions on pattern analysis and machine intelligence}, volume = {32}, year = {2010}, month = {2010///}, pages = {604 - 618}, abstract = {We propose a shape-based, hierarchical part-template matching approach to simultaneous human detection and segmentation combining local part-based and global shape-template-based schemes. The approach relies on the key idea of matching a part-template tree to images hierarchically to detect humans and estimate their poses. For learning a generic human detector, a pose-adaptive feature computation scheme is developed based on a tree matching approach. Instead of traditional concatenation-style image location-based feature encoding, we extract features adaptively in the context of human poses and train a kernel-SVM classifier to separate human/nonhuman patterns. Specifically, the features are collected in the local context of poses by tracing around the estimated shape boundaries. We also introduce an approach to multiple occluded human detection and segmentation based on an iterative occlusion compensation scheme. The output of our learned generic human detector can be used as an initial set of human hypotheses for the iterative optimization. We evaluate our approaches on three public pedestrian data sets (INRIA, MIT-CBCL, and USC-B) and two crowded sequences from Caviar Benchmark and Munich Airport data sets.}, author = {Zhe Lin and Davis, Larry S.} } @article {13090, title = {Shape-based human detection and segmentation via hierarchical part-template matching}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {32}, year = {2010}, month = {2010///}, pages = {604 - 618}, abstract = {We propose a shape-based, hierarchical part-template matching approach to simultaneous human detection and segmentation combining local part-based and global shape-template-based schemes. The approach relies on the key idea of matching a part-template tree to images hierarchically to detect humans and estimate their poses. For learning a generic human detector, a pose-adaptive feature computation scheme is developed based on a tree matching approach. Instead of traditional concatenation-style image location-based feature encoding, we extract features adaptively in the context of human poses and train a kernel-SVM classifier to separate human/nonhuman patterns. Specifically, the features are collected in the local context of poses by tracing around the estimated shape boundaries. We also introduce an approach to multiple occluded human detection and segmentation based on an iterative occlusion compensation scheme. The output of our learned generic human detector can be used as an initial set of human hypotheses for the iterative optimization. We evaluate our approaches on three public pedestrian data sets (INRIA, MIT-CBCL, and USC-B) and two crowded sequences from Caviar Benchmark and Munich Airport data sets.}, author = {Lin,Z. and Davis, Larry S.} } @article {13087, title = {SPECIAL SECTION ON SHAPE ANALYSIS AND ITS APPLICATIONS IN IMAGE UNDERSTANDING}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {32}, year = {2010}, month = {2010///}, pages = {0162 - 8828}, author = {Srivastava, A. and Damon,J.N. and Dryden,I.L. and Jermyn,I.H. and Das,S. and Vaswani, N. and Huckemann,S. and Hotz,T. and Munk,A. and Lin,Z. and others} } @article {18757, title = {Stochastic simulations with graphics hardware: Characterization of accuracy and performance}, journal = {Journal of Computing and Information Science in Engineering}, volume = {10}, year = {2010}, month = {2010///}, pages = {011010 - 011010}, author = {Balijepalli,A. and LeBrun,T. W. and Gupta,S.K.} } @inbook {17395, title = {Technology-Mediated Social Participation: Deep Science and Extreme Technology}, booktitle = {Active Media TechnologyActive Media Technology}, series = {Lecture Notes in Computer Science}, volume = {6335}, year = {2010}, month = {2010///}, pages = {1 - 4}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The dramatic success of social media such as Facebook, Twitter, YouTube, Flickr, blogs, and traditional discussion groups empowers individuals to become active in local and global communities. With modest redesign, these technologies can be harnessed to support national priorities such as healthcare/wellness, disaster response, community safety, energy sustainability, etc. This talk describes a research agenda for these topics that develops deep science questions and extreme technology challenges.}, isbn = {978-3-642-15469-0}, url = {http://dx.doi.org/10.1007/978-3-642-15470-6_1}, author = {Shneiderman, Ben}, editor = {An,Aijun and Lingras,Pawan and Petty,Sheila and Huang,Runhe} } @article {15054, title = {A tree-based approach to integrated action localization, recognition and segmentation}, journal = {ECCV Workshops}, year = {2010}, month = {2010///}, abstract = {A tree-based approach to integrated action segmentation,localization and recognition is proposed. An action is represented as a sequence of joint hog-flow descriptors extracted independently from each frame. During training, a set of action prototypes is first learned based on a k-means clustering, and then a binary tree model is constructed from the set of action prototypes based on hierarchical k-means cluster- ing. Each tree node is characterized by a shape-motion descriptor and a rejection threshold, and an action segmentation mask is defined for leaf nodes (corresponding to a prototype). During testing, an action is local- ized by mapping each test frame to a nearest neighbor prototype using a fast matching method to search the learned tree, followed by global fil- tering refinement. An action is recognized by maximizing the sum of the joint probabilities of the action category and action prototype over test frames. Our approach does not explicitly rely on human tracking and background subtraction, and enables action localization and recognition in realistic and challenging conditions (such as crowded backgrounds). Experimental results show that our approach can achieve recognition rates of 100\% on the CMU action dataset and 100\% on the Weizmann dataset. }, author = {Zhuolin Jiang and Lin,Z. and Davis, Larry S.} } @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} } @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} } @inbook {17503, title = {Visualizing Threaded Conversation Networks: Mining Message Boards and Email Lists for Actionable Insights}, booktitle = {Active Media TechnologyActive Media Technology}, series = {Lecture Notes in Computer Science}, volume = {6335}, year = {2010}, month = {2010///}, pages = {47 - 62}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analyzing complex online relationships is a difficult job, but new information visualization tools are enabling a wider range of users to make actionable insights from the growing volume of online data. This paper describes the challenges and methods for conducting analyses of threaded conversations such as found in enterprise message boards, email lists, and forums. After defining threaded conversation, we characterize the types of networks that can be extracted from them. We then provide 3 mini case studies to illustrate how actionable insights for community managers can be gained by applying the network analysis metrics and visualizations available in the free, open source NodeXL tool, which is a powerful, yet easy-to-use tool embedded in Excel 2007/2010.}, isbn = {978-3-642-15469-0}, url = {http://dx.doi.org/10.1007/978-3-642-15470-6_7}, author = {Hansen,Derek and Shneiderman, Ben and Smith,Marc}, editor = {An,Aijun and Lingras,Pawan and Petty,Sheila and Huang,Runhe} } @conference {18355, title = {VizWiz: nearly real-time answers to visual questions}, booktitle = {Proceedings of the 23nd annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {333 - 342}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The lack of access to visual information like text labels, icons, and colors can cause frustration and decrease independence for blind people. Current access technology uses automatic approaches to address some problems in this space, but the technology is error-prone, limited in scope, and quite expensive. In this paper, we introduce VizWiz, a talking application for mobile phones that offers a new alternative to answering visual questions in nearly real-time - asking multiple people on the web. To support answering questions quickly, we introduce a general approach for intelligently recruiting human workers in advance called quikTurkit so that workers are available when new questions arrive. A field deployment with 11 blind participants illustrates that blind people can effectively use VizWiz to cheaply answer questions in their everyday lives, highlighting issues that automatic approaches will need to address to be useful. Finally, we illustrate the potential of using VizWiz as part of the participatory design of advanced tools by using it to build and evaluate VizWiz::LocateIt, an interactive mobile tool that helps blind people solve general visual search problems.}, keywords = {blind users, non-visual interfaces, real-time human computation}, isbn = {978-1-4503-0271-5}, doi = {10.1145/1866029.1866080}, url = {http://doi.acm.org/10.1145/1866029.1866080}, author = {Bigham,Jeffrey P. and Jayant,Chandrika and Ji,Hanjie and Little,Greg and Miller,Andrew and Miller,Robert C. and Miller,Robin and Tatarowicz,Aubrey and White,Brandyn and White,Samual and Tom Yeh} } @conference {14351, title = {WATTR: a method for self-powered wireless sensing of water activity in the home}, booktitle = {Proceedings of the 12th ACM international conference on Ubiquitous computing}, series = {Ubicomp {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {169 - 172}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {power harvesting, sensing, water conservation}, isbn = {978-1-60558-843-8}, doi = {10.1145/1864349.1864378}, url = {http://doi.acm.org/10.1145/1864349.1864378}, author = {Campbell,Tim and Larson,Eric and Cohn,Gabe and Jon Froehlich and Alcaide,Ramses and Patel,Shwetak N.} } @conference {13086, title = {Web-scale computer vision using MapReduce for multimedia data mining}, booktitle = {Proceedings of the Tenth International Workshop on Multimedia Data Mining}, series = {MDMKDD {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {9:1{\textendash}9:10 - 9:1{\textendash}9:10}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This work explores computer vision applications of the MapReduce framework that are relevant to the data mining community. An overview of MapReduce and common design patterns are provided for those with limited MapReduce background. We discuss both the high level theory and the low level implementation for several computer vision algorithms: classifier training, sliding windows, clustering, bag-of-features, background subtraction, and image registration. Experimental results for the k-means clustering and single Gaussian background subtraction algorithms are performed on a 410 node Hadoop cluster.}, keywords = {background subtraction, bag-of-features, Cloud computing, clustering, Computer vision, image registration, MapReduce}, isbn = {978-1-4503-0220-3}, doi = {10.1145/1814245.1814254}, url = {http://doi.acm.org/10.1145/1814245.1814254}, author = {White,Brandyn and Tom Yeh and Jimmy Lin and Davis, Larry S.} } @article {18925, title = {When is it better not to look ahead?}, journal = {Artificial Intelligence}, volume = {174}, year = {2010}, month = {2010/11//}, pages = {1323 - 1338}, abstract = {In situations where one needs to make a sequence of decisions, it is often believed that looking ahead will help produce better decisions. However, it was shown 30 years ago that there are {\textquotedblleft}pathological{\textquotedblright} situations in which looking ahead is counterproductive. Two long-standing open questions are (a) what combinations of factors have the biggest influence on whether lookahead pathology occurs, and (b) whether it occurs in real-world decision-making.This paper includes simulation results for several synthetic game-tree models, and experimental results for three well-known board games: two chess endgames, kalah (with some modifications to facilitate experimentation), and the 8-puzzle. The simulations show the interplay between lookahead pathology and several factors that affect it; and the experiments confirm the trends predicted by the simulation models. The experiments also show that lookahead pathology is more common than has been thought: all three games contain situations where it occurs. }, keywords = {Game-tree search, Lookahead pathology, minimax}, isbn = {0004-3702}, doi = {10.1016/j.artint.2010.08.002}, url = {http://www.sciencedirect.com/science/article/pii/S0004370210001402}, author = {Nau, Dana S. and Lu{\v s}trek,Mitja and Parker,Austin and Bratko,Ivan and Gams,Matja{\v z}} } @article {12527, title = {3D Face Recognition: Technology and Applications}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {217 - 246}, author = {Tistarelli,M. and Li, S.Z. and Chellapa, Rama and Akarun, L.} } @article {12528, title = {Advanced Technologies for Touchless Fingerprint Recognition}, journal = {Handbook of Remote Biometrics}, year = {2009}, month = {2009///}, pages = {83 - 109}, author = {Tistarelli,M. and Li, S.Z. and Chellapa, Rama} } @article {18784, title = {Algorithms for extraction of nanowire lengths and positions from optical section microscopy image sequence}, journal = {Journal of Computing and Information Science in Engineering}, volume = {9}, year = {2009}, month = {2009///}, pages = {041007 - 041007}, author = {Peng,T. and Balijepalli,A. and Gupta,S.K. and LeBrun,T. W.} } @conference {12229, title = {All Bits Are Not Equal - A Study of IEEE 802.11 Communication Bit Errors}, booktitle = {INFOCOM 2009, IEEE}, year = {2009}, month = {2009/04//}, pages = {1602 - 1610}, abstract = {In IEEE 802.11 Wireless LAN (WLAN) systems, techniques such as acknowledgement, retransmission, and transmission rate adaptation, are frame-level mechanisms designed for combating transmission errors. Recently sub-frame level mechanisms such as frame combining have been proposed by the research community. In this paper, we present results obtained from our bit error study for identifying sub-frame error patterns because we believe that identifiable bit error patterns can potentially introduce new opportunities in channel coding, network coding, forward error correction (FEC), and frame combining mechanisms. We have constructed a number of IEEE 802.11 wireless LAN testbeds and conducted extensive experiments to study the characteristics of bit errors and their location distribution. Conventional wisdom dictates that bit error probability is the result of channel condition and ought to follow corresponding distribution. However our measurement results identify three repeatable bit error patterns that are not induced by channel conditions. We have verified that such error patterns are present in WLAN transmissions in different physical environments and across different wireless LAN hardware platforms. We also discuss our current hypotheses for the reasons behind these bit error probability patterns and how identifying these patterns may help improving WLAN transmission robustness.}, keywords = {802.11, bit, coding;error, coding;forward, coding;subframe, combining, Communication, correction;frame, correction;wireless, error, errors;channel, errors;wireless, IEEE, LAN;, LAN;channel, mechanisms;network, patterns;transmission, statistics;forward}, doi = {10.1109/INFCOM.2009.5062078}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Bhattacharjee, Bobby and Miller,R.R.} } @article {12522, title = {Appearance Modeling Using a Geometric Transform}, journal = {Image Processing, IEEE Transactions on}, volume = {18}, year = {2009}, month = {2009/04//}, pages = {889 - 902}, abstract = {A general transform, called the geometric transform (GeT), that models the appearance inside a closed contour is proposed. The proposed GeT is a functional of an image intensity function and a region indicator function derived from a closed contour. It can be designed to combine the shape and appearance information at different resolutions and to generate models invariant to deformation, articulation, or occlusion. By choosing appropriate functionals and region indicator functions, the GeT unifies Radon transform, trace transform, and a class of image warpings. By varying the region indicator and the types of features used for appearance modeling, five novel types of GeTs are introduced and applied to fingerprinting the appearance inside a contour. They include the GeTs based on a level set, shape matching, feature curves, and the GeT invariant to occlusion, and a multiresolution GeT (MRGeT). Applications of GeT to pedestrian identity recognition, human body part segmentation, and image synthesis are illustrated. The proposed approach produces promising results when applied to fingerprinting the appearance of a human and body parts despite the presence of nonrigid deformations and articulated motion.}, keywords = {body, contour;feature, curve;fingerprinting;geometric, function;image, function;shape, geometry;image, identity, indicator, INTENSITY, matching;trace, method;pedestrian, modeling;closed, part, Radon, recognition;region, resolution;image, segmentation;, segmentation;image, set, synthesis;image, transform;appearance, transform;human, transform;Radon, transforms;computational, warping;level}, isbn = {1057-7149}, doi = {10.1109/TIP.2008.2011381}, author = {Li,Jian and Zhou,S. K and Chellapa, Rama} } @article {16244, title = {ARDB-Antibiotic Resistance Genes Database}, journal = {Nucleic Acids Research}, volume = {37}, year = {2009}, month = {2009/01/01/}, pages = {D443-D447 - D443-D447}, abstract = {The treatment of infections is increasingly compromised by the ability of bacteria to develop resistance to antibiotics through mutations or through the acquisition of resistance genes. Antibiotic resistance genes also have the potential to be used for bio-terror purposes through genetically modified organisms. In order to facilitate the identification and characterization of these genes, we have created a manually curated database{\textemdash}the Antibiotic Resistance Genes Database (ARDB){\textemdash}unifying most of the publicly available information on antibiotic resistance. Each gene and resistance type is annotated with rich information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. Our database also supports sequence similarity searches and implements an initial version of a tool for characterizing common mutations that confer antibiotic resistance. The information we provide can be used as compendium of antibiotic resistance factors as well as to identify the resistance genes of newly sequenced genes, genomes, or metagenomes. Currently, ARDB contains resistance information for 13 293 genes, 377 types, 257 antibiotics, 632 genomes, 933 species and 124 genera. ARDB is available at http://ardb.cbcb.umd.edu/.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkn656}, url = {http://nar.oxfordjournals.org/content/37/suppl_1/D443.short}, author = {Liu,B. and Pop, Mihai} } @conference {15309, title = {Brute force and indexed approaches to pairwise document similarity comparisons with MapReduce}, booktitle = {Proceedings of the 32nd international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {155 - 162}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper explores the problem of computing pairwise similarity on document collections, focusing on the application of "more like this" queries in the life sciences domain. Three MapReduce algorithms are introduced: one based on brute force, a second where the problem is treated as large-scale ad hoc retrieval, and a third based on the Cartesian product of postings lists. Each algorithm supports one or more approximations that trade effectiveness for efficiency, the characteristics of which are studied experimentally. Results show that the brute force algorithm is the most efficient of the three when exact similarity is desired. However, the other two algorithms support approximations that yield large efficiency gains without significant loss of effectiveness.}, keywords = {distributed algorithms, hadoop}, isbn = {978-1-60558-483-6}, doi = {10.1145/1571941.1571970}, url = {http://doi.acm.org/10.1145/1571941.1571970}, author = {Jimmy Lin} } @article {14950, title = {Call for Papers: Special Issue of the Journal of Parallel and Distributed Computing: Cloud Computing}, journal = {J. Parallel Distrib. Comput.}, volume = {69}, year = {2009}, month = {2009/09//}, pages = {813{\textendash} - 813{\textendash}}, isbn = {0743-7315}, doi = {10.1016/j.jpdc.2009.07.002}, url = {http://dx.doi.org/10.1016/j.jpdc.2009.07.002}, author = {Chockler,Gregory and Dekel,Eliezer and JaJa, Joseph F. and Jimmy Lin} } @conference {12227, title = {Channel Access Throttling for Improving WLAN QoS}, booktitle = {Sensor, Mesh and Ad Hoc Communications and Networks, 2009. SECON {\textquoteright}09. 6th Annual IEEE Communications Society Conference on}, year = {2009}, month = {2009/06//}, pages = {1 - 9}, abstract = {The de facto QoS channel access method for the IEEE 802.11 Wireless LANs is the Enhanced Distributed Channel Access (EDCA) mechanism, which differentiates transmission treatments for data frames belonging to different traffic categories with four different levels of channel access priority. In this paper, we propose extending EDCA with Channel Access Throttling (CAT) for more flexible and efficient QoS support. By assigning different member stations different channel access parameters, CAT differentiates channel access priorities not between traffic categories but between member stations. Then by dynamically changing the channel access parameters of each member station based on a pre-computed schedule, CAT enables EDCA WLANs the benefits of scheduled access QoS. We also present evaluation results of CAT obtained from both simulations and experiments conducted using off-the-shelf WLAN hardware and open-source device driver. Our results show that CAT can proportionally partition channel capacity, significantly improve performance of multimedia applications, effectively achieve performance protection for admitted flows, and increase per cell VoIP call capacity by up to 41\%.}, keywords = {802.11, access, area, call, capacity;data, capacity;quality, capacity;WLAN, categories;transmission, channel, device, distributed, driver;quality, facto, frames;de, IEEE, LAN;, LAN;VoIP, local, mechanism;member, method;enhanced, multimedia, network;wireless, networks;channel, of, parameters;channel, priority;channel, QoS, QoS;channel, service;telecommunication, service;traffic, standards;telecommunication, stations;open-source, throttling;channel, traffic;wireless, treatments;wireless, wireless}, doi = {10.1109/SAHCN.2009.5168915}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Miller,R.R. and Bhattacharjee, Bobby} } @conference {12226, title = {Channel Access Throttling for Overlapping BSS Management}, booktitle = {Communications, 2009. ICC {\textquoteright}09. IEEE International Conference on}, year = {2009}, month = {2009/06//}, pages = {1 - 6}, abstract = {Multiple co-channel WLAN BSSes (i.e., WLAN cells) overlapping in coverage are generally considered undesirable because members of the OBSSes compete for channel access, which typically increases the contention level of wireless medium access and reduces overall system performance. In this paper, we propose to use channel access throttling (CAT) for managing Wireless LAN radio resources for overlapping BSSes (OBSSes). CAT provides an access point (AP) of each BSS with a mechanism to control channel access parameters of its member stations on the fly. By coordinating the CAT operations of the OBSS APs, we can enable privileged channel access to an individual BSS at a particular time, for example, by assigning high priority access parameters to member stations associated with the BSS. By controlling how much each BSS may be given the privileged channel access, we can also achieve a proportional partitioning of channel capacity among OBSSes. We present evaluation results obtained from both simulations and experiments using testbed built with commercial off-the-shelf (COTS) WLAN hardware and open-source device driver. Our results show that with CAT, not only can we proportionally partition channel capacity among the OBSSes, but also improve channel utilization efficiency and increase overall capacity.}, keywords = {access, access;cellular, allocation;channel, BSS, capacity;computer, capacity;proportional, cell;open-source, channel, channels;, co-channel, device, driver;overlapping, efficiency;high-priority, LAN;wireless, management;partition, management;wireless, medium, network, parameters;multiple, partitioning;radio, radio;channel, resources;wireless, throttling;channel, utilization, WLAN}, doi = {10.1109/ICC.2009.5198815}, author = {Han,Bo and Ji,Lusheng and Lee,Seungjoon and Miller,R.R. and Bhattacharjee, Bobby} } @article {15053, title = {Classic triangular mesh subdivision algorithm}, journal = {Jisuanji Gongcheng/ Computer Engineering}, volume = {35}, year = {2009}, month = {2009///}, pages = {7 - 10}, abstract = {This paper makes a concise introduction to seven classic algorithms of triangular mesh subdivision, and makes a classification and comparison between them according to their continuity, own advantage and application status. In order to improve the visualization of triangular mesh subdivision, interactive display control is implemented by using MFC and OpenGL while state machine model based on functional class is used as the software operating pattern. On the basis of this, the prototype implementation of Loop algorithm is performed. The improved method of solving existing problematic issues from prototype implementation is presented.}, author = {Zhuolin Jiang and Li,S.F. and Jia,X.P. and Zhu,H.L.} } @conference {13276, title = {Classification of non-manifold singularities from transformations of 2-manifolds}, booktitle = {Shape Modeling and Applications, 2009. SMI 2009. IEEE International Conference on}, year = {2009}, month = {2009/06//}, pages = {179 - 184}, abstract = {Non-manifold models are frequently encountered in engineering simulations and design as well as in computer graphics. However, these models lack shape characterization for modelling and searching purposes. Topological properties act as a kernel for deriving key features of objects. Here we propose a classification for the non-manifold singularities of non-manifold objects through continuous shape transformations of 2-manifolds without boundary up to the creation of non-manifold singularities. As a result, the non-manifold objects thus created can be categorized and contribute to the definition of a general purpose taxonomy for non-manifold shapes.}, keywords = {classification;search, Computer, graphic;continuous, graphics;pattern, model;nonmanifold, problems;topology;, property;computer, SHAPE, singularity;topological, transformation;nonmanifold}, doi = {10.1109/SMI.2009.5170146}, author = {Leon,J.-C. and De Floriani, Leila and Hetroy,F.} } @article {15077, title = {Collusion-free multiparty computation in the mediated model}, journal = {Advances in Cryptology-CRYPTO 2009}, year = {2009}, month = {2009///}, pages = {524 - 540}, abstract = {Collusion-free protocols prevent subliminal communication (i.e., covert channels) between parties running the protocol. In the standard communication model, if one-way functions exist, then protocols satisfying any reasonable degree of privacy cannot be collusion-free. To circumvent this impossibility, Alwen, shelat and Visconti (CRYPTO 2008) recently suggested the mediated model where all communication passes through a mediator. The goal is to design protocols where collusion-freeness is guaranteed as long as the mediator is honest, while standard security guarantees hold if the mediator is dishonest. In this model, they gave constructions of collusion-free protocols for commitments and zero-knowledge proofs in the two-party setting.We strengthen the definition of Alwen et al., and resolve the main open questions in this area by showing a collusion-free protocol (in the mediated model) for computing any multi-party functionality. }, doi = {10.1007/978-3-642-03356-8_31}, author = {Alwen,J. and Katz, Jonathan and Lindell,Y. and Persiano,G. and Shelat,A. and Visconti,I.} } @article {14482, title = {Common effect of antipsychotics on the biosynthesis and regulation of fatty acids and cholesterol supports a key role of lipid homeostasis in schizophrenia}, journal = {Schizophrenia Research}, volume = {108}, year = {2009}, month = {2009/03//}, pages = {134 - 142}, abstract = {For decades, the dopamine hypothesis has gained the most attention in an attempt to explain the origin and the symptoms of schizophrenia. While this hypothesis offers an explanation for the relationship between psychotic symptoms and dopamine kinetics, it does not provide a direct explanation of the etiology of schizophrenia which remains poorly understood. Consequently, current antipsychotics that target neurotransmitter receptors, have limited and inconsistent efficacy. To gain insights into the mechanism of action of these drugs, we studied the expression profile of 12,490 human genes in a cell line treated with 18 antipsychotics, and compared it to that of a library of 448 other compounds used in a variety of disorders. Analysis reveals a common effect of antipsychotics on the biosynthesis and regulation of fatty acids and cholesterol, which is discussed in the context of a lipid hypothesis where alterations in lipid homeostasis might underlie the pathogenesis of schizophrenia. This finding may help research aimed at the development of novel treatments for this devastating disease.}, keywords = {Antipsychotic action, Gene expression, Lipid homeostasis, Pathogenesis}, isbn = {0920-9964}, doi = {10.1016/j.schres.2008.11.025}, url = {http://www.sciencedirect.com/science/article/pii/S0920996408005306}, author = {Polymeropoulos,Mihael H. and Licamele,Louis and Volpi,Simona and Mack,Kendra and Mitkus,Shruti N. and Carstea,Eugene D. and Getoor, Lise and Thompson,Andrew and Lavedan,Christian} } @article {12895, title = {Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae}, journal = {Proceedings of the National Academy of Sciences}, volume = {106}, year = {2009}, month = {2009///}, pages = {15442 - 15447}, abstract = {Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a {\textquotedblleft}shift{\textquotedblright} between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a {\textquotedblleft}drift{\textquotedblright} between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0907787106}, url = {http://www.pnas.org/content/106/36/15442}, author = {Chun,J. and Grim,C. J. and Hasan,N. A. and Lee,J. H. and Choi,S. Y. and Haley,B. J. and Taviani,E. and Jeon,Y. S. and Kim,D.W. and Lee,J. H. and Rita R Colwell} } @article {18183, title = {Component forensics}, journal = {Signal Processing Magazine, IEEE}, volume = {26}, year = {2009}, month = {2009/03//}, pages = {38 - 48}, abstract = {Visual sensor technologies have experienced tremendous growth in recent decades, and digital devices are becoming ubiquitous. Digital images taken by various imaging devices have been used in a growing number of applications, from military and reconnaissance to medical diagnosis and consumer photography. Consequently, a series of new forensic issues arise amidst such rapid advancement and widespread adoption of imaging technologies. For example, one can readily ask what kinds of hardware and software components as well as their parameters have been employed inside these devices? Given a digital image, which imaging sensor or which brand of sensor was used to acquire the image? How was the image acquired? Was it captured using a digital camera, cell phone camera, image scanner, or was it created artificially using an imageediting software? Has the image undergone any manipulation after capture? Is it authentic, or has it been tampered in any way? Does it contain any hidden information or steganographic data? Many of these forensic questions are related to tracing the origin of the digital image to its creation process. Evidence obtained from such analysis would provide useful forensic information to law enforcement, security, and intelligence agencies. Knowledge of image acquisition techniques can also help answer further forensic questions regarding the nature of additional processing that the image might have undergone after capture.}, keywords = {ACQUISITION, component, data;, forensics;digital, image, of, processing;image, sensor, sensors;security, technique;visual, technology;image}, isbn = {1053-5888}, doi = {10.1109/MSP.2008.931076}, author = {Swaminathan,A. and M. Wu and Liu,K. J.R} } @article {15298, title = {Computational linguistics for metadata building (CLiMB): using text mining for the automatic identification, categorization, and disambiguation of subject terms for image metadata}, journal = {Multimedia Tools and Applications}, volume = {42}, year = {2009}, month = {2009///}, pages = {115 - 138}, abstract = {In this paper, we present a system using computational linguistic techniques to extract metadata for image access. We discuss the implementation, functionality and evaluation of an image catalogers{\textquoteright} toolkit, developed in the Computational Linguistics for Metadata Building (CLiMB) research project. We have tested components of the system, including phrase finding for the art and architecture domain, functional semantic labeling using machine learning, and disambiguation of terms in domain-specific text vis a vis a rich thesaurus of subject terms, geographic and artist names. We present specific results on disambiguation techniques and on the nature of the ambiguity problem given the thesaurus, resources, and domain-specific text resource, with a comparison of domain-general resources and text. Our primary user group for evaluation has been the cataloger expert with specific expertise in the fields of painting, sculpture, and vernacular and landscape architecture.}, doi = {10.1007/s11042-008-0253-9}, author = {Klavans,J. L and Sheffield,C. and Abels,E. and Jimmy Lin and Passonneau,R. and Sidhu,T. and Soergel,D.} } @article {13390, title = {On Computing Compression Trees for Data Collection in Sensor Networks}, journal = {arXiv:0907.5442}, year = {2009}, month = {2009/07/30/}, abstract = {We address the problem of efficiently gathering correlated data from a wired or a wireless sensor network, with the aim of designing algorithms with provable optimality guarantees, and understanding how close we can get to the known theoretical lower bounds. Our proposed approach is based on finding an optimal or a near-optimal {\em compression tree} for a given sensor network: a compression tree is a directed tree over the sensor network nodes such that the value of a node is compressed using the value of its parent. We consider this problem under different communication models, including the {\em broadcast communication} model that enables many new opportunities for energy-efficient data collection. We draw connections between the data collection problem and a previously studied graph concept, called {\em weakly connected dominating sets}, and we use this to develop novel approximation algorithms for the problem. We present comparative results on several synthetic and real-world datasets showing that our algorithms construct near-optimal compression trees that yield a significant reduction in the data collection cost.}, keywords = {Computer Science - Information Theory, Computer Science - Networking and Internet Architecture}, url = {http://arxiv.org/abs/0907.5442}, author = {Li,Jian and Deshpande, Amol and Khuller, Samir} } @conference {13360, title = {Consensus answers for queries over probabilistic databases}, booktitle = {Proceedings of the twenty-eighth ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems}, series = {PODS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {259 - 268}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We address the problem of finding a "best" deterministic query answer to a query over a probabilistic database. For this purpose, we propose the notion of a consensus world (or a consensus answer) which is a deterministic world (answer) that minimizes the expected distance to the possible worlds (answers). This problem can be seen as a generalization of the well-studied inconsistent information aggregation problems (e.g. rank aggregation) to probabilistic databases. We consider this problem for various types of queries including SPJ queries, Top-k ranking queries, group-by aggregate queries, and clustering. For different distance metrics, we obtain polynomial time optimal or approximation algorithms for computing the consensus answers (or prove NP-hardness). Most of our results are for a general probabilistic database model, called and/xor tree model, which significantly generalizes previous probabilistic database models like x-tuples and block-independent disjoint models, and is of independent interest.}, keywords = {consensus answers, probabilistic and/xor tree, Probabilistic databases, Query processing, rank aggregation}, isbn = {978-1-60558-553-6}, doi = {10.1145/1559795.1559835}, url = {http://doi.acm.org/10.1145/1559795.1559835}, author = {Li,Jian and Deshpande, Amol} } @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.} } @article {13701, title = {A cost-effective lexical acquisition process for large-scale thesaurus translation}, journal = {Language resources and evaluation}, volume = {43}, year = {2009}, month = {2009///}, pages = {27 - 40}, abstract = {Thesauri and controlled vocabularies facilitate access to digital collections by explicitly representing the underlying principles of organization. Translation of such resources into multiple languages is an important component for providing multilingual access. However, the specificity of vocabulary terms in most thesauri precludes fully-automatic translation using general-domain lexical resources. In this paper, we present an efficient process for leveraging human translations to construct domain-specific lexical resources. This process is illustrated on a thesaurus of 56,000 concepts used to catalog a large archive of oral histories. We elicited human translations on a small subset of concepts, induced a probabilistic phrase dictionary from these translations, and used the resulting resource to automatically translate the rest of the thesaurus. Two separate evaluations demonstrate the acceptability of the automatic translations and the cost-effectiveness of our approach.}, author = {Jimmy Lin and Murray,G. C and Dorr, Bonnie J and Haji{\v c},J. and Pecina,P.} } @article {15301, title = {The Curse of Zipf and Limits to Parallelization: A Look at the Stragglers Problem in MapReduce}, journal = {Proceedings of LSDS-IR workshop}, year = {2009}, month = {2009///}, pages = {57 - 62}, abstract = {This paper explores the problem of {\textquotedblleft}stragglers{\textquotedblright} in Map-Reduce: a common phenomenon where a small number of mappers or reducers takes significantly longer than the oth- ers to complete. The effects of these stragglers include un- necessarily long wall-clock running times and sub-optimal cluster utilization. In many cases, this problem cannot sim- ply be attributed to hardware idiosyncrasies, but is rather caused by the Zipfian distribution of input or intermedi- ate data. I present a simple theoretical model that shows how such distributions impose a fundamental limit on the amount of parallelism that can be extracted from a large class of algorithms where all occurrences of the same ele- ment must be processed together. A case study in parallel ad hoc query evaluation highlights the severity of the strag- glers problem. Fortunately, a simple modification of the in- put data cuts end-to-end running time in half. This example illustrates some of the issues associated with designing effi- cient MapReduce algorithms for real-world datasets. }, author = {Jimmy Lin} } @conference {18798, title = {A Decoupled and Prioritized Stochastic Dynamic Programming Approach for Automated Transport of Multiple Particles Using Optical Tweezers}, volume = {6}, year = {2009}, month = {2009///}, pages = {785 - 796}, publisher = {ASME}, organization = {ASME}, address = {San Diego, California, USA}, abstract = {Automated transport of multiple particles using optical tweezers requires the use of motion planning to move them simultaneously while avoiding collisions amongst themselves and with randomly moving obstacles. This paper develops a decoupled and prioritized stochastic dynamic programming based motion planning framework by sequentially applying a partially observable Markov decision process algorithm on every particle that needs to be transported. An iterative version of a maximum bipartite graph matching algorithm is used to assign given goal locations to such particles. The algorithm for individual particle transport is validated using silica beads in a holographic tweezer set-up. Once the individual plans are computed, a three-step method consisting of clustering, classification, and branch and bound optimization is employed to determine the final collision-free paths. Simulation results in the form of sample trajectories and performance characterization plots are presented to illustrate the usefulness of the developed approach.}, isbn = {978-0-7918-4903-3}, doi = {10.1115/DETC2009-87113}, url = {http://link.aip.org/link/ASMECP/v2009/i49033/p785/s1\&Agg=doi}, author = {Banerjee,Ashis Gopal and Losert,Wolfgang and Gupta, Satyandra K.} } @article {18195, title = {Design of data warehouse in teaching state based on OLAP and data mining}, journal = {Proceedings of SPIE}, volume = {7344}, year = {2009}, month = {2009///}, pages = {73440M - 73440M}, abstract = {The data warehouse and the data mining technology is one of information technology research hot topics. Atpresent the data warehouse and the data mining technology in aspects and so on commercial, financial industry as well as enterprise{\textquoteright}s production, market marketing obtained the widespread application, but is relatively less in educational fields{\textquoteright} application. Over the years, the teaching and management have been accumulating large amounts of data in colleges and universities, while the data can not be effectively used, in the light of social needs of the university development and the current status of data management, the establishment of data warehouse in university state, the better use of existing data, and on the basis dealing with a higher level of disposal --data mining are particularly important. In this paper, starting from the decision-making needs design data warehouse structure of university teaching state, and then through the design structure and data extraction, loading, conversion create a data warehouse model, finally make use of association rule mining algorithm for data mining, to get effective results applied in practice. Based on the data analysis and mining, get a lot of valuable information, which can be used to guide teaching management, thereby improving the quality of teaching and promoting teaching devotion in universities and enhancing teaching infrastructure. At the same time it can provide detailed, multi-dimensional information for universities assessment and higher education research. }, author = {Zhou,L. and Wu,M. and Li,S.} } @article {18528, title = {Designing Enforceable Network Contracts}, volume = {GT-CS-09-02}, year = {2009}, month = {2009///}, institution = {School of Computer Science, Georgia Tech}, abstract = {Internet connectivity depends on contractual agreements between cooperating entities, such as administrative domains (AD), where an agreement over a certain level of service is made. Contracts (e.g., SLAs) for providing certain levels of service must be enforceable, and ADs must have an incentive to meet their contractual obligations. Previous work has designed mechanisms for both pricing and network accountability, but no existing work examines contract structures with respect to different accountability frameworks, and how together they may affect an AD{\textquoteright}s incentives to fulfill contracts. We study how different contract structures{\textemdash}in particular, path-based versus pairwise contracts{\textemdash}affect ADs{\textquoteright} incentives to establish contracts (which, in turn, can affect overall connectivity) and, once contracts are established, to forward traffic according accordingly. This paper presents several contributions. First, we derive sufficient conditions for path-based contract systems and accountability frameworks for entities to have an incentive to forward traffic according to their contracts, provided that all parties involved are rational. Second, we show that for path-based contracts at equilibrium where nodes are encouraged to fulfill their contracts, only a constant amount of monitoring is required for every participant to make a positive profit; this is not the case for pairwise contracts. Third, we show how systems that rely on pairwise contracts are prone to depeering in presence of sufficient supply and demand due to coarse granularity, a contractual failure that systems which rely on path-based contracts are immune to. We propose modifications to pairwise contracts that could prevent such failures. Finally, we present situations of depeering that may be unpreventable due to maliciously behaving parties for both pairwise and path-based contract structures. For such scenarios, we show that while path-based contracts allow the sender of traffic to get reimbursed, this is not guaranteed in pairwise contract systems.}, url = {http://hdl.handle.net/1853/30626}, author = {Lychev,R. and Feamster, Nick} } @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} } @article {18209, title = {Enabling search over encrypted multimedia databases}, journal = {SPIE/IS\&T Media Forensics and Security}, year = {2009}, month = {2009///}, pages = {7254 - 18}, abstract = {Performing information retrieval tasks while preserving data confidentiality is a desirable capability when adatabase is stored on a server maintained by a third-party service provider. This paper addresses the problem of enabling content-based retrieval over encrypted multimedia databases. Search indexes, along with multimedia documents, are first encrypted by the content owner and then stored onto the server. Through jointly apply- ing cryptographic techniques, such as order preserving encryption and randomized hash functions, with image processing and information retrieval techniques, secure indexing schemes are designed to provide both privacy protection and rank-ordered search capability. Retrieval results on an encrypted color image database and se- curity analysis of the secure indexing schemes under different attack models show that data confidentiality can be preserved while retaining very good retrieval performance. This work has promising applications in secure multimedia management. }, author = {Lu,W. and Swaminathan,A. and Varna,A.L. and Wu,M.} } @conference {18829, title = {Enhanced force measurement techniques to extend optical trapping towards nanoscale manipulation}, year = {2009}, month = {2009/07//}, pages = {13 - 16}, abstract = {We have developed a new force measurement technique based on the random thermal motion of a nanoparticle in an optical trap. We demonstrate this method, in one-dimension, through numerical simulations and laboratory experiments. We show that computer simulations successfully recover the profile of the optical trapping force, beyond the inflection point of the trapping potential for a range of particle sizes. We show, through laboratory experiments, that this technique is effective in recovering higher order terms, in a power series expansion of the trapping force, beyond the widely reported linear trap stiffness. We also show that the first order (stiffness) term in our series expansion is consistent with values reported in the literature.}, keywords = {Brownian motion, extend optical trapping, Fokker-Planck equation, force measurement, inflection point, linear trap stiffness, nanoparticle, nanoparticles, nanoscale manipulation, nanotechnology, optical trapping force, power series expansion, radiation pressure, random thermal motion}, author = {Balijepalli,A. and LeBrun,T. W. and Gorman,J. J. and Gupta,S.K.} } @article {18701, title = {Evidence for Bidentate Substrate Binding as the Basis for the K48 Linkage Specificity of Otubain 1}, journal = {Journal of Molecular Biology}, volume = {386}, year = {2009}, month = {2009/03/06/}, pages = {1011 - 1023}, abstract = {Otubain 1 belongs to the ovarian tumor (OTU) domain class of cysteine protease deubiquitinating enzymes. We show here that human otubain 1 (hOtu1) is highly linkage-specific, cleaving Lys48 (K48)-linked polyubiquitin but not K63-, K29-, K6-, or K11-linked polyubiquitin, or linear α-linked polyubiquitin. Cleavage is not limited to either end of a polyubiquitin chain, and both free and substrate-linked polyubiquitin are disassembled. Intriguingly, cleavage of K48-diubiquitin by hOtu1 can be inhibited by diubiquitins of various linkage types, as well as by monoubiquitin. NMR studies and activity assays suggest that both the proximal and distal units of K48-diubiquitin bind to hOtu1. Reaction of Cys23 with ubiquitin-vinylsulfone identified a ubiquitin binding site that is distinct from the active site, which includes Cys91. Occupancy of the active site is needed to enable tight binding to the second site. We propose that distinct binding sites for the ubiquitins on either side of the scissile bond allow hOtu1 to discriminate among different isopeptide linkages in polyubiquitin substrates. Bidentate binding may be a general strategy used to achieve linkage-specific deubiquitination.}, keywords = {deubiquitination, isopeptide, linkage specificity, otubain, polyubiquitin}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2008.12.085}, url = {http://www.sciencedirect.com/science/article/pii/S0022283608016124}, author = {Wang,Tao and Yin,Luming and Cooper,Eric M. and Lai,Ming-Yih and Dickey,Seth and Pickart,Cecile M. and Fushman, David and Wilkinson,Keith D. and Cohen,Robert E. and Wolberger,Cynthia} } @article {14573, title = {Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart Failure / CLINICAL PERSPECTIVE}, journal = {Circulation: Cardiovascular Genetics}, volume = {2}, year = {2009}, month = {2009/06/01/}, pages = {212 - 219}, abstract = {Background{\textemdash} Pathological stresses induce heart failure in animal models through activation of multiple cardiac transcription factors (TFs) working cooperatively. However, interactions among TFs in human heart failure are less understood. Here, we use genomic data to examine the evidence that 5 candidate TF families coregulate gene expression in human heart failure.Methods and Results{\textemdash} RNA isolates from failing (n=86) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays. For each gene on the array, we determined conserved MEF2, NFAT, NKX , GATA , and FOX binding motifs within the -1-kb promoter region using human-murine sequence alignments and the TRANSFAC database. Across 9076 genes expressed in the heart, TF-binding motifs tended to cluster together in nonrandom patterns within promoters of specific genes (P values ranging from 10-2 to 10-21), suggesting coregulation. We then modeled differential expression as a function of TF combinations present in promoter regions. Several combinations predicted increased odds of differential expression in the failing heart, with the highest odds ratios noted for genes containing both MEF2 and NFAT binding motifs together in the same promoter region (peak odds ratio, 3.47; P=0.005).Conclusions{\textemdash} These findings provide genomic evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. In doing so, they extend the paradigm of combinatorial regulation of gene expression to the human heart and identify new target genes for mechanistic study. More broadly, we demonstrate how integrating diverse sources of genomic data yields novel insight into human cardiovascular disorders.}, doi = {10.1161/CIRCGENETICS.108.816686}, url = {http://circgenetics.ahajournals.org/content/2/3/212.abstract}, author = {Putt,Mary E. and Hannenhalli, Sridhar and Lu,Yun and Haines,Philip and Chandrupatla,Hareesh R. and Morrisey,Edward E. and Margulies,Kenneth B. and Cappola,Thomas P.} } @article {15055, title = {Fast and Accurate Method of Uniform-colored Video Text Extraction}, journal = {Jisuanji Gongcheng/ Computer Engineering}, volume = {35}, year = {2009}, month = {2009///}, abstract = {For most video text is rich in edge,uniform-colored and horizontally ranged,the candidate text areas in video image are determined by using a fast deriche edge based algorithm,and the accurate binary text images are extracted from the areas by using a color based algorithm.The experimental results show that the method is effective in text extraction in complex-background video frame,and has higher processing speed and better extraction result in comparison with color alone based method.}, author = {Shen,R.D. and Li,S.F. and Zhuolin Jiang} } @conference {18339, title = {Fast concurrent object localization and recognition}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {280 - 287}, publisher = {IEEE}, organization = {IEEE}, abstract = {Object localization and recognition are important problems in computer vision. However, in many applications, exhaustive search over all object models and image locations is computationally prohibitive. While several methods have been proposed to make either recognition or localization more efficient, few have dealt with both tasks simultaneously. This paper proposes an efficient method for concurrent object localization and recognition based on a data-dependent multi-class branch-and-bound formalism. Existing bag-of-features recognition techniques which can be expressed as weighted combinations of feature counts can be readily adapted to our method. We present experimental results that demonstrate the merit of our algorithm in terms of recognition accuracy, localization accuracy, and speed, compared to baseline approaches including exhaustive search, implicit-shape model (ISM), and efficient sub-window search (ESS). Moreover, we develop two extensions to consider non-rectangular bounding regions-composite boxes and polygons-and demonstrate their ability to achieve higher recognition scores compared to traditional rectangular bounding boxes.}, isbn = {978-1-4244-3992-8}, doi = {10.1109/CVPR.2009.5206805}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5206805}, author = {Tom Yeh and Lee,J.J. and Darrell,T.} } @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 {18764, title = {Generating simplified trapping probability models from simulation of optical tweezers system}, journal = {Journal of Computing and Information Science in Engineering}, volume = {9}, year = {2009}, month = {2009///}, pages = {021003 - 021003}, author = {Banerjee,A. G. and Balijepalli,A. and Gupta,S.K. and LeBrun,T. W.} } @article {12896, title = {Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains}, journal = {Nature}, year = {2009}, month = {2009///}, abstract = {Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the 6th and the current 7th pandemics, respectively. Cholera researchers continually face newly emerging and re-emerging pathogenic clones carrying combinations of new serogroups as well as of phenotypic and genotypic properties. These genotype and phenotype changes have hampered control of the disease. Here we compare the complete genome sequences of 23 strains of V. cholerae isolated from a variety of sources and geographical locations over the past 98 years in an effort to elucidate the evolutionary mechanisms governing genetic diversity and genesis of new pathogenic clones. The genome-based phylogeny revealed 12 distinct V. cholerae phyletic lineages, of which one, designated the V. cholerae core genome (CG), comprises both O1 classical and EI Tor biotypes. All 7th pandemic clones share nearly identical gene content, i.e., the same genome backbone. The transition from 6th to 7th pandemic strains is defined here as a {\textquoteright}shift{\textquoteright} between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages within the CG clade. In contrast, transition among clones during the present 7th pandemic period can be characterized as a {\textquoteright}drift{\textquoteright} between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V.cholerae serogroup O139 and V.cholerae O1 El Tor hybrid clones that produce cholera toxin of classical biotype. Based on the comprehensive comparative genomics presented in this study it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.}, keywords = {59; CHOLERA; GENES; GENETICS; GENOTYPE; ISLANDS; ORIGIN; PHENOTYPE; PUBLIC HEALTH; RECOMBINATION; STRAINS; TOXINS}, url = {http://www.osti.gov/energycitations/servlets/purl/962365-icnke9/}, author = {Brettin,Thomas S[Los Alamos National Laboratory and Bruce,David C[Los Alamos National Laboratory and Challacombe,Jean F[Los Alamos National Laboratory and Detter,John C[Los Alamos National Laboratory and Han,Cliff S[Los Alamos National Laboratory and Munik,A. C[Los Alamos National Laboratory and Chertkov,Olga[Los Alamos National Laboratory and Meincke,Linda[Los Alamos National Laboratory and Saunders,Elizabeth[Los Alamos National Laboratory and Choi,Seon Y[SEOUL NATL UNIV and Haley,Bradd J[U MARYLAND and Taviani,Elisa[U MARYLAND and Jeon,Yoon-Seong[INTL VACCINE INST SEOUL and Kim,Dong Wook[INTL VACCINE INST SEOUL and Lee,Jae-Hak[SEOUL NATL UNIV and Walters,Ronald A[PNNL and Hug,Anwar[NATL INST CHOLERIC ENTERIC DIS and Rita R Colwell} } @article {14553, title = {Hat guessing games}, journal = {SIAM review}, volume = {51}, year = {2009}, month = {2009///}, pages = {399 - 413}, author = {Butler,S. and Hajiaghayi, Mohammad T. and Kleinberg,R. D and Leighton,T.} } @conference {14321, title = {HydroSense: infrastructure-mediated single-point sensing of whole-home water activity}, booktitle = {Proceedings of the 11th international conference on Ubiquitous computing, September}, year = {2009}, month = {2009///}, author = {Jon Froehlich and Larson,E. and Campbell,T. and Haggerty,C. and Fogarty,J. and Patel,S.N.} } @conference {17242, title = {Interacting with eHealth: towards grand challenges for HCI}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, year = {2009}, month = {2009///}, pages = {3309 - 3312}, abstract = {While health records are increasingly stored electronically, we, as citizens, have little access to this data about ourselves. We are not used to thinking of these official records either as ours or as useful to us. We increasingly turn to the Web, however, to query any ache, pain or health goal we may have before consulting with health care professionals. Likewise, for proactive health care such as nutrition or fitness, or to find fellow-sufferers for post diagnosis support, we turn to online resources. There is a potential disconnect between points at which professional and lay eHealth data and resources intersect for preventative or proactive health care. Such gaps in information sharing may have direct impact on practices we decide to take up, the care we seek, or the support professionals offer. In this panel, we consider several places within proactive, preventative health care in particular HCI has a role towards enhancing health knowledge discovery and health support interaction. Our goal is to demonstrate how now is the time for eHealth to come to the forefront of the HCI research agenda.}, author = {Andr{\'e},P. and White,R. and Tan,D. and Berners-Lee,T. and Consolvo,S. and Jacobs,R. and Kohane,I. and Le Dantec,C.A. and Mamykina,L. and Marsden,G.} } @inbook {13797, title = {Interlingual annotation of multilingual text corpora and FrameNet}, booktitle = {Multilingual FrameNets in Computational LexicographyMultilingual FrameNets in Computational Lexicography}, volume = {200}, year = {2009}, month = {2009/07/14/}, pages = {287 - 318}, publisher = {Mouton de Gruyter}, organization = {Mouton de Gruyter}, address = {Berlin, New York}, isbn = {978-3-11-021296-9, 978-3-11-021297-6}, url = {http://www.degruyter.com/view/books/9783110212976/9783110212976.4.287/9783110212976.4.287.xml}, author = {Farwell,David and Dorr, Bonnie J and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Green,Rebecca and Levin,Lori and Miller,Keith and Mitamura,Teruko and Rambow,Owen and Reeder,Flo and Siddharthan,Advaith}, editor = {Bisang,Walter and Hock,Hans Henrich and Winter,Werner and Boas,Hans C.} } @article {13579, title = {Language Identification for Handwritten Document Images Using AShape Codebook}, journal = {Pattern Recognition}, volume = {42}, year = {2009}, month = {2009/12//}, pages = {3184 - 3191}, abstract = {Language identification for handwritten document images is an open document analysis problem. In this paper, we propose a novel approach to language identification for documents containing mixture of handwritten and machine printed text using image descriptors constructed from a codebook of shape features. We encode local text structures using scale and rotation invariant codewords, each representing a segmentation-free shape feature that is generic enough to be detected repeatably. We learn a concise, structurally indexed shape codebook from training by clustering and partitioning similar feature types through graph cuts. Our approach is easily extensible and does not require skew correction, scale normalization, or segmentation. We quantitatively evaluate our approach using a large real-world document image collection, which is composed of 1,512 documents in eight languages (Arabic, Chinese, English, Hindi, Japanese, Korean, Russian, and Thai) and contains a complex mixture of handwritten and machine printed content. Experiments demonstrate the robustness and flexibility of our approach, and show exceptional language identification performance that exceeds the state of the art.}, author = {Zhu,Guangyu and Yu,Xiaodong and Li,Yi and David Doermann} } @conference {12519, title = {Learning multi-modal densities on Discriminative Temporal Interaction Manifold for group activity recognition}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {2450 - 2457}, abstract = {While video-based activity analysis and recognition has received much attention, existing body of work mostly deals with single object/person case. Coordinated multi-object activities, or group activities, present in a variety of applications such as surveillance, sports, and biological monitoring records, etc., are the main focus of this paper. Unlike earlier attempts which model the complex spatial temporal constraints among multiple objects with a parametric Bayesian network, we propose a Discriminative Temporal Interaction Manifold (DTIM) framework as a data-driven strategy to characterize the group motion pattern without employing specific domain knowledge. In particular, we establish probability densities on the DTIM, whose element, the discriminative temporal interaction matrix, compactly describes the coordination and interaction among multiple objects in a group activity. For each class of group activity we learn a multi-modal density function on the DTIM. A Maximum a Posteriori (MAP) classifier on the manifold is then designed for recognizing new activities. Experiments on football play recognition demonstrate the effectiveness of the approach.}, keywords = {a, activities;parametric, activity, analysis;belief, analysis;pattern, Bayesian, classification;image, classifier;multimodal, complex, constraints;data-driven, density, equipment;video, function;multiobject, interaction, manifold;discriminative, matrix;football, MOTION, network;video-based, networks;image, play, posteriori, processing;, recognition, recognition;group, recognition;maximum, signal, spatial, strategy;discriminative, temporal}, doi = {10.1109/CVPR.2009.5206676}, author = {Ruonan Li and Chellapa, Rama and Zhou,S. K} } @article {13895, title = {The Maryland Modular Method: An Approach to Doctoral Education in Information Studies}, journal = {Journal of education for library and information science}, volume = {50}, year = {2009}, month = {2009///}, pages = {293 - 301}, author = {Druin, Allison and Jaeger,P. T and Golbeck,J. and Fleischmann,K.R. and Jimmy Lin and Qu,Y. and Wang,P. and Xie,B.} } @conference {13453, title = {Measuring General Relational Structure Using the Block Modularity Clustering Objective}, booktitle = {Twenty-Second International FLAIRS Conference}, year = {2009}, month = {2009/03/16/}, abstract = {The performance of all relational learning techniques has an implicit dependence on the underlying connectivity structure of the relations that are used as input. In this paper, we show how clustering can be used to develop an efficient optimization strategy can be used to effectively measure the structure of a graph in the absence of labeled instances.}, url = {http://www.aaai.org/ocs/index.php/FLAIRS/2009/paper/viewPaper/46}, author = {Anthony,Adam Paul and desJardins, Marie and Lombardi,Michael} } @conference {13385, title = {Minimizing Communication Cost in Distributed Multi-query Processing}, booktitle = {IEEE 25th International Conference on Data Engineering, 2009. ICDE {\textquoteright}09}, year = {2009}, month = {2009/04/29/March}, pages = {772 - 783}, publisher = {IEEE}, organization = {IEEE}, abstract = {Increasing prevalence of large-scale distributed monitoring and computing environments such as sensor networks, scientific federations, Grids etc., has led to a renewed interest in the area of distributed query processing and optimization. In this paper we address a general, distributed multi-query processing problem motivated by the need to minimize the communication cost in these environments. Specifically we address the problem of optimally sharing data movement across the communication edges in a distributed communication network given a set of overlapping queries and query plans for them (specifying the operations to be executed). Most of the problem variations of our general problem can be shown to be NP-Hard by a reduction from the Steiner tree problem. However, we show that the problem can be solved optimally if the communication network is a tree, and present a novel algorithm for finding an optimal data movement plan. For general communication networks, we present efficient approximation algorithms for several variations of the problem. Finally, we present an experimental study over synthetic datasets showing both the need for exploiting the sharing of data movement and the effectiveness of our algorithms at finding such plans.}, keywords = {Approximation algorithms, Communication networks, Computer science, Cost function, Data engineering, distributed communication network, distributed databases, distributed multi-query processing, grid computing, Large-scale systems, NP-hard, optimisation, Polynomials, Publish-subscribe, publish-subscribe systems, Query optimization, Query processing, sensor networks, Steiner tree problem, Tree graphs, trees (mathematics)}, isbn = {978-1-4244-3422-0}, doi = {10.1109/ICDE.2009.85}, author = {Li,Jian and Deshpande, Amol and Khuller, Samir} } @article {15293, title = {Modeling actions of PubMed users with n-gram language models}, journal = {Information retrieval}, volume = {12}, year = {2009}, month = {2009///}, pages = {487 - 503}, abstract = {Transaction logs from online search engines are valuable for two reasons: First, they provide insight into human information-seeking behavior. Second, log data can be used to train user models, which can then be applied to improve retrieval systems. This article presents a study of logs from PubMed{\textregistered}, the public gateway to the MEDLINE{\textregistered} database of bibliographic records from the medical and biomedical primary literature. Unlike most previous studies on general Web search, our work examines user activities with a highly-specialized search engine. We encode user actions as string sequences and model these sequences using n-gram language models. The models are evaluated in terms of perplexity and in a sequence prediction task. They help us better understand how PubMed users search for information and provide an enabler for improving users{\textquoteright} search experience.}, doi = {10.1007/s10791-008-9067-7}, author = {Jimmy Lin and Wilbur,W. J} } @article {14630, title = {Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/07/01/}, pages = {R72 - R72}, abstract = {Hundreds of proteins modulate neurotransmitter release and synaptic plasticity during neuronal development and in response to synaptic activity. The expression of genes in the pre- and post-synaptic neurons is under stringent spatio-temporal control, but the mechanism underlying the neuronal expression of these genes remains largely unknown.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-7-r72}, url = {http://genomebiology.com/2009/10/7/R72}, author = {Liu,Rui and Hannenhalli, Sridhar and Bucan,Maja} } @conference {13113, title = {Multiple instance Feature for robust part-based object detection}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009///}, pages = {405 - 412}, author = {Lin,Z. and Hua,G. and Davis, Larry S.} } @article {15321, title = {Pairwise Document Similarity in Large Collections with MapReduce}, journal = {Relation}, volume = {10}, year = {2009}, month = {2009///}, pages = {8372 - 8372}, author = {Elsayed,T. and Jimmy Lin and Oard, Douglas} } @article {12892, title = {Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study}, journal = {EcoHealth}, volume = {6}, year = {2009}, month = {2009///}, pages = {378 - 389}, abstract = {Vibrio cholerae, the causative agent of cholera, is a naturally occurring inhabitant of the Chesapeake Bay and serves as a predictor for other clinically important vibrios, including Vibrio parahaemolyticus and Vibrio vulnificus. A system was constructed to predict the likelihood of the presence of V. cholerae in surface waters of the Chesapeake Bay, with the goal to provide forecasts of the occurrence of this and related pathogenic Vibrio spp. Prediction was achieved by driving an available multivariate empirical habitat model estimating the probability of V. cholerae within a range of temperatures and salinities in the Bay, with hydrodynamically generated predictions of ambient temperature and salinity. The experimental predictions provided both an improved understanding of the in situ variability of V. cholerae, including identification of potential hotspots of occurrence, and usefulness as an early warning system. With further development of the system, prediction of the probability of the occurrence of related pathogenic vibrios in the Chesapeake Bay, notably V. parahaemolyticus and V. vulnificus, will be possible, as well as its transport to any geographical location where sufficient relevant data are available.}, doi = {10.1007/s10393-009-0273-6}, author = {Constantin de Magny,G. and Long,W. and Brown,C. W. and Hood,R. R. and Huq,A. and Murtugudde,R. and Rita R Colwell} } @conference {14251, title = {Real-time shape retrieval for robotics using skip Tri-Grams}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems, 2009. IROS 2009}, year = {2009}, month = {2009/10/10/15}, pages = {4731 - 4738}, publisher = {IEEE}, organization = {IEEE}, abstract = {The real time requirement is an additional constraint on many intelligent applications in robotics, such as shape recognition and retrieval using a mobile robot platform. In this paper, we present a scalable approach for efficiently retrieving closed contour shapes. The contour of an object is represented by piecewise linear segments. A skip Tri-Gram is obtained by selecting three segments in the clockwise order while allowing a constant number of segments to be {\~A}‚{\^A}{\textquestiondown}skipped{\~A}‚{\^A}{\textquestiondown} in between. The main idea is to use skip Tri-Grams of the segments to implicitly encode the distant dependency of the shape. All skip Tri-Grams are used for efficiently retrieving closed contour shapes without pairwise matching feature points from two shapes. The retrieval is at least an order of magnitude faster than other state-of-the-art algorithms. We score 80\% in the Bullseye retrieval test on the whole MPEG 7 shape dataset. We further test the algorithm using a mobile robot platform in an indoor environment. 8 objects are used for testing from different viewing directions, and we achieve 82\% accuracy.}, keywords = {Bullseye retrieval test, Clocks, closed contour shape retrieval, Image retrieval, Image segmentation, Indexing, Information retrieval, Intelligent robots, Jacobian matrices, mobile robot, Mobile robots, MPEG 7 shape dataset, piecewise linear segments, Piecewise linear techniques, Real time systems, real-time shape retrieval, robot vision, SHAPE, shape recognition, shape representation, skip Tri-Grams, Testing}, isbn = {978-1-4244-3803-7}, doi = {10.1109/IROS.2009.5354738}, author = {Li,Yi and Bitsakos,K. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {13100, title = {Recognizing actions by shape-motion prototype trees}, booktitle = {Computer Vision, 2009 IEEE 12th International Conference on}, year = {2009}, month = {2009/10/29/2}, pages = {444 - 451}, abstract = {A prototype-based approach is introduced for action recognition. The approach represents an action as a sequence of prototypes for efficient and flexible action matching in long video sequences. During training, first, an action prototype tree is learned in a joint shape and motion space via hierarchical k-means clustering; then a lookup table of prototype-to-prototype distances is generated. During testing, based on a joint likelihood model of the actor location and action prototype, the actor is tracked while a frame-to-prototype correspondence is established by maximizing the joint likelihood, which is efficiently performed by searching the learned prototype tree; then actions are recognized using dynamic prototype sequence matching. Distance matrices used for sequence matching are rapidly obtained by look-up table indexing, which is an order of magnitude faster than brute-force computation of frame-to-frame distances. Our approach enables robust action matching in very challenging situations (such as moving cameras, dynamic backgrounds) and allows automatic alignment of action sequences. Experimental results demonstrate that our approach achieves recognition rates of 91.07\% on a large gesture dataset (with dynamic backgrounds), 100\% on the Weizmann action dataset and 95.77\% on the KTH action dataset.}, doi = {10.1109/ICCV.2009.5459184}, author = {Zhe Lin and Zhuolin Jiang and Davis, Larry S.} } @conference {12521, title = {Recognizing coordinated multi-object activities using a dynamic event ensemble model}, booktitle = {Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on}, year = {2009}, month = {2009/04//}, pages = {3541 - 3544}, abstract = {While video-based activity analysis and recognition has received broad attention, existing body of work mostly deals with single object/person case. Modeling involving multiple objects and recognition of coordinated group activities, present in a variety of applications such as surveillance, sports, biological records, and so on, is the main focus of this paper. Unlike earlier attempts which model the complex spatial temporal constraints among different activities of multiple objects with a parametric Bayesian network, we propose a dynamic dasiaevent ensemblepsila framework as a data-driven strategy to characterize the group motion pattern without employing any specific domain knowledge. In particular, we exploit the Riemannian geometric property of the set of ensemble description functions and develop a compact representation for group activities on the ensemble manifold. An appropriate classifier on the manifold is then designed for recognizing new activities. Experiments on football play recognition demonstrate the effectiveness of the framework.}, keywords = {activities, activity, analysis;Bayes, Bayesian, classification;video, description, ensemble, event, framework;dynamic, functions;ensemble, geometric, manifold;football, methods;geometry;image, model;ensemble, multiobject, network;video-based, play, processing;, property;classifier;coordinated, recognition;data-driven, recognition;parametric, Riemannian, signal, strategy;dynamic}, doi = {10.1109/ICASSP.2009.4960390}, author = {Ruonan Li and Chellapa, Rama} } @conference {12773, title = {Recovering Views of Inter-System Interaction Behaviors}, booktitle = {Reverse Engineering, Working Conference on}, year = {2009}, month = {2009///}, pages = {53 - 61}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper presents an approach for recovering application-level views of the interaction behaviors between systems that communicate via networks. Rather than illustrating a single behavior, a sequence diagram is constructed that describes the characteristics of multiple combined behaviors. The approach has several properties that make it particularly suitable for analyzing heterogeneous systems. First, since the interactions are retrieved from observing the network communication, our technique can be applied to systems that are implemented in different languages and run on different platforms. Second, it does not require the availability or modification of source code. After the behaviors are extracted, we employ methods to merge multiple observed behaviors to a single sequence diagram that illustrates the overall behavior.The contributions of this paper are a technique for observing and processing the network communication to derive a model of the behavior. Furthermore, it describes a series of model transformations to construct a sequence diagram view of all observed behaviors.}, keywords = {distributed systems, program understanding, reliability}, doi = {http://doi.ieeecomputersociety.org/10.1109/WCRE.2009.34}, author = {Ackermann,Christopher and Lindvall,Mikael and Cleaveland, Rance} } @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} } @article {17926, title = {Saliency-guided lighting}, journal = {IEICE TRANSACTIONS on Information and Systems}, volume = {2}, year = {2009}, month = {2009///}, pages = {369 - 73}, author = {Lee,C. H and Kim,Y. and Varshney, Amitabh} } @article {13114, title = {Scene it or not? incremental multiple kernel learning for object detection}, journal = {Proceedings of the International Conference on Computer Vision}, year = {2009}, month = {2009///}, author = {Kembhavi,A. and Siddiquie,B. and Miezianko,R. and McCloskey,S. and Davis, Larry S. and Schwartz, W.R. and Harwood,D. and Gupta,A. and Farrell,R. and Luo,Y. and others} } @article {16283, title = {Searching for SNPs with cloud computing}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/11/20/}, pages = {R134 - R134}, abstract = {As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-11-r134}, url = {http://genomebiology.com/2009/10/11/R134}, author = {Langmead,Ben and Schatz,Michael C and Jimmy Lin and Pop, Mihai and Salzberg,Steven L.} } @conference {18275, title = {Secure image retrieval through feature protection}, booktitle = {Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on}, year = {2009}, month = {2009/04//}, pages = {1533 - 1536}, abstract = {This paper addresses the problem of image retrieval from an encrypted database, where data confidentiality is preserved both in the storage and retrieval process. The paper focuses on image feature protection techniques which enable similarity comparison among protected features. By utilizing both signal processing and cryptographic techniques, three schemes are investigated and compared, including bit-plane randomization, random projection, and randomized unary encoding. Experimental results show that secure image retrieval can achieve comparable retrieval performance to conventional image retrieval techniques without revealing information about image content. This work enriches the area of secure information retrieval and can find applications in secure online services for images and videos.}, keywords = {bit-plane, confidentiality;data, database;image, databases;, encoding;signal, extraction;image, feature, processes;visual, processing;content-based, projection;randomized, protection;image, randomization;cryptographic, retrieval;cryptography;feature, retrieval;random, storage;encrypted, technique;data, unary}, doi = {10.1109/ICASSP.2009.4959888}, author = {Lu,Wenjun and Varna,A.L. and Swaminathan,A. and M. Wu} } @proceedings {19206, title = {Sensing opportunities for personalized feedback technology to reduce consumption}, year = {2009}, month = {2009}, author = {Jon Froehlich and Everitt,K. and Fogarty,J. and Patel,S. and Landay,J.} } @article {12882, title = {Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/10/01/}, pages = {6268 - 6274}, abstract = {Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41\%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23\%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94\%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., {\textquotedblleft}clonal cluster,{\textquotedblright} as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00266-09}, url = {http://aem.asm.org/content/75/19/6268}, author = {Alam,Munirul and Chowdhury,Wasimul B. and Bhuiyan,N. A. and Islam,Atiqul and Hasan,Nur A. and Nair,G. Balakrish and Watanabe,H. and Siddique,A. K. and Huq,Anwar and Sack,R. Bradley and Akhter,M. Z. and Grim,Christopher J. and Kam,K.-M. and Luey,C. K. Y. and Endtz,Hubert P. and Cravioto,Alejandro and Rita R Colwell} } @inbook {14908, title = {Shape Matching for Foliage Database Retrieval}, booktitle = {Semantic Mining Technologies for Multimedia DatabasesSemantic Mining Technologies for Multimedia Databases}, year = {2009}, month = {2009///}, pages = {100 - 100}, author = {Ling,H. and Jacobs, David W.} } @conference {14863, title = {Sparse representation of cast shadows via l1-regularized least squares}, booktitle = {Computer Vision, 2009 IEEE 12th International Conference on}, year = {2009}, month = {2009///}, pages = {583 - 590}, abstract = {Scenes with cast shadows can produce complex sets of images. These images cannot be well approximated by low-dimensional linear subspaces. However, in this paper we show that the set of images produced by a Lambertian scene with cast shadows can be efficiently represented by a sparse set of images generated by directional light sources. We first model an image with cast shadows as composed of a diffusive part (without cast shadows) and a residual part that captures cast shadows. Then, we express the problem in an $\#$x2113;1-regularized least squares formulation, with nonnegativity constraints. This sparse representation enjoys an effective and fast solution, thanks to recent advances in compressive sensing. In experiments on both synthetic and real data, our approach performs favorably in comparison to several previously proposed methods.}, keywords = {$\#$x2113;1-regularized, approximations;lighting;, formulation;Lambertian, least, representation;image, representation;least, scene;cast, sensing;sparse, shadows;compressive, squares}, doi = {10.1109/ICCV.2009.5459185}, author = {Mei,Xue and Ling,Haibin and Jacobs, David W.} } @conference {16833, title = {Spatio-textual spreadsheets: geotagging via spatial coherence}, booktitle = {Proceedings of the 17th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {524 - 527}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The spatio-textual spreadsheet is a conventional spreadsheet where spatial attribute values are specified textually. Techniques are presented to automatically find the textually-specified spatial attributes that are present in spreadsheets. Once the spatial attributes have been identified, an accurate translation of the values of the spatial attributes to their actual geographic locations is needed (known as geotagging). The key observation is that spreadsheets with spatial data exhibit spatial coherence --- that is, cells with spatial data that are nearby in the spreadsheet contain data that share spatial characteristics in the real world. These techniques also allow richer search engine results by returning actual tuples from spreadsheets instead of simply links to the spreadsheets. Moreover, when the search key is a particular location, results in proximity to the query can be provided rather than just exact matches.}, keywords = {geotagging, spatial coherence, spatio-textual, spreadsheets}, isbn = {978-1-60558-649-6}, doi = {10.1145/1653771.1653860}, url = {http://doi.acm.org/10.1145/1653771.1653860}, author = {Lieberman,Michael D. and Samet, Hanan and Sankaranarayanan,Jagan and Sperling,Jon} } @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.} } @conference {12236, title = {Symbiotic relationships in internet routing overlays}, booktitle = {Proceedings of the 6th USENIX symposium on Networked systems design and implementation}, series = {NSDI{\textquoteright}09}, year = {2009}, month = {2009///}, pages = {467 - 480}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {We propose to construct routing overlay networks using the following principle: that overlay edges should be based on mutual advantage between pairs of hosts. Upon this principle, we design, implement, and evaluate Peer-Wise, a latency-reducing overlay network. To show the feasibility of PeerWise, we must show first that mutual advantage exists in the Internet: perhaps contrary to expectation, that there are not only "haves" and "have nots" of low-latency connectivity. Second, we must provide a scalable means of finding promising edges and overlay routes; we seek embedding error in network coordinates to expose both shorter-than-default "detour" routes and longer-than-expected default routes. We evaluate the cost of limiting PeerWise to mutually advantageous links, then build the intelligent components that put PeerWise into practice. We design and evaluate "virtual" network coordinates for destinations not participating in the overlay, neighbor selection algorithms to find promising relays, and relay selection algorithms to choose the neighbor to traverse for a good detour. Finally, we show that PeerWise is practical through a wide-area deployment and evaluation.}, url = {http://dl.acm.org/citation.cfm?id=1558977.1559009}, author = {Lumezanu,Cristian and Baden,Randy and Levin,Dave and Spring, Neil and Bhattacharjee, Bobby} } @article {13110, title = {System and method for fast illumination-invariant background subtraction ...}, volume = {11/282,513}, year = {2009}, month = {2009/03/31/}, abstract = {A method for eliminating errors in foreground object detection in digitized images comprises providing a reference camera and a secondary camera, vertically aligning each said camera with a baseline that is approximately perpendicular to a ground plane, wherein said reference camera is placed lower than said secondary camera, selecting a foreground pixel in a reference view of a first point in a foreground object, finding a conjugate pixel of the foreground pixel in a secondary view, using the foreground and conjugate pixels to determine an image base pixel of a base point in the reference view, wherein said base point is a point on the ground plane below the first point, and using the foreground and image base pixels to find a location where the ground plane is first visible.}, url = {http://www.google.com/patents?id=8yK_AAAAEBAJ}, author = {Lim,Ser-Nam and Mittal,Anurag and Davis, Larry S.}, editor = {Siemens Corporate Research, Inc.} } @conference {12228, title = {Systems-compatible incentives}, booktitle = {Game Theory for Networks, 2009. GameNets {\textquoteright}09. International Conference on}, year = {2009}, month = {2009/05//}, pages = {100 - 106}, abstract = {Selfish participants in a distributed system attempt to gain from the system without regard to how their actions may affect others. To maintain desirable system-wide properties in the presence of selfish users, designers are increasingly turning to the powerful mechanisms offered by economics and game theory. Combining the two fields of economics and systems design introduces new challenges of achieving incentive-compatibility in systems we can deploy in today{\textquoteright}s Internet. In this paper, we explore the interactions between systems and the mechanisms that give users incentives to cooperate. Using findings from recent work on incentive-compatible systems, we discuss several economic mechanisms and assumptions: money, punishment, and altruism. We seek to understand when these mechanisms violate system properties. Among the potential pitfalls we present is a phenomenon we call the price of altruism: altruistic peers can impose a loss of social good in some systems. We also discuss systems-compatible mechanisms that have been used in real, distributed systems, and attempt to extract the underlying design principles that have led to their success.}, keywords = {computing;, incentives;game, Internet;distributed, system;distributed, systems;game, systems;systems-compatible, theory;incentive-compatible, theory;peer-to-peer}, doi = {10.1109/GAMENETS.2009.5137390}, author = {Levin,D. and Spring, Neil and Bhattacharjee, Bobby} } @conference {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} } @inbook {12235, title = {Triangle Inequality and Routing Policy Violations in the Internet}, booktitle = {Passive and Active Network MeasurementPassive and Active Network Measurement}, series = {Lecture Notes in Computer Science}, volume = {5448}, year = {2009}, month = {2009///}, pages = {45 - 54}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Triangle inequality violations (TIVs) are the effect of packets between two nodes being routed on the longer direct path between them when a shorter detour path through an intermediary is available. TIVs are a natural, widespread and persistent consequence of Internet routing policies. By exposing opportunities to improve the delay between two nodes, TIVs can help myriad applications that seek to minimize end-to-end latency. However, sending traffic along the detour paths revealed by TIVs may influence Internet routing negatively. In this paper we study the interaction between triangle inequality violations and policy routing in the Internet. We use measured and predicted AS paths between Internet nodes to show that 25\% of the detour paths exposed by TIVs are in fact available to BGP but are simply deemed {\textquotedblleft}less efficient{\textquotedblright}. We also compare the AS paths of detours and direct paths and find that detours use AS edges that are rarely followed by default Internet paths, while avoiding others that BGP seems to prefer. Our study is important both for understanding the various interactions that occur at the routing layer as well as their effects on applications that seek to use TIVs to minimize latency.}, keywords = {Computer, Science}, isbn = {978-3-642-00974-7}, url = {http://dx.doi.org/10.1007/978-3-642-00975-4_5}, author = {Lumezanu,Cristian and Baden,Randy and Spring, Neil and Bhattacharjee, Bobby}, editor = {Moon,Sue and Teixeira,Renata and Uhlig,Steve} } @conference {12234, title = {Triangle inequality variations in the internet}, booktitle = {Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference}, series = {IMC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {177 - 183}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Triangle inequality violations (TIVs) are important for latency sensitive distributed applications. On one hand, they can expose opportunities to improve network routing by finding shorter paths between nodes. On the other hand, TIVs can frustrate network embedding or positioning systems that treat the Internet as a metric space where the triangle inequality holds. Even though triangle inequality violations are both significant and curious, their study has been limited to aggregate data sets that combine measurements taken over long periods of time. The limitations of these data sets open crucial questions in the design of systems that exploit (or avoid) TIVs: are TIVs stable or transient? Or are they illusions caused by aggregating measurements taken at different times? We collect latency matrices at varying sizes and time granularities and study dynamic properties of triangle inequality violations in the Internet. We show that TIVs are not results of measurement error and that their number varies with time. We examine how latency aggregates of data measured over longer periods of time preserve TIVs. Using medians to compute violations eliminates most of the TIVs that appear sporadically during the measurement but it misses many of the ones that are present for more than five hours.}, keywords = {latency, tiv, triangle inequality violation, variation}, isbn = {978-1-60558-771-4}, doi = {10.1145/1644893.1644914}, url = {http://doi.acm.org/10.1145/1644893.1644914}, author = {Lumezanu,Cristian and Baden,Randy and Spring, Neil and Bhattacharjee, Bobby} } @conference {16830, title = {TwitterStand: news in tweets}, booktitle = {Proceedings of the 17th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {42 - 51}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Twitter is an electronic medium that allows a large user populace to communicate with each other simultaneously. Inherent to Twitter is an asymmetrical relationship between friends and followers that provides an interesting social network like structure among the users of Twitter. Twitter messages, called tweets, are restricted to 140 characters and thus are usually very focused. We investigate the use of Twitter to build a news processing system, called TwitterStand, from Twitter tweets. The idea is to capture tweets that correspond to late breaking news. The result is analogous to a distributed news wire service. The difference is that the identities of the contributors/reporters are not known in advance and there may be many of them. Furthermore, tweets are not sent according to a schedule: they occur as news is happening, and tend to be noisy while usually arriving at a high throughput rate. Some of the issues addressed include removing the noise, determining tweet clusters of interest bearing in mind that the methods must be online, and determining the relevant locations associated with the tweets.}, keywords = {geotagging, news, online clustering, Twitter}, isbn = {978-1-60558-649-6}, doi = {10.1145/1653771.1653781}, url = {http://doi.acm.org/10.1145/1653771.1653781}, author = {Sankaranarayanan,Jagan and Samet, Hanan and Teitler,Benjamin E. and Lieberman,Michael D. and Sperling,Jon} } @conference {14346, title = {UbiGreen: investigating a mobile tool for tracking and supporting green transportation habits}, booktitle = {Proceedings of the 27th international conference on Human factors in computing systems}, series = {CHI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1043 - 1052}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {ambient displays, mobile phones, sensing, Sustainability, transportation, ubicomp}, isbn = {978-1-60558-246-7}, doi = {10.1145/1518701.1518861}, url = {http://doi.acm.org/10.1145/1518701.1518861}, author = {Jon Froehlich and Dillahunt,Tawanna and Klasnja,Predrag and Mankoff,Jennifer and Consolvo,Sunny and Harrison,Beverly and Landay,James A.} } @article {16292, title = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome}, journal = {Genome Biology}, volume = {10}, year = {2009}, month = {2009/03/04/}, pages = {R25 - R25}, abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu.}, isbn = {1465-6906}, doi = {10.1186/gb-2009-10-3-r25}, url = {http://genomebiology.com/2009/10/3/R25}, author = {Langmead,Ben and Trapnell,Cole and Pop, Mihai and Salzberg,Steven L.} } @article {13350, title = {A unified approach to ranking in probabilistic databases}, journal = {Proceedings of the VLDB Endowment}, volume = {2}, year = {2009}, month = {2009/08//}, pages = {502 - 513}, abstract = {The dramatic growth in the number of application domains that naturally generate probabilistic, uncertain data has resulted in a need for efficiently supporting complex querying and decision-making over such data. In this paper, we present a unified approach to ranking and top-k query processing in probabilistic databases by viewing it as a multi-criteria optimization problem, and by deriving a set of features that capture the key properties of a probabilistic dataset that dictate the ranked result. We contend that a single, specific ranking function may not suffice for probabilistic databases, and we instead propose two parameterized ranking functions, called PRFω and PRFe, that generalize or can approximate many of the previously proposed ranking functions. We present novel generating functions-based algorithms for efficiently ranking large datasets according to these ranking functions, even if the datasets exhibit complex correlations modeled using probabilistic and/xor trees or Markov networks. We further propose that the parameters of the ranking function be learned from user preferences, and we develop an approach to learn those parameters. Finally, we present a comprehensive experimental study that illustrates the effectiveness of our parameterized ranking functions, especially PRFe, at approximating other ranking functions and the scalability of our proposed algorithms for exact or approximate ranking.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=1687627.1687685}, author = {Li,Jian and Saha,Barna and Deshpande, Amol} } @article {12846, title = {Using formal specifications to support testing}, journal = {ACM Computing Surveys}, volume = {41}, year = {2009}, month = {2009/02/01/}, pages = {1 - 76}, isbn = {03600300}, doi = {10.1145/1459352.1459354}, url = {http://dl.acm.org/citation.cfm?id=1459352.1459354}, author = {Hierons,Robert M. and Krause,Paul and L{\"u}ttgen,Gerald and Simons,Anthony J. H. and Vilkomir,Sergiy and Woodward,Martin R. and Zedan,Hussein and Bogdanov,Kirill and Bowen,Jonathan P. and Cleaveland, Rance and Derrick,John and Dick,Jeremy and Gheorghe,Marian and Harman,Mark and Kapoor,Kalpesh} } @conference {13484, title = {ACamera Phone Based Currency Reader for the Visually Impaired}, booktitle = {The Tenth International ACMSIG ACCESS Conference on Computers and Accessibility}, year = {2008}, month = {2008/10//}, pages = {305 - 306}, abstract = {In this paper we present a camera phone-based currency reader for the visually impaired to denominate face values of the U.S. paper dollars. Currently, they can only be identified visually and this situation will continue in foreseeable future. Our solution harvests the imaging and computational power on camera phones to read bills. Considering it is impractical for the visually impaired to capture high quality image, our currency reader performs real time processing for each captured frame as the camera approaches the bill. We develop efficient background subtraction and perspective correction algorithms and train our currency reader using the Ada-boost framework, which is efficient. Our currency reader processes 10 frames/second and achieves a false positive rate of 10^-4. Major smart phone platforms, including Symbian and Windows Mobile, are supported.}, author = {Liu,Xu and David Doermann} } @conference {13485, title = {ACamera-based Mobile Data Channel: Capacity and Analysis}, booktitle = {ACM International Conference on Multimedia}, year = {2008}, month = {2008///}, pages = {359 - 368}, abstract = {In this paper we propose a novel application, color Video Code (V-Code) and analyze its data transmission capacity through camera-based mobile data channels. Users can use the camera on a mobile device (PDA or camera phone) as a passive and pervasive data channel to download data encoded as a sequence of color visual patterns. The color V-Code is animated on a display, acquired by the camera and decoded by the pre-embedded software in the mobile device. One interesting question is what is the data transmission capacity it can achieve, theoretically and practically. To answer this question we build a camera channel model to measure color degradation using information theory and show that the capacity of the camera channel can be improved with the optimized color selection through color calibration. After initialization color models are learned automatically as downloading proceeds. We address the problem of precise registration, and implemented a fast perspective correction method to accelerate the decoder in real-time on a resource constrained device. With the optimized color set and efficient implementation we achieve a transmission bit rate of 15.4kbps on a common iMate Jamin phone (200MHz CPU). This speed is faster than the average GPRS bit rate (12kbps).}, author = {Liu,Xu and David Doermann and Li,H.} } @article {13874, title = {The acl anthology reference corpus: A reference dataset for bibliographic research in computational linguistics}, journal = {Proc. of the 6th International Conference on Language Resources and Evaluation Conference (LREC{\textquoteright}08)}, year = {2008}, month = {2008///}, pages = {1755 - 1759}, abstract = {The ACL Anthology is a digital archive of conference and journal papers in natural language processing and computational linguistics.Its primary purpose is to serve as a reference repository of research results, but we believe that it can also be an object of study and a platform for research in its own right. We describe an enriched and standardized reference corpus derived from the ACL Anthology that can be used for research in scholarly document processing. This corpus, which we call the ACL Anthology Reference Corpus (ACL ARC), brings together the recent activities of a number of research groups around the world. Our goal is to make the corpus widely available, and to encourage other researchers to use it as a standard testbed for experiments in both bibliographic and bibliometric research. }, author = {Bird,S. and Dale,R. and Dorr, Bonnie J and Gibson,B. and Joseph,M.T. and Kan,M.Y. and Lee,D. and Powley,B. and Radev,D.R. and Tan,Y.F.} } @conference {14323, title = {Activity sensing in the wild: a field trial of ubifit garden}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {1797 - 1806}, author = {Consolvo,S. and McDonald,D.W. and Toscos,T. and Chen,M.Y. and Jon Froehlich and Harrison,B. and Klasnja,P. and LaMarca,A. and LeGrand,L. and Libby,R. and others} } @article {15181, title = {Aggregate message authentication codes}, journal = {Topics in Cryptology{\textendash}CT-RSA 2008}, year = {2008}, month = {2008///}, pages = {155 - 169}, abstract = {We propose and investigate the notion of aggregate message authentication codes (MACs) which have the property that multiple MAC tags, computed by (possibly) different senders on multiple (possibly different) messages, can be aggregated into a shorter tag that can still be verified by a recipient who shares a distinct key with each sender. We suggest aggregate MACs as an appropriate tool for authenticated communication in mobile ad-hoc networks or other settings where resource-constrained devices share distinct keys with a single entity (such as a base station), and communication is an expensive resource.}, doi = {10.1007/978-3-540-79263-5_10}, author = {Katz, Jonathan and Lindell,A.} } @article {17684, title = {Algorithm 879: EIGENTEST{\textemdash}a test matrix generator for large-scale eigenproblems}, journal = {ACM Trans. Math. Softw.}, volume = {35}, year = {2008}, month = {2008/07//}, pages = {7:1{\textendash}7:11 - 7:1{\textendash}7:11}, abstract = {Eigentest is a package that produces real test matrices with known eigensystems. A test matrix, called an eigenmat, is generated in a factored form, in which the user can specify the eigenvalues and has some control over the condition of the eigenvalues and eigenvectors. An eigenmat A of order n requires only O(n) storage for its representation. Auxiliary programs permit the computation of (A - sI)b, (A - sI)Tb, (A - sI)-1 b, and (A - sI)-T b in O(n) operations. A special routine computes specified eigenvectors of an eigenmat and the condition of its eigenvalue. Thus eigenmats are suitable for testing algorithms based on Krylov sequences, as well as others based on matrix-vector products. This article introduces the eigenmat and describes implementations in Fortran 77, Fortran 95, C, and Matlab.}, keywords = {Eigensystem, test matrix generation}, isbn = {0098-3500}, doi = {10.1145/1377603.1377610}, url = {http://doi.acm.org/10.1145/1377603.1377610}, author = {Lee,Che-Rung and Stewart, G.W.} } @conference {16837, title = {Augmenting spatio-textual search with an infectious disease ontology}, booktitle = {Data Engineering Workshop, 2008. ICDEW 2008. IEEE 24th International Conference on}, year = {2008}, month = {2008/04//}, pages = {266 - 269}, abstract = {A system is described that automatically categorizes and classifies infectious disease incidence reports by type and geographic location, to aid analysis by domain experts. It identifies references to infectious diseases by using a disease ontology. The system leverages the textual and spatial search capabilities of the STEWARD system to enable queries such as reports on "influenza" near "Hong Kong", possibly within a particular time period. Documents from the U.S. National Library of Medicine (http://www.pubmed.gov) and the World Health Organization (http://www.who.int) are tagged so that spatial relationships to specific disease occurrences can be presented graphically via a map interface. In addition, newspaper articles can be tagged and indexed to bolster the surveillance of ongoing epidemics. Examining past epidemics using this system may lead to improved understanding of the cause and spread of infectious diseases.}, keywords = {(artificial, article;ontology;spatio-textual, disease;map, engines;, information, intelligence);search, interface;newspaper, search;classification;diseases;indexing;medical, STEWARD, system;classification;epidemics;indexing;infectious, systems;ontologies}, doi = {10.1109/ICDEW.2008.4498330}, author = {Lieberman,M.D. and Sankaranarayanan,J. and Samet, Hanan and Sperling,J.} } @article {13052, title = {A Bayesian statistics approach to multiscale coarse graining}, journal = {The Journal of chemical physics}, volume = {129}, year = {2008}, month = {2008///}, pages = {214114 - 214114}, author = {Liu,P. and Shi,Q. and Daum{\'e}, Hal and Voth,G. A} } @conference {12246, title = {Bittorrent is an auction: analyzing and improving bittorrent{\textquoteright}s incentives}, booktitle = {Proceedings of the ACM SIGCOMM 2008 conference on Data communication}, series = {SIGCOMM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {243 - 254}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Incentives play a crucial role in BitTorrent, motivating users to upload to others to achieve fast download times for all peers. Though long believed to be robust to strategic manipulation, recent work has empirically shown that BitTorrent does not provide its users incentive to follow the protocol. We propose an auction-based model to study and improve upon BitTorrent{\textquoteright}s incentives. The insight behind our model is that BitTorrent uses, not tit-for-tat as widely believed, but an auction to decide which peers to serve. Our model not only captures known, performance-improving strategies, it shapes our thinking toward new, effective strategies. For example, our analysis demonstrates, counter-intuitively, that BitTorrent peers have incentive to intelligently under-report what pieces of the file they have to their neighbors. We implement and evaluate a modification to BitTorrent in which peers reward one another with proportional shares of bandwidth. Within our game-theoretic model, we prove that a proportional-share client is strategy-proof. With experiments on PlanetLab, a local cluster, and live downloads, we show that a proportional-share unchoker yields faster downloads against BitTorrent and BitTyrant clients, and that under-reporting pieces yields prolonged neighbor interest.}, keywords = {auctions, bittorrent, incentive systems, proportional share, tit-for-tat}, isbn = {978-1-60558-175-0}, doi = {10.1145/1402958.1402987}, url = {http://doi.acm.org/10.1145/1402958.1402987}, author = {Levin,Dave and LaCurts,Katrina and Spring, Neil and Bhattacharjee, Bobby} } @conference {13517, title = {Camera Phone Based Tools for People with Visual Impairments}, booktitle = {The First International Workshop on Mobile Multimedia Processing}, year = {2008}, month = {2008///}, abstract = {In this paper we describe a set of applications that utilize a camera phone to help the visually impaired with daily tasks. Our {\textquotedblleft}MobileEye{\textquotedblright} software suite turns a camera enabled mobile device into a multi-purpose vision tool that helps individuals with visual disabilities. MobileEye consists of four subsystems for different types of visual disabilities. A color channel mapper helps distinguish colors, a software magnifier helps low vision individuals see detail, a pattern recognizer helps the severely impaired recognize objects and a document retriever provides access to printed materials. We apply cutting edge computer vision and image processing technologies on the mobile devices and tackle the challenges of limited computational resources and low image quality. We also consider the usability for the visually impaired so our system requires minimum keyboard operation. We provide a full software solution which runs on Symbian and Windows Mobile handsets. This paper provides a high level overview of the system.}, author = {Liu,Xu and David Doermann and Li,H.} } @conference {13978, title = {Canny edge detection on NVIDIA CUDA}, booktitle = {Computer Vision and Pattern Recognition Workshops, 2008. CVPRW {\textquoteright}08. IEEE Computer Society Conference on}, year = {2008}, month = {2008/06//}, pages = {1 - 8}, abstract = {The Canny edge detector is a very popular and effective edge feature detector that is used as a pre-processing step in many computer vision algorithms. It is a multi-step detector which performs smoothing and filtering, non-maxima suppression, followed by a connected-component analysis stage to detect ldquotruerdquo edges, while suppressing ldquofalserdquo non edge filter responses. While there have been previous (partial) implementations of the Canny and other edge detectors on GPUs, they have been focussed on the old style GPGPU computing with programming using graphical application layers. Using the more programmer friendly CUDA framework, we are able to implement the entire Canny algorithm. Details are presented along with a comparison with CPU implementations. We also integrate our detector in to MATLAB, a popular interactive simulation package often used by researchers. The source code will be made available as open source.}, keywords = {algorithms;connected-component, analysis, application, Canny, CUDA;computer, detection;feature, detection;NVIDIA, detector;filtering;graphical, detector;non, edge, extraction;smoothing, feature, filter, layers;multistep, methods;, responses;nonmaxima, stage;edge, suppression;smoothing;computer, VISION, vision;edge}, doi = {10.1109/CVPRW.2008.4563088}, author = {Luo,Yuancheng and Duraiswami, Ramani} } @conference {17570, title = {Capacity of Asynchronous Random-Access Scheduling in Wireless Networks}, booktitle = {IEEE INFOCOM 2008. The 27th Conference on Computer Communications}, year = {2008}, month = {2008/04/13/18}, pages = {1148 - 1156}, publisher = {IEEE}, organization = {IEEE}, abstract = {We study the throughput capacity of wireless networks which employ (asynchronous) random-access scheduling as opposed to deterministic scheduling. The central question we answer is: how should we set the channel-access probability for each link in the network so that the network operates close to its optimal throughput capacity? We design simple and distributed channel-access strategies for random-access networks which are provably competitive with respect to the optimal scheduling strategy, which is deterministic, centralized, and computationally infeasible. We show that the competitiveness of our strategies are nearly the best achievable via random-access scheduling, thus establishing fundamental limits on the performance of random- access. A notable outcome of our work is that random access compares well with deterministic scheduling when link transmission durations differ by small factors, and much worse otherwise. The distinguishing aspects of our work include modeling and rigorous analysis of asynchronous communication, asymmetry in link transmission durations, and hidden terminals under arbitrary link-conflict based wireless interference models.}, keywords = {asynchronous random-access scheduling, channel access probability, Computer networks, Computer science, Educational institutions, Interference, Optimal scheduling, Peer to peer computing, probability, Processor scheduling, radio link, radio links, radio networks, Routing, scheduling, Throughput, throughput capacity, wireless channels, Wireless networks}, isbn = {978-1-4244-2025-4}, doi = {10.1109/INFOCOM.2008.170}, author = {Chafekar,D. and Levin,D. and Kumar,V. S.A and Marathe,M. V and Parthasarathy,S. and Srinivasan, Aravind} } @article {12898, title = {The Complete Genome Sequence of Thermococcus Onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism}, journal = {Journal of BacteriologyJ. Bacteriol.}, volume = {190}, year = {2008}, month = {2008/11/15/}, pages = {7491 - 7499}, abstract = {Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus.}, isbn = {0021-9193, 1098-5530}, doi = {10.1128/JB.00746-08}, url = {http://jb.asm.org/content/190/22/7491}, author = {Lee,Hyun Sook and Kang,Sung Gyun and Bae,Seung Seob and Lim,Jae Kyu and Cho,Yona and Kim,Yun Jae and Jeon,Jeong Ho and Cha,Sun-Shin and Kwon,Kae Kyoung and Kim,Hyung-Tae and Park,Cheol-Joo and Lee,Hee-Wook and Kim,Seung Il and Jongsik Chun and Rita R Colwell and Kim,Sang-Jin and Lee,Jung-Hyun} } @article {13526, title = {Computer Vision and Image Processing Techniques for Mobile Application}, volume = {LAMP-TR-151}, year = {2008}, month = {2008/11//}, institution = {Center for Automation Research, University of Maryland}, abstract = {Camera phones have penetrated every corner of society and have become a focal point for communications. In our research we extend the traditional use of such devices to help bridge the gap between physical and digital worlds. Their combined image acquisition, processing, storage, and communication capabilities in a compact, portable device make them an ideal platform for embedding computer vision and image processing capabilities in the pursuit of new mobile applications. This technical report is presented as a series of computer vision and image processing techniques together with their applications on the mobile device. We have developed a set of techniques for ego-motion estimation, enhancement, feature extraction, perspective correction, object detection, and document retrieval that serve as a basis for such applications. Our applications include a dynamic video barcode that can transfer significant amounts of information visually, a document retrieval system that can retrieve documents from low resolution snapshots, and a series of applications for the users with visual disabilities such as a currency reader. Solutions for mobile devices require a fundamentally different approach than traditional vision techniques that run on traditional computers, so we consider user-device interaction and the fact that these algorithms must execute in a resource constrained environment. For each problem we perform both theoretical and empirical analysis in an attempt to optimize performance and usability. The thesis makes contributions related to efficient implementation of image processing and computer vision techniques, analysis of information theory, feature extraction and analysis of low quality images, and device usability.}, author = {Liu,Xu and David Doermann} } @article {13282, title = {Contribution to a Taxonomy of Non-Manifold Models Based on Topological Properties}, journal = {ASME Conference Proceedings}, volume = {2008}, year = {2008}, month = {2008///}, pages = {187 - 197}, abstract = {Non-manifold models have classically been used in Finite Element (FE) simulations to describe the shape of a mechanical part. Sketching the shape of an object is also important in a design stage, where non-manifold models could be of help for the designer. The purpose of the taxonomy proposed here is to be able either to accept or reject them based on the design context and on the type of product. This will contribute to model non-manifold objects and to their binary classification. The proposed taxonomy is also based on the topological properties of non-manifold objects, and especially on topological invariants. We will classify several topological properties as local or global ones, and we will illustrate how such properties can help either modelling these objects or searching for them in industrial data bases when large numbers of FE models have been stored.}, doi = {10.1115/DETC2008-49529}, url = {http://link.aip.org/link/abstract/ASMECP/v2008/i43277/p187/s1}, author = {Leon,Jean-Claude and De Floriani, Leila} } @article {16065, title = {Data Sonification for Users with Visual Impairment: A Case Study with Georeferenced Data}, journal = {ACM Trans. Comput.-Hum. Interact.}, volume = {15}, year = {2008}, month = {2008/05//}, pages = {4:1{\textendash}4:28 - 4:1{\textendash}4:28}, abstract = {We describe the development and evaluation of a tool, iSonic, to assist users with visual impairment in exploring georeferenced data using coordinated maps and tables, augmented with nontextual sounds and speech output. Our in-depth case studies with 7 blind users during 42 hours of data collection, showed that iSonic enabled them to find facts and discover trends in georeferenced data, even in unfamiliar geographical contexts, without special devices. Our design was guided by an Action-by-Design-Component (ADC) framework, which was also applied to scatterplots to demonstrate its generalizability. Video and download is available at www.cs.umd.edu/hcil/iSonic/.}, keywords = {auditory user interfaces, information seeking, Interactive sonification, universal usability, users with visual impairment}, isbn = {1073-0516}, doi = {10.1145/1352782.1352786}, url = {http://doi.acm.org/10.1145/1352782.1352786}, author = {Zhao,Haixia and Plaisant, Catherine and Shneiderman, Ben and Lazar,Jonathan} } @article {15056, title = {Design and implementation of blackboard-based system for human detection}, journal = {Jisuanji Gongcheng/ Computer Engineering}, volume = {34}, year = {2008}, month = {2008///}, author = {Zhuolin Jiang and Li,S.F. and Gao,D.F.} } @article {18197, title = {Digital image forensics via intrinsic fingerprints}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {3}, year = {2008}, month = {2008/03//}, pages = {101 - 117}, abstract = {Digital imaging has experienced tremendous growth in recent decades, and digital camera images have been used in a growing number of applications. With such increasing popularity and the availability of low-cost image editing software, the integrity of digital image content can no longer be taken for granted. This paper introduces a new methodology for the forensic analysis of digital camera images. The proposed method is based on the observation that many processing operations, both inside and outside acquisition devices, leave distinct intrinsic traces on digital images, and these intrinsic fingerprints can be identified and employed to verify the integrity of digital data. The intrinsic fingerprints of the various in-camera processing operations can be estimated through a detailed imaging model and its component analysis. Further processing applied to the camera captured image is modelled as a manipulation filter, for which a blind deconvolution technique is applied to obtain a linear time-invariant approximation and to estimate the intrinsic fingerprints associated with these postcamera operations. The absence of camera-imposed fingerprints from a test image indicates that the test image is not a camera output and is possibly generated by other image production processes. Any change or inconsistencies among the estimated camera-imposed fingerprints, or the presence of new types of fingerprints suggest that the image has undergone some kind of processing after the initial capture, such as tampering or steganographic embedding. Through analysis and extensive experimental studies, this paper demonstrates the effectiveness of the proposed framework for nonintrusive digital image forensics.}, keywords = {ACQUISITION, analysis;intrinsic, approximation;cameras;digital, camera, deconvolution;digital, devices;blind, fingerprints;time, forensics;forensic, identification;image, image, images;digital, invariant, photography;fingerprint, sensors;}, isbn = {1556-6013}, doi = {10.1109/TIFS.2007.916010}, author = {Swaminathan,A. and M. Wu and Liu,K. J.R} } @article {18961, title = {The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008///}, pages = {991 - 996}, abstract = {Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3 draft genome sequence of {\textquoteright}SunUp{\textquoteright} papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica{\textquoteright}s distinguishing morpho-physiological, medicinal and nutritional properties.}, isbn = {0028-0836}, doi = {10.1038/nature06856}, url = {http://www.nature.com/nature/journal/v452/n7190/full/nature06856.html}, author = {Ming,R. and Hou,S. and Feng,Y. and Yu,Q. and Dionne-Laporte,A. and Saw,J.H. and Senin,P. and Wang,W. and Ly,B.V. and Lewis,K.L.T. and others} } @article {12239, title = {Efficient and Resilient Backbones for Multihop Wireless Networks}, journal = {Mobile Computing, IEEE Transactions on}, volume = {7}, year = {2008}, month = {2008/11//}, pages = {1349 - 1362}, abstract = {We consider the problem of finding "backbones" in multihop wireless networks. The backbone provides end-to-end connectivity, allowing nonbackbone nodes to save energy since they do not have to route nonlocal data or participate in the routing protocol. Ideally, such a backbone would be small, consist primarily of high capacity nodes, and remain connected even when nodes are mobile or fail. Unfortunately, it is often infeasible to construct a backbone that has all of these properties; e.g., a small optimal backbone is often too sparse to handle node failures or high mobility. We present a parameterized backbone construction algorithm that permits explicit trade-offs between backbone size, resilience to node movement and failure, energy consumption, and path lengths. We prove that our scheme can construct essentially best possible backbones (with respect to energy consumption and backbone size) when the network is relatively static. We generalize our scheme to build more robust structures better suited to networks with higher mobility. We present a distributed protocol based upon our algorithm and show that this protocol builds and maintains a connected backbone in dynamic networks. Finally, we present detailed packet-level simulation results to evaluate and compare our scheme with existing energy-saving techniques. Our results show that, depending on the network environment, our scheme increases network lifetimes by 20 percent to 220 percent without adversely affecting delivery ratio or end-to-end latency.}, keywords = {algorithm;protocols;wireless, backbone, channels;, CONSTRUCTION, distributed, networks;parameterized, protocol;multihop, wireless}, isbn = {1536-1233}, doi = {10.1109/TMC.2008.69}, author = {Lee,Seungjoon and Bhattacharjee, Bobby and Srinivasan, Aravind and Khuller, Samir} } @inbook {13365, title = {Energy Efficient Monitoring in Sensor Networks}, booktitle = {LATIN 2008: Theoretical InformaticsLATIN 2008: Theoretical Informatics}, series = {Lecture Notes in Computer Science}, volume = {4957}, year = {2008}, month = {2008///}, pages = {436 - 448}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper we study a set of problems related to efficient energy management for monitoring applications in wireless sensor networks. We study several generalizations of a basic problem called Set k -Cover, which can be described as follows: we are given a set of sensors, and a set of regions to be monitored. Each region can be monitored by a subset of the sensors. To increase the lifetime of the sensor network, we would like to partition the sensors into k sets (or time-slots) and activate each partition in a different time-slot. The goal is to find the partitioning that maximizes the coverage of the regions. This problem is known to be NP -hard. We first develop improved approximation algorithms for this problem based on its similarities to the max k -cut problem. We then consider a variation, called Set ( k , α )-cover, where each sensor is allowed to be active in α different time-slots. We develop a randomized routing algorithm for this problem. We then consider extensions where each sensor can monitor only a bounded number of regions in any time-slot. We develop the first approximation algorithms for this problem. An experimental evaluation of the algorithms we propose can be found in the full version of the paper.}, isbn = {978-3-540-78772-3}, url = {http://dx.doi.org/10.1007/978-3-540-78773-0_38}, author = {Deshpande, Amol and Khuller, Samir and Malekian,Azarakhsh and Toossi,Mohammed}, editor = {Laber,Eduardo and Bornstein,Claudson and Nogueira,Loana and Faria,Luerbio} } @article {12913, title = {Environmental signatures associated with cholera epidemics}, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, year = {2008}, month = {2008///}, pages = {17676 - 17676}, abstract = {The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998{\textendash}2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing }, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0809654105}, url = {http://www.pnas.org/content/105/46/17676}, author = {Constantin de Magny,G. and Murtugudde,R. and Sapiano,M. R. P. and Nizam,A. and Brown,C. W. and Busalacchi,A. J. and Yunus,M. and Nair,G. B. and Gil,A. I. and Lanata,C. F. and Rita R Colwell} } @article {12908, title = {Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons}, journal = {FEMS Microbiology Ecology}, volume = {64}, year = {2008}, month = {2008/04/01/}, pages = {45 - 54}, abstract = {Circulation of mobile genetic elements linked to drug resistance spread was studied in Vibrio strains isolated from surface urban water (river and sea) and shellfish samples in 2002{\textendash}2003 in Maputo, Mozambique. Class 1 integrons and integrating conjugative elements (ICE) were investigated by PCR and mating experiments in strains of major health interest: 10 Vibrio cholerae, six Vibrio parahaemolyticus, two Vibrio alginolyticus and one Vibrio fluvialis. Resistance to at least two antibiotics (predominantly β-lactams) was detected in all the strains, with additional resistances to sulfamethoxazole, spectinomycin, streptomycin and/or trimethoprim. Class 1 integrons contributed partially to the expression of drug resistance and were found in five isolates: four V. cholerae (blaP1 cassette, one strain also contained the dfrA15 cassette) and one V. alginolyticus (aadA2 cassette). ICEs, apparently devoid of resistance genes, were found in eight V. cholerae, three V. parahaemolyticus and one V. fluvialis isolates. A wide variability was observed by molecular characterization of ICEs. Five ICEs were included in the SXT/R391 family and seven ICEs were not classified. Our results indicate that the SXT/R391 family and related ICEs comprise a large class of polymorphic genetic elements widely circulating in environmental Vibrio strains in Africa, beside those evidently linked to drug resistance in clinical isolates.}, keywords = {ICE, integron, Mozambique, Vibrio}, isbn = {1574-6941}, doi = {10.1111/j.1574-6941.2008.00455.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2008.00455.x/full}, author = {Taviani,Elisa and Ceccarelli,Daniela and Lazaro,Nivalda and Bani,Stefania and Cappuccinelli,Piero and Rita R Colwell and Colombo,Mauro M.} } @article {16066, title = {Evaluating Visual Analytics at the 2007 VAST Symposium Contest}, journal = {Computer Graphics and Applications, IEEE}, volume = {28}, year = {2008}, month = {2008/04//march}, pages = {12 - 21}, abstract = {In this article, we report on the contest{\textquoteright}s data set and tasks, the judging criteria, the winning tools, and the overall lessons learned in the competition. We believe that by organizing these contests, we{\textquoteright}re creating useful resources for researchers and are beginning to understand how to better evaluate VA tools. Competitions encourage the community to work on difficult problems, improve their tools, and develop baselines for others to build or improve upon. We continue to evolve a collection of data sets, scenarios, and evaluation methodologies that reflect the richness of the many VA tasks and applications.}, keywords = {2007, analytics, analytics;data, and, Contest;Visual, Science, Symposium, Technology;data, VAST, visualisation;, visualization;visual}, isbn = {0272-1716}, doi = {10.1109/MCG.2008.27}, author = {Plaisant, Catherine and Grinstein,G. and Scholtz,J. and Whiting,M. and O{\textquoteright}Connell,T. and Laskowski,S. and Chien,L. and Tat,A. and Wright,W. and Gorg,C. and Zhicheng Liu and Parekh,N. and Singhal,K. and Stasko,J.} } @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 {18338, title = {Fast concurrent object classification and localization}, journal = {CSAIL Technical Reports (July 1, 2003 - present)}, year = {2008}, month = {2008/06/10/}, abstract = {Object localization and classification are important problems incomputer vision. However, in many applications, exhaustive searchover all class labels and image locations is computationallyprohibitive. While several methods have been proposed to makeeither classification or localization more efficient, few havedealt with both tasks simultaneously. This paper proposes anefficient method for concurrent object localization andclassification based on a data-dependent multi-classbranch-and-bound formalism. Existing bag-of-featuresclassification schemes, which can be expressed as weightedcombinations of feature counts can be readily adapted to ourmethod. We present experimental results that demonstrate the meritof our algorithm in terms of classification accuracy, localizationaccuracy, and speed, compared to baseline approaches includingexhaustive search, the ISM method, and single-class branch andbound.}, url = {http://dspace.mit.edu/handle/1721.1/41862}, author = {Tom Yeh and Lee,John J and Darrell,Trevor} } @conference {15317, title = {Fast, easy, and cheap: Construction of statistical machine translation models with MapReduce}, booktitle = {Proceedings of the Third Workshop on Statistical Machine Translation}, year = {2008}, month = {2008///}, pages = {199 - 207}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, abstract = {In recent years, the quantity of parallel train-ing data available for statistical machine trans- lation has increased far more rapidly than the performance of individual computers, re- sulting in a potentially serious impediment to progress. Parallelization of the model- building algorithms that process this data on computer clusters is fraught with challenges such as synchronization, data exchange, and fault tolerance. However, the MapReduce programming paradigm has recently emerged as one solution to these issues: a powerful functional abstraction hides system-level de- tails from the researcher, allowing programs to be transparently distributed across potentially very large clusters of commodity hardware. We describe MapReduce implementations of two algorithms used to estimate the parame- ters for two word alignment models and one phrase-based translation model, all of which rely on maximum likelihood probability esti- mates. On a 20-machine cluster, experimental results show that our solutions exhibit good scaling characteristics compared to a hypo- thetical, optimally-parallelized version of cur- rent state-of-the-art single-core tools. }, author = {Dyer,C. and Cordova,A. and Mont,A. and Jimmy Lin} } @conference {16838, title = {A Fast Similarity Join Algorithm Using Graphics Processing Units}, booktitle = {Data Engineering, 2008. ICDE 2008. IEEE 24th International Conference on}, year = {2008}, month = {2008/04//}, pages = {1111 - 1120}, abstract = {A similarity join operation A BOWTIEepsiv B takes two sets of points A, B and a value epsiv isin Ropf, and outputs pairs of points p isin A,q isin B, such that the distance D(p, q) les epsiv. Similarity joins find use in a variety of fields, such as clustering, text mining, and multimedia databases. A novel similarity join algorithm called LSS is presented that executes on a graphics processing unit (GPU), exploiting its parallelism and high data throughput. As GPUs only allow simple data operations such as the sorting and searching of arrays, LSS uses these two operations to cast a similarity join operation as a GPU sort-and-search problem. It first creates, on the fly, a set of space-filling curves on one of its input datasets, using a parallel GPU sort routine. Next, LSS processes each point p of the other dataset in parallel. For each p, it searches an interval of one of the space-filling curves guaranteed to contain all the pairs in which p participates. Using extensive theoretical and experimental analysis, LSS is shown to offer a good balance between time and work efficiency. Experimental results demonstrate that LSS is suitable for similarity joins in large high-dimensional datasets, and that it performs well when compared against two existing prominent similarity join methods.}, keywords = {algorithm;graphics, algorithms;quadtrees;set, arrays, curves;parallel, join, problem;space-filling, PROCESSING, searching;fast, similarity, theory;sorting;, units;sort-and-search}, doi = {10.1109/ICDE.2008.4497520}, author = {Lieberman,M.D. and Sankaranarayanan,J. and Samet, Hanan} } @conference {17517, title = {On the fidelity of 802.11 packet traces}, booktitle = {Proceedings of the 9th international conference on Passive and active network measurement}, year = {2008}, month = {2008///}, pages = {132 - 141}, author = {Schulman,A. and Levin,D. and Spring, Neil} } @conference {14331, title = {Flowers or a robot army?: encouraging awareness \& activity with personal, mobile displays}, booktitle = {Proceedings of the 10th international conference on Ubiquitous computing}, series = {UbiComp {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {54 - 63}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Personal, mobile displays, such as those on mobile phones, are ubiquitous, yet for the most part, underutilized. We present results from a field experiment that investigated the effectiveness of these displays as a means for improving awareness of daily life (in our case, self-monitoring of physical activity). Twenty-eight participants in three experimental conditions used our UbiFit system for a period of three months in their day-to-day lives over the winter holiday season. Our results show, for example, that participants who had an awareness display were able to maintain their physical activity level (even during the holidays), while the level of physical activity for participants who did not have an awareness display dropped significantly. We discuss our results and their general implications for the use of everyday mobile devices as awareness displays.}, keywords = {ambient display, awareness, calm technology, field experiment, fitness, glanceable display, mobile phone, personal mobile display, persuasive technology, physical activity}, isbn = {978-1-60558-136-1}, doi = {10.1145/1409635.1409644}, url = {http://doi.acm.org/10.1145/1409635.1409644}, author = {Consolvo,Sunny and Klasnja,Predrag and McDonald,David W. and Avrahami,Daniel and Jon Froehlich and LeGrand,Louis and Libby,Ryan and Mosher,Keith and Landay,James A.} } @article {15123, title = {Handling expected polynomial-time strategies in simulation-based security proofs}, journal = {Journal of Cryptology}, volume = {21}, year = {2008}, month = {2008///}, pages = {303 - 349}, abstract = {The standard class of adversaries considered in cryptography is that of strict polynomial-time probabilistic machines. However, expected polynomial-time machines are often also considered. For example, there are many zero-knowledge protocols for which the only known simulation techniques run in expected (and not strict) polynomial time. In addition, it has been shown that expected polynomial-time simulation is essential for achieving constant-round black-box zero-knowledge protocols. This reliance on expected polynomial-time simulation introduces a number of conceptual and technical difficulties. In this paper, we develop techniques for dealing with expected polynomial-time adversaries in simulation-based security proofs.}, doi = {10.1007/s00145-007-9004-8}, author = {Katz, Jonathan and Lindell,Y.} } @book {13565, title = {Handwritten Document Image Processing}, year = {2008}, month = {2008///}, publisher = {VDMVerlang Dr. Muller}, organization = {VDMVerlang Dr. Muller}, author = {Yefeng Zheng and David Doermann and Huiping Li} } @conference {19450, title = {Hci for community and international development}, booktitle = {SIGCHI EA {\textquoteright}08}, series = {CHI EA {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {3909 - 3912}, publisher = {ACM}, organization = {ACM}, abstract = {This workshop explores the challenges in applying, extending and inventing appropriate methods and contributions of Human Computer Interaction (HCI) to International economic and community Development. We address interaction design for parts of the world that are often marginalized by the Global North as well as people in the Global North who are themselves similarly marginalized by poverty or other barriers. We hope to extend the boundaries of the field of Human Computer Interaction by spurring a discussion on how existing methods and practices can be adapted and modified, and how new practices can be developed, to deal with the unique challenges posed by these contexts.}, keywords = {community design, ict4d, information and communication technology, international development, participatory design, ucd4id, User centered design}, isbn = {978-1-60558-012-8}, url = {http://doi.acm.org/10.1145/1358628.1358954}, author = {Thomas, John and Dearden, Andy and Dray, Susan and Light, Ann and Best, Michael and Arkin, Nuray and Maunder, Andrew and Kam, Mathew and Marshini Chetty and Sambasivan, Nithya and Buckhalter, Celeste and Krishnan, Gaurishankar} } @article {15324, title = {How Do Users Find Things with PubMed? Towards Automatic Utility Evaluation with User Simulations}, year = {2008}, month = {2008/02//}, institution = {Human-Computer Interaction Lab, University of Maryland, College Park}, abstract = {In the context of document retrieval in the biomedical domain, this paper explores the complex relationship between the quality of initial query results and the overall utility of an interactive system. We demonstrate that a content-similarity browsing tool can compensate for poor retrieval results, and that the relationship between retrieval performance and overall utility is non-linear. Arguments are advanced with user simulations, which characterize the relevance of documents that a user might encounter with different browsing strategies. With broader implications to IR, this work provides a case study of how user simulations can be exploited as a formative tool for automatic utility evaluation. Simulation-based studies provide researchers with an additional evaluation tool to complement interactive and Cranfield-style experiments.}, keywords = {*BIOMEDICAL INFORMATION SYSTEMS, *BROWSING, *INFORMATION RETRIEVAL, *PUBMED, *SIMILARITY, *SIMULATION, *USER NEEDS, DOCUMENTS, FIND-SIMILAR, HUMAN FACTORS ENGINEERING \& MAN MACHINE SYSTEM, INFORMATION SCIENCE, MAN COMPUTER INTERFACE, QUALITY, queries, searching, TEST AND EVALUATION, UTILITY}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA478703}, author = {Jimmy Lin and Smucker,Mark D.} } @article {19195, title = {ilearn on the iphone: Real-time human activity classification on commodity mobile phones}, journal = {University of Washington CSE Tech Report UW-CSE-08-04-02}, year = {2008}, month = {2008}, author = {Saponas,T. and Lester,J. and Jon Froehlich and Fogarty,J. and Landay,J.} } @conference {15694, title = {Immunity-Based Epidemic Routing in Intermittent Networks}, booktitle = {5th Annual IEEE Communications Society Conference on Sensor, Mesh and Ad Hoc Communications and Networks, 2008. SECON {\textquoteright}08}, year = {2008}, month = {2008/06/16/20}, pages = {609 - 611}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this research, we propose to modify and extend epidemic routing used in intermittent networks. In particular, we propose to include immunity-based information disseminated in the reverse once messages get delivered to their destination. The goal is to design a more efficient routing protocol in terms of resource utilization. The idea is to analyze and evaluate the network performance using an immunity scheme in the context of epidemic routing and its variants. The reverse dissemination of such information requires minimal resources and the tradeoff in timely purging of delivered messages can be significant. We are using ns2 to implement a detailed simulation of the proposed immunity-based epidemic routing.}, keywords = {Analytical models, Delay, delivered messages, Disruption tolerant networking, Educational institutions, immunity-based epidemic routing, information dissemination, intermittent networks, Mobile ad hoc networks, Network topology, Performance analysis, Resource management, resource utilization, routing protocol, routing protocols, telecommunication network topology}, isbn = {978-1-4244-1777-3}, doi = {10.1109/SAHCN.2008.86}, author = {Mundur, Padma and Seligman,M. and Jin Na Lee} } @conference {15064, title = {An improved mean shift tracking method based on nonparametric clustering and adaptive bandwidth}, booktitle = {Machine Learning and Cybernetics, 2008 International Conference on}, volume = {5}, year = {2008}, month = {2008/07//}, pages = {2779 - 2784}, abstract = {An improved mean shift method for object tracking based on nonparametric clustering and adaptive bandwidth is presented in this paper. Based on partitioning the color space of a tracked object by using a modified nonparametric clustering, an appearance model of the tracked object is built. It captures both the color information and spatial layout of the tracked object. The similarity measure between the target model and the target candidate is derived from the Bhattacharyya coefficient. The kernel bandwidth parameters are automatically selected by maximizing the lower bound of a log-likelihood function, which is derived from a kernel density estimate using the bandwidth matrix and the modified weight function. The experimental results show that the method can converge in an average of 2.6 iterations per frame.}, keywords = {adaptive bandwidth, appearance model, bandwidth matrix, Bhattacharyya coefficient, color information, color space partitioning, image colour analysis, iterative procedure, kernel bandwidth parameter, kernel density estimate, log-likelihood function, mean shift tracking method, modified weight function, nonparametric clustering, Object detection, object representation, object tracking, pattern clustering, similarity measure, spatial layout, target candidate, target model, tracking}, doi = {10.1109/ICMLC.2008.4620880}, author = {Zhuolin Jiang and Li,Shao-Fa and Jia,Xi-Ping and Zhu,Hong-Li} } @article {16068, title = {Interactive auditory data exploration: A framework and evaluation with geo-referenced data sonification}, journal = {ACM Transactions on Computer-Human Interaction}, year = {2008}, month = {2008///}, abstract = {We describe an Action-by-Design-Component (ADC) framework to guide auditory interface designers for exploratory data analysis. The framework characterizes data interaction in the auditory mode as a set of Auditory Information Seeking Actions (AISAs). Contrasting AISAs with actions in visualizations, the framework also discusses design considerations for a set of Design Components to support AISAs. Applying the framework to geo-referenced data, we systematically explored and evaluated its design space. A data exploration tool, iSonic, was built for blind users. In depth case studies with 7 blind users, with over 42 hours of data collection, showed that iSonic enabled them to find facts and discover trends of geo-referenced data, even in unfamiliar geographical contexts, without special devices. The results also showed that blind users dramatically benefited from the rich set of task-oriented actions (AISAs) and the use of multiple highly coordinated data views provided by the ADC framework. Some widely used techniques in visualization, with appropriate adaptation, also work in the auditory mode. The application of the framework to scatterplots shows that the framework can be generalized and lead to the design of a unified auditory workspace for general exploratory data analysis. Readers can view a supplementary video demonstration of iSonic by visiting www.cs.umd.edu/hcil/iSonic/}, author = {Zhao,H. and Plaisant, Catherine and Shneiderman, Ben and Lazar,J.} } @article {17250, title = {Interactive Entity Resolution in Relational Data: A Visual Analytic Tool and Its Evaluation}, journal = {IEEE Transactions on Visualization and Computer Graphics}, volume = {14}, year = {2008}, month = {2008/10//Sept}, pages = {999 - 1014}, abstract = {Databases often contain uncertain and imprecise references to real-world entities. Entity resolution, the process of reconciling multiple references to underlying real-world entities, is an important data cleaning process required before accurate visualization or analysis of the data is possible. In many cases, in addition to noisy data describing entities, there is data describing the relationships among the entities. This relational data is important during the entity resolution process; it is useful both for the algorithms which determine likely database references to be resolved and for visual analytic tools which support the entity resolution process. In this paper, we introduce a novel user interface, D-Dupe, for interactive entity resolution in relational data. D-Dupe effectively combines relational entity resolution algorithms with a novel network visualization that enables users to make use of an entity{\textquoteright}s relational context for making resolution decisions. Since resolution decisions often are interdependent, D-Dupe facilitates understanding this complex process through animations which highlight combined inferences and a history mechanism which allows users to inspect chains of resolution decisions. An empirical study with 12 users confirmed the benefits of the relational context visualization on the performance of entity resolution tasks in relational data in terms of time as well as users{\textquoteright} confidence and satisfaction.}, keywords = {algorithms, Computer Graphics, D-Dupe, data visualisation, database management systems, Databases, Factual, graphical user interface, Graphical user interfaces, human-centered computing, Image Interpretation, Computer-Assisted, Information Storage and Retrieval, Information Visualization, interactive entity resolution, relational context visualization, Relational databases, relational entity resolution algorithm, User interfaces, user-centered design, User-Computer Interface, visual analytic tool}, isbn = {1077-2626}, doi = {10.1109/TVCG.2008.55}, author = {Kang,Hyunmo and Getoor, Lise and Shneiderman, Ben and Bilgic,M. and Licamele,L.} } @book {15195, title = {Introduction to Modern Cryptography}, year = {2008}, month = {2008///}, publisher = {CRC Press}, organization = {CRC Press}, abstract = {Cryptography plays a key role in ensuring the privacy and integrity of data and the security of computer networks. Introduction to Modern Cryptography provides a rigorous yet accessible treatment of modern cryptography, with a focus on formal definitions, precise assumptions, and rigorous proofs. The authors introduce the core principles of modern cryptography, including the modern, computational approach to security that overcomes the limitations of perfect secrecy. An extensive treatment of private-key encryption and message authentication follows. The authors also illustrate design principles for block ciphers, such as the Data Encryption Standard (DES) and the Advanced Encryption Standard (AES), and present provably secure constructions of block ciphers from lower-level primitives. The second half of the book focuses on public-key cryptography, beginning with a self-contained introduction to the number theory needed to understand the RSA, Diffie-Hellman, El Gamal, and other cryptosystems. After exploring public-key encryption and digital signatures, the book concludes with a discussion of the random oracle model and its applications. Serving as a textbook, a reference, or for self-study, Introduction to Modern Cryptography presents the necessary tools to fully understand this fascinating subject.}, keywords = {Computer networks, computer security, Computers / Operating Systems / General, Computers / Security / General, cryptography, Language Arts \& Disciplines / Communication Studies, Mathematics / Combinatorics}, isbn = {9781584885511}, author = {Katz, Jonathan and Lindell,Yehuda} } @article {13131, title = {Learning pairwise dissimilarity profiles for appearance recognition in visual surveillance}, journal = {Advances in Visual Computing}, year = {2008}, month = {2008///}, pages = {23 - 34}, abstract = {Training discriminative classifiers for a large number of classes is a challenging problem due to increased ambiguities between classes. In order to better handle the ambiguities and to improve the scalability of classifiers to larger number of categories, we learn pairwise dissimilarity profiles (functions of spatial location) between categories and adapt them into nearest neighbor classification. We introduce a dissimilarity distance measure and linearly or nonlinearly combine it with direct distances. We illustrate and demonstrate the approach mainly in the context of appearance-based person recognition.}, author = {Lin,Z. and Davis, Larry S.} } @conference {13581, title = {Learning Visual Shape Lexicon for Document Image Content Recognition}, booktitle = {The 10th European Conference on Computer Vision (ECCV 2008)}, year = {2008}, month = {2008///}, pages = {745 - 758}, address = {Marseille, France}, abstract = {Developing effective content recognition methods for diverse imagery continues to challenge computer vision researchers. We present a new approach for document image content categorization using a lexicon of shape features. Each lexical word corresponds to a scale and rotation invariant shape feature that is generic enough to be detected repeatably and segmentation free. We learn a concise, structurally indexed shape lexicon from training by clustering and partitioning feature types through graph cuts. We demonstrate our approach on two challenging document image content recognition problems: 1) The classification of 4,500 Web images crawled from Google Image Search into three content categories {\textemdash} pure image, image with text, and document image, and 2) Language identification of 8 languages (Arabic, Chinese, English, Hindi, Japanese, Korean, Russian, and Thai) on a 1,512 complex document image database composed of mixed machine printed text and handwriting. Our approach is capable to handle high intra-class variability and shows results that exceed other state-of-the-art approaches, allowing it to be used as a content recognizer in image indexing and retrieval systems.}, author = {Zhu,Guangyu and Yu,Xiaodong and Li,Yi and David Doermann} } @conference {14454, title = {Leveraging social context for searching social media}, booktitle = {Proceedings of the 2008 ACM workshop on Search in social media}, series = {SSM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {91 - 94}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The ability to utilize and benefit from today{\textquoteright}s explosion of social media sites depends on providing tools that allow users to productively participate. In order to participate, users must be able to find resources (both people and information) that they find valuable. Here, we argue that in order to do this effectively, we should make use of a user{\textquoteright}s "social context". A user{\textquoteright}s social context includes both their personal social context (their friends and the communities to which they belong) and their community social context (their role and identity in different communities).}, keywords = {social context, social media, social search}, isbn = {978-1-60558-258-0}, doi = {10.1145/1458583.1458602}, url = {http://doi.acm.org/10.1145/1458583.1458602}, author = {Smith,Marc and Barash,Vladimir and Getoor, Lise and Lauw,Hady W.} } @conference {12244, title = {Matchmaking and implementation issues for a P2P desktop grid}, booktitle = {Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on}, year = {2008}, month = {2008/04//}, pages = {1 - 5}, abstract = {We present some recent and ongoing work in our decentralized desktop computing grid project. Specifically, we discuss matching jobs with compute nodes in a peer-to-peer grid of heterogeneous platforms, and the implementation of our algorithms in a concrete system.}, keywords = {computing, computing;, computing;peer-to-peer, desktop, grid;decentralized, grid;grid, grid;peer-to-peer, P2P}, doi = {10.1109/IPDPS.2008.4536388}, author = {Marsh,M. and Kim,Jik-Soo and Nam,Beomseok and Jaehwan Lee and Ratanasanya,S. and Bhattacharjee, Bobby and Keleher,P. and Richardson,D. and Wellnitz,D.} } @article {14569, title = {Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development}, journal = {Development}, volume = {135}, year = {2008}, month = {2008///}, pages = {2729 - 2738}, abstract = {CTCF is a multifunctional nuclear factor involved in epigenetic regulation. Despite recent advances that include the systematic discovery of CTCF-binding sites throughout the mammalian genome, the in vivo roles of CTCF in adult tissues and during embryonic development are largely unknown. Using transgenic RNAi, we depleted maternal stores of CTCF from growing mouse oocytes, and identified hundreds of misregulated genes. Moreover, our analysis suggests that CTCF predominantly activates or derepresses transcription in oocytes. CTCF depletion causes meiotic defects in the egg, and mitotic defects in the embryo that are accompanied by defects in zygotic gene expression, and culminate in apoptosis. Maternal pronuclear transfer and CTCF mRNA microinjection experiments indicate that CTCF is a mammalian maternal effect gene, and that persistent transcriptional defects rather than persistent chromosomal defects perturb early embryonic development. This is the first study detailing a global and essential role for CTCF in mouse oocytes and preimplantation embryos.}, doi = {10.1242/dev.024539}, url = {http://dev.biologists.org/content/135/16/2729.abstract}, author = {Wan,Le-Ben and Pan,Hua and Hannenhalli, Sridhar and Cheng,Yong and Ma,Jun and Fedoriw,Andrew and Lobanenkov,Victor and Latham,Keith E. and Schultz,Richard M. and Bartolomei,Marisa S.} } @conference {17536, title = {Measurement Manipulation and Space Selection in Network Coordinates}, booktitle = {Distributed Computing Systems, International Conference on}, year = {2008}, month = {2008///}, pages = {361 - 368}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Internet coordinate systems have emerged as an efficient method to estimate the latency between pairs of nodes without any communication between them. However, most coordinate systems have been evaluated solely on data sets built by their authors from measurements gathered over large periods of time. Although they show good prediction results, it is unclear whether the accuracy is the result of the system design properties or is more connected to the characteristics of the data sets. In this paper, we revisit a simple question: how do the features of the embedding space and the inherent attributes of the data sets interact in producing good embeddings? We adapt the Vivaldi algorithm to use Hyperbolic space for embedding and evaluate both Euclidean and Hyperbolic Vivaldi on seven sets of real-world latencies. Our results show that node filtering and latency distributions can significantly influence the accuracy of the predictions. For example, although Euclidean Vivaldi performs well on data sets that were chosen, constructed and filtered by the designers of the algorithm, its performance and robustness decrease considerably when run on third party data sets that were not filtered a priori. Our results offer important insight into designing and building coordinate systems that are both robust and accurate in Internet-like environments.}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICDCS.2008.27}, author = {Lumezanu,Cristian and Spring, Neil} } @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.} } @conference {18775, title = {Methods to directly measure the trapping potential in optical tweezers}, year = {2008}, month = {2008///}, pages = {70380V{\textendash}1 - 70380V{\textendash}1}, abstract = {Techniques to measure the trapping force in an optical tweezers without any prior assumptions about the trapshape have been developed. The response of a trapped micro or nanoparticle to a step input is measured and then used to calculate the trapping force experienced by the particle as a function of it{\textquoteright}s position in the trap. This method will provide new insight into the trapping behavior of nanoparticles, which are more weakly bound than microparticles and thereby explore larger regions of the trapping potential due to Brownian motion. Langevin dynamics simulations are presented to model the system and are used to demonstrate this technique. Preliminary experimental results are then presented to validate the simulations. Finally, the measured trapping forces, from simulations and laboratory experiments, are integrated to recover the trapping potential. }, url = {http://144.206.159.178/FT/CONF/16419087/16419102.pdf}, author = {Balijepalli,A. and LeBrun,T. W. and Gorman,J. J. and Gupta,S.K.} } @article {13599, title = {Mobile Retriever: Access to Digital Documents from their Physical Source}, journal = {International Journal on Document Analysis and Recognition}, volume = {11}, year = {2008}, month = {2008/09//}, pages = {19 - 27}, abstract = {In this paper, we describe an image based document retrieval system which runs on camera enabled mobile devices. {\textquotedblleft}Mobile Retriever{\textquotedblright} aims to seamlessly link physical and digital documents by allowing users to snap a picture of the text of a document and retrieve its electronic version from a database. Experiments show that for a database of 100,093 pages, the correct document can be retrieved in less than 4 s at a success rate over 95\%. Our system extracts token pairs from the text, to efficiently index and retrieve candidate pages using only a small portion of the image. We use token triplets that define the orientation of three corresponding tokens to effectively prune the false positives and identify the correct page to retrieve. We stress the importance of geometrical relationship between feature points and show its effectiveness in our camera based image retrieval system.}, author = {Liu,Xu and David Doermann} } @inbook {13455, title = {Modeling Transfer Relationships Between Learning Tasks for Improved Inductive Transfer}, booktitle = {Machine Learning and Knowledge Discovery in DatabasesMachine Learning and Knowledge Discovery in Databases}, series = {Lecture Notes in Computer Science}, volume = {5211}, year = {2008}, month = {2008///}, pages = {317 - 332}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper, we propose a novel graph-based method for knowledge transfer. We model the transfer relationships between source tasks by embedding the set of learned source models in a graph using transferability as the metric. Transfer to a new problem proceeds by mapping the problem into the graph, then learning a function on this graph that automatically determines the parameters to transfer to the new learning task. This method is analogous to inductive transfer along a manifold that captures the transfer relationships between the tasks. We demonstrate improved transfer performance using this method against existing approaches in several real-world domains.}, isbn = {978-3-540-87478-2}, url = {http://dx.doi.org/10.1007/978-3-540-87479-9_39}, author = {Eaton,Eric and desJardins, Marie and Lane,Terran}, editor = {Daelemans,Walter and Goethals,Bart and Morik,Katharina} } @article {12976, title = {A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13}, journal = {J Mol Evol}, volume = {67}, year = {2008}, month = {2008/12//}, pages = {581 - 593}, abstract = {The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42\%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss and possible limb re-evolution.}, doi = {10.1007/s00239-008-9156-7}, author = {Kohlsdorf,T and Cummings, Michael P. and Lynch,VJ and Stopper,GF and Takahashi,K and Wagner,GP} } @conference {12247, title = {Motivating participation in internet routing overlays}, booktitle = {Proceedings of the 3rd international workshop on Economics of networked systems}, series = {NetEcon {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {91 - 96}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {PeerWise is an Internet routing overlay that reduces end-to-end latencies by allowing peers to forward through a relay instead of connecting directly to their destinations. Fundamental to PeerWise is the notion of peering agreements between two peers, wherein they agree to forward for one another. In this paper, we consider the problem of motivating users to establish and maintain peerings in a completely decentralized, scalable manner. We show that routing overlays present unique challenges and goals. For instance, since participants can always "fall back" on standard Internet routing, we must encourage users to stay in the system and maintain long-lived peering agreements. To address these challenges, we propose two mechanisms: First, we use Service Level Agreements (SLAs) to expressively negotiate peers{\textquoteright} demands and the recourses they will take when SLAs are violated. Second, we propose a mechanism to address SLA violations that differs from the standard notion of punishment via service degradation. Our simulation results demonstrate that our mechanism causes peers to avoid SLA violators in favor of long-lived peerings. Lastly, we discuss potential, emergent behaviors in a selfish routing overlay.}, keywords = {incentives, internet routing overlays, service-level agreements}, isbn = {978-1-60558-179-8}, doi = {10.1145/1403027.1403048}, url = {http://doi.acm.org/10.1145/1403027.1403048}, author = {Levin,Dave and Baden,Randolph and Lumezanu,Cristian and Spring, Neil and Bhattacharjee, Bobby} } @article {18247, title = {Mpeg recompression detection based on block artifacts}, journal = {Proc. of SPIE Electronic Imaging, Security, Steganography, and Watermarking of Multimedia Contents}, volume = {6819}, year = {2008}, month = {2008///}, abstract = {With sophisticated video editing technologies, it is becoming increasingly easy to tamper digital video withoutleaving visual clues. One of the common tampering operations on video is to remove some frames and then re-encode the resulting video. In this paper, we propose a new method for detecting this type of tampering by exploring the temporal patterns of the block artifacts in video sequences. We show that MPEG compression introduces different block artifacts into various types of frames and that the strength of the block artifacts as a function over time has a regular pattern for a given group of pictures (GOP) structure. When some frames are removed from an MPEG video file and the file is then recompressed, the block artifacts introduced by the previous compression would remain and affect the average of block artifact strength of the recompressed one in such a way that depends on the number of deleted frames and the type of GOP used previously. We propose a feature curve to reveal the compression history of an MPEG video file with a given GOP structure, and use it as evidence to detect tampering. Experimental results evaluated on common video benchmark clips demonstrate the effectiveness of the proposed method. }, author = {Luo,W. and Wu,M. and Huang,J.} } @article {13833, title = {Multiple alternative sentence compressions and word-pair antonymy for automatic text summarization and recognizing textual entailment}, journal = {Proceedings of the Text Analysis Conference (TAC-2008), Gaithersburg, MD}, year = {2008}, month = {2008///}, abstract = {The University of Maryland participatedin three tasks organized by the Text Anal- ysis Conference 2008 (TAC 2008): (1) the update task of text summarization; (2) the opinion task of text summariza- tion; and (3) recognizing textual entail- ment (RTE). At the heart of our summa- rization system is Trimmer, which gener- ates multiple alternative compressed ver- sions of the source sentences that act as candidate sentences for inclusion in the summary. For the first time, we investi- gated the use of automatically generated antonym pairs for both text summariza- tion and recognizing textual entailment. We used an antonymy feature in both the opinion summarization task and for rec- ognizing textual entailment. More coher- ent summaries resulted when using the antonymy feature as compared to when not using it. However, performance on ROUGE dropped. The RTE system per- formed almost equally well when using antonyms from WordNet and when using automatically generated antonyms. }, author = {Mohammad,S. and Dorr, Bonnie J and Egan,M. and Jimmy Lin and Zajic, David} } @article {15290, title = {Navigating information spaces: A case study of related article search in PubMed}, journal = {Information Processing \& Management}, volume = {44}, year = {2008}, month = {2008///}, pages = {1771 - 1783}, abstract = {The concept of an {\^a}{\texteuro}{\oe}information space{\^a}{\texteuro} provides a powerful metaphor for guiding the design of interactive retrieval systems. We present a case study of related article search, a browsing tool designed to help users navigate the information space defined by results of the PubMed{\^A}{\textregistered} search engine. This feature leverages content-similarity links that tie MEDLINE{\^A}{\textregistered} citations together in a vast document network. We examine the effectiveness of related article search from two perspectives: a topological analysis of networks generated from information needs represented in the TREC 2005 genomics track and a query log analysis of real PubMed users. Together, data suggest that related article search is a useful feature and that browsing related articles has become an integral part of how users interact with PubMed.}, keywords = {Browsing, Interactive IR, MEDLINE, TREC genomics}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2008.04.002}, url = {http://www.sciencedirect.com/science/article/pii/S0306457308000502}, author = {Jimmy Lin and DiCuccio,Michael and Grigoryan,Vahan and Wilbur,W. John} } @conference {16839, title = {NewsStand: a new view on news}, booktitle = {Proceedings of the 16th ACM SIGSPATIAL international conference on Advances in geographic information systems}, series = {GIS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {18:1{\textendash}18:10 - 18:1{\textendash}18:10}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {News articles contain a wealth of implicit geographic content that if exposed to readers improves understanding of today{\textquoteright}s news. However, most articles are not explicitly geotagged with their geographic content, and few news aggregation systems expose this content to users. A new system named NewsStand is presented that collects, analyzes, and displays news stories in a map interface, thus leveraging on their implicit geographic content. NewsStand monitors RSS feeds from thousands of online news sources and retrieves articles within minutes of publication. It then extracts geographic content from articles using a custom-built geotagger, and groups articles into story clusters using a fast online clustering algorithm. By panning and zooming in NewsStand{\textquoteright}s map interface, users can retrieve stories based on both topical significance and geographic region, and see substantially different stories depending on position and zoom level.}, keywords = {clustering, geotagging, knowledge discovery, text mining}, isbn = {978-1-60558-323-5}, doi = {10.1145/1463434.1463458}, url = {http://doi.acm.org/10.1145/1463434.1463458}, author = {Teitler,Benjamin E. and Lieberman,Michael D. and Panozzo,Daniele and Sankaranarayanan,Jagan and Samet, Hanan and Sperling,Jon} } @inbook {19642, title = {Optimal Cryptographic Hardness of Learning Monotone Functions}, booktitle = {Automata, Languages and Programming}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {36 - 47}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {A wide range of positive and negative results have been established for learning different classes of Boolean functions from uniformly distributed random examples. However, polynomial-time algorithms have thus far been obtained almost exclusively for various classes of monotone functions, while the computational hardness results obtained to date have all been for various classes of general (nonmonotone) functions. Motivated by this disparity between known positive results (for monotone functions) and negative results (for nonmonotone functions), we establish strong computational limitations on the efficient learnability of various classes of monotone functions. We give several such hardness results which are provably almost optimal since they nearly match known positive results. Some of our results show cryptographic hardness of learning polynomial-size monotone circuits to accuracy only slightly greater than 1/2+1/n--√1/2 + 1/\sqrt{n} ; this accuracy bound is close to optimal by known positive results (Blum et al., FOCS {\textquoteright}98). Other results show that under a plausible cryptographic hardness assumption, a class of constant-depth, sub-polynomial-size circuits computing monotone functions is hard to learn; this result is close to optimal in terms of the circuit size parameter by known positive results as well (Servedio, Information and Computation {\textquoteright}04). Our main tool is a complexity-theoretic approach to hardness amplification via noise sensitivity of monotone functions that was pioneered by O{\textquoteright}Donnell (JCSS {\textquoteright}04).}, keywords = {Data structures, Data Structures, Cryptology and Information Theory, Discrete Mathematics in Computer Science, Numeric Computing, Software Engineering/Programming and Operating Systems, Theory of computation}, isbn = {978-3-540-70574-1, 978-3-540-70575-8}, url = {http://link.springer.com/chapter/10.1007/978-3-540-70575-8_4}, author = {Dana Dachman-Soled and Lee, Homin K. and Malkin, Tal and Servedio, Rocco A. and Wan, Andrew and Wee, Hoeteck}, editor = {Aceto, Luca and Damg{\r a}rd, Ivan and Goldberg, Leslie Ann and Halld{\'o}rsson, Magn{\'u}s M. and Ing{\'o}lfsd{\'o}ttir, Anna and Walukiewicz, Igor} } @conference {18155, title = {A pattern classification framework for theoretical analysis of component forensics}, booktitle = {Acoustics, Speech and Signal Processing, 2008. ICASSP 2008. IEEE International Conference on}, year = {2008}, month = {2008/04/31/4}, pages = {1665 - 1668}, abstract = {Component forensics is an emerging methodology for forensic analysis that aims at estimating the algorithms and parameters in each component of a digital device. This paper proposes a theoretical foundation to examine the performance limits of component forensics. Using ideas from pattern classification theory, we define formal notions of identifiability of components in the information processing chain. We show that the parameters of certain device components can be accurately identified only in controlled settings through semi non-intrusive forensics, while the parameters of some others can be computed directly from the available sample data via complete non-intrusive analysis. We then extend the proposed theoretical framework to quantify and improve the accuracies and confidence in component parameter identification for several forensic applications.}, keywords = {analysis;information, classification;, classification;parameter, component, estimation;pattern, forensics;component, forensics;pattern, identification;forensic, parameter, processing;nonintrusive}, doi = {10.1109/ICASSP.2008.4517947}, author = {Swaminathan,A. and M. Wu and Liu,K. J.R} } @conference {18350, title = {Photo-based question answering}, booktitle = {Proceedings of the 16th ACM international conference on Multimedia}, series = {MM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {389 - 398}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Photo-based question answering is a useful way of finding information about physical objects. Current question answering (QA) systems are text-based and can be difficult to use when a question involves an object with distinct visual features. A photo-based QA system allows direct use of a photo to refer to the object. We develop a three-layer system architecture for photo-based QA that brings together recent technical achievements in question answering and image matching. The first, template-based QA layer matches a query photo to online images and extracts structured data from multimedia databases to answer questions about the photo. To simplify image matching, it exploits the question text to filter images based on categories and keywords. The second, information retrieval QA layer searches an internal repository of resolved photo-based questions to retrieve relevant answers. The third, human-computation QA layer leverages community experts to handle the most difficult cases. A series of experiments performed on a pilot dataset of 30,000 images of books, movie DVD covers, grocery items, and landmarks demonstrate the technical feasibility of this architecture. We present three prototypes to show how photo-based QA can be built into an online album, a text-based QA, and a mobile application.}, keywords = {Computer vision, Information retrieval, Question answering}, isbn = {978-1-60558-303-7}, doi = {10.1145/1459359.1459412}, url = {http://doi.acm.org/10.1145/1459359.1459412}, author = {Tom Yeh and Lee,John J and Darrell,Trevor} } @article {16338, title = {Pooled ANOVA}, journal = {Computational Statistics \& Data Analysis}, volume = {52}, year = {2008}, month = {2008/08/15/}, pages = {5215 - 5228}, abstract = {We introduce Pooled ANOVA, a greedy algorithm to sequentially select the rare important factors from a large set of factors. Problems such as computer simulations and software performance tuning involve a large number of factors, few of which have an important effect on the outcome or performance measure. We pool multiple factors together, and test the pool for significance. If the pool has a significant effect we retain the factors for deconfounding. If not, we either declare that none of the factors are important, or retain them for follow-up decoding, depending on our assumptions and stage of testing. The sparser important factors are, the bigger the savings. Pooled ANOVA requires fewer assumptions than other, similar methods (e.g.~sequential bifurcation), such as not requiring all important effects to have the same sign. We demonstrate savings of 25\%-35\% when compared to a conventional ANOVA, and also the ability to work in a setting where Sequential Bifurcation fails.}, isbn = {0167-9473}, doi = {16/j.csda.2008.04.024}, url = {http://www.sciencedirect.com/science/article/pii/S0167947308002168}, author = {Last,Michael and Luta,Gheorghe and Orso,Alex and Porter, Adam and Young,Stan} } @article {13132, title = {A pose-invariant descriptor for human detection and segmentation}, journal = {Computer Vision{\textendash}ECCV 2008}, year = {2008}, month = {2008///}, pages = {423 - 436}, abstract = {We present a learning-based, sliding window-style approach for the problem of detecting humans in still images. Instead of traditional concatenation-style image location-based feature encoding, a global descriptor more invariant to pose variation is introduced. Specifically, we propose a principled approach to learning and classifying human/non-human image patterns by simultaneously segmenting human shapes and poses, and extracting articulation-insensitive features. The shapes and poses are segmented by an efficient, probabilistic hierarchical part-template matching algorithm, and the features are collected in the context of poses by tracing around the estimated shape boundaries. Histograms of oriented gradients are used as a source of low-level features from which our pose-invariant descriptors are computed, and kernel SVMs are adopted as the test classifiers. We evaluate our detection and segmentation approach on two public pedestrian datasets.}, author = {Lin,Z. and Davis, Larry S.} } @article {14291, title = {Rule-based static analysis of network protocol implementations}, journal = {Information and Computation}, volume = {206}, year = {2008}, month = {2008///}, pages = {130 - 157}, author = {Udrea,O. and Lumezanu,C. and Foster, Jeffrey S.} } @conference {18351, title = {Scalable classifiers for Internet vision tasks}, booktitle = {Computer Vision and Pattern Recognition Workshops, 2008. CVPRW{\textquoteright}08. IEEE Computer Society Conference on}, year = {2008}, month = {2008/06//}, pages = {1 - 8}, publisher = {IEEE}, organization = {IEEE}, abstract = {Object recognition systems designed for Internet applications typically need to adapt to userspsila needs in a flexible fashion and scale up to very large data sets. In this paper, we analyze the complexity of several multiclass SVM-based algorithms and highlight the computational bottleneck they suffer at test time: comparing the input image to every training image. We propose an algorithm that overcomes this bottleneck; it offers not only the efficiency of a simple nearest-neighbor classifier, by voting on class labels based on the k nearest neighbors quickly determined by a vocabulary tree, but also the recognition accuracy comparable to that of a complex SVM classifier, by incorporating SVM parameters into the voting scores incrementally accumulated from individual image features. Empirical results demonstrate that adjusting votes by relevant support vector weights can improve the recognition accuracy of a nearest-neighbor classifier without sacrificing speed. Compared to existing methods, our algorithm achieves a ten-fold speed increase while incurring an acceptable accuracy loss that can be easily offset by showing about two more labels in the result. The speed, scalability, and adaptability of our algorithm makes it suitable for Internet vision applications.}, isbn = {978-1-4244-2339-2}, doi = {10.1109/CVPRW.2008.4562958}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4562958}, author = {Tom Yeh and Lee,John J and Darrell,Trevor} } @article {12241, title = {A scalable key management and clustering scheme for wireless ad hoc and sensor networks}, journal = {Future Generation Computer Systems}, volume = {24}, year = {2008}, month = {2008/10//}, pages = {860 - 869}, abstract = {This paper describes a scalable key management and clustering scheme for secure group communications in ad hoc and sensor networks. The scalability problem is solved by partitioning the communicating devices into subgroups, with a leader in each subgroup, and further organizing the subgroups into hierarchies. Each level of the hierarchy is called a tier or layer. Key generation, distribution, and actual data transmissions follow the hierarchy. The distributed, efficient clustering approach (DECA) provides robust clustering to form subgroups, and analytical and simulation results demonstrate that DECA is energy-efficient and resilient against node mobility. Comparing with most other schemes, our approach is extremely scalable and efficient, provides more security guarantees, and is selective, adaptive and robust.}, keywords = {ad hoc networks, clustering, Group communications, Key management, sensor networks}, isbn = {0167-739X}, doi = {10.1016/j.future.2008.03.007}, url = {http://www.sciencedirect.com/science/article/pii/S0167739X08000782}, author = {Li,Jason H. and Bhattacharjee, Bobby and Yu,Miao and Levy,Renato} } @conference {15312, title = {Scalable language processing algorithms for the masses: a case study in computing word co-occurrence matrices with MapReduce}, booktitle = {Proceedings of the Conference on Empirical Methods in Natural Language Processing}, series = {EMNLP {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {419 - 428}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper explores the challenge of scaling up language processing algorithms to increasingly large datasets. While cluster computing has been available in commercial environments for several years, academic researchers have fallen behind in their ability to work on large datasets. I discuss two barriers contributing to this problem: lack of a suitable programming model for managing concurrency and difficulty in obtaining access to hardware. Hadoop, an open-source implementation of Google{\textquoteright}s MapReduce framework, provides a compelling solution to both issues. Its simple programming model hides system-level details from the developer, and its ability to run on commodity hardware puts cluster computing within the reach of many academic research groups. This paper illustrates these points with a case study in building word cooccurrence matrices from large corpora. I conclude with an analysis of an alternative computing model based on renting instead of buying computer clusters.}, url = {http://dl.acm.org/citation.cfm?id=1613715.1613769}, author = {Jimmy Lin} } @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 {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 {15292, title = {Single-document and multi-document summarization techniques for email threads using sentence compression}, journal = {Information Processing \& Management}, volume = {44}, year = {2008}, month = {2008/07//}, pages = {1600 - 1610}, abstract = {We present two approaches to email thread summarization: collective message summarization (CMS) applies a multi-document summarization approach, while individual message summarization (IMS) treats the problem as a sequence of single-document summarization tasks. Both approaches are implemented in our general framework driven by sentence compression. Instead of a purely extractive approach, we employ linguistic and statistical methods to generate multiple compressions, and then select from those candidates to produce a final summary. We demonstrate these ideas on the Enron email collection {\^a}{\texteuro}{\textquotedblleft} a very challenging corpus because of the highly technical language. Experimental results point to two findings: that CMS represents a better approach to email thread summarization, and that current sentence compression techniques do not improve summarization performance in this genre.}, keywords = {Email summarization, Enron, Informal media, Sentence compression, Trimming}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2007.09.007}, url = {http://www.sciencedirect.com/science/article/pii/S0306457307001768}, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin} } @conference {15062, title = {A topic-based Document Correlation Model}, booktitle = {Machine Learning and Cybernetics, 2008 International Conference on}, volume = {5}, year = {2008}, month = {2008/07//}, pages = {2487 - 2491}, abstract = {Document correlation analysis is now a focus of study in text mining. This paper proposed a Document Correlation Model to capture the correlation between documents from topic level. The model represents the document correlation as the Optimal Matching of a bipartite graph, of which each partition is a document, each node is a topic, and each edge is the similarity between two topics. The topics of each document are retrieved by the Latent Dirichlet Allocation model and Gibbs sampling. Experiments on correlated document search show that the Document Correlation Model outperforms the Vector Space Model on two aspects: 1) it has higher average retrieval precision; 2) it needs less space to store a documentpsilas information.}, keywords = {bipartite graph optimal matching, data mining, document correlation analysis, document retrieval, Gibbs sampling, Information retrieval, latent Dirichlet allocation model, text analysis, text mining, topic-based document correlation model}, doi = {10.1109/ICMLC.2008.4620826}, author = {Jia,Xi-Ping and Peng,Hong and Zheng,Qi-Lun and Zhuolin Jiang and Li,Zhao} } @article {15282, title = {Toward automatic facet analysis and need negotiation: Lessons from mediated search}, journal = {ACM Transactions on Information Systems (TOIS)}, volume = {27}, year = {2008}, month = {2008/12//}, pages = {6:1{\textendash}6:42 - 6:1{\textendash}6:42}, abstract = {This work explores the hypothesis that interactions between a trained human search intermediary and an information seeker can inform the design of interactive IR systems. We discuss results from a controlled Wizard-of-Oz case study, set in the context of the TREC 2005 HARD track evaluation, in which a trained intermediary executed an integrated search and interaction strategy based on conceptual facet analysis and informed by need negotiation techniques common in reference interviews. Having a human {\textquotedblleft}in the loop{\textquotedblright} yielded large improvements over fully automated systems as measured by standard ranked-retrieval metrics, demonstrating the value of mediated search. We present a detailed analysis of the intermediary{\textquoteright}s actions to gain a deeper understanding of what worked and why. One contribution is a taxonomy of clarification types informed both by empirical results and existing theories in library and information science. We discuss how these findings can guide the development of future systems. Overall, this work illustrates how studying human information-seeking processes can lead to better information retrieval applications.}, keywords = {interactive information retrieval, Reference interview}, isbn = {1046-8188}, doi = {10.1145/1416950.1416956}, url = {http://doi.acm.org/10.1145/1416950.1416956}, author = {Jimmy Lin and Wu,Philip and Abels,Eileen} } @conference {13126, title = {Tracking Down Under: Following the Satin Bowerbird}, booktitle = {Applications of Computer Vision, 2008. WACV 2008. IEEE Workshop on}, year = {2008}, month = {2008/01//}, pages = {1 - 7}, abstract = {Socio biologists collect huge volumes of video to study animal behavior (our collaborators work with 30,000 hours of video). The scale of these datasets demands the development of automated video analysis tools. Detecting and tracking animals is a critical first step in this process. However, off-the-shelf methods prove incapable of handling videos characterized by poor quality, drastic illumination changes, non-stationary scenery and foreground objects that become motionless for long stretches of time. We improve on existing approaches by taking advantage of specific aspects of this problem: by using information from the entire video we are able to find animals that become motionless for long intervals of time; we make robust decisions based on regional features; for different parts of the image, we tailor the selection of model features, choosing the features most helpful in differentiating the target animal from the background in that part of the image. We evaluate our method, achieving almost 83\% tracking accuracy on a more than 200,000 frame dataset of Satin Bowerbird courtship videos.}, keywords = {analysis, behavior;animal, Bowerbird;animal, computing;feature, detection;animal, extraction;tracking;video, processing;zoology;, Satin, sciences, selection;behavioural, signal, tool;feature, tracking;automated, video}, doi = {10.1109/WACV.2008.4544004}, author = {Kembhavi,A. and Farrell,R. and Luo,Yuancheng and Jacobs, David W. and Duraiswami, Ramani and Davis, Larry S.} } @article {13127, title = {UMD_VDT, an Integration of Detection and Tracking Methods for Multiple Human Tracking}, journal = {Multimodal Technologies for Perception of Humans}, year = {2008}, month = {2008///}, pages = {179 - 190}, abstract = {This paper presents a cooperative body part labeling and tracking algorithm for locating body parts in a videoimage sequence. The body part labeling procedure is used to initialize the tracking procedure and to prevent tracking from getting lost; and the tracking procedure is used to analyze frames that cannot be handled reliably by the labeling procedure. This results in an automatic and robust body part tracking system. Unlike previous work that always start tracking from the first frame which may be difficult to analyze, our tracking procedure starts with some key frames in which body parts can be located reliably. Key frames are selected based on a labeling confidence measure which evaluates the similarity between the human model and the image features. The labeled body parts are tracked in-between frames based on such cues as shape, color, and location interpolated between key frames iteratively. The proposed algorithm has been applied to analyze NASA videotapes in which crew members present challenging postures of bending, twisting, and rotating in a space station. The experimental results demonstrate the effectiveness of the proposed algorithm. }, author = {Tran,S. and Lin,Z. and Harwood,D. and Davis, Larry S.} } @conference {13683, title = {Unconstrained Language Identification Using AShape Codebook}, booktitle = {The 11th International Conference on Frontiers in Handwritting Recognition (ICFHR 2008)}, year = {2008}, month = {2008///}, pages = {13 - 18}, address = {Montreal, Canada}, abstract = {We propose a novel approach to language identification in document images containing handwriting and machine printed text using image descriptors constructed from a codebook of shape features. We encode local text structures using scale and rotation invariant codewords, each representing a characteristic shape feature that is generic enough to appear repeatably. We learn a concise, structurally indexed shape codebook from training data by clustering similar features and partitioning the feature space by graph cuts. Our approach is segmentation free and easily extensible. We quantitatively evaluate our approach using a large real-world document image collection, which consists of more than 1,500 documents in 8 languages (Arabic, Chinese, English, Hindi, Japanese, Korean, Russian, and Thai) and contains a complex mixture of handwritten and machine printed content. Experimental results demonstrate the robustness and flexibility of our approach, and show exceptional language identification performance that exceeds the state of art.}, author = {Zhu,Guangyu and Yu,Xiaodong and Li,Yi and David Doermann} } @article {12242, title = {A Unified Framework for Multipath Routing for Unicast and Multicast Traffic}, journal = {Networking, IEEE/ACM Transactions on}, volume = {16}, year = {2008}, month = {2008/10//}, pages = {1038 - 1051}, abstract = {We study the problem of load balancing the traffic from a set of unicast and multicast sessions. The problem is formulated as an optimization problem. However, we assume that the gradient of the network cost function is not available and needs to be estimated. Multiple paths are provided between a source and a destination using application-layer overlay. We propose a novel algorithm that is based on what is known as simultaneous perturbation stochastic approximation and utilizes only noisy measurements collected and reported to the sources, using an overlay architecture. We consider three network models that reflect different sets of assumptions regarding multicast capabilities of the network. Using an analytical model we first prove the almost sure convergence of the algorithm to a corresponding optimal solution under each network model considered in this paper with decreasing step sizes. Then, we establish the weak convergence (or convergence in distribution) with a fixed step size. In addition, we investigate the benefits acquired from implementing additional multicast capabilities by studying the relative performance of our algorithm under the three network models.}, keywords = {application-layer, approximation;unicast, balancing;multicast, channels;stochastic, communication;multipath, cost, function;optimization, network, overlay;load, perturbation, problem;simultaneous, processes;telecommunication, routing;network, routing;telecommunication, Stochastic, traffic;, traffic;multicast, traffic;multipath}, isbn = {1063-6692}, doi = {10.1109/TNET.2007.909686}, author = {Guven,T. and La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @conference {14348, title = {Using wearable sensors and real time inference to understand human recall of routine activities}, booktitle = {Proceedings of the 10th international conference on Ubiquitous computing}, series = {UbiComp {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {154 - 163}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {empirical evaluation, ESM, experience sampling method, recall accuracy, self-reports, survey frequency, user study}, isbn = {978-1-60558-136-1}, doi = {10.1145/1409635.1409656}, url = {http://doi.acm.org/10.1145/1409635.1409656}, author = {Klasnja,Predrag and Harrison,Beverly L. and LeGrand,Louis and LaMarca,Anthony and Jon Froehlich and Hudson,Scott E.} } @conference {16064, title = {VAST 2008 Challenge: Introducing mini-challenges}, booktitle = {Visual Analytics Science and Technology, 2008. VAST {\textquoteright}08. IEEE Symposium on}, year = {2008}, month = {2008/10//}, pages = {195 - 196}, abstract = {Visual analytics experts realize that one effective way to push the field forward and to develop metrics for measuring the performance of various visual analytics components is to hold an annual competition. The VAST 2008 Challenge is the third year that such a competition was held in conjunction with the IEEE Visual Analytics Science and Technology (VAST) symposium. The authors restructured the contest format used in 2006 and 2007 to reduce the barriers to participation and offered four mini-challenges and a Grand Challenge. Mini Challenge participants were to use visual analytic tools to explore one of four heterogeneous data collections to analyze specific activities of a fictitious, controversial movement. Questions asked in the Grand Challenge required the participants to synthesize data from all four data sets. In this paper we give a brief overview of the data sets, the tasks, the participation, the judging, and the results.}, keywords = {2008, analytics;data, Challenge;heterogeneous, collections;visual, data, VAST, visualisation;}, doi = {10.1109/VAST.2008.4677383}, author = {Grinstein,G. and Plaisant, Catherine and Laskowski,S. and O{\textquoteright}Connell,T. and Scholtz,J. and Whiting,M.} } @article {13688, title = {VCode - Pervasive Data Transfer Using Video Barcode}, journal = {IEEETransactions on Multimedia}, volume = {10}, year = {2008}, month = {2008/04//}, pages = {361 - 371}, abstract = {In this paper we describe a novel data transfer scheme that uses the camera in a smart phone as an alternative data channel. The data is encoded as a sequence of 2D barcode images, displayed on a flat panel display, acquired by the camera, and decoded in real time by the software embedded in device. The decoded data is written to a file. Compared with existing data channels, such as CDMA/GPRS, cables, Bluetooth, and Infrared, our method relies on visual communication and does not require special hardware or data plans. Users only need to point the camera at a monitor displaying the VCode to download. Technical challenges to overcome include correction of perspective distortion, compensation for contrast variation, and efficient implementation of small footprint software into a mobile device. We address these challenges and present our solution in detail. We have implemented a prototype which allows users to download various types of files successfully, including pictures, ring tones and Java games onto camera phones running Symbian and Windows Mobile platforms. We discuss the limitations of our solution and outline future work to overcome these limitations.}, author = {Liu,Xu and David Doermann and Huiping Li} } @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} } @conference {12263, title = {Accountability as a service}, booktitle = {Proceedings of the 3rd USENIX workshop on Steps to reducing unwanted traffic on the internet}, series = {SRUTI{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {5:1{\textendash}5:6 - 5:1{\textendash}5:6}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {We propose that accountability be a first-class network service, independent of addressing and routing. We design a scheme for allowing accountability services, rather than connectivity-providing ISPs, to vouch for traffic, allowing victims to report abuse, filter abusive traffic, and isolate malicious senders. We discuss how accountability services may evolve, how they may facilitate new applications, and the implications of shifting the burden of network policing to a dedicated service.}, url = {http://dl.acm.org/citation.cfm?id=1361436.1361441}, author = {Bender,Adam and Spring, Neil and Levin,Dave and Bhattacharjee, Bobby} } @conference {15063, title = {An adaptive mean shift tracking method using multiscale images}, booktitle = {Wavelet Analysis and Pattern Recognition, 2007. ICWAPR {\textquoteright}07. International Conference on}, volume = {3}, year = {2007}, month = {2007/11//}, pages = {1060 - 1066}, abstract = {An adaptive mean shift tracking method for object tracking using multiscale images is presented in this paper. A bandwidth matrix and a Gaussian kernel are used to extend the definition of target model. The method can exactly estimate the position of the tracked object using multiscale images from Gaussian pyramid. The tracking method determines the parameters of kernel bandwidth by maximizing the lower bound of a log-likelihood function, which is derived from a kernel density estimate with the bandwidth matrix and the modified weight function. The experimental results show that it can averagely converge in 2.55 iterations per frame.}, keywords = {adaptive mean shift tracking method, bandwidth matrix, Gaussian kernel, Gaussian processes, Image sequences, log-likelihood function, matrix algebra, maximum likelihood estimation, multiscale image, Object detection, object tracking}, doi = {10.1109/ICWAPR.2007.4421589}, author = {Zhuolin Jiang and Li,Shao-Fa and Gao,Dong-Fa} } @conference {18331, title = {Adaptive Vocabulary Forests br Dynamic Indexing and Category Learning}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10/14/21}, pages = {1 - 8}, publisher = {IEEE}, organization = {IEEE}, abstract = {Histogram pyramid representations computed from a vocabulary tree of visual words have proven valuable for a range of image indexing and recognition tasks; however, they have only used a single, fixed partition of feature space. We present a new efficient algorithm to incrementally compute set-of-trees (forest) vocabulary representations, and show that they improve recognition and indexing performance in methods which use histogram pyramids. Our algorithm incrementally adapts a vocabulary forest with an Inverted file system at the leaf nodes and automatically keeps existing histogram pyramid database entries up-to-date in a forward filesystem. It is possible not only to apply vocabulary tree indexing algorithms directly, but also to compute pyramid match kernel values efficiently. On dynamic recognition tasks where categories or objects under consideration may change over time, we show that adaptive vocabularies offer significant performance advantages in comparison to a single, fixed vocabulary.}, isbn = {978-1-4244-1630-1}, doi = {10.1109/ICCV.2007.4409053}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4409053}, author = {Tom Yeh and Lee,John and Darrell,Trevor} } @article {18734, title = {Algorithms for on-line monitoring of micro spheres in an optical tweezers-based assembly cell}, journal = {Journal of Computing and Information Science in Engineering}, volume = {7}, year = {2007}, month = {2007///}, pages = {330 - 330}, abstract = {Optical tweezers have emerged as a powerful tool for microand nanomanipulation. Using optical tweezers to perform auto- mated assembly requires on-line monitoring of components in the assembly workspace. This paper presents algorithms for estimat- ing positions and orientations of microscale and nanoscale com- ponents in the 3-Dimensional assembly workspace. Algorithms presented in this paper use images obtained by optical section microscopy. The images are first segmented to locate areas of in- terest and then image gradient information from the areas of in- terest is used to generate probable locations and orientations of components in the XY-plane. Finally, signature curves are com- puted and utilized to obtain component locations and orienta- tions in 3-D space. We have tested these algorithms with silica micro-spheres as well as metallic nanowires. We believe that the algorithms described in this paper will provide the foundation for realizing automated assembly operations in optical tweezers- based assembly cells. }, author = {Peng,T. and Balijepalli,A. and Gupta,S.K. and LeBrun,T.} } @article {13421, title = {Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids}, journal = {Protein Engineering Design and SelectionProtein Engineering, Design and Selection}, volume = {20}, year = {2007}, month = {2007/07/01/}, pages = {347 - 351}, abstract = {Here, we present the AA-QSPR Db (Amino Acid Quantitative Structure Property Relationship Database): a novel, freely available web-resource of data pertaining to amino acids, both engineered and naturally occurring. In addition to presenting fundamental molecular descriptors of size, charge and hydrophobicity, it also includes online visualization tools for users to perform instant, interactive analyses of amino acid sub-sets in which they are interested. The database has been designed with extensible markup language technology to provide a flexible structure, suitable for future development. In addition to providing easy access for queries by external computers, it also offers a user-friendly web-based interface that facilitates human interactions (submission, storage and retrieval of amino acid data) and an associated e-forum that encourages users to question and discuss current and future database contents.}, keywords = {Amino acids, database, QSPR, XML}, isbn = {1741-0126, 1741-0134}, doi = {10.1093/protein/gzm027}, url = {http://peds.oxfordjournals.org/content/20/7/347}, author = {Lu,Yi and Bulka,Blazej and desJardins, Marie and Freeland,Stephen J} } @article {17690, title = {Analysis of the Residual Arnoldi Method}, volume = {UMIACS-TR-2007-45}, year = {2007}, month = {2007/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The Arnoldi method generates a nested squences of orthonormal bases$U_{1},U_{2}, \ldots$ by orthonormalizing $Au_{k}$ against $U_{k}$. Frequently these bases contain increasingly accurate approximations of eigenparis from the periphery of the spectrum of $A$. However, the convergence of these approximations stagnates if $u_{k}$ is contaminated by error. It has been observed that if one chooses a Rayleigh--Ritz approximation $(\mu_{k}, z_{k})$ to a chosen target eigenpair $(\lambda, x)$ and orthonormalizes the residual $Az_{k - }\mu_{k} z_{k}$, the approximations to $x$ (but not the other eigenvectors) continue to converge, even when the residual is contaminated by error. The same is true of the shift-invert variant of Arnoldi{\textquoteright}s method. In this paper we give a mathematical analysis of these new methods. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/7428}, author = {Lee,Che-Rung and Stewart, G.W.} } @article {15284, title = {Answering Clinical Questions with Knowledge-Based and Statistical Techniques}, journal = {Computational Linguistics}, volume = {33}, year = {2007}, month = {2007///}, pages = {63 - 103}, abstract = {The combination of recent developments in question-answering research and the availability of unparalleled resources developed specifically for automatic semantic processing of text in the medical domain provides a unique opportunity to explore complex question answering in the domain of clinical medicine. This article presents a system designed to satisfy the information needs of physicians practicing evidence-based medicine. We have developed a series of knowledge extractors, which employ a combination of knowledge-based and statistical techniques, for automatically identifying clinically relevant aspects of MEDLINE abstracts. These extracted elements serve as the input to an algorithm that scores the relevance of citations with respect to structured representations of information needs, in accordance with the principles of evidence-based medicine. Starting with an initial list of citations retrieved by PubMed, our system can bring relevant abstracts into higher ranking positions, and from these abstracts generate responses that directly answer physicians{\textquoteright} questions. We describe three separate evaluations: one focused on the accuracy of the knowledge extractors, one conceptualized as a document reranking task, and finally, an evaluation of answers by two physicians. Experiments on a collection of real-world clinical questions show that our approach significantly outperforms the already competitive PubMed baseline.}, isbn = {0891-2017}, doi = {i: 10.1162/coli.2007.33.1.63}, url = {http://dx.doi.org/10.1162/coli.2007.33.1.63}, author = {Demner-Fushman,Dina and Jimmy Lin} } @conference {12258, title = {Backbone construction in selfish wireless networks}, booktitle = {Proceedings of the 2007 ACM SIGMETRICS international conference on Measurement and modeling of computer systems}, series = {SIGMETRICS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {121 - 132}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a protocol to construct routing backbones in wireless networks composed of selfish participants. Backbones are inherently cooperative, so constructing them in selfish environments is particularly difficult; participants want a backbone to exist (soothers relay their packets) but do not want to join the backbone (so they do not have to relay packets for others). We model the wireless backbone as a public good and use impatience as an incentive for cooperation. To determine if and when to donate to this public good, each participant calculates how patient it should be in obtaining the public good. We quantify patience using the Volunteer{\textquoteright}s Timing Dilemma (VTD), which we extend to general multihop network settings. Using our generalized VTD analysis, each node individually computes as its dominant strategy the amount of time to wait before joining the backbone. We evaluate our protocol using both simulations and an implementation. Our results show that, even though participants in our system deliberately wait before volunteering, a backbone is formed quickly. Further, the quality of the backbone (such as the size and resulting network lifetime) is comparable to that of existing backbone protocols that assume altruistic behavior.}, keywords = {incentives, public good, selfish network, volunteer{\textquoteright}s dilemma, wireless backbone}, isbn = {978-1-59593-639-4}, doi = {10.1145/1254882.1254896}, url = {http://doi.acm.org/10.1145/1254882.1254896}, author = {Lee,Seungjoon and Levin,Dave and Gopalakrishnan,Vijay and Bhattacharjee, Bobby} } @article {12982, title = {Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences}, journal = {Future Generation Comp Syst}, volume = {23}, year = {2007}, month = {2007/03//}, pages = {497 - 509}, abstract = {Life science research is becoming evermore computationally intensive. Hence, from a computational resource perspective, Grid computing provides a logical approach to meeting many of the computational needs of life science research. However, there are several barriers to the widespread use of Grid computing in life sciences. In this paper, we attempt to address one particular barrier: the difficulty of using Grid computing by life scientists. Life science research often involves connecting multiple applications together to form a workflow. This process of constructing a workflow is complex. When combined with the difficulty of using Grid services, composing a meaningful workflow using Grid services can present a challenge to life scientists. Our proposed solution is a Semantic Web-enabled computing environment, called Bio-STEER. In BioSTEER, bioinformatics Grid services are mapped to Semantic Web services, described in OWL-S. We also defined an ontology in OWL to model bioinformatics applications. A graphical user interface helps to construct a scientific workflow by showing a list of services that are semantically sound: that is, the output of one service is semantically compatible with the input of the connecting service. Bio-STEER can help users take full advantaue of Grid services through a user-friendly graphical user interface (GUI), which allows them to easily construct the workflows they need. (c) 2006 Elsevier B.V. All rights reserved.}, keywords = {client/server;, distributed, environments;, integrated, interface, management;, semantics;, services;, systems;, user, web-base, workflow}, doi = {DOI 10.1016/j.future.2006.07.011}, author = {Lee,S. and Wang,T. D and Hashmi,N. and Cummings, Michael P.} } @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 {12257, title = {Boycotting and extorting nodes in an internetwork}, journal = {NetE-con+ IBC}, year = {2007}, month = {2007///}, author = {Levin,D. and Bender,A. and Lumezanu,C. and Spring, Neil and Bhattacharjee, Bobby} } @article {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 {18178, title = {Collusion-Resistant Fingerprinting for Compressed Multimedia Signals}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {2}, year = {2007}, month = {2007/04//}, pages = {II-165 -II-168 - II-165 -II-168}, abstract = {Most existing collusion-resistant fingerprinting techniques are for fingerprinting uncompressed signals. In this paper, we first study the performance of the traditional Gaussian based spread spectrum sequences for fingerprinting compressed signals and show that the system can be easily defeated by averaging or taking the median of a few copies. To overcome the collusion problem for compressed multimedia host signals, we propose a technique called anti-collusion dithering to mimic an uncompressed signal. Results show higher probability of catching a colluder using the proposed scheme compared to using Gaussian based fingerprints.}, keywords = {based, compression;Gaussian, compression;multimedia, dithering;collusion-resistant, fingerprinting;multimedia, Gaussian, processes;data, sequences;anticollusion, signals, spectrum, spread, systems;}, doi = {10.1109/ICASSP.2007.366198}, author = {Varna,A.L. and He,Shan and Swaminathan,A. and M. Wu and Lu,Haiming and Lu,Zengxiang} } @conference {18150, title = {A Component Estimation Framework for Information Forensics}, booktitle = {Multimedia Signal Processing, 2007. MMSP 2007. IEEE 9th Workshop on}, year = {2007}, month = {2007/10//}, pages = {397 - 400}, abstract = {With a rapid growth of imaging technologies and an increasingly widespread usage of digital images and videos for a large number of high security and forensic applications, there is a strong need for techniques to verify the source and integrity of digital data. Component forensics is new approach for forensic analysis that aims to estimate the algorithms and parameters in each component of the digital device. In this paper, we develop a novel theoretical foundation to understand the fundamental performance limits of component forensics. We define formal notions of identifiability of components in the information processing chain, and present methods to quantify the accuracies at which the component parameters can be estimated. Building upon the proposed theoretical framework, we devise methods to improve the accuracies of component parameter estimation for a wide range of forensic applications.}, keywords = {component, data, data;, Estimation, estimation;image, forensics;parameter, framework;digital, integrity;imaging, of, processing;security, technologies;information}, doi = {10.1109/MMSP.2007.4412900}, author = {Swaminathan,A. and M. Wu and Liu,K. J.R} } @article {14600, title = {COMPUTATIONAL BIOLOGY}, journal = {Nucleic acids research}, volume = {35}, year = {2007}, month = {2007///}, pages = {3163 - 3163}, author = {Leparc,GG and Mitra,RD and Vardhanabhuti,S. and Wang,J. and Hannenhalli, Sridhar and Smit,S. and Widmann,J. and Knight,R. and Wu,S. and Zhang,Y. and others} } @article {15320, title = {Concept disambiguation for improved subject access using multiple knowledge sources}, journal = {Proceedings of the Workshop on Language Technology for Cultural Heritage Data (LaTeCH 2007)}, year = {2007}, month = {2007///}, pages = {25 - 25}, abstract = {We address the problem of mining text forrelevant image metadata. Our work is situ- ated in the art and architecture domain, where highly specialized technical vocabu- lary presents challenges for NLP tech- niques. To extract high quality metadata, the problem of word sense disambiguation must be addressed in order to avoid leading the searcher to the wrong image as a result of ambiguous{\textemdash}and thus faulty{\textemdash}meta- data. In this paper, we present a disam- biguation algorithm that attempts to select the correct sense of nouns in textual de- scriptions of art objects, with respect to a rich domain-specific thesaurus, the Art and Architecture Thesaurus (AAT). We per- formed a series of intrinsic evaluations us- ing a data set of 600 subject terms ex- tracted from an online National Gallery of Art (NGA) collection of images and text. Our results showed that the use of external knowledge sources shows an improvement over a baseline. }, author = {Sidhu,T. and Klavans,J. and Jimmy Lin} } @article {15175, title = {Concurrently-secure blind signatures without random oracles or setup assumptions}, journal = {Theory of Cryptography}, year = {2007}, month = {2007///}, pages = {323 - 341}, abstract = {We show a new protocol for blind signatures in which security is preserved even under arbitrarily-many concurrent executions. The protocol can be based on standard cryptographic assumptions and is the first to be proven secure in a concurrent setting (under any assumptions) without random oracles or a trusted setup assumption such as a common reference string. Along the way, we also introduce new definitions of security for blind signature schemes.This research was supported by US-Israel Binational Science Foundation grant $\#$2004240. Work of the first author was also supported by an Eshkol fellowship from the Israel Ministry of Science and Technology. Work of the second author was also supported by NSF CAREER award $\#$0447075. }, doi = {10.1007/978-3-540-70936-7_18}, author = {Hazay,C. and Katz, Jonathan and Koo,C. Y and Lindell,Y.} } @article {14327, title = {Conducting In Situ Evaluations for and With Ubiquitous Computing Technologies}, journal = {International Journal of Human-Computer Interaction}, volume = {22}, year = {2007}, month = {2007///}, pages = {103 - 118}, abstract = {Abstract To evaluate ubiquitous computing technologies, which may be embedded in the environment, embedded in objects, worn, or carried by the user throughout everyday life, it is essential to use methods that accommodate the often unpredictable, real-world environments in which the technologies are used. This article discusses how we have adapted and applied traditional methods from psychology and human-computer interaction, such as Wizard of Oz and Experience Sampling, to be more amenable to the in situ evaluations of ubiquitous computing applications, particularly in the early stages of design. The way that ubiquitous computing technologies can facilitate the in situ collection of self-report data is also discussed. Although the focus is on ubiquitous computing applications and tools for their assessment, it is believed that the in situ evaluation tools that are proposed will be generally useful for field trials of other technology, applications, or formative studies that are concerned with collecting data in situ.Abstract To evaluate ubiquitous computing technologies, which may be embedded in the environment, embedded in objects, worn, or carried by the user throughout everyday life, it is essential to use methods that accommodate the often unpredictable, real-world environments in which the technologies are used. This article discusses how we have adapted and applied traditional methods from psychology and human-computer interaction, such as Wizard of Oz and Experience Sampling, to be more amenable to the in situ evaluations of ubiquitous computing applications, particularly in the early stages of design. The way that ubiquitous computing technologies can facilitate the in situ collection of self-report data is also discussed. Although the focus is on ubiquitous computing applications and tools for their assessment, it is believed that the in situ evaluation tools that are proposed will be generally useful for field trials of other technology, applications, or formative studies that are concerned with collecting data in situ. }, isbn = {1044-7318}, doi = {10.1080/10447310709336957}, url = {http://www.tandfonline.com/doi/abs/10.1080/10447310709336957}, author = {Consolvo,Sunny and Harrison,Beverly and Smith,Ian and Chen,Mike Y. and Everitt,Katherine and Jon Froehlich and Landay,James A.} } @article {13361, title = {Data Management in the Worldwide Sensor Web}, journal = {IEEE Pervasive Computing}, volume = {6}, year = {2007}, month = {2007///}, pages = {30 - 40}, abstract = {Advances in hardware and miniaturization technologies have led to a rapid increase in the number of large-scale sensor network deployments around the world, bringing us closer to the vision of a worldwide sensor web. Exploiting the sensor web to its full potential, however, raises several hard data management challenges. Addressing these challenges requires a concerted multidisciplinary effort encompassing many computer science fields. This article outlines some of the key data management challenges of a worldwide sensor web. It also presents recent advances in data management research that aim to address these challenges. Hopefully, the scientific, ubiquitous computing, and sensor network communities will adopt some of these solutions for managing their data. The article also attempts to bring many of the remaining open issues to the attention of the database community. This article is part of a special issue on Building a Sensor-Rich World.}, keywords = {data modeling, data streams, data uncertainty, distributed systems, interoperability, sensor networks}, isbn = {1536-1268}, author = {Balazinska,Magdalena and Deshpande, Amol and Franklin,Michael J. and Gibbons,Phillip B. and Gray,Jim and Hansen,Mark and Liebhold,Michael and Nath,Suman and Szalay,Alexander and Tao,Vincent} } @article {12326, title = {Dataflow-based mapping of computer vision algorithms onto FPGAs}, journal = {EURASIP Journal on Embedded Systems}, volume = {2007}, year = {2007}, month = {2007///}, pages = {29 - 29}, author = {Sen,M. and Corretjer,I. and Haim,F. and Saha,S. and Schlessman,J. and Lv,T. and Bhattacharyya, Shuvra S. and Wolf,W.} } @conference {15308, title = {Deconstructing nuggets: the stability and reliability of complex question answering evaluation}, booktitle = {Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {327 - 334}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A methodology based on "information nuggets" has recently emerged as the de facto standard by which answers to complex questions are evaluated. After several implementations in the TREC question answering tracks, the community has gained a better understanding of its many characteristics. This paper focuses on one particular aspect of the evaluation: the human assignment of nuggets to answer strings, which serves as the basis of the F-score computation. As a byproduct of the TREC 2006 ciQA task, identical answer strings were independently evaluated twice, which allowed us to assess the consistency of human judgments. Based on these results, we explored simulations of assessor behavior that provide a method to quantify scoring variations. Understanding these variations in turn lets researchers be more confident in their comparisons of systems.}, keywords = {complex information needs, human judgments, trec}, isbn = {978-1-59593-597-7}, doi = {10.1145/1277741.1277799}, url = {http://doi.acm.org/10.1145/1277741.1277799}, author = {Jimmy Lin and Zhang,Pengyi} } @article {18564, title = {Diagnosing network disruptions with network-wide analysis}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {35}, year = {2007}, month = {2007/06//}, pages = {61 - 72}, abstract = {To maintain high availability in the face of changing network conditions, network operators must quickly detect, identify, and react to events that cause network disruptions. One way to accomplish this goal is to monitor routing dynamics, by analyzing routing update streams collected from routers. Existing monitoring approaches typically treat streams of routing updates from different routers as independent signals, and report only the "loud" events (i.e., events that involve large volume of routing messages). In this paper, we examine BGP routing data from all routers in the Abilene backbone for six months and correlate them with a catalog of all known disruptions to its nodes and links. We find that many important events are not loud enough to be detected from a single stream. Instead, they become detectable only when multiple BGP update streams are simultaneously examined. This is because routing updates exhibit network-wide dependencies. This paper proposes using network-wide analysis of routing information to diagnose (i.e., detect and identify) network disruptions. To detect network disruptions, we apply a multivariate analysis technique on dynamic routing information, (i.e., update traffic from all the Abilene routers) and find that this technique can detect every reported disruption to nodes and links within the network with a low rate of false alarms. To identify the type of disruption, we jointly analyze both the network-wide static configuration and details in the dynamic routing updates; we find that our method can correctly explain the scenario that caused the disruption. Although much work remains to make network-wide analysis of routing data operationally practical, our results illustrate the importance and potential of such an approach.}, keywords = {anomaly detection, network management, statistical inference}, isbn = {0163-5999}, doi = {10.1145/1269899.1254890}, url = {http://doi.acm.org/10.1145/1269899.1254890}, author = {Huang,Yiyi and Feamster, Nick and Lakhina,Anukool and Xu,Jim (Jun)} } @conference {13543, title = {Document Image Mosaicing with Mobile Phones}, booktitle = {International Conference on Image Analysis and Processing (ICIAP{\textquoteright}07)}, year = {2007}, month = {2007/09//}, pages = {1 - 8}, abstract = {This paper presents a novel user interaction oncept for document image scanning with mobile phones. A high resolution mosaic image is constructed in two main stages. Firstly, online camera motion estimation is applied on the phone to assist the user to capture small image batches of the document page. Automatic image stitching process with a help of estimated device motion is carried out to reconstruct the full view of the document. Experiments on document images captured and processed with the mosaicing software clearly show the feasibility of the approach.}, author = {Hannuksela,J. and Sangi,P. and Heikkila,J. and Liu,X. and David Doermann} } @article {16257, title = {Draft Genome of the Filarial Nematode Parasite Brugia Malayi}, journal = {Science}, volume = {317}, year = {2007}, month = {2007/09/21/}, pages = {1756 - 1760}, abstract = {Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the \~{}90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict \~{}11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during \~{}350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1145406}, url = {http://www.sciencemag.org/content/317/5845/1756}, author = {Ghedin,Elodie and Wang,Shiliang and Spiro,David and Caler,Elisabet and Zhao,Qi and Crabtree,Jonathan and Allen,Jonathan E and Delcher,Arthur L. and Guiliano,David B and Miranda-Saavedra,Diego and Angiuoli,Samuel V and Creasy,Todd and Amedeo,Paolo and Haas,Brian and El-Sayed, Najib M. and Wortman,Jennifer R. and Feldblyum,Tamara and Tallon,Luke and Schatz,Michael and Shumway,Martin and Koo,Hean and Salzberg,Steven L. and Schobel,Seth and Pertea,Mihaela and Pop, Mihai and White,Owen and Barton,Geoffrey J and Carlow,Clotilde K. S and Crawford,Michael J and Daub,Jennifer and Dimmic,Matthew W and Estes,Chris F and Foster,Jeremy M and Ganatra,Mehul and Gregory,William F and Johnson,Nicholas M and Jin,Jinming and Komuniecki,Richard and Korf,Ian and Kumar,Sanjay and Laney,Sandra and Li,Ben-Wen and Li,Wen and Lindblom,Tim H and Lustigman,Sara and Ma,Dong and Maina,Claude V and Martin,David M. A and McCarter,James P and McReynolds,Larry and Mitreva,Makedonka and Nutman,Thomas B and Parkinson,John and Peregr{\'\i}n-Alvarez,Jos{\'e} M and Poole,Catherine and Ren,Qinghu and Saunders,Lori and Sluder,Ann E and Smith,Katherine and Stanke,Mario and Unnasch,Thomas R and Ware,Jenna and Wei,Aguan D and Weil,Gary and Williams,Deryck J and Zhang,Yinhua and Williams,Steven A and Fraser-Liggett,Claire and Slatko,Barton and Blaxter,Mark L and Scott,Alan L} } @article {13155, title = {An ease-of-use stereo-based particle filter for tracking under occlusion}, journal = {Human Motion{\textendash}Understanding, Modeling, Capture and Animation}, year = {2007}, month = {2007///}, pages = {225 - 239}, abstract = {We describe a tracker that handles occlusion by clustering foreground pixels based on their disparity values. Stereo-matched foreground pixels, mapped from multiple views to a reference view, allow the tracker to recover occluded foreground regions in the reference view. The stereo algorithm utilizes a common plan view into which foreground regions from multiple views are projected and intersected to construct polygons that contain the ground plane locations of objects, followed by constraining the epipolar search to only those pixels with ground plane locations lying within these polygons. Consequently, a stereo-matched foreground pixel is easily mapped between views by first mapping its ground plane location using pre-computed homography, followed by intersecting the vertical axis passing through the mapped location with the epipolar line. Finally, tracking in a reference view allows a particle filter to be {\textquotedblleft}seamlessly{\textquotedblright} integrated, so that uncertainties can be effectively dealt with. Experimental results illustrate the effectiveness of our algorithm.}, author = {Lim,S.N. and Davis, Larry S.} } @article {12186, title = {EcoLens: Integration and interactive visualization of ecological datasets}, journal = {Ecological Informatics}, volume = {2}, year = {2007}, month = {2007/01/01/}, pages = {61 - 69}, abstract = {Complex multi-dimensional datasets are now pervasive in science and elsewhere in society. Better interactive tools are needed for visual data exploration so that patterns in such data may be easily discovered, data can be proofread, and subsets of data can be chosen for algorithmic analysis. In particular, synthetic research such as ecological interaction research demands effective ways to examine multiple datasets. This paper describes our integration of hundreds of food-web datasets into a common platform, and the visualization software, EcoLens, we developed for exploring this information. This publicly-available application and integrated dataset have been useful for our research predicting large complex food webs, and EcoLens is favorably reviewed by other researchers. Many habitats are not well represented in our large database. We confirm earlier results about the small size and lack of taxonomic resolution in early food webs but find that they and a non-food-web source provide trophic information about a large number of taxa absent from more modern studies. Corroboration of Tuesday Lake trophic links across studies is usually possible, but lack of links among congeners may have several explanations. While EcoLens does not provide all kinds of analytical support, its label- and item-based approach is effective at addressing concerns about the comparability and taxonomic resolution of food-web data.}, keywords = {Data integration, Food webs, Taxonomy, Visualization}, isbn = {1574-9541}, doi = {10.1016/j.ecoinf.2007.03.005}, url = {http://www.sciencedirect.com/science/article/pii/S1574954107000118}, author = {Parr,Cynthia Sims and Lee,Bongshin and Bederson, Benjamin B.} } @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} } @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 {15281, title = {An exploration of the principles underlying redundancy-based factoid question answering}, journal = {ACM Transactions on Information Systems}, volume = {25}, year = {2007}, month = {2007/04//}, abstract = {The so-called {\textquotedblleft}redundancy-based{\textquotedblright} approach to question answering represents a successful strategy for mining answers to factoid questions such as {\textquotedblleft}Who shot Abraham Lincoln?{\textquotedblright} from the World Wide Web. Through contrastive and ablation experiments with Aranea, a system that has performed well in several TREC QA evaluations, this work examines the underlying assumptions and principles behind redundancy-based techniques. Specifically, we develop two theses: that stable characteristics of data redundancy allow factoid systems to rely on external {\textquotedblleft}black box{\textquotedblright} components, and that despite embodying a data-driven approach, redundancy-based methods encode a substantial amount of knowledge in the form of heuristics. Overall, this work attempts to address the broader question of {\textquotedblleft}what really matters{\textquotedblright} and to provide guidance for future researchers.}, keywords = {Data redundancy, Web search}, isbn = {1046-8188}, doi = {10.1145/1229179.1229180}, url = {http://doi.acm.org/10.1145/1229179.1229180}, author = {Jimmy Lin} } @article {15606, title = {A fast implementation of the ISODATA clustering algorithm}, journal = {International Journal of Computational Geometry and Applications}, volume = {17}, year = {2007}, month = {2007///}, pages = {71 - 103}, abstract = {Clustering is central to many image processing and remote sensing applications. isodatais one of the most popular and widely used clustering methods in geoscience applications, but it can run slowly, particularly with large data sets. We present a more efficient approach to isodata clustering, which achieves better running times by storing the points in a kd-tree and through a modification of the way in which the algorithm estimates the dispersion of each cluster. We also present an approximate version of the algorithm which allows the user to further improve the running time, at the expense of lower fidelity in computing the nearest cluster center to each point. We provide both theoretical and empirical justification that our modified approach produces clusterings that are very similar to those produced by the standard isodata approach. We also provide empirical studies on both synthetic data and remotely sensed Landsat and MODIS images that show that our approach has significantly lower running times. }, author = {Memarsadeghi,N. and Mount, Dave and Netanyahu,N. S and Le Moigne,J. and de Berg,M.} } @conference {13989, title = {Fast Time-Domain Spherical Microphone Array Beamforming}, booktitle = {Applications of Signal Processing to Audio and Acoustics, 2007 IEEE Workshop on}, year = {2007}, month = {2007/10//}, pages = {155 - 158}, abstract = {Capturing and reproducing 3D audio has several applications. Spherical array based beamforming is an important technique in this field. However, such a beamformer is very expensive to implement, especially for interactive applications. In this paper, we propose a fast spherical beamforming algorithm in the time domain. It uses pre-computed data and can be steered to arbitrary 3D directions. It is ideal for interactive audio applications such as 3D games, etc. Simulation and experimental results are demonstrated to verify our algorithm.}, doi = {10.1109/ASPAA.2007.4393043}, author = {Zhiyun Li and Duraiswami, Ramani} } @article {13995, title = {Flexible and Optimal Design of Spherical Microphone Arrays for Beamforming}, journal = {Audio, Speech, and Language Processing, IEEE Transactions on}, volume = {15}, year = {2007}, month = {2007/02//}, pages = {702 - 714}, abstract = {This paper describes a methodology for designing a flexible and optimal spherical microphone array for beamforming. Using the approach presented, a spherical microphone array can have very flexible layouts of microphones on the spherical surface, yet optimally approximate a desired beampattern of higher order within a specified robustness constraint. Depending on the specified beampattern order, our approach automatically achieves optimal performances in two cases: when the specified beampattern order is reachable within the robustness constraint we achieve a beamformer with optimal approximation of the desired beampattern; otherwise we achieve a beamformer with maximum directivity, both robustly. For efficient implementation, we also developed an adaptive algorithm for computing the beamformer weights. It converges to the optimal performance quickly while exactly satisfying the specified frequency response and robustness constraint in each step. One application of the method is to allow the building of a real-world system, where microphones may not be placeable on regions, such as near cable outlets and/or a mounting base, while having a minimal effect on the performance. Simulation results are presented}, keywords = {adaptive, algorithm;beamforming;beampattern;frequency, arrays;, arrays;acoustic, directivity;optimal, microphone, processing;array, processing;microphone, response;maximum, signal, spherical}, isbn = {1558-7916}, doi = {10.1109/TASL.2006.876764}, author = {Li,Z. and Duraiswami, Ramani} } @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 {13139, title = {Hierarchical Part-Template Matching for Human Detection and Segmentation}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {Local part-based human detectors are capable of handling partial occlusions efficiently and modeling shape articulations flexibly, while global shape template-based human detectors are capable of detecting and segmenting human shapes simultaneously. We describe a Bayesian approach to human detection and segmentation combining local part-based and global template-based schemes. The approach relies on the key ideas of matching a part-template tree to images hierarchically to generate a reliable set of detection hypotheses and optimizing it under a Bayesian MAP framework through global likelihood re-evaluation and fine occlusion analysis. In addition to detection, our approach is able to obtain human shapes and poses simultaneously. We applied the approach to human detection and segmentation in crowded scenes with and without background subtraction. Experimental results show that our approach achieves good performance on images and video sequences with severe occlusion.}, keywords = {analysis;global, approach;background, articulations;video, Bayesian, detection;human, detectors;hierarchical, detectors;partial, framework;Bayesian, human, likelihood, MAP, matching;human, matching;image, methods;image, occlusion, occlusions;shape, part-based, part-template, re-evaluation;global, segmentation;image, segmentation;local, sequences;, sequences;Bayes, SHAPE, subtraction;fine, template-based}, doi = {10.1109/ICCV.2007.4408975}, author = {Zhe Lin and Davis, Larry S. and David Doermann and DeMenthon,D.} } @article {18851, title = {Incorporating manufacturability considerations during design of injection molded multi-material objects}, journal = {Research in Engineering Design}, volume = {17}, year = {2007}, month = {2007///}, pages = {207 - 231}, abstract = {The presence of an already molded component during the second and subsequent molding stages makes multi-material injection molding different from traditional injection molding process. Therefore, designing multi-material molded objects requires addressing many additional manufacturability considerations. In this paper, we first present an approach to systematically identifying potential manufacturability problems that are unique to the multi-material molding processes and design rules to avoid these problems. Then we present a comprehensive manufacturability analysis approach that incorporates both the traditional single material molding rules as well as the specific rules that have been identified for multi-material molding. Our analysis shows that sometimes the traditional rules need to be suppressed or modified. Lastly, for each of the new manufacturability problem, this paper describes algorithms for automatically detecting potential occurrences and generating redesign suggestions. These algorithms have been implemented in a computer-aided manufacturability analysis system. The approach presented in this paper is applicable to multi-shot and over molding processes. We expect that the manufacturability analysis techniques presented in this paper will help in decreasing the product development time for the injection molded multi-material objects.}, keywords = {engineering}, isbn = {0934-9839}, doi = {10.1007/s00163-007-0027-9}, url = {http://www.springerlink.com/content/c35337h3r5129525/abstract/}, author = {Banerjee,Ashis and Li,Xuejun and Fowler,Greg and Gupta, Satyandra K.} } @conference {14334, title = {Increasing the breadth: applying sensors, inference and self-report in field studies with the MyExperience tool}, booktitle = {Proceedings of the 1st international workshop on System evaluation for mobile platforms}, series = {MobiEval {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {27 - 27}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {In situ evaluation, context-aware systems, experience sampling method (ESM), field studies, Mobile computing, toolkits}, isbn = {978-1-59593-762-9}, doi = {10.1145/1247721.1247727}, url = {http://doi.acm.org/10.1145/1247721.1247727}, author = {Jon Froehlich and Chen,Mike Y. and Consolvo,Sunny and Harrison,Beverly and Landay,James A.} } @conference {13138, title = {An Interactive Approach to Pose-Assisted and Appearance-based Segmentation of Humans}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {An interactive human segmentation approach is described. Given regions of interest provided by users, the approach iteratively estimates segmentation via a generalized EM algorithm. Specifically, it encodes both spatial and color information in a nonparametric kernel density estimator, and incorporates local MRF constraints and global pose inferences to propagate beliefs over image space iteratively to determine a coherent segmentation. This ensures the segmented humans resemble the shapes of human poses. Additionally, a layered occlusion model and a probabilistic occlusion reasoning method are proposed to handle segmentation of multiple humans in occlusion. The approach is tested on a wide variety of images containing single or multiple occluded humans, and the segmentation performance is evaluated quantitatively.}, keywords = {algorithm;appearance-based, algorithm;hidden, approach;layered, density, EM, Estimation, estimation;, estimator;pose-assisted, feature, human, Kernel, mechanisms;pose, method;expectation-maximisation, model;nonparametric, occlusion, reasoning, removal;image, segmentation;inference, segmentation;interactive, segmentation;probabilistic}, doi = {10.1109/ICCV.2007.4409123}, author = {Zhe Lin and Davis, Larry S. and David Doermann and DeMenthon,D.} } @article {18229, title = {Intrinsic fingerprints for image authentication and steganalysis}, journal = {Proc. SPIE Conf. Security, Steganography, Watermarking of Multimedia Contents}, year = {2007}, month = {2007///}, abstract = {With growing popularity of digital imaging devices and low-cost image editing software, the integrity of imagecontent can no longer be taken for granted. This paper introduces a methodology for forensic analysis of digital camera images, based on the observation that many in-camera and post-camera processing operations leave distinct traces on digital images. We present methods to identify these intrinsic fingerprint traces of the various processing operations and employ them to verify the authenticity of digital data. We develop an explicit imaging model to characterize the properties that should be satisfied by a direct camera output, and model any further processing applied to the camera captured image by a manipulation filter. Utilizing the manipulation filter coefficients and reference patterns estimated from direct camera outputs using blind deconvolution techniques, the proposed methods are capable of detecting manipulations made by previously unseen operations and steganographic embedding. }, author = {Swaminathan,A. and Wu,M. and Liu,K. J.R} } @article {18236, title = {Joint Uplink and Downlink Optimization for Real-Time Multiuser Video Streaming Over WLANs}, journal = {Selected Topics in Signal Processing, IEEE Journal of}, volume = {1}, year = {2007}, month = {2007/08//}, pages = {280 - 294}, abstract = {In this paper, a network-aware and source-aware video streaming system is proposed to support interactive multiuser communications within single-cell and multicell IEEE 802.11 networks. Unlike the traditional streaming video services, the strict delay constraints of an interactive video streaming system pose more challenges. These challenges include the heterogeneity of uplink and downlink channel conditions experienced by different users, the multiuser resource allocation of limited radio resources, the incorporation of the cross-layer design, and the diversity of content complexities exhibited by different video sequences. With the awareness of video content and network resources, the proposed system integrates cross-layer error protection mechanism and performs dynamic resource allocation across multiple users. We formulate the proposed system as to minimize the maximal end-to-end expected distortion received by all users, subject to maximal transmission power and delay constraints. To reduce the high dimensionality of the search space, fast multiuser algorithms are proposed to find the near-optimal solutions. Compared to the strategy without dynamically and jointly allocating bandwidth resource for uplinks and downlinks, the proposed framework outperforms by 2.18 7.95 dB in terms of the average received PSNR of all users and by 3.82 11.50 dB in terms of the lowest received PSNR among all users. Furthermore, the proposed scheme can provide more uniform video quality for all users and lower quality fluctuation for each received video sequence.}, keywords = {802.11, allocation;image, allocation;real-time, communications;maximal, distortion;multiuser, end-to-end, error, expected, IEEE, LAN;, mechanism;downlink, multiuser, networks;WLAN;cross-layer, optimization;interactive, optimization;video, Protection, quality;video, resource, sequences;video, streaming, streaming;uplink, streaming;wireless, system;bandwidth, video}, isbn = {1932-4553}, doi = {10.1109/JSTSP.2007.901518}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @conference {12592, title = {Markerless Monocular Tracking of Articulated Human Motion}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {1}, year = {2007}, month = {2007/04//}, pages = {I-693 -I-696 - I-693 -I-696}, abstract = {This paper presents a method for tracking general 3D general articulated human motion using a single camera with unknown calibration data. No markers, special clothes, or devices are assumed to be attached to the subject. In addition, both the camera and the subject are allowed to move freely, so that long-term view-independent human motion tracking and recognition are possible. We exploit the fact that the anatomical structure of the human body can be approximated by an articulated blob model. The optical flow under scaled orthographic projection is used to relate the spatial-temporal intensity change of the image sequence to the human motion parameters. These motion parameters are obtained by solving a set of linear equations to achieve global optimization. The correctness and robustness of the proposed method are demonstrated using Tai Chi sequences}, keywords = {analysis;image, blob, camera;spatial-temporal, Chi, equations;markerless, flow;scaled, human, intensity;cameras;gait, model;articulated, monocular, MOTION, motion;global, optimization;human, orthographic, projection;single, recognition;image, sequence;linear, sequences;anatomical, sequences;optimisation;, structure;articulated, Tai, tracking;optical}, doi = {10.1109/ICASSP.2007.366002}, author = {Liu,Haiying and Chellapa, Rama} } @article {14088, title = {Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni}, journal = {BMC Genomics}, volume = {8}, year = {2007}, month = {2007///}, pages = {181 - 181}, abstract = {BACKGROUND:The parasitic trematode Schistosoma mansoni is one of the major causative agents of Schistosomiasis, a disease that affects approximately 200 million people, mostly in developing countries. Since much of the pathology is associated with eggs laid by the female worm, understanding the mechanisms involved in oogenesis and sexual maturation is an important step towards the discovery of new targets for effective drug therapy. It is known that the adult female worm only develops fully in the presence of a male worm and that the rates of oviposition and maturation of eggs are significantly increased by mating. In order to study gene transcripts associated with sexual maturation and oviposition, we compared the gene expression profiles of sexually mature and immature parasites using DNA microarrays.RESULTS:For each experiment, three amplified RNA microarray hybridizations and their dye swaps were analyzed. Our results show that 265 transcripts are differentially expressed in adult females and 53 in adult males when mature and immature worms are compared. Of the genes differentially expressed, 55\% are expressed at higher levels in paired females while the remaining 45\% are more expressed in unpaired ones and 56.6\% are expressed at higher levels in paired male worms while the remaining 43.4\% are more expressed in immature parasites. Real-time RT-PCR analysis validated the microarray results. Several new maturation associated transcripts were identified. Genes that were up-regulated in single-sex females were mostly related to energy generation (i.e. carbohydrate and protein metabolism, generation of precursor metabolites and energy, cellular catabolism, and organelle organization and biogenesis) while genes that were down-regulated related to RNA metabolism, reactive oxygen species metabolism, electron transport, organelle organization and biogenesis and protein biosynthesis.CONCLUSION:Our results confirm previous observations related to gene expression induced by sexual maturation in female schistosome worms. They also increase the list of S. mansoni maturation associated transcripts considerably, therefore opening new and exciting avenues for the study of the conjugal biology and development of new drugs against schistosomes.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-8-181}, url = {http://www.biomedcentral.com/1471-2164/8/181}, author = {Waisberg,Michael and Lobo,Francisco and Cerqueira,Gustavo and Passos,Liana and Carvalho,Omar and Franco,Gloria and El-Sayed, Najib M.} } @conference {18586, title = {MobCast: Overlay Architecture for Seamless IP Mobility using Scalable Anycast Proxies}, booktitle = {Wireless Communications and Networking Conference, 2007.WCNC 2007. IEEE}, year = {2007}, month = {2007/03//}, pages = {3872 - 3876}, abstract = {We propose a routing overlay system, MobCast, for simple and efficient routing to mobile hosts. Mobcast nodes advertise the same address space at each proxy location, and each mobile host is assigned a "universal" IP address from this address space, so packets sent to a mobile host{\textquoteright}s universal IP address automatically go to the nearest proxy on the overlay. The overlay then delivers the packets to the mobile host. Our architecture enables seamless mobility for both micro and macro mobility. While our initial design is not as mature as Mobile IP, it shows great promise to solve the traditional problems of ingress routing, firewalls, NATs, and rapid mobility with much lower complexity. We present our design as a scalable and deployable alternative to mobile IP. In this paper, we focus on describing the MobCast system architecture. We form our arguments for scalability, handoff-speed, and simplicity, and give our initial results for scalability. We postpone a detailed discussion of MobCast{\textquoteright}s security model for future work.}, keywords = {address space, handoff-speed, IP networks, MobCast, mobile hosts, mobile radio, overlay architecture, proxy location, routing overlay system, scalable anycast proxies, seamless IP mobility, telecommunication network routing, universal IP address}, doi = {10.1109/WCNC.2007.708}, author = {Lee,C.P. and Attrey,K. and Caballero,C. and Feamster, Nick and Mihail,M. and Copeland,J.A.} } @conference {13598, title = {Mobile Retriever - Finding Document with a Snapshot}, booktitle = {CBDAR}, year = {2007}, month = {2007/09//}, pages = {29 - 34}, abstract = {In this paper we describe a camera based document image retrieval system which is targeted toward camera phones. Our goal is to enable the device to identify which of a known set of documents it is {\textquotedblleft}looking at{\textquotedblright}. This paper provides two key contributions 1) a local context descriptor that effectively rules out irrelevant documents using only a small patch of the document image and 2) a layout verification approach that boosts the accuracy of retrieval even under severe degradation such as warping or crinkling. We have implemented the mobile retriever client on an iMate Jamin camera phone and tested it with a document database of 12742 pages. Experiments show that our verification approach clearly separates successful retrievals from unsuccessful retrievals.}, author = {Liu,Xu and David Doermann} } @conference {18002, title = {Models for advancing PRAM and other algorithms into parallel programs for a PRAM-On-Chip platform}, booktitle = {IN HANDBOOK OF PARALLEL COMPUTING: MODELS, ALGORITHMS AND APPLICATIONS, EDITORS}, year = {2007}, month = {2007///}, publisher = {CRC Press}, organization = {CRC Press}, abstract = {A bold vision that guided this work is as follows: (i) a parallel algorithms and programming course could become a standard course in every undergraduate computer science program, and (ii) this course could be coupled with a so-called PRAM-On-Chip architecture {\textemdash} a commodity high-end multi-core computer architecture. In fact, the current paper is a tutorial on how to convert PRAM algorithms intoefficient PRAM-On-Chip programs. Coupled with a text on PRAM algorithms as well as an available PRAM-On-Chip tool-chain, comprising a compiler and a simulator, the paper provides the missing link for upgrading a standard theoretical PRAM algorithms class to a parallel algorithms and programming class. Having demonstrated that such a course could cover similar programming projects and material to what is covered by a typical first serial algorithms and programming course, the paper suggests that parallel programming in the emerging multi-core era does not need to be more difficult than serial programming. If true, a powerful answer to the so-called parallel programming open problem is being provided. This open problem is currently the main stumbling block for the industry in getting the upcoming generation of multi-core architectures to improve single task completion time using easy-to-program application programmer interfaces. Known constraints of this open problem, such as backwards compatibility on serial code, are also addressed by the overall approach. More concretely, a widely used methodology for advancing parallel algorithmic thinking into parallel algorithms is revisited, and is extended into a methodology for advancing parallel algorithms to PRAM-On-Chip programs. A performance cost model for the PRAM-On-Chip is also presented. It uses as complexity metrics the length of sequence of round trips to memory (LSRTM) and queuing delay (QD) from memory access queues, in addition to standard PRAM computation costs. Highlighting the importance of LSRTM in determining performance is another contribution of the paper. Finally, some alternatives to PRAM algorithms, which, on one hand, are easier-to-think, but, on the other hand, suppress more architecture details, are also discussed. }, author = {Vishkin, Uzi and Caragea,George C. and Lee,Bryant} } @article {13831, title = {Multi-candidate reduction: Sentence compression as a tool for document summarization tasks}, journal = {Information Processing \& Management}, volume = {43}, year = {2007}, month = {2007/11//}, pages = {1549 - 1570}, abstract = {This article examines the application of two single-document sentence compression techniques to the problem of multi-document summarization{\textemdash}a {\textquotedblleft}parse-and-trim{\textquotedblright} approach and a statistical noisy-channel approach. We introduce the multi-candidate reduction (MCR) framework for multi-document summarization, in which many compressed candidates are generated for each source sentence. These candidates are then selected for inclusion in the final summary based on a combination of static and dynamic features. Evaluations demonstrate that sentence compression is a valuable component of a larger multi-document summarization framework.}, keywords = {Headline generation, Hidden Markov model, Parse-and-trim, Summarization}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2007.01.016}, url = {http://www.sciencedirect.com/science/article/pii/S0306457307000295}, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin and Schwartz,Richard} } @article {13834, title = {Multiple alternative sentence compressions for automatic text summarization}, journal = {Proceedings of DUC}, year = {2007}, month = {2007///}, abstract = {We perform multi-document summariza-tion by generating compressed versions of source sentences as summary candi- dates and using weighted features of these candidates to construct summaries. We combine a parse-and-trim approach with a novel technique for producing multiple alternative compressions for source sen- tences. In addition, we use a novel method for tuning the feature weights that maxi- mizes the change in the ROUGE-2 score (∆ROUGE) between the already existing summary state and the new state that re- sults from the addition of the candidate under consideration. We also describe ex- periments using a new paraphrase-based feature for redundancy checking. Finally, we present the results of our DUC2007 submissions and some ideas for future work. }, author = {Madnani,N. and Zajic, David and Dorr, Bonnie J and Ayan,N.F. and Jimmy Lin} } @conference {14338, title = {MyExperience: a system for in situ tracing and capturing of user feedback on mobile phones}, booktitle = {Proceedings of the 5th international conference on Mobile systems, applications and services}, series = {MobiSys {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {57 - 70}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper presents MyExperience, a system for capturing both objective and subjective in situ data on mobile computing activities. MyExperience combines the following two techniques: 1) passive logging of device usage, user context, and environmental sensor readings, and 2) active context-triggered user experience sampling to collect in situ, subjective user feedback. MyExperience currently runs on mobile phones and supports logging of more than 140 event types, including: 1) device usage such as communication, application usage, and media capture, 2) user context such as calendar appointments, and 3) environmental sensing such as Bluetooth and GPS. In addition, user experience sampling can be targeted to moments of interest by triggering off sensor readings. We present several case studies of field deployments on people{\textquoteright}s personal phones to demonstrate how MyExperience can be used effectively to understand how people use and experience mobile technology.}, keywords = {context-aware systems, experience sampling method (ESM), field studies, in situ evaluation, Mobile computing, SmartPhones, toolkit, usage logging, user surveys, user-centered design}, isbn = {978-1-59593-614-1}, doi = {10.1145/1247660.1247670}, url = {http://doi.acm.org/10.1145/1247660.1247670}, author = {Jon Froehlich and Chen,Mike Y. and Consolvo,Sunny and Harrison,Beverly and Landay,James A.} } @article {16077, title = {NetLens: Iterative Exploration of Content-Actor Network Data}, journal = {Information VisualizationInformation Visualization}, volume = {6}, year = {2007}, month = {2007/03/20/}, pages = {18 - 31}, abstract = {Networks have remained a challenge for information retrieval and visualization because of the rich set of tasks that users want to accomplish. This paper offers an abstract Content-Actor network data model, a classification of tasks, and a tool to support them. The NetLens interface was designed around the abstract Content-Actor network data model to allow users to pose a series of elementary queries and iteratively refine visual overviews and sorted lists. This enables the support of complex queries that are traditionally hard to specify. NetLens is general and scalable in that it applies to any data set that can be represented with our abstract data model. This paper describes the use of NetLens with a subset of the ACM Digital Library consisting of about 4000 papers from the CHI conference written by about 6000 authors, and reports on a usability study with nine participants.}, keywords = {content-actor network data, digital library, incremental data exploration, iterative query refinement, User interfaces}, isbn = {1473-8716, 1473-8724}, doi = {10.1057/palgrave.ivs.9500143}, url = {http://ivi.sagepub.com/content/6/1/18}, author = {Kang,Hyunmo and Plaisant, Catherine and Lee,Bongshin and Bederson, Benjamin B.} } @article {12214, title = {NetLens: iterative exploration of content-actor network data}, journal = {Information Visualization}, volume = {6}, year = {2007}, month = {2007///}, pages = {18 - 31}, author = {Kang,H. and Plaisant, Catherine and Lee,B. and Bederson, Benjamin B.} } @article {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 {18257, title = {Nonintrusive component forensics of visual sensors using output images}, journal = {Information Forensics and Security, IEEE Transactions on}, volume = {2}, year = {2007}, month = {2007/03//}, pages = {91 - 106}, abstract = {Rapid technology development and the widespread use of visual sensors have led to a number of new problems related to protecting intellectual property rights, handling patent infringements, authenticating acquisition sources, and identifying content manipulations. This paper introduces nonintrusive component forensics as a new methodology for the forensic analysis of visual sensing information, aiming to identify the algorithms and parameters employed inside various processing modules of a digital device by only using the device output data without breaking the device apart. We propose techniques to estimate the algorithms and parameters employed by important camera components, such as color filter array and color interpolation modules. The estimated interpolation coefficients provide useful features to construct an efficient camera identifier to determine the brand and model from which an image was captured. The results obtained from such component analysis are also useful to examine the similarities between the technologies employed by different camera models to identify potential infringement/licensing and to facilitate studies on technology evolution}, keywords = {ACQUISITION, array;color, authenticating, component, filter, forensics;patent, infringements;visual, Interpolation, manipulations;intellectual, modules;content, property, property;, protection;nonintrusive, rights, sensors;image, sensors;industrial, sources;color}, isbn = {1556-6013}, doi = {10.1109/TIFS.2006.890307}, author = {Swaminathan,A. and M. Wu and Liu,K. J.R} } @conference {13611, title = {Object Detection Using Shape Codebook}, booktitle = {British Machine Vision Conference (BMVC{\textquoteright}07)}, year = {2007}, month = {2007/12//}, publisher = {BMVC07}, organization = {BMVC07}, abstract = {This paper presents a method for detecting categories of objects in real-world images. Given training images of an object category, our goal is to recognize and localize instances of those objects in a candidate image. The main contribution of this work is a novel structure of the shape codebook for object detection. A shape codebook entry consists of two components: a shape codeword and a group of associated vectors that specify the object centroids. Like their counterpart in language, the shape codewords are simple and generic such that they can be easily extracted from most object categories. The associated vectors store the geometrical relationships between the shape codewords, which specify the characteristics of a particular object category. Thus they can be considered as the {\textquotedblleft}grammar{\textquotedblright} of the shape codebook. In this paper, we use Triple-Adjacent-Segments (TAS) extracted from image edges as the shape codewords. Object detection is performed in a probabilistic voting framework. Experimental results on public datasets show performance similar to the state-of-the-art, yet our method has significantly lower complexity and requires considerably less supervision in the training (We only need bounding boxes for a few training samples, do not need figure/ground segmentation and do not need a validation dataset).}, author = {Yu,Xiaodong and Li,Yi and Ferm{\"u}ller, Cornelia and David Doermann} } @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 {17528, title = {PeerWise discovery and negotiation of faster paths}, booktitle = {Proc. Workshop on Hot Topics in Networks (HotNets)}, year = {2007}, month = {2007///}, author = {Lumezanu,C. and Levin,D. and Spring, Neil} } @article {13153, title = {Poster Session 5: Matching and Registration-Simultaneous Appearance Modeling and Segmentation for Matching People Under Occlusion}, journal = {Lecture Notes in Computer Science}, volume = {4844}, year = {2007}, month = {2007///}, pages = {404 - 413}, author = {Lin,Z. and Davis, Larry S. and David Doermann and DeMenthon,D.} } @article {14508, title = {Predicting Protein-Protein Interactions Using Relational Features}, volume = {CS-TR-4909}, year = {2007}, month = {2007/01/07/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {Proteins play a fundamental role in ever y process within the cell.Understanding how proteins interact, and the functional units they are par t of, is important to furthering our knowledge of the entire biological process. There has been a growing amount of work, both experimental and computational, on determining the protein-protein interaction network. Recently researchers have had success looking at this as a relational learning problem. In this work, we further this investigation, proposing several novel relational features for predicting protein-protein interaction. These features can be used in any classifier. Our approach allows large and complex networks to be analyzed and is an alternative to using more expensive relational methods. We show that we are able to get an accuracy of 81.7\% when predicting new links from noisy high throughput data. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/7555}, author = {Licamele,Louis and Getoor, Lise} } @article {12795, title = {Priority and abstraction in process algebra}, journal = {Information and Computation}, volume = {205}, year = {2007}, month = {2007/09//}, pages = {1426 - 1458}, abstract = {More than 15 years ago, Cleaveland and Hennessy proposed an extension of the process algebra CCS in which some actions may take priority over others. The theory was equipped with a behavioral congruence based on strong bisimulation.This article gives a full account of the challenges in, and the solutions employed for, defining a semantic theory of observation congruence for this process algebra. A full-abstraction result is presented whose proof relies on a novel approach based on successive approximations for identifying the largest congruence contained in an intuitive but na{\~A}{\textasciimacron}ve equivalence. Prioritized observation congruence is also characterized equationally for the class of finite processes, while its utility for system verification is demonstrated by an illustrative example. }, keywords = {Axiomatization, Bisimulation, Full abstraction, Observation congruence, Priority, Process algebra}, isbn = {0890-5401}, doi = {10.1016/j.ic.2007.05.001}, url = {http://www.sciencedirect.com/science/article/pii/S0890540107000624}, author = {Cleaveland, Rance and L{\~A}{\textonequarter}ttgen,Gerald and Natarajan,V.} } @article {13400, title = {Report on the Fourth International Workshop on Data Management for Sensor Networks (DMSN 2007)}, journal = {SIGMOD Rec.}, volume = {36}, year = {2007}, month = {2007/12//}, pages = {53 - 55}, abstract = {Sensor networks enable an unprecedented level of access to the physical world, and hold tremendous potential to revolutionize many application domains. Research on sensor networks spans many areas of computer science, and there are now major conferences, e.g., IPSN and SenSys, devoted to sensor networks. However, there is no focused forum for discussion of early and innovative work on data management in sensor networks. The International Workshop on Data Management for Sensor Networks (DMSN), inaugurated in 2004, aims to fill this significant gap in the database and sensor network communities.}, isbn = {0163-5808}, doi = {10.1145/1361348.1361362}, url = {http://doi.acm.org/10.1145/1361348.1361362}, author = {Balazinska,Magdalena and Deshpande, Amol and Labrinidis,Alexandros and Luo,Qiong and Madden,Samuel and Yang,Jun} } @conference {12250, title = {Robust Routing with Unknown Traffic Matrices}, booktitle = {INFOCOM 2007. 26th IEEE International Conference on Computer Communications. IEEE}, year = {2007}, month = {2007/05//}, pages = {2436 - 2440}, abstract = {In this paper, we present an algorithm for intra-domain traffic engineering. We assume that the traffic matrix, which specifies traffic load between every source-destination pair in the network, is unknown and varies with time, but that always lies inside an explicitly defined region. Our goal is to compute a fixed robust routing with best worst case performance for all traffic matrices inside the bounding region. We formulate this problem as a semi-infinite programming problem. Then, we focus on a special case with practical merits, where (1) the traffic matrix region is assumed to be a polytope specified by a finite set of linear inequalities, and (2) our objective is to find the routing that minimizes the maximum link utilization. Under these assumptions, the problem can be formulated as a polynomial size linear programming (LP) problem with finite number of constraints. We further consider two specific set of constraints for the traffic matrix region. The first set is based on the hose model and limits the total traffic rate of network point of presence (PoP) nodes. The second set is based on the pipe model and limits the traffic between source-destination pairs. We study the effectiveness of each set of constraints using extensive simulations.}, keywords = {engineering;linear, inequalities;maximum, intradomain, linear, link, matrices;linear, matrix, network, nodes;polynomial, of, point, presence, problem;traffic, Programming, programming;semiinfinite, programming;telecommunication, region;unknown, routing;telecommunication, size, traffic, traffic;, utilization;network}, doi = {10.1109/INFCOM.2007.296}, author = {Tabatabaee,V. and Kashyap,A. and Bhattacharjee, Bobby and La,R.J. and Shayman,M.A.} } @article {14099, title = {Schistosoma mansoni genome: Closing in on a final gene set}, journal = {Experimental Parasitology}, volume = {117}, year = {2007}, month = {2007/11//}, pages = {225 - 228}, abstract = {The Schistosoma mansoni genome sequencing consortium has recently released the latest versions of the genome assembly as well as an automated preliminary gene structure annotation. The combined datasets constitute a vast resource for researchers to exploit in a variety of post-genomic studies with an emphasis of transcriptomic and proteomic tools. Here we present an innovative method used for combining diverse sources of evidence including ab initio gene predictions, protein and transcript sequence homologies, and cross-genome sequence homologies between S. mansoni and Schistosoma japonicum to define a comprehensive list of protein-coding genes.}, keywords = {Annotation, Gene finding, Genome, Schistosoma mansoni}, isbn = {0014-4894}, doi = {16/j.exppara.2007.06.005}, url = {http://www.sciencedirect.com/science/article/pii/S0014489407001683}, author = {Haas,Brian J. and Berriman,Matthew and Hirai,Hirohisa and Cerqueira,Gustavo G. and LoVerde,Philip T. and El-Sayed, Najib M.} } @article {12248, title = {A Secure DHT via the Pigeonhole Principle}, journal = {Technical Reports of the Computer Science Department, CS-TR-4884}, year = {2007}, month = {2007/09/24/}, abstract = {The standard Byzantine attack model assumes no more than some fixedfraction of the participants are faulty. This assumption does not accurately apply to peer-to-peer settings, where Sybil attacks and botnets are realistic threats. We propose an attack model that permits an arbitrary number of malicious nodes under the assumption that each node can be classified based on some of its attributes, such as autonomous system number or operating system, and that the number of classes with malicious nodes is bounded (e.g., an attacker may exploit at most a few operating systems at a time). In this model, we present a secure DHT, evilTwin, which replaces a single, large DHT with sufficiently many smaller instances such that it is impossible for an adversary to corrupt every instance. Our system ensures high availability and low-latency lookups, is easy to implement, does not require a complex Byzantine agreement protocol, and its proof of security is a straightforward application of the pigeonhole principle. The cost of security comes in the form of increased storage and bandwidth overhead; we show how to reduce these costs by replicating data and adaptively querying participants who historically perform well. We use implementation and simulation to show that evilTwin imposes a relatively small additional cost compared to conventional DHTs. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/7136}, author = {Baden,Randy and Bender,Adam and Levin,Dave and Sherwood,Rob and Spring, Neil and Bhattacharjee, Bobby} } @article {14892, title = {Shape Classification Using the Inner-Distance}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {29}, year = {2007}, month = {2007/02//}, pages = {286 - 299}, abstract = {Part structure and articulation are of fundamental importance in computer and human vision. We propose using the inner-distance to build shape descriptors that are robust to articulation and capture part structure. The inner-distance is defined as the length of the shortest path between landmark points within the shape silhouette. We show that it is articulation insensitive and more effective at capturing part structures than the Euclidean distance. This suggests that the inner-distance can be used as a replacement for the Euclidean distance to build more accurate descriptors for complex shapes, especially for those with articulated parts. In addition, texture information along the shortest path can be used to further improve shape classification. With this idea, we propose three approaches to using the inner-distance. The first method combines the inner-distance and multidimensional scaling (MDS) to build articulation invariant signatures for articulated shapes. The second method uses the inner-distance to build a new shape descriptor based on shape contexts. The third one extends the second one by considering the texture information along shortest paths. The proposed approaches have been tested on a variety of shape databases, including an articulated shape data set, MPEG7 CE-Shape-1, Kimia silhouettes, the ETH-80 data set, two leaf data sets, and a human motion silhouette data set. In all the experiments, our methods demonstrate effective performance compared with other algorithms}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;, Computer-Assisted;Imaging, Euclidean distance;articulation invariant signatures;computer vision;inner distance;multidimensional scaling;part structure;shape classification;shape descriptors;shape silhouette;shortest path;computational geometry;computer vision;graph theory;image cla, Three-Dimensional;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.41}, author = {Ling,Haibin and Jacobs, David W.} } @conference {13152, title = {Simultaneous appearance modeling and segmentation for matching people under occlusion}, booktitle = {Proceedings of the 8th Asian conference on Computer vision - Volume Part II}, series = {ACCV{\textquoteright}07}, year = {2007}, month = {2007///}, pages = {404 - 413}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, abstract = {We describe an approach to segmenting foreground regions corresponding to a group of people into individual humans. Given background subtraction and ground plane homography, hierarchical parttemplate matching is employed to determine a reliable set of human detection hypotheses, and progressive greedy optimization is performed to estimate the best configuration of humans under a Bayesian MAP framework. Then, appearance models and segmentations are simultaneously estimated in an iterative sampling-expectation paradigm. Each human appearance is represented by a nonparametric kernel density estimator in a joint spatial-color space and a recursive probability update scheme is employed for soft segmentation at each iteration. Additionally, an automatic occlusion reasoning method is used to determine the layered occlusion status between humans. The approach is evaluated on a number of images and videos, and also applied to human appearance matching using a symmetric distance measure derived from the Kullback-Leiber divergence.}, isbn = {3-540-76389-9, 978-3-540-76389-5}, url = {http://dl.acm.org/citation.cfm?id=1775728.1775777}, author = {Zhe Lin and Davis, Larry S. and David Doermann and DeMenthon,Daniel} } @article {18998, title = {Spliceosomal small nuclear RNA genes in 11 insect genomes}, journal = {RNARNA}, volume = {13}, year = {2007}, month = {2007/01/01/}, pages = {5 - 14}, abstract = {A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms}, keywords = {honeybee, Insecta, secondary structure, snRNA, spliceosomal snRNA, U12 introns}, isbn = {1355-8382, 1469-9001}, doi = {10.1261/rna.259207}, url = {http://rnajournal.cshlp.org/content/13/1/5}, author = {Mount, Stephen M. and Gotea,Valer and Lin,Chiao-Feng and Hernandez,Kristina and Maka{\l}owski,Wojciech} } @conference {16859, title = {STEWARD: architecture of a spatio-textual search engine}, booktitle = {Proceedings of the 15th annual ACM international symposium on Advances in geographic information systems}, series = {GIS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {25:1{\textendash}25:8 - 25:1{\textendash}25:8}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {STEWARD ("Spatio-Textual Extraction on the Web Aiding Retrieval of Documents"), a system for extracting, querying, and visualizing textual references to geographic locations in unstructured text documents, is presented. Methods for retrieving and processing web documents, extracting and disambiguating georeferences, and identifying geographic focus are described. A brief overview of STEWARD{\textquoteright}s querying capabilities, as well as the design of an intuitive user interface, are provided. Finally, several application scenarios and future extensions to STEWARD are discussed.}, keywords = {geocoding, spatio-textual search engine, STEWARD}, isbn = {978-1-59593-914-2}, doi = {10.1145/1341012.1341045}, url = {http://doi.acm.org/10.1145/1341012.1341045}, author = {Lieberman,Michael D. and Samet, Hanan and Sankaranarayanan,Jagan and Sperling,Jon} } @conference {16855, title = {STEWARD: demo of spatio-textual extraction on the web aiding the retrieval of documents}, booktitle = {Proceedings of the 8th annual international conference on Digital government research: bridging disciplines \& domains}, series = {dg.o {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {300 - 301}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {A spatio-textual search engine, termed "STEWARD" is demonstrated where document similarity is based on both the textual similarity as well as the spatial proximity of the locations in the document to the spatial search input. STEWARD{\textquoteright}s performance is enhanced by the presence of a document tagger that is able to identify textual references to geographical entities. The user-interface of STEWARD provides the ability to browse results, thereby making it a valuable "knowledge discovery" tool.}, keywords = {geocoding, spatio-textual search engine, STEWARD}, isbn = {1-59593-599-1}, url = {http://dl.acm.org/citation.cfm?id=1248460.1248529}, author = {Samet, Hanan and Lieberman,Michael D. and Sankaranarayanan,Jagan and Sperling,Jon} } @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 {14893, title = {Surface Dependent Representations for Illumination Insensitive Image Comparison}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {29}, year = {2007}, month = {2007/01//}, pages = {98 - 111}, abstract = {We consider the problem of matching images to tell whether they come from the same scene viewed under different lighting conditions. We show that the surface characteristics determine the type of image comparison method that should be used. Previous work has shown the effectiveness of comparing the image gradient direction for surfaces with material properties that change rapidly in one direction. We show analytically that two other widely used methods, normalized correlation of small windows and comparison of multiscale oriented filters, essentially compute the same thing. Then, we show that for surfaces whose properties change more slowly, comparison of the output of whitening filters is most effective. This suggests that a combination of these strategies should be employed to compare general objects. We discuss indications that Gabor jets use such a mixed strategy effectively, and we propose a new mixed strategy. We validate our results on synthetic and real images}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Subtraction Technique;, Computer-Assisted;Imaging, Gabor jets;Gaussian random surface;filter whitening;illumination;image comparison;image matching;lighting condition;multiscale oriented filter;surface dependent representation;image matching;image representation;Algorithms;Artificial Intelligence;Image En, Three-Dimensional;Information Storage and Retrieval;Lighting;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.250602}, author = {Osadchy,M. and Jacobs, David W. and Lindenbaum,M.} } @article {15295, title = {Syntactic sentence compression in the biomedical domain: facilitating access to related articles}, journal = {Information Retrieval}, volume = {10}, year = {2007}, month = {2007///}, pages = {393 - 414}, abstract = {We explore a syntactic approach to sentence compression in the biomedical domain, grounded in the context of result presentation for related article search in the PubMed search engine. By automatically trimming inessential fragments of article titles, a system can effectively display more results in the same amount of space. Our implemented prototype operates by applying a sequence of syntactic trimming rules over the parse trees of article titles. Two separate studies were conducted using a corpus of manually compressed examples from MEDLINE: an automatic evaluation using Bleu and a summative evaluation involving human assessors. Experiments show that a syntactic approach to sentence compression is effective in the biomedical domain and that the presentation of compressed article titles supports accurate {\textquotedblleft}interest judgments{\textquotedblright}, decisions by users as to whether an article is worth examining in more detail.}, doi = {10.1007/s10791-007-9029-5}, author = {Jimmy Lin and Wilbur,W. J} } @article {13154, title = {Task scheduling in large camera networks}, journal = {Computer Vision{\textendash}ACCV 2007}, year = {2007}, month = {2007///}, pages = {397 - 407}, abstract = {Visibility in architectural layouts affects humannavigation, so a suitable representation of visibility context is useful in understanding human activity. Motivated by studies of spatial behavior, we use a set of features from visibility analysis to represent spatial context in the interpretation of human activity. An agent{\textquoteright}s goal, belief about the world, trajectory and visible layout are considered to be random variables that evolve with time during the agent{\textquoteright}s movement, and are modeled in a Bayesian framework. We design a search-based task in a sprite-world, and compare the results of our framework to those of human subject experiments. Our findings confirm that knowledge of spatial layout improves human interpretations of the trajectories (implying that visibility context is useful in this task). Since our framework demonstrates performance close to that of human subjects with knowledge of spatial layout, our findings confirm that our model makes adequate use of visibility context. In addition, the representation we use for visibility context allows our model to generalize well when presented with new scenes. }, author = {Lim,S.N. and Davis, Larry S. and Mittal,A.} } @article {16322, title = {Techniques for Classifying Executions of Deployed Software to Support Software Engineering Tasks}, journal = {IEEE Transactions on Software Engineering}, volume = {33}, year = {2007}, month = {2007///}, pages = {287 - 304}, abstract = {There is an increasing interest in techniques that support analysis and measurement of fielded software systems. These techniques typically deploy numerous instrumented instances of a software system, collect execution data when the instances run in the field, and analyze the remotely collected data to better understand the system{\textquoteright}s in-the-field behavior. One common need for these techniques is the ability to distinguish execution outcomes (e.g., to collect only data corresponding to some behavior or to determine how often and under which condition a specific behavior occurs). Most current approaches, however, do not perform any kind of classification of remote executions and either focus on easily observable behaviors (e.g., crashes) or assume that outcomes{\textquoteright} classifications are externally provided (e.g., by the users). To address the limitations of existing approaches, we have developed three techniques for automatically classifying execution data as belonging to one of several classes. In this paper, we introduce our techniques and apply them to the binary classification of passing and failing behaviors. Our three techniques impose different overheads on program instances and, thus, each is appropriate for different application scenarios. We performed several empirical studies to evaluate and refine our techniques and to investigate the trade-offs among them. Our results show that 1) the first technique can build very accurate models, but requires a complete set of execution data; 2) the second technique produces slightly less accurate models, but needs only a small fraction of the total execution data; and 3) the third technique allows for even further cost reductions by building the models incrementally, but requires some sequential ordering of the software instances{\textquoteright} instrumentation.}, keywords = {execution classification, remote analysis/measurement.}, isbn = {0098-5589}, doi = {http://doi.ieeecomputersociety.org/10.1109/TSE.2007.1004}, author = {Haran,Murali and Karr,Alan and Last,Michael and Orso,Alessandro and Porter, Adam and Sanil,Ashish and Fouch?,Sandro} } @article {13880, title = {TREC 2007 ciQA Task: University of Maryland}, journal = {Proceedings of TREC}, year = {2007}, month = {2007///}, author = {Madnani,N. and Jimmy Lin and Dorr, Bonnie J} } @article {15289, title = {User simulations for evaluating answers to question series}, journal = {Information Processing \& Management}, volume = {43}, year = {2007}, month = {2007/05//}, pages = {717 - 729}, abstract = {Recently, question series have become one focus of research in question answering. These series are comprised of individual factoid, list, and {\textquotedblleft}other{\textquotedblright} questions organized around a central topic, and represent abstractions of user{\textendash}system dialogs. Existing evaluation methodologies have yet to catch up with this richer task model, as they fail to take into account contextual dependencies and different user behaviors. This paper presents a novel simulation-based methodology for evaluating answers to question series that addresses some of these shortcomings. Using this methodology, we examine two different behavior models: a {\textquotedblleft}QA-styled{\textquotedblright} user and an {\textquotedblleft}IR-styled{\textquotedblright} user. Results suggest that an off-the-shelf document retrieval system is competitive with state-of-the-art QA systems in this task. Advantages and limitations of evaluations based on user simulations are also discussed.}, keywords = {Evaluation, Question answering, User simulations}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2006.06.006}, url = {http://www.sciencedirect.com/science/article/pii/S0306457306000963}, author = {Jimmy Lin} } @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.} } @article {14572, title = {Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes}, journal = {Virology}, volume = {365}, year = {2007}, month = {2007/08/15/}, pages = {60 - 69}, abstract = {Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5{\textquoteright}-(T/C)CCTT-3{\textquoteright}. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13~bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.}, keywords = {Annotation of topoisomerase sites, Sequence specific recognition, Topoisomerase IB, Variola virus}, isbn = {0042-6822}, doi = {16/j.virol.2007.02.037}, url = {http://www.sciencedirect.com/science/article/pii/S0042682207001225}, author = {Minkah,Nana and Hwang,Young and Perry,Kay and Van Duyne,Gregory D. and Hendrickson,Robert and Lefkowitz,Elliot J. and Hannenhalli, Sridhar and Bushman,Frederic D.} } @conference {16074, title = {VAST 2007 Contest - Blue Iguanodon}, booktitle = {Visual Analytics Science and Technology, 2007. VAST 2007. IEEE Symposium on}, year = {2007}, month = {2007/11/30/1}, pages = {231 - 232}, abstract = {Visual analytics experts realize that one effective way to push the field forward and to develop metrics for measuring the performance of various visual analytics components is to hold an annual competition. The second visual analytics science and technology (VAST) contest was held in conjunction with the 2007 IEEE VAST symposium. In this contest participants were to use visual analytic tools to explore a large heterogeneous data collection to construct a scenario and find evidence buried in the data of illegal and terrorist activities that were occurring. A synthetic data set was made available as well as tasks. In this paper we describe some of the advances we have made from the first competition held in 2006.}, keywords = {activities;large, activities;visual, analytic, collection;terrorist, data, heterogeneous, illegal, interfaces;, tools;data, user, visualisation;graphical}, doi = {10.1109/VAST.2007.4389032}, author = {Grinstein,G. and Plaisant, Catherine and Laskowski,S. and O{\textquoteright}Connell,T. and Scholtz,J. and Whiting,M.} } @article {15657, title = {Vision Geometry XV}, journal = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series}, volume = {6499}, year = {2007}, month = {2007///}, author = {Latecki,L.J. and Mount, Dave and Wu,A. Y} } @conference {18758, title = {Algorithms for on-line monitoring of components in an optical tweezers-based assembly cell}, year = {2006}, month = {2006///}, pages = {1 - 13}, abstract = {Optical tweezers have emerged as a powerful tool for microand nanomanipulation. Using optical tweezers to perform auto- mated assembly requires on-line monitoring of components in the assembly workspace. This paper presents algorithms for estimat- ing positions and orientations of microscale and nanoscale com- ponents in the 3-Dimensional assembly workspace. Algorithms presented in this paper use images obtained by optical section microscopy. The images are first segmented to locate areas of in- terest and then image gradient information from the areas of in- terest is used to generate probable locations and orientations of components in the XY-plane. Finally, signature curves are com- puted and utilized to obtain component locations and orienta- tions in 3-D space. We have tested these algorithms with silica micro-spheres as well as metallic nanowires. We believe that the algorithms described in this paper will provide the foundation for realizing automated assembly operations in optical tweezers- based assembly cells. }, url = {http://www.glue.umd.edu/~skgupta/Publication/CIE06_Peng1.pdf}, author = {Peng,T. and Balijepalli,A. and Gupta,S.K. and LeBrun,T. W.} } @conference {13496, title = {ANew Algorithm for Detecting Text Line in Handwritten Documents}, booktitle = {10th International Workshop on Frontiers in Handwriting Recognition}, year = {2006}, month = {2006///}, pages = {35 - 40}, address = {La Baule, France}, abstract = {Curvilinear text line detection and segmentation in handwritten documents is a significant challenge for handwriting recognition. Given no prior knowledge of script, we model text line detection as an image segmentation problem by enhancing text line structure using a Gaussian window, and adopting the level set method to evolve text line boundaries. Experiments show that the proposed method achieves high accuracy for detecting text lines in both handwritten and machine printed documents with many scripts.}, author = {Li,Yi and Yefeng Zheng and David Doermann and Jaeger,Stefan} } @conference {13723, title = {Annotation compatibility working group report}, booktitle = {Proceedings of the Workshop on Frontiers in Linguistically Annotated Corpora 2006}, series = {LAC {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {38 - 53}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This report explores the question of compatibility between annotation projects including translating annotation formalisms to each other or to common forms. Compatibility issues are crucial for systems that use the results of multiple annotation projects. We hope that this report will begin a concerted effort in the field to track the compatibility of annotation schemes for part of speech tagging, time annotation, treebanking, role labeling and other phenomena.}, isbn = {1-932432-78-7}, url = {http://dl.acm.org/citation.cfm?id=1641991.1641997}, author = {Meyers,A. and Fang,A. C. and Ferro,L. and K{\"u}bler,S. and Jia-Lin,T. and Palmer,M. and Poesio,M. and Dolbey,A. and Schuler,K. K. and Loper,E. and Zinsmeister,H. and Penn,G. and Xue,N. and Hinrichs,E. and Wiebe,J. and Pustejovsky,J. and Farwell,D. and Hajicova,E. and Dorr, Bonnie J and Hovy,E. and Onyshkevych,B. A. and Levin,L.} } @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 {18008, title = {Bootstrapping free-space optical networks}, journal = {Selected Areas in Communications, IEEE Journal on}, volume = {24}, year = {2006}, month = {2006/12//}, pages = {13 - 22}, abstract = {We introduce a challenging problem in establishing and initially configuring or bootstrapping a Free Space Optical (FSO) network. In such networks, it is assumed that each communication node is a base station, including a router and wireless optical communications hardware, and its number of transceivers is limited. In addition, the FSO networks are characterized by narrow beam, directional links (e.g., operating at 1550 nm) and support up to Gbps data rates. The problem of initially configuring the transceivers to form a connected topology is NP-complete because of the transceiver limitation. What makes this problem even more challenging is the need to configure the transceiver in a "distributed" fashion, because a node can have only direct knowledge of its neighbors. We have developed a fully distributed approximation algorithm, which constructs a spanning tree with maximal node degree at most one larger than that in the optimal solution. Due to its distributed nature, this algorithm outperforms known serial algorithms. For a graph with 200 nodes generated in some randomized model, speed-ups greater than 6 have been demonstrated.}, keywords = {algorithm;free-space, algorithms;optical, approximation, communication;telecommunication, communications, configuration;randomized, FSO;base, hardware;distributed, model;spanning, network, network;network, node;connected, optical, router;optical, routing;telecommunication, searching;, station;bootstrapping;communication, topology;distributed, topology;transceivers;tree, transceiver, tree;wireless}, isbn = {0733-8716}, doi = {10.1109/JSAC.2006.258219}, author = {Liu,F. and Vishkin, Uzi and Milner,S.} } @article {18007, title = {A bootstrapping model for directional wireless networks}, journal = {Communications Letters, IEEE}, volume = {10}, year = {2006}, month = {2006/12//}, pages = {840 - 842}, abstract = {Initially configuring or bootstrapping a connected topology in directional wireless networks is a challenging problem, especially when nodes only have local connectivity information and a limited number of transceivers. This paper presents a scalable bootstrapping model which integrates: 1) a distributed bottom-up algorithm that constructs a spanning tree with degree at most one larger than the optimal 2) a resource discovery algorithm for efficient dissemination of local connectivity information, and 3) synchronization protocols to guarantee the efficient emergence of overall network connectivity from local interactions. We investigate the feasibility and scalability of the proposed model. Results are presented for different network systems, with varying size and signaling data rates.}, keywords = {(mathematics);, algorithm;resource, algorithm;spanning, bootstrapping, bottom-up, discovery, model;directional, network;distributed, networks;trees, protocols;protocols;radio, tree;synchronization, wireless}, isbn = {1089-7798}, doi = {10.1109/LCOMM.2006.060808}, author = {Milner,S. and Llorca,J. and Anibha,A. and Vishkin, Uzi} } @conference {12264, title = {CAM04-6: Single-Path Routing of Time-varying Traffic}, booktitle = {Global Telecommunications Conference, 2006. GLOBECOM {\textquoteright}06. IEEE}, year = {2006}, month = {2006/12/27/1}, pages = {1 - 6}, abstract = {We consider the problem of finding a single-path intra-domain routing for time-varying traffic. We characterize the traffic variations by a finite set of traffic profiles with given non-zero fractions of occurrence. Our goal is to optimize the average performance over all of these traffic profiles. We solve the optimal multi-path version of this problem using linear programming and develop heuristic single-path solutions using randomized rounding and iterated rounding. We analyze our single-path heuristic (finding the optimal single-path routing is NP-hard), and prove that the randomized rounding algorithm has a worst case performance bound of O(log(KN)/log(log(KN))) compared to the optimal multi-path routing with a high probability, where K is the number of traffic profiles, and N the number of nodes in the network. Further, our simulations show the iterated rounding heuristics perform close to the optimal multi-path routing on a wide range of measured ISP topologies, in both the average and the worst-case. Overall, these results are extremely positive since they show that in a wide-range of practical situations, it is not necessary to deploy multi-path routing; instead, an appropriately computed single-path routing is sufficient to provide good performance.}, keywords = {algorithm;linear, algorithm;time-varying, algorithms;telecommunication, bound;IP, case, complexity;iterative, intra-domain, IP, methods;linear, multipath, network, network;ISP, networks;Internet;computational, optimal, performance, problem;heuristic, profile;worst, programming;optimal, programming;probability;randomised, rounding, routing;iterated, routing;probability;randomized, routing;telecommunication, single-path, topology;NP-hard, topology;telecommunication, traffic, traffic;}, doi = {10.1109/GLOCOM.2006.29}, author = {Kashyap,A. and Bhattacharjee, Bobby and La,R. and Shayman,M. and Tabatabaee,V.} } @conference {13519, title = {Camera-Based Document Image Mosaicing}, booktitle = {ICPR{\textquoteright}06}, year = {2006}, month = {2006///}, pages = {476 - 479}, abstract = {In this paper we present an image mosaicing method for camera-captured document images. Our method is unique in not restricting the camera position, thus allowing greater flexibility than scanner-based or fixed-camera-based approaches. To accommodate for the perspective distortions introduced by varying poses, we implement a two-step image registration process that relies on accurately computing the projectivity between any two document images with an overlapping area as small as 10\%. In the overlapping area, we apply a sharpness based selection process to obtain seamless blending across the border and within. Experiments show that our approach can produce a very sharp, high resolution and accurate full page mosaic from small image patches of a document.}, author = {Liang,Jian and DeMenthon,Daniel and David Doermann} } @conference {18184, title = {Component Forensics of Digital Cameras: A Non-Intrusive Approach}, booktitle = {Information Sciences and Systems, 2006 40th Annual Conference on}, year = {2006}, month = {2006/03//}, pages = {1194 - 1199}, abstract = {This paper considers the problem of component forensics and proposes a methodology to identify the algorithms and parameters employed by various processing modules inside a digital camera. The proposed analysis techniques are non-intrusive, using only sample output images collected from the camera to find the color filter array pattern; and the algorithm and parameters of color interpolation employed in cameras. As demonstrated by various case studies in the paper, the features obtained from component forensic analysis provide useful evidence for such applications as detecting technology infringement, protecting intellectual property rights, determining camera source, and identifying image tampering.}, keywords = {analysis;image, approach;processing, array, camera;image, Color, colour, detection;optical, filter, filters;, forensics;detecting, identification;intellectual, infringement;digital, interpolation;component, intrusive, module;cameras;image, pattern;color, property, protection;non, right, sensors;interpolation;object, tampering, technology}, doi = {10.1109/CISS.2006.286646}, author = {Swaminathan,A. and Wu,M. and Liu,K. J.R} } @article {17952, title = {Computing and displaying intermolecular negative volume for docking}, journal = {Scientific visualization: the visual extraction of knowledge from data}, volume = {I}, year = {2006}, month = {2006///}, pages = {49 - 64}, abstract = {Protein docking is a Grand Challenge problem that is crucial to our understanding of biochemical processes. Several protein docking algorithms use shape complementarity as the primary criterion for evaluating the docking candidates. The intermolecular volume and area between docked molecules is useful as a measure of the shape complementarity. In this paper we discuss an algorithm for interactively computing intermolecular negative volume and the area of docking site using graphics hardware. We also present the design considerations for building an interactive 3D visualization tool for visualizing intermolecular negative volumes.}, doi = {10.1007/3-540-30790-7_4}, author = {Lee,C. and Varshney, Amitabh} } @article {13176, title = {Constructing task visibility intervals for video surveillance}, journal = {Multimedia systems}, volume = {12}, year = {2006}, month = {2006///}, pages = {211 - 226}, abstract = {Vision systems are increasingly being deployed to perform complex surveillance tasks. While improved algorithms are being developed to perform these tasks, it is also important that data suitable for these algorithms be acquired {\textendash} a non-trivial task in a dynamic and crowded scene viewed by multiple PTZ cameras. In this paper, we describe a real-time multi-camera system that collects images and videos of moving objects in such scenes, subject to task constraints. The system constructs {\textquotedblleft}task visibility intervals{\textquotedblright} that contain information about what can be sensed in future time intervals. Constructing these intervals requires prediction of future object motion and consideration of several factors such as object occlusion and camera control parameters. Such intervals can also be combined to form multi-task intervals, during which a single camera can collect videos suitable for multiple tasks simultaneously. Experimental results are provided to illustrate the system capabilities in constructing such task visibility intervals, followed by scheduling them using a greedy algorithm.}, author = {Lim,S.N. and Davis, Larry S. and Mittal,A.} } @article {12268, title = {Cooperative peer groups in NICE}, journal = {Computer Networks}, volume = {50}, year = {2006}, month = {2006/03/15/}, pages = {523 - 544}, abstract = {We present a distributed scheme for trust inference in peer-to-peer networks. Our work is in the context of the NICE system, which is a platform for implementing cooperative applications over the Internet. We describe a technique for efficiently storing user reputation information in a completely decentralized manner, and show how this information can be used to efficiently identify non-cooperative users in NICE. We present a simulation-based study of our algorithms, in which we show our scheme scales to thousands of users using modest amounts of storage, processing, and bandwidth at any individual node. Lastly we show that our scheme is robust and can form cooperative groups in systems where the vast majority of users are malicious.}, keywords = {distributed algorithms, P2P, Reputation base trust}, isbn = {1389-1286}, doi = {10.1016/j.comnet.2005.07.012}, url = {http://www.sciencedirect.com/science/article/pii/S1389128605002185}, author = {Sherwood,Rob and Lee,Seungjoon and Bhattacharjee, Bobby} } @article {17837, title = {Data redistribution and remote method invocation for coupled components}, journal = {Journal of Parallel and Distributed Computing}, volume = {66}, year = {2006}, month = {2006/07//}, pages = {931 - 946}, abstract = {With the increasing availability of high-performance massively parallel computer systems, the prevalence of sophisticated scientific simulation has grown rapidly. The complexity of the scientific models being simulated has also evolved, leading to a variety of coupled multi-physics simulation codes. Such cooperating parallel programs require fundamentally new interaction capabilities, to efficiently exchange parallel data structures and collectively invoke methods across programs. So-called {\textquotedblleft} M {\texttimes} N {\textquotedblright} research, as part of the common component architecture (CCA) effort, addresses these special and challenging needs, to provide generalized interfaces and tools that support flexible parallel data redistribution and parallel remote method invocation. Using this technology, distinct simulation codes with disparate distributed data decompositions can work together to achieve greater scientific discoveries.}, keywords = {Common component architecture, Model coupling, Parallel data redistribution, Parallel remote method invocation}, isbn = {0743-7315}, doi = {10.1016/j.jpdc.2005.12.009}, url = {http://www.sciencedirect.com/science/article/pii/S0743731506000700}, author = {Bertrand,Felipe and Bramley,Randall and Bernholdt,David E. and Kohl,James A. and Sussman, Alan and Larson,Jay W. and Damevski,Kostadin B.} } @conference {14498, title = {D-Dupe: An Interactive Tool for Entity Resolution in Social Networks}, booktitle = {Visual Analytics Science And Technology, 2006 IEEE Symposium On}, year = {2006}, month = {2006/11/31/2}, pages = {43 - 50}, abstract = {Visualizing and analyzing social networks is a challenging problem that has been receiving growing attention. An important first step, before analysis can begin, is ensuring that the data is accurate. A common data quality problem is that the data may inadvertently contain several distinct references to the same underlying entity; the process of reconciling these references is called entity-resolution. D-Dupe is an interactive tool that combines data mining algorithms for entity resolution with a task-specific network visualization. Users cope with complexity of cleaning large networks by focusing on a small subnetwork containing a potential duplicate pair. The subnetwork highlights relationships in the social network, making the common relationships easy to visually identify. D-Dupe users resolve ambiguities either by merging nodes or by marking them distinct. The entity resolution process is iterative: as pairs of nodes are resolved, additional duplicates may be revealed; therefore, resolution decisions are often chained together. We give examples of how users can flexibly apply sequences of actions to produce a high quality entity resolution result. We illustrate and evaluate the benefits of D-Dupe on three bibliographic collections. Two of the datasets had already been cleaned, and therefore should not have contained duplicates; despite this fact, many duplicates were rapidly identified using D-Dupe{\textquoteright}s unique combination of entity resolution algorithms within a task-specific visual interface}, keywords = {algorithm;data, analysis;social, computing;user, D-Dupe, interactive, interface;data, interfaces;, mining, mining;interactive, network, problem;entity, QUALITY, resolution;entity-resolution;social, sciences, systems;social, tool;data, visual, visualization;task-specific}, doi = {10.1109/VAST.2006.261429}, author = {Bilgic,M. and Licamele,L. and Getoor, Lise and Shneiderman, Ben} } @conference {12271, title = {Decentralized message ordering for publish/subscribe systems}, booktitle = {Proceedings of the ACM/IFIP/USENIX 2006 International Conference on Middleware}, series = {Middleware {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {162 - 179}, publisher = {Springer-Verlag New York, Inc.}, organization = {Springer-Verlag New York, Inc.}, address = {New York, NY, USA}, abstract = {We describe a method to order messages across groups in a publish/subscribe system without centralized control or large vector timestamps. We show that our scheme is practical---little state is required; that it is scalable---the maximum message load is limited by receivers; and that it performs well---the paths messages traverse to be ordered are not made much longer than necessary. Our insight is that only messages to groups that overlap in membership can be observed to arrive out of order: sequencing messages to these groups is sufficient to provide a consistent order, and when publishers subscribe to the groups to which they send, this message order is a causal order.}, url = {http://dl.acm.org/citation.cfm?id=1515984.1515997}, author = {Lumezanu,Cristian and Spring, Neil and Bhattacharjee, Bobby} } @conference {13536, title = {Detecting Text Line in Handwritten Documents}, booktitle = {ICPR{\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1030 - 1033}, address = {Hong Kong, China}, abstract = {Although detecting text lines in machine printed documents is typically considered as a solved problem, it is still a challenge to segment handwritten text lines in the general sense given no prior knowledge of scrip. This paper models text line detection as an image segmentation problem by enhancing text line structure using a Gaussian window, and adopting the level set method to evolve text line boundaries. Experiments show that the method, which is script independent, achieves high accuracy for detecting text lines in both handwritten and machine printed documents.}, author = {Li,Yi and Yefeng Zheng and David Doermann} } @article {17696, title = {EIGENTEST: A Test Matrix Generator for Large-Scale Eigenproblems}, volume = {UMIACS-TR-2006-07}, year = {2006}, month = {2006/02/13/T19:4}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Eigentest is a package that produces real test matrices with knowneigensystems. A test matrix, called an eigenmat, is generated in a factored form, in which the user can specify the eigenvalues and has some control over the condition of the eigenvalues and eigenvectors. An eigenmat A of order n requires only O(n) storage for its representation. Auxiliary programs permit the computation of (A - sI)*b, (A - sI){\textquoteright}*b, inv(A - sI)*b, and inv(A - sI)*b in O(n) operations. A special routine computes specified eigenvectors of an eigenmat and the condition of its eigenvalue. Thus eigenmats are suitable for testing algorithms based on Krylov sequences, as well as others based on matrix-vector products. This paper introduces the eigenmat and describes implementations in Fortran~77, Fortran~95, C, and Matlab. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3328}, author = {Lee,Che Rung and Stewart, G.W.} } @article {14068, title = {Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements}, journal = {Molecular and Biochemical Parasitology}, volume = {145}, year = {2006}, month = {2006/02//}, pages = {158 - 170}, abstract = {The ingi and L1Tc non-LTR retrotransposons - which constitute the ingi clade - are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5{\textquoteright}-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.}, keywords = {Degenerate retroelement, Evolution, Ingi, L1Tc, Leishmania major, Non-LTR retrotransposon, Retroposon, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/j.molbiopara.2005.09.017}, url = {http://www.sciencedirect.com/science/article/pii/S0166685105002963}, author = {Bringaud,Fr{\'e}d{\'e}ric and Ghedin,Elodie and Blandin,Ga{\"e}lle and Bartholomeu,Daniella C. and Caler,Elisabet and Levin,Mariano J. and Baltz,Th{\'e}o and El-Sayed, Najib M.} } @conference {16085, title = {Exploring content-actor paired network data using iterative query refinement with NetLens}, booktitle = {Digital Libraries, 2006. JCDL {\textquoteright}06. Proceedings of the 6th ACM/IEEE-CS Joint Conference on}, year = {2006}, month = {2006/06//}, pages = {372 - 372}, abstract = {Networks have remained a challenge for information retrieval and visualization because of the rich set of tasks that users want to accomplish. This paper demonstrates a tool, NetLens, to explore a content-actor paired network data model. The NetLens interface was designed to allow users to pose a series of elementary queries and iteratively refine visual overviews and sorted lists. This enables the support of complex queries that are traditionally hard to specify in node-link visualizations. NetLens is general and scalable in that it applies to any dataset that can be represented with our abstract content-actor data model}, keywords = {data, interface, libraries;query, management, model;data, models;data, NetLens;content-actor, network, pair, processing;user, query, refinement;data, retrieval;iterative, systems;, visualisation;digital, visualization;information}, doi = {10.1145/1141753.1141868}, author = {Lee,Bongshin and Kang,Hyunmo and Plaisant, Catherine and Bederson, Benjamin B.} } @conference {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} } @conference {15306, title = {Exploring the limits of single-iteration clarification dialogs}, booktitle = {Proceedings of the 29th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {469 - 476}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Single-iteration clarification dialogs, as implemented in the TREC HARD track, represent an attempt to introduce interaction into ad hoc retrieval, while preserving the many benefits of large-scale evaluations. Although previous experiments have not conclusively demonstrated performance gains resulting from such interactions, it is unclear whether these findings speak to the nature of clarification dialogs, or simply the limitations of current systems. To probe the limits of such interactions, we employed a human intermediary to formulate clarification questions and exploit user responses. In addition to establishing a plausible upper bound on performance, we were also able to induce an "ontology of clarifications" to characterize human behavior. This ontology, in turn, serves as the input to a regression model that attempts to determine which types of clarification questions are most helpful. Our work can serve to inform the design of interactive systems that initiate user dialogs.}, keywords = {interactive retrieval, intermediated search, TREC HARD}, isbn = {1-59593-369-7}, doi = {10.1145/1148170.1148251}, url = {http://doi.acm.org/10.1145/1148170.1148251}, author = {Jimmy Lin and Wu,Philip and Demner-Fushman,Dina and Abels,Eileen} } @conference {19493, title = {Eye of the Beholder: Phone-Based Text-Recognition for the Visually-Impaired}, booktitle = {2006 10th IEEE International Symposium on Wearable Computers}, year = {2006}, month = {2006///}, pages = {145 - 146}, abstract = {Blind and visually-impaired people cannot access essential information in the form of written text in our environment (e.g., on restaurant menus, street signs, door labels, product names and instructions, expiration dates). In this paper, we present and evaluate a mobile text-recognition system capable of extracting written information from a wide variety of sources and communicating it on-demand to the user. The user needs no additional hardware except an ordinary, Internet- enabled mobile camera-phone - a device that many visually-impaired individuals already own. This approach fills a gap in assistive technologies for the visually- impaired because it makes users aware of textual information not available to them through any other means.}, keywords = {CAMERAS, data mining, handicapped aids, Hardware, Image quality, Internet, Land mobile radio cellular systems, Mobile computing, mobile handsets, mobile text-recognition system, Optical character recognition software, phone-based text-recognition, Product safety, Text recognition, visually-impaired}, author = {Tudor Dumitras and Lee, M. and Quinones, P. and Smailagic, A. and Siewiorek, Dan and Narasimhan, P.} } @conference {12273, title = {Fair file swarming with FOX}, booktitle = {Proc. 5th IPTPS}, year = {2006}, month = {2006///}, abstract = {File swarming is a popular method of coordi-nated download by which peers obtain a file from an under- provisioned server. Critical problems arise within this domain when users act selfishly, yet most systems are built with altru- ism assumed. Working under the assumption that all peers are greedy, we introduce the Fair, Optimal eXchange (FOX) protocol. FOX, in addition to effective and robust application of the tit-for-tat incentive mechanism, provides theoretically optimal download times when everyone cooperates. Under our assumption of server and peer capabilities, we develop a strong threat model that provides peers with the incentives to not deviate from the protocol. From a theoretical perspective, we prove FOX{\textquoteright}s optimality and incentive properties, even when the network consists only of purely self-interested peers. We also discuss issues in implementing and deploying such a system, and address the cost of ensuring fairness in a domain where efficiency is so important. }, author = {Levin,D. and Sherwood,R. and Bhattacharjee, Bobby} } @article {14909, title = {First Steps Toward an Electronic Field Guide for Plants}, journal = {Taxon}, volume = {55}, year = {2006}, month = {2006///}, pages = {597 - 610}, abstract = {this paper, we will describe our progress towards building a digital collection of the Smithsonian{\textquoteright}s type specimens, developing recognition algorithms that can match an image of a leaf to the species of plant from which it comes, and designing user interfaces for interacting with an electronic field guide. To start, we are developing a prototype electronic field guide for the flora of Plummers Island, a small, well-studied island in the Potomac River. This prototype system contains multiple images for each of about 130 species of plants on the island, and should soon grow to cover all 200+ species currently recorded (Shetler et al., 2005). Images of full specimens are available, as well as images of isolated leaves of each species. A zoomable user interface allows a user to browse these images, zooming in on ones of interest. Visual recognition algorithms assist a botanist in locating the specimens that are most relevant to identify the species of a plant. The system currently runs on a small hand-held computer. We will describe the components of this prototype, and also describe some of the future challenges we anticipate if we are to provide botanists in the field with all the resources that are now currently available in the world{\textquoteright}s museums and herbaria. Type Specimen Digital Collection The first challenge in producing our electronic field guide is to create a digital collection covering all of the Smithsonian{\textquoteright}s 85,000 vascular plant type specimens. For each type specimen, the database should eventually include systematically acquired high-resolution digital images of the specimen, textual descriptions, links to decision trees, images of live plants, and 3D models. Figure 1: On the left, our set-up at the Smithsonian for digitally photographing type specimens. On the...}, author = {Haibin,Gaurav Agarwal and Agarwal,Gaurav and Ling,Haibin and Jacobs, David W. and Shirdhonkar,Sameer and Kress,W. John and Russell,Rusty and Belhumeur,Peter and Dixit,An and Feiner,Steve and Mahajan,Dhruv and Sunkavalli,Kalyan and Ramamoorthi,Ravi and White,Sean} } @conference {18755, title = {A flexible system framework for a nanoassembly cell using optical tweezers}, year = {2006}, month = {2006///}, address = {Philadelphia, Pennsylvania, USA}, abstract = {The optical tweezers instrument is a unique tool fordirected assembly of nanocomponents. In order to function as a viable nanomanufacturing tool, a software architecture is needed to run the optical tweezers hardware, provide an effective user interface, and allow automated operation. A flexible software system framework is described to utilize the optical tweezers hardware to its full potential. Initially we lay out the requirements for the system framework and define the broad architectural choices made while implementing the different modules. Implementation details of key system modules are then described. The flexible nature of the architecture is demonstrated by showing how a simulation module can be seamlessly included into the framework to replace the optical tweezers hardware as necessary. Finally, we show some representative assembly operations to demonstrate the capabilities of the system. }, url = {http://terpconnect.umd.edu/~skgupta/Publication/CIE06_Balijepalli.pdf}, author = {Balijepalli,A. and LeBrun,T. W. and Gupta,S.K.} } @article {17968, title = {Geometry-dependent lighting}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {12}, year = {2006}, month = {2006/04//march}, pages = {197 - 207}, abstract = {In this paper, we introduce geometry-dependent lighting that allows lighting parameters to be defined independently and possibly discrepantly over an object or scene based on the local geometry. We present and discuss light collages, a lighting design system with geometry-dependent lights for effective feature-enhanced visualization. Our algorithm segments the objects into local surface patches and places lights that are locally consistent but globally discrepant to enhance the perception of shape. We use spherical harmonics for efficiently storing and computing light placement and assignment. We also outline a method to find the minimal number of light sources sufficient to illuminate an object well with our globally discrepant lighting approach.}, keywords = {Computer-Assisted;Imaging, feature-enhanced visualization;geometry-dependent light;light collage;light placement;lighting design system;computational geometry;data visualisation;lighting;Algorithms;Computer Graphics;Image Enhancement;Image Interpretation, Three-Dimensional;Information Storage and Retrieval;Lighting;User-Computer Interface;}, isbn = {1077-2626}, doi = {10.1109/TVCG.2006.30}, author = {Lee,C. H and Hao,X. and Varshney, Amitabh} } @conference {14007, title = {Headphone-Based Reproduction of 3D Auditory Scenes Captured by Spherical/Hemispherical Microphone Arrays}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {We propose a method to reproduce 3D auditory scenes captured by spherical microphone arrays over headphones. This algorithm employs expansions of the captured sound and the head related transfer function over the sphere and uses the orthonormality of the spherical harmonics. Using a spherical microphone array, we first record the 3D auditory scene, then the recordings are spatially filtered and reproduced through headphones in the orthogonal beam-space of the head related transfer functions (HRTFs). We use the KEMAR HRTF measurements to verify our algorithm}, keywords = {3D, analysis;headphones;microphone, arrays;orthogonal, arrays;spatial, auditory, beam-space;spatial, filter;spherical, filters;, function;headphone-based, harmonics;array, microphone, processing;audio, processing;harmonic, related, reproduction;hemispherical, scenes;head, signal, transfer}, doi = {10.1109/ICASSP.2006.1661281}, author = {Zhiyun Li and Duraiswami, Ramani} } @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.} } @article {14623, title = {Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements}, journal = {Osteoarthritis and Cartilage}, volume = {14}, year = {2006}, month = {2006/08//}, pages = {830 - 838}, abstract = {SummaryObjectiveTo better understand transcription regulation of osteoarthritis (OA) by examining common promoter motifs in canine osteoarthritic genes, to identify other genes containing these motifs and to assess the conservation of these motifs between canine, human, mouse and rat. Design Differentially expressed transcripts in canine OA were mapped to the human genome. We thus identified 20 orthologous human transcripts representing 19 up-regulated genes and 62 orthologous transcripts representing 60 down-regulated genes. The 5\&$\#$xa0;kbp upstream regions of these transcripts were used to identify binding sites and build promoter models based on those sites. The human genome was subsequently searched for other transcripts likely to be regulated by the same promoter models. Orthologous transcripts were then identified in canine, rat and mouse for determination of potential cross-species conservation of binding sites comprising the promoter model. Results Four promoter models containing 5{\textendash}6 transcripts and 5{\textendash}8 common transcription factor binding sites were developed. They include binding sites for AP-4, AP-2α and γ, and E2F. Several hundred other human genes were found to contain these promoter motifs. Furthermore these motifs were significantly over represented in the orthologous genes in canine, rat and mouse genomes. Conclusions We have developed and applied a computational methodology to identify common promoter elements implicated in OA and shared amongst four higher vertebrates. The transcription factors associated with these binding sites and other genes driven by these promoter motifs have been implicated in OA, chondrocyte development and with other biological factors involved in the disease. }, keywords = {Chondrocyte, Gene expression, Osteoarthritis, Promoter}, isbn = {1063-4584}, doi = {10.1016/j.joca.2006.02.007}, url = {http://www.sciencedirect.com/science/article/pii/S1063458406000379}, author = {Hannenhalli, Sridhar and Middleton,R.P. and Levy,S. and Perroud,B. and Holzwarth,J.A. and McDonald,K. and Hannah,S.S.} } @article {15590, title = {Image fusion using cokriging}, journal = {Geosci. and Remote Sens. Symp., 2006. IGARSS 2006. IEEE Int. Conf. on}, year = {2006}, month = {2006///}, pages = {2518 - 2521}, author = {Memarsadeghi,N. and Le Moigne,J. and Mount, Dave} } @conference {15543, title = {Image Registration and Fusion Studies for the Integration of Multiple Remote Sensing Data}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {The future of remote sensing will see the development of spacecraft formations, and with this development will come a number of complex challenges such as maintaining precise relative position and specified attitudes. At the same time, there will be increasing needs to understand planetary system processes and build accurate prediction models. One essential technology to accomplish these goals is the integration of multiple source data. For this integration, image registration and fusion represent the first steps and need to be performed with very high accuracy. In this paper, we describe studies performed in both image registration and fusion, including a modular framework that was built to describe registration algorithms, a Web-based image registration toolbox, and the comparison of several image fusion techniques using data from the EO-1/ALI and Hyperion sensors}, keywords = {ALI, EO-1, fusion studies, geophysical signal processing, Hyperion sensors, image registration, Internet, multiple remote sensing data, multiple source data, Remote sensing, Web-based image registration toolbox}, doi = {10.1109/ICASSP.2006.1661494}, author = {Le Moigne,J. and Cole-Rhodes,A. and Eastman,R. and Jain,P. and Joshua,A. and Memarsadeghi,N. and Mount, Dave and Netanyahu,N. and Morisette,J. and Uko-Ozoro,E.} } @conference {18226, title = {Image Tampering Identification using Blind Deconvolution}, booktitle = {Image Processing, 2006 IEEE International Conference on}, year = {2006}, month = {2006/10//}, pages = {2309 - 2312}, abstract = {Digital images have been used in growing number of applications from law enforcement and surveillance, to medical diagnosis and consumer photography. With such widespread popularity and the presence of low-cost image editing softwares, the integrity of image content can no longer be taken for granted. In this paper, we propose a novel technique based on blind deconvolution to verify image authenticity. We consider the direct output images of a camera as authentic, and introduce algorithms to detect further processing such as tampering applied to the image. Our proposed method is based on the observation that many tampering operations can be approximated as a combination of linear and non-linear components. We model the linear part of the tampering process as a filter, and obtain its coefficients using blind deconvolution. These estimated coefficients are then used to identify possible manipulations. We demonstrate the effectiveness of the proposed image authentication technique and compare our results with existing works}, keywords = {(access, approximation;blind, authentication;image, coding;, compression;deconvolution;filtering, control);data, deconvolution;camera;consumer, diagnosis;surveillance;tampering, editing, identification;approximation, images;filter, photography;digital, process;image, softwares;medical, theory;biometrics, theory;image}, doi = {10.1109/ICIP.2006.312848}, author = {Swaminathan,A. and M. Wu and Liu,K. J.R} } @conference {13574, title = {Imaging as an Alternative Data Channel for Camera Phones}, booktitle = {ACM International Conference Proceeding Series; Proceedings of the 5th International Conference on Mobile and Ubiquitous Multimedia}, year = {2006}, month = {2006/12//}, pages = {No. 5 - No. 5}, abstract = {In this paper, we demonstrate a solution to use cameras to download data to cell phones as an alternative to existing wireless (CDMA/GPRS, BlueTooth), infrared or cable connections. In our method the data is encoded as a sequence of images, which can be displayed on any flat display, captured by users with their camera phones, and decoded by pre-embedded software. To solve this problem we need to be able to (1) encode arbitrary data as a sequence of images, (2) process captured images under various lighting variations and perspective distortions while maintaining real-time performance, and (3) decode the processed images robustly even when partial data is lost. In the paper we address these challenges in detail and present our solution. We have implemented a prototype which allows users to successfully download various types of files, including pictures, ring tones and Java programs to the camera phones. We discuss the limitations of our solution, and future works to overcome these limitations.}, author = {Liu,Xu and Huiping Li and David Doermann} } @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} } @conference {14547, title = {Improved lower and upper bounds for universal TSP in planar metrics}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {649 - 658}, author = {Hajiaghayi, Mohammad T. and Kleinberg,R. and Leighton,T.} } @article {18231, title = {JET: dynamic join-exit-tree amortization and scheduling for contributory key management}, journal = {IEEE/ACM Trans. Netw.}, volume = {14}, year = {2006}, month = {2006/10//}, pages = {1128 - 1140}, abstract = {In secure group communications, the time cost associated with key updates in the events of member join and departure is an important aspect of quality of service, especially in large groups with highly dynamic membership. To achieve better time efficiency, we propose a join-exit-tree (JET) key management framework. First, a special key tree topology with join and exit subtrees is introduced to handle key updates for dynamic membership. Then, optimization techniques are employed to determine the capacities of join and exit subtrees for achieving the best time efficiency, and algorithms are designed to dynamically update the join and exit trees. We show that, on average, the asymptotic time cost for each member join/departure event is reduced to O(log (log n)) from the previous cost of O(log n), where n is the group size. Our experimental results based on simulated user activities as well as the real MBone data demonstrate that the proposed JET scheme can significantly improve the time efficiency, while maintaining low communication and computation cost, of tree-based contributory key management.}, keywords = {contributory key management, dynamic tree topology, secure group communications, time efficiency}, isbn = {1063-6692}, doi = {10.1109/TNET.2006.882851}, url = {http://dx.doi.org/10.1109/TNET.2006.882851}, author = {Mao,Yinian and Sun,Yan and M. Wu and Liu,K. J.R} } @article {13812, title = {Leveraging recurrent phrase structure in large-scale ontology translation}, journal = {Proceedings of the 11th Annual Conference of the European Association for Machine Translation}, year = {2006}, month = {2006///}, abstract = {This paper presents a process for leveraging structural relationships and reusablephrases when translating large-scale ontologies. Digital libraries are becoming more and more prevalent. An important step in providing universal access to such material is to pro- vide multi-lingual access to the underlying principles of organization via ontologies, thesauri, and controlled vocabularies. Machine translation of these resources requires high accuracy and a deep vocabulary. Human input is often required, but full manual translation can be slow and expensive. We report on a cost-effective approach to ontology translation. We describe our technique of prioritization, our process of collecting aligned translations and generating a new lexicon, and the resulting improvement to translation system output. Our preliminary evaluation indicates that this technique provides significant cost savings for human-assisted translation. The process we developed can be applied to ontologies in other domains and is easily incorporated into other translation systems. }, author = {Murray,G. C and Dorr, Bonnie J and Jimmy Lin and Haji{\v c},J. and Pecina,P.} } @conference {13813, title = {Leveraging reusability: cost-effective lexical acquisition for large-scale ontology translation}, 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 = {945 - 952}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Thesauri and ontologies provide important value in facilitating access to digital archives by representing underlying principles of organization. Translation of such resources into multiple languages is an important component for providing multilingual access. However, the specificity of vocabulary terms in most ontologies precludes fully-automated machine translation using general-domain lexical resources. In this paper, we present an efficient process for leveraging human translations when constructing domain-specific lexical resources. We evaluate the effectiveness of this process by producing a probabilistic phrase dictionary and translating a thesaurus of 56,000 concepts used to catalogue a large archive of oral histories. Our experiments demonstrate a cost-effective technique for accurate machine translation of large ontologies.}, doi = {10.3115/1220175.1220294}, url = {http://dx.doi.org/10.3115/1220175.1220294}, author = {Murray,G. Craig and Dorr, Bonnie J and Jimmy Lin and Haji{\v c},Jan and Pecina,Pavel} } @inbook {13825, title = {Machine Translation: Interlingual Methods}, booktitle = {Encyclopedia of Language \& Linguistics (Second Edition)Encyclopedia of Language \& Linguistics (Second Edition)}, year = {2006}, month = {2006///}, pages = {383 - 394}, publisher = {Elsevier}, organization = {Elsevier}, address = {Oxford}, abstract = {An interlingua is a notation for representing the content of a text that abstracts away from the characteristics of the language itself and focuses on the meaning (semantics) alone. Interlinguas are typically used as pivot representations in machine translation, allowing the contents of a source text to be generated in many different target languages. Because of the complexities involved, few interlinguas are more than demonstration prototypes, and only one has been used in a commercial MT system. In this article, we define the components of an interlingua and the principal issues faced by designers and builders of interlinguas and interlingua MT systems, illustrating with examples from operational systems and research prototypes. We discuss current efforts to annotate texts with interlingua-based information.}, keywords = {approximate interlingua, compositionality, conceptual knowledge, cross-language divergences, interlingua, interlingual speech translation, language-independent representation, lexical-conceptual structure, Machine translation, ontology, predicate-argument structure, semantic annotation, semantic frames, semantic zones, text-meaning representations, THEMATIC ROLES}, isbn = {978-0-08-044854-1}, url = {http://www.sciencedirect.com/science/article/pii/B0080448542009391}, author = {Dorr, Bonnie J and Hovy,E. and Levin,L.}, editor = {Editor-in-Chief:~~ Keith Brown} } @conference {17285, title = {Making a difference: integrating socially relevant projects into HCI teaching}, booktitle = {CHI {\textquoteright}06 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {41 - 44}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Enriching courses on human-computer interaction with socially-relevant projects provides a compelling opportunity for students to improve their education and make socially beneficial contributions. By having clearly defined user communities outside the classroom, students have the chance to practice their interview, observation, and usability testing skills, while developing projects that continue beyond the semester. These projects often give students life-changing exposure to genuine needs and impressive results to include in their portfolio when seeking employment. Educators will present their strategies for arranging, supervising, and grading these projects. Students will describe their experience and how it influenced them.}, keywords = {education, making a difference, relevance, service learning, social impact, team projects}, isbn = {1-59593-298-4}, doi = {10.1145/1125451.1125463}, url = {http://doi.acm.org/10.1145/1125451.1125463}, author = {Shneiderman, Ben and Bishop,Ann and Friedman,Batya and Lazar,Jonathan and Marsden,Gary and Nass,Cliff} } @article {12274, title = {Measurement-based optimal routing on overlay architectures for unicast sessions}, journal = {Computer Networks}, volume = {50}, year = {2006}, month = {2006///}, pages = {1938 - 1951}, abstract = {We propose a measurement-based routing algorithm to load-balance intradomain traffic along multiple paths for multi-ple unicast sources. Multiple paths are established using overlay nodes. The distributed algorithm is derived from simul- taneous perturbation stochastic approximation (SPSA) and does not assume that the gradient of an analytical cost function is known. Instead, we rely on (potentially) noisy estimates from local measurements. Using the analytical model presented in the paper, we first show the almost sure convergence of the algorithm to the optimal solution under a decreas- ing step size policy (as with a standard SPSA model). Motivated by practical concerns, we next consider the constant step size case, for which we establish weak convergence. We provide simulation results to demonstrate the advantages of our proposed algorithm under various network scenarios, and also present a comparative study with MATE (an existing opti- mal routing algorithm) }, author = {La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @article {15294, title = {Methods for automatically evaluating answers to complex questions}, journal = {Information Retrieval}, volume = {9}, year = {2006}, month = {2006///}, pages = {565 - 587}, abstract = {Evaluation is a major driving force in advancing the state of the art in language technologies. In particular, methods for automatically assessing the quality of machine output is the preferred method for measuring progress, provided that these metrics have been validated against human judgments. Following recent developments in the automatic evaluation of machine translation and document summarization, we present a similar approach, implemented in a measure called POURPRE, an automatic technique for evaluating answers to complex questions based on n-gram co-occurrences between machine output and a human-generated answer key. Until now, the only way to assess the correctness of answers to such questions involves manual determination of whether an information {\textquotedblleft}nugget{\textquotedblright} appears in a system{\textquoteright}s response. The lack of automatic methods for scoring system output is an impediment to progress in the field, which we address with this work. Experiments with the TREC 2003, TREC 2004, and TREC 2005 QA tracks indicate that rankings produced by our metric correlate highly with official rankings, and that POURPRE outperforms direct application of existing metrics.}, doi = {10.1007/s10791-006-9003-7}, author = {Jimmy Lin and Demner-Fushman,D.} } @article {18011, title = {Models for Advancing PRAM and Other Algorithms into Parallel Programs for a PRAM-On-Chip Platform}, year = {2006}, month = {2006/05/18/}, abstract = {A bold vision that guided this work is as follows: (i) a parallel algorithms and programming course could become a standard course in every undergraduate computer science program, and (ii) this course could be coupled with a so-called PRAM-On-Chip architecture --- a commodity high-end multi-core computer architecture.In fact, the current paper is a tutorial on how to convert PRAM algorithms into efficient PRAM-On-Chip programs. Coupled with a text on PRAM algorithms as well as an available PRAM-On-Chip tool-chain, comprising a compiler and a simulator, the paper provides the missing link for upgrading a standard theoretical PRAM algorithms class to a parallel algorithms and programming class. Having demonstrated that such a course could cover similar programming projects and material to what is covered by a typical first serial algorithms and programming course, the paper suggests that parallel programming in the emerging multi-core era does not need to be more difficult than serial programming. If true, a powerful answer to the so-called parallel programming open problem is being provided. This open problem is currently the main stumbling block for the industry in getting the upcoming generation of multi-core architectures to improve single task completion time using easy-to-program application programmer interfaces. Known constraints of this open problem, such as backwards compatibility on serial code, are also addressed by the overall approach. More concretely, a widely used methodology for advancing parallel algorithmic thinking into parallel algorithms is revisited, and is extended into a methodology for advancing parallel algorithms to PRAM-On-Chip programs. A performance cost model for the PRAM-On-Chip is also presented. It uses as complexity metrics the length of sequence of round trips to memory (LSRTM) and queuing delay (QD) from memory access queues, in addition to standard PRAM computation costs. Highlighting the importance of LSRTM in determining performance is another contribution of the paper. Finally, some alternatives to PRAM algorithms, which, on one hand, are easier-to-think, but, on the other hand, suppress more architecture details, are also discussed. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3338}, author = {Vishkin, Uzi and Caragea,George C. and Lee,Bryant} } @article {13605, title = {Mosaicing of Camera-captured Documents Without Pose Restriction}, journal = {Computer Vision and Image Understanding}, year = {2006}, month = {2006///}, abstract = {In this paper we present an image mosaicing method for camera-captured documents. Our method is unique in not restricting the camera position, thus allowing greater flexibility than approaches using scanner or fixed-cameras. To accommodate for the perspective distortions introduced by varying poses, we implement a two step image registration process that accurately computes the projectivity between any two document images with an overlapping area that may be as small as 10\%. In the overlapping area, we apply a sharpness based selection process to obtain seamless composition across the border and within. Experiments show that our approach can produce a very sharp, high resolution and accurate full page mosaic from small image patches of a document captured from unconstrained positions.}, author = {Liang,Jian and DeMenthon,Daniel and David Doermann} } @conference {12616, title = {Motion Based Correspondence for 3D Tracking of Multiple Dim Objects}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {2}, year = {2006}, month = {2006/05//}, pages = {II - II}, abstract = {Tracking multiple objects in a video is a demanding task that is frequently encountered in several systems such as surveillance and motion analysis. Ability to track objects in 3D requires the use of multiple cameras. While tracking multiple objects using multiples video cameras, establishing correspondence between objects in the various cameras is a nontrivial task. Specifically, when the targets are dim or are very far away from the camera, appearance cannot be used in order to establish this correspondence. Here, we propose a technique to establish correspondence across cameras using the motion features extracted from the targets, even when the relative position of the cameras is unknown. Experimental results are provided for the problem of tracking multiple bees in natural flight using two cameras. The reconstructed 3D flight paths of the bees show some interesting flight patterns}, keywords = {3D, analysis;motion, analysis;video, based, cameras;feature, correspondence;motion, dim, extraction;image, extraction;multiple, features, MOTION, objects;video, processing;, signal, tracking;motion}, doi = {10.1109/ICASSP.2006.1660431}, author = {Veeraraghavan,A. and Srinivasan, M. and Chellapa, Rama and Baird, E. and Lamont, R.} } @article {18253, title = {Multiuser cross-layer resource allocation for video transmission over wireless networks}, journal = {Network, IEEE}, volume = {20}, year = {2006}, month = {2006/04//march}, pages = {21 - 27}, abstract = {With the advancement of video-compression technology and the wide deployment of wireless networks, there is an increasing demand for wireless video communication services, and many design challenges remain to be overcome. In this article, we discuss how to dynamically allocate resources according to the changing environments and requirements, so as to improve the overall system performance and ensure individual quality of service (QoS). Specifically, we consider two aspects with regard to design issues: cross-layer design, which jointly optimizes resource utilization from the physical layer to the application layer, and multiuser diversity, which explores source and channel heterogeneity for different users. We study how to efficiently transmit multiple video streams, encoded by current and future video codecs, over resource-limited wireless networks such as 3G/4G cellular system and future wireless local/metropolitan area networks (WLANs/WMANs)}, keywords = {3G, allocation;multiuser, allocation;video, cellular, channels;quality, codecs;video, coding;video, communication;4G, communication;data, compression;diversity, cross-layer, diversity;physical, layer;multiple, layer;quality, mobile, networks;3G, of, reception;multiuser, resource, service;resource, service;video, streaming;, streams;multiuser, system;4G, system;QoS;application, technology;wireless, transmission;video-compression, video}, isbn = {0890-8044}, doi = {10.1109/MNET.2006.1607892}, author = {Su,Guan-Ming and Man,Zhu and M. Wu and Liu,K. J.R} } @article {18254, title = {Multiuser distortion management of layered video over resource limited downlink multicode-CDMA}, journal = {Wireless Communications, IEEE Transactions on}, volume = {5}, year = {2006}, month = {2006/11//}, pages = {3056 - 3067}, abstract = {Transmitting multiple real-time encoded videos to multiple users over wireless cellular networks is a key driving force for developing broadband technology. We propose a new framework to transmit multiple users{\textquoteright} video programs encoded by MPEG-4 FGS codec over downlink multicode CDMA networks in real time. The proposed framework jointly manages the rate adaptation of source and channel coding, CDMA code allocation, and power control. Subject to the limited system resources, such as the number of pseudo-random codes and the maximal power for CDMA transmission, we develop an adaptive scheme of distortion management to ensure baseline video quality for each user and further reduce the overall distortion received by all users. To efficiently utilize system resources, the proposed scheme maintains a balanced ratio between the power and code usages. We also investigate three special scenarios where demand, power, or code is limited, respectively. Compared with existing methods in the literature, the proposed algorithm can reduce the overall system{\textquoteright}s distortion by 14\% to 26\%. In the demand-limited case and the code-limited but power-unlimited case, the proposed scheme achieves the optimal solutions. In the power-limited but code-unlimited case, the proposed scheme has a performance very close to a performance upper bound}, keywords = {(mobile, access;combined, allocation;broadband, case;layered, CDMA, cellular, code, codes;radio, codes;real-time, codes;telecommunication, coding;mobility, coding;video, coding;wireless, communication;, control;pseudo-random, control;pseudonoise, control;video, distortion, division, downlink, encoded, limited, links;random, management, management;power, multicode-CDMA;source-channel, multiple, networks;broadband, networks;cellular, radio);power, radio;code, source-channel, technology;code-unlimited, video;multiuser, videos;resource}, isbn = {1536-1276}, doi = {10.1109/TWC.2006.258231}, author = {Han,Z. and Su,Guan-Ming and Kwasinski,A. and M. Wu and Liu,K. J.R} } @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.} } @conference {18256, title = {Non-Intrusive Forensic Analysis of Visual Sensors Using Output Images}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {This paper considers the problem of non-intrusive forensic analysis of the individual components in visual sensors and its implementation. As a new addition to the emerging area of forensic engineering, we present a framework for analyzing technologies employed inside digital cameras based on output images, and develop a set of forensic signal processing algorithms for visual sensors based on color array sensor and interpolation methods. We show through simulations that the proposed method is robust against compression and noise, and can help identify various processing components inside the camera. Such a non-intrusive forensic framework would provide useful evidence for analyzing technology infringement and evolution for visual sensors}, keywords = {algorithms;interpolation, analysis;image, analysis;output, array, cameras;forensic, Color, colour, engineering;forensic, forensic, images;visual, methods;nonintrusive, PROCESSING, sensor;digital, sensors;cameras;image, sensors;interpolation;, signal}, doi = {10.1109/ICASSP.2006.1661297}, author = {Swaminathan,A. and M. Wu and Liu,K. J.R} } @article {13166, title = {A One-Threshold Algorithm for Detecting Abandoned Packages Under Severe Occlusions Using a Single Camera}, journal = {Technical Reports from UMIACS}, year = {2006}, month = {2006/02/13/T21:4}, abstract = {We describe a single-camera system capable of detecting abandoned packages under severe occlusions, which leads to complications on several levels. The first arises when frames containing only background pixels are unavailable for initializing the background model - a problem for which we apply a novel discriminative measure. The proposed measure is essentially the probability of observing a particular pixel value, conditioned on the probability that no motion is detected, with the pdf on which the latter is based being estimated as a zero-mean and unimodal Gaussian distribution from observing the difference values between successive frames. We will show that such a measure is a powerful discriminant even under severe occlusions, and can deal robustly with the foreground aperture effect - a problem inherently caused by differencing successive frames. The detection of abandoned packages then follows at both the pixel and region level. At the pixel-level, an {\textquoteleft}{\textquoteleft}abandoned pixel{\textquoteright}{\textquoteright} is detected as a foreground pixel, at which no motion is observed. At the region-level, abandoned pixels are ascertained in a Markov Random Field (MRF), after which they are clustered. These clusters are only finally classified as abandoned packages, if they display temporal persistency in their size, shape, position and color properties, which is determined using conditional probabilities of these attributes. The algorithm is also carefully designed to avoid any thresholding, which is the pitfall of many vision systems, and which significantly improves the robustness of our system. Experimental results from real-life train station sequences demonstrate the robustness and applicability of our algorithm.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3329}, author = {Lim,Ser-Nam and Davis, Larry S.} } @conference {12390, title = {Optimization of signal processing software for control system implementation}, booktitle = {Computer Aided Control System Design, 2006 IEEE International Conference on Control Applications, 2006 IEEE International Symposium on Intelligent Control, 2006 IEEE}, year = {2006}, month = {2006/10//}, pages = {1562 - 1567}, abstract = {Signal processing plays a fundamental role in the design of control systems $\#$x2014; the portion of a digitally-implemented control system between the sensor outputs and the actuator inputs is precisely a digital signal processor (DSP). Consequently, effective techniques for design and optimization of signal processing software are important in achieving efficient controller implementations. Motivated by these relationships, this paper reviews techniques for modeling signal processing functionality in a manner that exposes aspects of application structure that are useful for mapping the functionality into efficient implementations. The paper then introduces some representative techniques that operate on such models to systematically derive optimized implementations from them.}, doi = {10.1109/CACSD-CCA-ISIC.2006.4776874}, author = {Bhattacharyya, Shuvra S. and Levine,William S.} } @article {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 {12410, title = {Participatory design with proxies: developing a desktop-PDA system to support people with aphasia}, booktitle = {Proceedings of the SIGCHI conference on Human Factors in computing systems}, series = {CHI {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {151 - 160}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we describe the design and preliminary evaluation of a hybrid desktop-handheld system developed to support individuals with aphasia, a disorder which impairs the ability to speak, read, write, or understand language. The system allows its users to develop speech communication through images and sound on a desktop computer and download this speech to a mobile device that can then support communication outside the home. Using a desktop computer for input addresses some of this population{\textquoteright}s difficulties interacting with handheld devices, while the mobile device addresses stigma and portability issues. A modified participatory design approach was used in which proxies, that is, speech-language pathologists who work with aphasic individuals, assumed the role normally filled by users. This was done because of the difficulties in communicating with the target population and the high variability in aphasic disorders. In addition, the paper presents a case study of the proxy-use participatory design process that illustrates how different interview techniques resulted in different user feedback.}, keywords = {aphasia, assistive technology, multi-modal interfaces, participatory design}, isbn = {1-59593-372-7}, doi = {10.1145/1124772.1124797}, url = {http://doi.acm.org/10.1145/1124772.1124797}, author = {Jordan Boyd-Graber and Nikolova,Sonya S. and Moffatt,Karyn A. and Kin,Kenrick C. and Lee,Joshua Y. and Mackey,Lester W. and Tremaine,Marilyn M. and Klawe,Maria M.} } @conference {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 {16875, title = {A probabilistic analysis of trie-based sorting of large collections of line segments in spatial databases}, journal = {SIAM Journal on Computing}, volume = {35}, year = {2006}, month = {2006///}, pages = {22 - 58}, author = {Lindenbaum,M. and Samet, Hanan and Hjaltason,G. R} } @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 {15565, title = {Proximity problems on line segments spanned by points}, journal = {Computational Geometry}, volume = {33}, year = {2006}, month = {2006/02//}, pages = {115 - 129}, abstract = {Finding the closest or farthest line segment (line) from a point are fundamental proximity problems. Given a set S of n points in the plane and another point q, we present optimal O ( n log n ) time, O ( n ) space algorithms for finding the closest and farthest line segments (lines) from q among those spanned by the points in S. We further show how to apply our techniques to find the minimum (maximum) area triangle with a vertex at q and the other two vertices in S \ { q } in optimal O ( n log n ) time and O ( n ) space. Finally, we give an O ( n log n ) time, O ( n ) space algorithm to find the kth closest line from q and show how to find the k closest lines from q in O ( n log n + k ) time and O ( n + k ) space.}, keywords = {Closest, Farthest, k closest lines, Minimum (maximum) area triangle, Proximity problem}, isbn = {0925-7721}, doi = {10.1016/j.comgeo.2005.08.007}, url = {http://www.sciencedirect.com/science/article/pii/S0925772105000805}, author = {Daescu,Ovidiu and Luo,Jun and Mount, Dave} } @conference {14407, title = {Query-time entity resolution}, booktitle = {International conference on knowledge discovery and data mining}, year = {2006}, month = {2006///}, pages = {529 - 534}, abstract = {The goal of entity resolution is to reconcile database references corresponding to the same real-world entities. Given the abundance of publicly available databases where entities are not resolved, we motivate the problem of quickly processing queries that require resolved entities from such {\textquoteright}unclean{\textquoteright} databases. We propose a two-stage collective resolution strategy for processing queries. We then show how it can be performed on-the-fly by adaptively extracting and resolving those database references that are the most helpful for resolving the query. We validate our approach on two large real-world publication databases where we show the usefulness of collective resolution and at the same time demonstrate the need for adaptive strategies for query processing. We then show how the same queries can be answered in real time using our adaptive approach while preserving the gains of collective resolution.}, author = {BHATTACHARVA,I. and Getoor, Lise and Licamele,L.} } @article {14394, title = {Relational clustering for entity resolution queries}, journal = {ICML 2006 Workshop on Statistical Relational Learning (SRL)}, year = {2006}, month = {2006///}, abstract = {The goal of entity resolution is to recon-cile database references corresponding to the same real-world entities. Given the abun- dance of publicly available databases where entities are not resolved, we motivate the problem of quickly processing queries that require resolved entities from such {\textquoteleft}unclean{\textquoteright} databases. We first propose a cut-based rela- tional clustering formulation for collective en- tity resolution. We then show how it can be performed on-the-fly by adaptively extract- ing and resolving those database references that are the most helpful for resolving the query. We validate our approach on two large real-world publication databases, where we show the usefulness of collective resolution and at the same time demonstrate the need for adaptive strategies for query processing. We then show how the same queries can be answered in real time using our adaptive ap- proach while preserving the gains of collective resolution. }, author = {Bhattacharya,I. and Licamele,L. and Getoor, Lise} } @conference {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.} } @article {17348, title = {Research-based web design \& usability guidelines}, journal = {Background and Methodology. US Department of Health and Human Services. Washington}, year = {2006}, month = {2006///}, author = {Leavitt,M.O. and Shneiderman, Ben} } @article {17650, title = {Resilient multicast using overlays}, journal = {IEEE/ACM Transactions on Networking}, volume = {14}, year = {2006}, month = {2006/04//}, pages = {237 - 248}, abstract = {We introduce Probabilistic Resilient Multicast (PRM): a multicast data recovery scheme that improves data delivery ratios while maintaining low end-to-end latencies. PRM has both a proactive and a reactive components; in this paper we describe how PRM can be used to improve the performance of application-layer multicast protocols especially when there are high packet losses and host failures. Through detailed analysis in this paper, we show that this loss recovery technique has efficient scaling properties-the overheads at each overlay node asymptotically decrease to zero with increasing group sizes. As a detailed case study, we show how PRM can be applied to the NICE application-layer multicast protocol. We present detailed simulations of the PRM-enhanced NICE protocol for 10 000 node Internet-like topologies. Simulations show that PRM achieves a high delivery ratio (>97\%) with a low latency bound (600 ms) for environments with high end-to-end network losses (1\%-5\%) and high topology change rates (5 changes per second) while incurring very low overheads (<5\%).}, keywords = {application-layer multicast protocols, Computer science, Data communication, Delay, Internet, Internet-like topologies, IP networks, loss recovery technique, Multicast, multicast data recovery scheme, Multicast protocols, Network topology, NETWORKS, overlays, Performance loss, probabilistic forwarding, probabilistic resilient multicast, Protocols, Resilience, Streaming media, telecommunication network topology, Terminology}, isbn = {1063-6692}, doi = {10.1109/TNET.2006.872579}, author = {Banerjee,S. and Lee,Seungjoon and Bhattacharjee, Bobby and Srinivasan, Aravind} } @article {14641, title = {Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection}, journal = {PLoS PathogPLoS Pathog}, volume = {2}, year = {2006}, month = {2006/06/23/}, pages = {e60 - e60}, abstract = {Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I{\textendash}hypersensitive sites (i.e., +/- 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.}, doi = {10.1371/journal.ppat.0020060}, url = {UR - http://dx.plos.org/10.1371/journal.ppat.0020060,http://dx.plos.org/10.1371/journal.ppat.0020060}, author = {Lewinski,Mary K and Yamashita,Masahiro and Emerman,Michael and Ciuffi,Angela and Marshall,Heather and Crawford,Gregory and Collins,Francis and Shinn,Paul and Leipzig,Jeremy and Hannenhalli, Sridhar and Berry,Charles C and Ecker,Joseph R and Bushman,Frederic D.} } @conference {15305, title = {The role of knowledge in conceptual retrieval: a study in the domain of clinical medicine}, booktitle = {Proceedings of the 29th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {99 - 106}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Despite its intuitive appeal, the hypothesis that retrieval at the level of "concepts" should outperform purely term-based approaches remains unverified empirically. In addition, the use of "knowledge" has not consistently resulted in performance gains. After identifying possible reasons for previous negative results, we present a novel framework for "conceptual retrieval" that articulates the types of knowledge that are important for information seeking. We instantiate this general framework in the domain of clinical medicine based on the principles of evidence-based medicine (EBM). Experiments show that an EBM-based scoring algorithm dramatically outperforms a state-of-the-art baseline that employs only term statistics. Ablation studies further yield a better understanding of the performance contributions of different components. Finally, we discuss how other domains can benefit from knowledge-based approaches.}, keywords = {Question answering, reranking, semantic models}, isbn = {1-59593-369-7}, doi = {10.1145/1148170.1148191}, url = {http://doi.acm.org/10.1145/1148170.1148191}, author = {Jimmy Lin and Demner-Fushman,Dina} } @conference {15677, title = {Routing for data delivery in dynamic networks}, booktitle = {Proceedings of the IEEE MILCOM}, year = {2006}, month = {2006///}, pages = {1 - 7}, author = {Mundur, Padma and Lee,S. and Seligman,M.} } @article {15695, title = {Routing in Delay Tolerant Networks Using Storage Domains}, volume = {UMIACS-TR-2007-01}, year = {2006}, month = {2006/11/20/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In this paper, we present a routing algorithm for a class ofdynamic networks called the Delay Tolerant Networks (DTNs). The proposed algorithm takes into account the quintessential DTN characteristic namely, intermittent link connectivity. We modify the breadth first search (BFS) algorithm to take into account link state changes and find the quickest route between source and destination nodes. We adopt a message drop policy at intermediate nodes to incorporate storage constraint. We also introduce the idea of time-varying storage domains where all nodes connected for a length of time act as a single storage unit by sharing the aggregated storage capacity of the nodes. We evaluate the routing algorithm with and without storage domain in an extensive simulation. We analyze the performance using metrics such as delivery ratio, incomplete transfers with no routes and dropped messages. The DTN topology dynamics are analyzed by varying: number of nodes generating traffic, link probability, link availability through combinations of downtime/uptime values, storage per node, message size, and traffic. The delay performance of the proposed algorithms is conceptually the same as flooding-based algorithms but without the penalty of multiple copies. More significantly, we show that the Quickest Storage Domain (Quickest SD) algorithm distributes the storage demand across many nodes in the network topology, enabling balanced load and higher network utilization. In fact, we show that for the same level of performance, we can actually cut the storage requirement in half using the Quickest SD algorithm. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/4024}, author = {Mundur, Padma and Lee,Sookyoung and Seligman,Matthew} } @conference {15686, title = {Routing in intermittent network topologies}, booktitle = {Proceedings of the 9th ACM international symposium on Modeling analysis and simulation of wireless and mobile systems}, series = {MSWiM {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {385 - 389}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {delay tolerant network (DTN), performance evaluation, routing algorithms}, isbn = {1-59593-477-4}, doi = {10.1145/1164717.1164782}, url = {http://doi.acm.org/10.1145/1164717.1164782}, author = {Mundur, Padma and Lee,Sookyoung and Seligman,Matthew} } @conference {12272, title = {A scalable key management and clustering scheme for ad hoc networks}, booktitle = {Proceedings of the 1st international conference on Scalable information systems}, series = {InfoScale {\textquoteright}06}, year = {2006}, month = {2006///}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a scalable key management and clustering scheme for secure group communications in ad hoc and sensor networks. The scalability problem is solved by partitioning the communicating devices into subgroups, with a leader in each subgroup, and further organizing the subgroups into hierarchies. Each level of the hierarchy is called a tier or layer. Key generation, distribution, and actual data transmissions follow the hierarchy. The Distributed, Efficient Clustering Approach (DECA) provides robust clustering to form subgroups, and analytical and simulation results demonstrate that DECA is energy-efficient and resilient against node mobility. Comparing with most other schemes, our approach is extremely scalable and efficient, provides more security guarantees, and is selective, adaptive and robust.}, isbn = {1-59593-428-6}, doi = {10.1145/1146847.1146875}, url = {http://doi.acm.org/10.1145/1146847.1146875}, author = {Li,Jason H. and Levy,Renato and Yu,Miao and Bhattacharjee, Bobby} } @article {18159, title = {A Scalable Multiuser Framework for Video Over OFDM Networks: Fairness and Efficiency}, journal = {Circuits and Systems for Video Technology, IEEE Transactions on}, volume = {16}, year = {2006}, month = {2006/10//}, pages = {1217 - 1231}, abstract = {In this paper, we propose a framework to transmit multiple scalable video programs over downlink multiuser orthogonal frequency division multiplex (OFDM) networks in real time. The framework explores the scalability of the video codec and multidimensional diversity of multiuser OFDM systems to achieve the optimal service objectives subject to constraints on delay and limited system resources. We consider two essential service objectives, namely, the fairness and efficiency. Fairness concerns the video quality deviation among users who subscribe the same quality of service, and efficiency relates to how to attain the highest overall video quality using the available system resources. We formulate the fairness problem as minimizing the maximal end-to-end distortion received among all users and the efficiency problem as minimizing total end-to-end distortion of all users. Fast suboptimal algorithms are proposed to solve the above two optimization problems. The simulation results demonstrated that the proposed fairness algorithm outperforms a time division multiple (TDM) algorithm by 0.5 3 dB in terms of the worst received video quality among all users. In addition, the proposed framework can achieve a desired tradeoff between fairness and efficiency. For achieving the same average video quality among all users, the proposed framework can provide fairer video quality with 1 1.8 dB lower PSNR deviation than a TDM algorithm}, keywords = {algorithm;video, codec;video, coding;video, communication;, deviation;downlink, deviation;OFDM, distortion;multidimensional, diversity;multiple, division, end-to-end, framework;time, Frequency, modulation;diversity, multiple, multiplex, multiuser, network;efficiency, networks;video, objectives;optimization, of, OFDM, orthogonal, over, problem;fairness, problem;maximal, problems;quality, programs;multiuser, PSNR, QUALITY, reception;image, resolution;optimisation;quality, scalable, service, service;scalable, service;video, systems;optimal, video}, isbn = {1051-8215}, doi = {10.1109/TCSVT.2006.883513}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @article {14069, title = {Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: Sixteen new members and a novel subfamily}, journal = {Gene}, volume = {366}, year = {2006}, month = {2006/02/01/}, pages = {303 - 315}, abstract = {Nuclear receptors (NRs) are important transcriptional modulators in metazoans. Sixteen new NRs were identified in the Platyhelminth trematode, Schistosoma mansoni. Three were found to possess novel tandem DNA-binding domains that identify a new subfamily of NR. Two NRs are homologues of the thyroid hormone receptor that previously were thought to be restricted to chordates. This study brings the total number of identified NR in S. mansoni to 21. Phylogenetic and comparative genomic analyses demonstrate that S. mansoni NRs share an evolutionary lineage with that of arthropods and vertebrates. Phylogenic analysis shows that more than half of the S. mansoni nuclear receptors evolved from a second gene duplication. As the second gene duplication of NRs was thought to be specific to vertebrates, our data challenge the current theory of NR evolution.}, keywords = {Nuclear receptors, Schistosoma mansoni}, isbn = {0378-1119}, doi = {16/j.gene.2005.09.013}, url = {http://www.sciencedirect.com/science/article/pii/S0378111905005871}, author = {Wu,Wenjie and Niles,Edward G. and El-Sayed, Najib M. and Berriman,Matthew and LoVerde,Philip T.} } @article {13639, title = {Script-Independent Text Line Segmentation in Freestyle Handwritten Documents}, volume = {LAMP-TR-136, CS-TR-4836, UMIACS-TR-2006-51, CFAR-TR-1017}, year = {2006}, month = {2006/11//}, institution = {University of Maryland, College Park}, abstract = {Text line segmentation in freestyle handwritten documents remains an open document analysis problem. Curvilinear text lines and small gaps between neighboring text lines present a challenge to algorithms developed for machine printed or hand-printed documents. In this paper, we propose a novel approach based on density estimation and a state-of-the-art image segmentation technique, the level set method. From an input document image, we estimate a probability map, where each element represents the probability that the underlying pixel belongs to a text line. The level set method is then exploited to determine the boundary of neighboring text lines by evolving an initial estimate. Unlike most connected component based methods [1, 2], the proposed algorithm does not use any script-specific knowledge. Extensive quantitative experiments on freestyle handwritten documents with diverse scripts, such as Arabic, Chinese, Korean, and Hindi, demonstrate that our algorithm consistently outperforms previous methods [3, 1, 2]. Further experiments show the proposed algorithm is robust to scale change, rotation, and noise.}, author = {Li,Yi and Yefeng Zheng and David Doermann and Jaeger,Stefan} } @article {14642, title = {Selection of Target Sites for Mobile DNA Integration in the Human Genome}, journal = {PLoS Comput BiolPLoS Comput Biol}, volume = {2}, year = {2006}, month = {2006/11/24/}, pages = {e157 - e157}, abstract = {DNA sequences from retroviruses, retrotransposons, DNA transposons, and parvoviruses can all become integrated into the human genome. Accumulation of such sequences accounts for at least 40\% of our genome today. These integrating elements are also of interest as gene-delivery vectors for human gene therapy. Here we present a comprehensive bioinformatic analysis of integration targeting by HIV, MLV, ASLV, SFV, L1, SB, and AAV. We used a mathematical method which allowed annotation of each base pair in the human genome for its likelihood of hosting an integration event by each type of element, taking advantage of more than 200 types of genomic annotation. This bioinformatic resource documents a wealth of new associations between genomic features and integration targeting. The study also revealed that the length of genomic intervals analyzed strongly affected the conclusions drawn{\textemdash}thus, answering the question {\textquotedblleft}What genomic features affect integration?{\textquotedblright} requires carefully specifying the length scale of interest.}, doi = {10.1371/journal.pcbi.0020157}, url = {UR - http://dx.plos.org/10.1371/journal.pcbi.0020157,http://dx.plos.org/10.1371/journal.pcbi.0020157}, author = {Berry,Charles and Hannenhalli, Sridhar and Leipzig,Jeremy and Bushman,Frederic D.} } @conference {11979, title = {A sensory grammar for inferring behaviors in sensor networks}, booktitle = {Proceedings of the 5th international conference on Information processing in sensor networks}, series = {IPSN {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {251 - 259}, publisher = {ACM}, organization = {ACM}, address = {Nashville, Tennessee, USA}, abstract = {The ability of a sensor network to parse out observable activities into a set of distinguishable actions is a powerful feature that can potentially enable many applications of sensor networks to everyday life situations. In this paper we introduce a framework that uses a hierarchy of Probabilistic Context Free Grammars (PCFGs) to perform such parsing. The power of the framework comes from the hierarchical organization of grammars that allows the use of simple local sensor measurements for reasoning about more macroscopic behaviors. Our presentation describes how to use a set of phonemes to construct grammars and how to achieve distributed operation using a messaging model. The proposed framework is flexible. It can be mapped to a network hierarchy or can be applied sequentially and across the network to infer behaviors as they unfold in space and time. We demonstrate this functionality by inferring simple motion patterns using a sequence of simple direction vectors obtained from our camera sensor network testbed.}, keywords = {algorithms, behavior identification, human activity, human factors, pcfg, real-time and embedded systems, sensor grammars, sensor networks}, isbn = {1-59593-334-4}, doi = {10.1145/1127777.1127817}, author = {Lymberopoulos, Dimitrios and Ogale, Abhijit S. and Savvides, Andreas and Aloimonos, J.} } @article {13857, title = {Sentence compression as a component of a multi-document summarization system}, journal = {Proceedings of the 2006 Document Understanding Workshop, New York}, year = {2006}, month = {2006///}, abstract = {We applied a single-document sentence-trimming approach (Trimmer) to the problem of multi-document summariza- tion. Trimmer was designed with the in- tention of compressing a lead sentence into a space consisting of tens of char- acters. In our Multi-Document Trimmer (MDT), we use Trimmer to generate multiple trimmed candidates for each sentence. Sentence selection is used to determine which trimmed candidates provide the best combination of topic coverage and brevity. We demonstrate that we were able to port Trimmer easily to this new problem. We also show that MDT generally ranked higher for recall than for precision, suggesting that MDT is currently more successful at finding relevant content than it is at weeding out irrelevant content. Finally, we present an error analysis that shows that, while sentence compressions is making space for additional sentences, more work is needed in the area of generating and se- lecting the right candidates. }, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin and Schwartz,R.} } @inbook {15806, title = {Sentence Trimming and Selection: Mixing and Matching}, booktitle = {DUC 06 Conference Proceedings}, year = {2006}, month = {2006///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {We describe how components from two distinct multi-document summarization systems were combined. Twenty four possible combinations of components were considered. We observed some contrasts between conservative and aggressive sentence compression (i.e., trimming) in the context of multi-document summarization. }, url = {http://duc.nist.gov/}, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin and O{\textquoteright}Leary, Dianne P. and Conroy,John M. and Schlesinger,Judith D.} } @article {17356, title = {Severity and impact of computer user frustration: A comparison of student and workplace users}, journal = {Interacting with Computers}, volume = {18}, year = {2006}, month = {2006/03//}, pages = {187 - 207}, abstract = {User frustration with information and computing technology is a pervasive 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. Our exploratory study of 107 student computer users and 50 workplace computer users shows high levels of frustration and loss of 1/3{\textendash}1/2 of time spent. This paper reports on the incident and individual factors that cause of frustration, and how they raise frustration severity. It examines the frustration impacts on the daily interactions of the users. The time lost and time to fix problem, and importance of task, strongly correlate with frustration levels for both student and workplace users. Differences between students and workplace users are discussed in the paper, as are implications for researchers.}, keywords = {Computer anxiety, Computer experience, Helpdesk, Training, User frustration, user interface design}, isbn = {0953-5438}, doi = {10.1016/j.intcom.2005.06.001}, url = {http://www.sciencedirect.com/science/article/pii/S0953543805000561}, author = {Lazar,Jonathan and Jones,Adam and Hackley,Mary and Shneiderman, Ben} } @conference {14391, title = {Social Capital in Friendship-Event Networks}, booktitle = {Data Mining, 2006. ICDM {\textquoteright}06. Sixth International Conference on}, year = {2006}, month = {2006///}, pages = {959 - 964}, abstract = {In this paper, we examine a particular form of social network which we call a friendship-event network. A friendship-event network captures both the friendship relationship among a set of actors, and also the organizer and participation relationships of actors in a series of events. Within these networks, we formulate the notion of social capital based on the actor-organizer friendship relationship and the notion of benefit, based on event participation. We investigate appropriate definitions for the social capital of both a single actor and a collection of actors. 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 show that our definitions of capital and benefit capture interesting qualitative properties of event series. In addition, we show that social capital is a better publication predictor than publication history.}, keywords = {academic, based, capital;Internet;groupware;knowledge, Collaboration, friendship;friendship-event, network;actor-organizer, network;social, systems;}, doi = {10.1109/ICDM.2006.149}, author = {Licamele,L. and Getoor, Lise} } @article {13648, title = {SOFTCBIR: Object Searching in Videos Combining Keypoint Matching and Graduated Assignment}, volume = {LAMP-TR-132,CAR-TR-1013,CS-TR-4804,UMIACS-TR-2006-25}, year = {2006}, month = {2006/05//}, institution = {University of Maryland, College Park}, abstract = {This paper proposes a new approach to object searching in video databases, SoftCBIR, which combines a keypoint matching algorithm and a graduated assignment algorithm based on softassign. Compared with previous approaches, SoftCBIR is an innovative combination of two powerful techniques: 1) An energy minimization algorithm is applied to match two groups of keypoints while accounting for both their similarity in descriptor space and the consistency of their geometric configuration. The algorithm computes correspondence and pose transformation between two groups of keypoints iteratively and alternately toward an optimal result. The objective energy function combines normalized distance errors in descriptor space and in the spatial domain. 2) Initial individual keypoint matching relies on Approximate K-Nearest Neighbor (ANN) search. ANN achieves much more accurate initial keypoint matching results in the descriptor space than K-means labeling. Experiments prove the effectiveness of our approach, and demonstrate the performance improvements rising from the combination of the two proposed techniques in the SoftCBIR algorithm. The support of this research by the Department of Defense under contract MDA-9040-2C-0406 is gratefully acknowledged.}, author = {Luo,Ming and DeMenthon,Daniel and Yu,Xiaodong and David Doermann} } @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 {14016, title = {Spherical and hemispherical microphone arrays for capture and analysis of sound fields}, journal = {The Journal of the Acoustical Society of America}, volume = {120}, year = {2006}, month = {2006///}, pages = {3225 - 3225}, abstract = {The capture of the spatial structure of a sound field and analysis is important in many fields including creating virtual environments, source localization and detection, noise suppression, and beamforming. Spherical microphone arrays are a promising development to help achieve such capture and analysis, and have been studied by several groups. We develop a practical spherical microphone array and demonstrate its utility in applications for sound capture, room measurement and for beamforming and tracking. To accommodate equipment failure and manufacturing imprecision we extend their theory to handle arbitrary microphone placement. To handle speech capture and surveillance we describe the development of a new sensor, the hemispherical microphone array. For each array the practical performance follows that predicted by theory. Future applications and improvements are also discussed. [Work supported by NSF.]}, url = {http://link.aip.org/link/?JAS/120/3225/3}, author = {Duraiswami, Ramani and Zhiyun Li and Zotkin,Dmitry N and Grassi,Elena} } @article {12604, title = {Structure From Planar Motion}, journal = {Image Processing, IEEE Transactions on}, volume = {15}, year = {2006}, month = {2006/11//}, pages = {3466 - 3477}, abstract = {Planar motion is arguably the most dominant type of motion in surveillance videos. The constraints on motion lead to a simplified factorization method for structure from planar motion when using a stationary perspective camera. Compared with methods for general motion , our approach has two major advantages: a measurement matrix that fully exploits the motion constraints is formed such that the new measurement matrix has a rank of at most 3, instead of 4; the measurement matrix needs similar scalings, but the estimation of fundamental matrices or epipoles is not needed. Experimental results show that the algorithm is accurate and fairly robust to noise and inaccurate calibration. As the new measurement matrix is a nonlinear function of the observed variables, a different method is introduced to deal with the directional uncertainty in the observed variables. Differences and the dual relationship between planar motion and planar object are also clarified. Based on our method, a fully automated vehicle reconstruction system has been designed}, keywords = {algebra;road, analysis;matrix, camera;surveillance, directional, matrix;planar, MOTION, motion;stationary, perspective, processing;, reconstruction, signal, system;image, uncertainty;measurement, vehicles;surveillance;video, videos;vehicle}, isbn = {1057-7149}, doi = {10.1109/TIP.2006.881943}, author = {Li,Jian and Chellapa, Rama} } @article {15031, title = {Synthetic-perturbation techniques for screening shared memory programs}, journal = {Software: Practice and Experience}, volume = {24}, year = {2006}, month = {2006/10/30/}, pages = {679 - 701}, abstract = {The synthetic-perturbation screening (SPS) methodology is based on an empirical approach; SPS introduces artificial perturbations into the MIMD program and captures the effects of such perturbations by using the modern branch of statistics called design of experiments. SPS can provide the basis of a powerful tool for screening MIMD programs for performance bottlenecks. This technique is portable across machines and architectures, and scales extremely well on massively parallel processors. The purpose of this paper is to explain the general approach and to extend it to address specific features that are the main source of poor performance on the shared memory programming model. These include performance degradation due to load imbalance and insufficient parallelism, and overhead introduced by synchronizations and by accessing shared data structures. We illustrate the practicality of SPS by demonstrating its use on two very different case studies: a large image understanding benchmark and a parallel quicksort.}, keywords = {Design of experiments, parallel programs, performance, Shared memory programming model, Synthetic perturbation}, isbn = {1097-024X}, doi = {10.1002/spe.4380240802}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.4380240802/abstract}, author = {Snelick,Robert and JaJa, Joseph F. and Kacker,Raghu and Lyon,Gordon} } @article {13164, title = {SYSTEM AND METHOD FOR FAST ILLUMINATION-INVARIANT BACKGROUND SUBTRACTION USING TWO VIEWS}, volume = {PCT/EP2005/056207}, year = {2006}, month = {2006/06//}, abstract = {A method for eliminating errors in foreground object detection in digitized images comprises providing (1101) a reference camera and a secondary camera, vertically aligning each said camera with a baseline that is approximately perpendicular to a ground plane, wherein said reference camera is placed lower than said secondary camera, selecting (1104) a foreground pixel in a reference view of a first point in a foreground object, finding (1105) a conjugate pixel of the foreground pixel in a secondary view, using (1106) the foreground and conjugate pixels to determine an image base pixel of a base point in the reference view, wherein said base point is a point on the ground plane below the first point, and using (1107) the foreground and image base pixels to find a location where the ground plane is first visible.}, author = {Davis, Larry S. and Lim,S.N. and Mittal,A.} } @conference {16089, title = {Task taxonomy for graph visualization}, booktitle = {Proceedings of the 2006 AVI workshop on BEyond time and errors: novel evaluation methods for information visualization}, series = {BELIV {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {1 - 5}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Our goal is to define a list of tasks for graph visualization that has enough detail and specificity to be useful to: 1) designers who want to improve their system and 2) to evaluators who want to compare graph visualization systems. In this paper, we suggest a list of tasks we believe are commonly encountered while analyzing graph data. We define graph specific objects and demonstrate how all complex tasks could be seen as a series of low-level tasks performed on those objects. We believe that our taxonomy, associated with benchmark datasets and specific tasks, would help evaluators generalize results collected through a series of controlled experiments.}, keywords = {Evaluation, graph visualization, task taxonomy}, isbn = {1-59593-562-2}, doi = {10.1145/1168149.1168168}, url = {http://doi.acm.org/10.1145/1168149.1168168}, author = {Lee,Bongshin and Plaisant, Catherine and Parr,Cynthia Sims and Fekete,Jean-Daniel and Henry,Nathalie} } @article {13167, title = {Task-Driven Video Collection}, journal = {Technical Reports from UMIACS}, year = {2006}, month = {2006/01/23/T17:1}, abstract = {Vision systems are increasingly being deployed to perform complexsurveillance tasks. While improved algorithms are being developed to perform these tasks, it is also important that data suitable for these algorithms be acquired - a non-trivial task in a dynamic and crowded scene viewed by multiple PTZ cameras. In this paper, we describe a multi-camera system that collects images and videos of moving objects in such scenes, subject to task constraints. The system constructs "task visibility intervals" that contain information about what can be sensed in future time intervals. Constructing these intervals requires prediction of future object motion and consideration of several factors such as object occlusion and camera control parameters. Using a plane-sweep algorithm, these atomic intervals can be combined to form multi-task intervals, during which a single camera can collect videos suitable for multiple tasks simultaneously. Although cameras can then be scheduled based on the constructed intervals, finding an optimal schedule is a typical NP-hard problem. Due to this, and the lack of exact future information in a dynamic environment, we propose several methods for fast camera scheduling that yield solutions within a small constant factor of optimal. Experimental results illustrate system capabilities for both real and more complicated simulated scenarios. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/3042}, author = {Lim,Ser-Nam and Mittal,Anuarg and Davis, Larry S.} } @conference {15061, title = {A Time Saving Method for Human Detection in Wide Angle Camera Images}, booktitle = {Machine Learning and Cybernetics, 2006 International Conference on}, year = {2006}, month = {2006/08//}, pages = {4029 - 4034}, abstract = {A time-saving method for human detection in an indoor environment in wide angle camera images is presented in this paper, without using time-consuming template operations such as edge detection and morphological operations. It excludes other objects in motion to detect humans including cases of the partial occlusion of humans, rotation of the head and variation of skin colors. This algorithm is applicable where the memory space is limited and the time requirements are strict, such as in an embedded system. The experimental results show that it took about 0.35 seconds to process the algorithm after the scene study time}, keywords = {CAMERAS, Embedded system, human detection, image recognition, Image segmentation, indoor environment, Motion estimation, time-saving method, wide angle camera images}, doi = {10.1109/ICMLC.2006.258804}, author = {Zhuolin Jiang and Li,Shao-Fa and Gao,Dong-Fa} } @article {17434, title = {Toward an enriched (and revitalized) sense of help: Summary of an ASIS\&T 2005 panel session}, journal = {Bulletin of the American Society for Information Science and Technology}, volume = {32}, year = {2006}, month = {2006/06/01/}, pages = {23 - 26}, isbn = {1550-8366}, doi = {10.1002/bult.2006.1720320509}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bult.2006.1720320509/abstract}, author = {Haas,Stephanie W and Denn,Sheila and Locke,David and Shneiderman, Ben and Brown,Laurie} } @article {16082, title = {TreePlus: Interactive Exploration of Networks with Enhanced Tree Layouts}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {12}, year = {2006}, month = {2006/12//nov}, pages = {1414 - 1426}, abstract = {Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food Webs, ontologies and social networks difficult to understand and interact with. We propose a new interactive visual analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus}, keywords = {Automated;Software;User-Computer Interface;, Biological;Pattern Recognition, data visualization;graph structure;graphical user interface;interactive visual analytics;occlusion;tree-style layout;data visualisation;graphical user interfaces;hidden feature removal;interactive systems;trees (mathematics);Algorithms;Computer Graphics;C}, isbn = {1077-2626}, doi = {10.1109/TVCG.2006.106}, author = {Lee,B. and Parr,C.S. and Plaisant, Catherine and Bederson, Benjamin B. and Veksler,V.D. and Gray,W.D. and Kotfila,C.} } @conference {16083, title = {VAST 2006 Contest - A Tale of Alderwood}, booktitle = {Visual Analytics Science And Technology, 2006 IEEE Symposium On}, year = {2006}, month = {2006/11/31/2}, pages = {215 - 216}, abstract = {Visual analytics experts realize that one effective way to push the field forward and to develop metrics for measuring the performance of various visual analytics components is to hold an annual competition. The first visual analytics science and technology (VAST) contest was held in conjunction with the 2006 IEEE VAST Symposium. The competition entailed the identification of possible political shenanigans in the fictitious town of Alderwood. A synthetic data set was made available as well as tasks. We summarize how we prepared and advertised the contest, developed some initial metrics for evaluation, and selected the winners. The winners were invited to participate at an additional live competition at the symposium to provide them with feedback from senior analysts}, keywords = {Alderwood;human, analysis;data, analytics, and, contest;data, information, interaction;sense, making;visual, Science, technology, visualisation;}, doi = {10.1109/VAST.2006.261420}, author = {Grinstein,G. and O{\textquoteright}Connell,T. and Laskowski,S. and Plaisant, Catherine and Scholtz,J. and Whiting,M.} } @article {17919, title = {Vertex{\textendash}transformation streams}, journal = {Graphical Models}, volume = {68}, year = {2006}, month = {2006/07//}, pages = {371 - 383}, abstract = {Recent trends in parallel computer architecture strongly suggest the need to improve the arithmetic intensity (the compute to bandwidth ratio) for greater performance in time-critical applications, such as interactive 3D graphics. At the same time, advances in stream programming abstraction for graphics processors (GPUs) have enabled us to use parallel algorithm design methods for GPU programming. Inspired by these developments, this paper explores the interactions between multiple data streams to improve arithmetic intensity and address the input geometry bandwidth bottleneck for interactive 3D graphics applications. We introduce the idea of creating vertex and transformation streams that represent large point datasets via their interaction. We discuss how to factor such point datasets into a set of source vertices and transformation streams by identifying the most common translations amongst vertices. We accomplish this by identifying peaks in the cross-power spectrum of the dataset in the Fourier domain. We validate our approach by integrating it with a view-dependent point rendering system and show significant improvements in input geometry bandwidth requirements as well as rendering frame rates.}, keywords = {Arithmetic intensity, Geometry instancing, Stream programming, Streaming algorithms, Transformation encoding}, isbn = {1524-0703}, doi = {10.1016/j.gmod.2006.03.005}, url = {http://www.sciencedirect.com/science/article/pii/S1524070306000373}, author = {Kim,Youngmin and Lee,Chang Ha and Varshney, Amitabh} } @inbook {12638, title = {Video Mensuration Using a Stationary Camera}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3953}, year = {2006}, month = {2006///}, pages = {164 - 176}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents a method for video mensuration using a single stationary camera. The problem we address is simple, i.e., the mensuration of any arbitrary line segment on the reference plane using multiple frames with minimal calibration. Unlike previous solutions that are based on planar rectification, our approach is based on fitting the image of multiple concentric circles on the plane. Further, the proposed method aims to minimize the error in mensuration. Hence we can calculate the mensuration of the line segments not lying on the reference plane. Using an algorithm for detecting and tracking wheels of an automobile, we have implemented a fully automatic system for wheel base mensuration. The mensuration results are accurate enough that they can be used to determine the vehicle classes. Furthermore, we measure the line segment between any two points on the vehicle and plot them in top and side views.}, isbn = {978-3-540-33836-9}, url = {http://dx.doi.org/10.1007/11744078_13}, author = {Guo,Feng and Chellapa, Rama}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @inbook {16090, title = {Visualizing Graphs as Trees: Plant a Seed and Watch it Grow}, booktitle = {Graph DrawingGraph Drawing}, series = {Lecture Notes in Computer Science}, volume = {3843}, year = {2006}, month = {2006///}, pages = {516 - 518}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {TreePlus is a graph browsing technique based on a tree-style layout. It shows the missing graph structure using interaction techniques and enables users to start with a specific node and incrementally explore the local structure of graphs. We believe that it supports particularly well tasks that require rapid reading of labels.}, isbn = {978-3-540-31425-7}, url = {http://dx.doi.org/10.1007/11618058_50}, author = {Lee,Bongshin and Parr,Cynthia and Plaisant, Catherine and Bederson, Benjamin B.}, editor = {Healy,Patrick and Nikolov,Nikola} } @inbook {14276, title = {Wavelet-Based Super-Resolution Reconstruction: Theory and Algorithm}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3954}, year = {2006}, month = {2006///}, pages = {295 - 307}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present a theoretical analysis and a new algorithm for the problem of super-resolution imaging: the reconstruction of HR (high-resolution) images from a sequence of LR (low-resolution) images. Super-resolution imaging entails solutions to two problems. One is the alignment of image frames. The other is the reconstruction of a HR image from multiple aligned LR images. Our analysis of the latter problem reveals insights into the theoretical limits of super-resolution reconstruction. We find that at best we can reconstruct a HR image blurred by a specific low-pass filter. Based on the analysis we present a new wavelet-based iterative reconstruction algorithm which is very robust to noise. Furthermore, it has a computationally efficient built-in denoising scheme with a nearly optimal risk bound. Roughly speaking, our method could be described as a better-conditioned iterative back-projection scheme with a fast and optimal regularization criteria in each iteration step. Experiments with both simulated and real data demonstrate that our approach has significantly better performance than existing super-resolution methods. It has the ability to remove even large amounts of mixed noise without creating smoothing artifacts.}, isbn = {978-3-540-33838-3}, url = {http://dx.doi.org/10.1007/11744085_23}, author = {Hui Ji and Ferm{\"u}ller, Cornelia}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @inbook {12642, title = {What Is the Range of Surface Reconstructions from a Gradient Field?}, booktitle = {Computer Vision {\textendash} ECCV 2006Computer Vision {\textendash} ECCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3951}, year = {2006}, month = {2006///}, pages = {578 - 591}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We propose a generalized equation to represent a continuum of surface reconstruction solutions of a given non-integrable gradient field. We show that common approaches such as Poisson solver and Frankot-Chellappa algorithm are special cases of this generalized equation. For a N {\texttimes} N pixel grid, the subspace of all integrable gradient fields is of dimension N 2 {\textendash} 1. Our framework can be applied to derive a range of meaningful surface reconstructions from this high dimensional space. The key observation is that the range of solutions is related to the degree of anisotropy in applying weights to the gradients in the integration process. While common approaches use isotropic weights, we show that by using a progression of spatially varying anisotropic weights, we can achieve significant improvement in reconstructions. We propose (a) α-surfaces using binary weights, where the parameter α allows trade off between smoothness and robustness, (b) M-estimators and edge preserving regularization using continuous weights and (c) Diffusion using affine transformation of gradients. We provide results on photometric stereo, compare with previous approaches and show that anisotropic treatment discounts noise while recovering salient features in reconstructions.}, isbn = {978-3-540-33832-1}, url = {http://dx.doi.org/10.1007/11744023_45}, author = {Agrawal,Amit and Raskar,Ramesh and Chellapa, Rama}, editor = {Leonardis,Ale{\v s} and Bischof,Horst and Pinz,Axel} } @conference {15315, title = {Will pyramids built of nuggets topple over?}, booktitle = {Proceedings of the main conference on Human Language Technology Conference of the North American Chapter of the Association of Computational Linguistics}, series = {HLT-NAACL {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {383 - 390}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {The present methodology for evaluating complex questions at TREC analyzes answers in terms of facts called "nuggets". The official F-score metric represents the harmonic mean between recall and precision at the nugget level. There is an implicit assumption that some facts are more important than others, which is implemented in a binary split between "vital" and "okay" nuggets. This distinction holds important implications for the TREC scoring model---essentially, systems only receive credit for retrieving vital nuggets---and is a source of evaluation instability. The upshot is that for many questions in the TREC testsets, the median score across all submitted runs is zero. In this work, we introduce a scoring model based on judgments from multiple assessors that captures a more refined notion of nugget importance. We demonstrate on TREC 2003, 2004, and 2005 data that our "nugget pyramids" address many shortcomings of the present methodology, while introducing only minimal additional overhead on the evaluation flow.}, doi = {10.3115/1220835.1220884}, url = {http://dx.doi.org/10.3115/1220835.1220884}, author = {Jimmy Lin and Demner-Fushman,Dina} } @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 {17513, title = {Workplace user frustration with computers: an exploratory investigation of the causes and severity}, journal = {Behaviour \& Information Technology}, volume = {25}, year = {2006}, month = {2006///}, pages = {239 - 251}, abstract = {When hard-to-use computers cause users to become frustrated, it can affect workplace productivity, user mood and interactions with other co-workers. Previous research has examined the frustration that students and their families face in using computers. To learn more about the causes and measure the severity of user frustration with computers in the workplace, we collected modified time diaries from 50 workplace users, who spent an average of 5.1 hours on the computer. In this exploratory research, users reported wasting on average, 42~?~43\% of their time on the computer due to frustrating experiences. The largest number of frustrating experiences occurred while using word processors, email and web browsers. The causes of the frustrating experiences, the time lost due to the frustrating experiences, and the effects of the frustrating experiences on the mood of the users are discussed in this paper. Implications for designers, managers, users, information technology staff and policymakers are discussed.When hard-to-use computers cause users to become frustrated, it can affect workplace productivity, user mood and interactions with other co-workers. Previous research has examined the frustration that students and their families face in using computers. To learn more about the causes and measure the severity of user frustration with computers in the workplace, we collected modified time diaries from 50 workplace users, who spent an average of 5.1 hours on the computer. In this exploratory research, users reported wasting on average, 42~?~43\% of their time on the computer due to frustrating experiences. The largest number of frustrating experiences occurred while using word processors, email and web browsers. The causes of the frustrating experiences, the time lost due to the frustrating experiences, and the effects of the frustrating experiences on the mood of the users are discussed in this paper. Implications for designers, managers, users, information technology staff and policymakers are discussed. }, isbn = {0144-929X}, doi = {10.1080/01449290500196963}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449290500196963}, author = {Lazar,Jonathan and Jones,Adam and Shneiderman, Ben} } @article {18752, title = {Algorithms for constructing 3-D point clouds using multiple digital fringe projection patterns}, journal = {Computer-Aided Design and Applications}, volume = {2}, year = {2005}, month = {2005///}, pages = {737 - 746}, abstract = {This paper describes algorithms for generating 3-D point clouds from a set of digital imagesobtained from projecting phase-shifted sinusoidal fringe patterns onto object. In this paper, a mathematical model is introduced for describing the geometric relationship between the fringe patterns being projected, the image captured and the shape of the object being measured. This model allows considerable flexibility in the spatial configuration of shape measurement system. The algorithms for point cloud construction described in this paper present an improvement over the existing algorithms in terms of accuracy, ease of system calibration, and sensitivity to parameter errors. These algorithms have been incorporated in a shape measurement system and shown to have a very good performance. }, url = {http://cadanda.homestead.com/V2No6_04.pdf}, author = {Peng,T. and Gupta,S.K. and Lau,K.} } @article {18168, title = {Anti-collusion forensics of multimedia fingerprinting using orthogonal modulation}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/06//}, pages = {804 - 821}, abstract = {Digital fingerprinting is a method for protecting digital data in which fingerprints that are embedded in multimedia are capable of identifying unauthorized use of digital content. A powerful attack that can be employed to reduce this tracing capability is collusion, where several users combine their copies of the same content to attenuate/remove the original fingerprints. In this paper, we study the collusion resistance of a fingerprinting system employing Gaussian distributed fingerprints and orthogonal modulation. We introduce the maximum detector and the thresholding detector for colluder identification. We then analyze the collusion resistance of a system to the averaging collusion attack for the performance criteria represented by the probability of a false negative and the probability of a false positive. Lower and upper bounds for the maximum number of colluders Kmax are derived. We then show that the detectors are robust to different collusion attacks. We further study different sets of performance criteria, and our results indicate that attacks based on a few dozen independent copies can confound such a fingerprinting system. We also propose a likelihood-based approach to estimate the number of colluders. Finally, we demonstrate the performance for detecting colluders through experiments using real images.}, keywords = {Automated;Product Labeling;Signal Processing, Computer-Assisted;, Computer-Assisted;Multimedia;Patents as Topic;Pattern Recognition, Gaussian distribution;anticollusion forensic;colluder identification;collusion resistance;digital fingerprinting;false probability;likelihood-based approach;multimedia fingerprinting;orthogonal modulation;spread spectrum embedding;Gaussian distribution;fi}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.847284}, author = {Wang,Z.J. and M. Wu and Zhao,H.V. and Trappe,W. and Liu,K. J.R} } @article {13498, title = {AParallel-Line Detection Algorithm Based on HMMDecoding}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {27}, year = {2005}, month = {2005/05//}, pages = {777 - 792}, abstract = {The detection of groups of parallel lines is important in applications such as form processing and text (handwriting) extraction from rule lined paper. These tasks can be very challenging in degraded documents where the lines are severely broken. In this paper we propose a novel model-based method which incorporates high level context to detect these lines. After preprocessing (such as skew correction and text filtering), we use trained Hidden Markov Models (HMM) to locate the optimal positions of all lines simultaneously on the horizontal or vertical projection profiles, based on the Viterbi decoding. The algorithm is trainable so it can be easily adapted to different application scenarios. The experiments conducted on known form processing and rule line detection show our method is robust, and achieves better results than other widely used line detection methods.}, author = {Yefeng Zheng and Huiping Li and David Doermann} } @conference {12649, title = {Appearance modeling under geometric context}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/10//}, pages = {1252 -1259 Vol. 2 - 1252 -1259 Vol. 2}, abstract = {We propose a unified framework based on a general definition of geometric transform (GeT) for modeling appearance. GeT represents the appearance by applying designed functionals over certain geometric sets. We show that image warping, Radon transform, trace transform, etc. are special cases of our definition. Moreover, three different types of GeTs are designed to handle deformation, articulation and occlusion and applied to fingerprinting the appearance inside a contour. They include the contour-driven GeT, the feature curve based GeT and selecting functionals to model the appearance inside the convex hull of the contour. A multi-resolution representation that combines both shape and appearance information is also proposed. We apply our approach to image synthesis and object recognition. The proposed approach produces promising results when applied to fingerprinting the appearance of human and body parts despite the challenges due to articulated motion and deformations}, keywords = {based, curve, geometry;image, GeT;convex, GeT;fingerprinting;geometric, hull;feature, information;trace, modeling;contour-driven, Radon, recognition;, recognition;shape, representation;object, synthesis;image, transform;appearance, transform;image, transform;Radon, transforms;computational, warping;multi-resolution}, doi = {10.1109/ICCV.2005.38}, author = {Li,Jian and Zhou,S. K and Chellapa, Rama} } @conference {14325, title = {Are GSM phones THE solution for localization?}, booktitle = {Mobile Computing Systems and Applications, 2006. WMCSA{\textquoteright}06. Proceedings. 7th IEEE Workshop on}, year = {2005}, month = {2005///}, pages = {34 - 42}, author = {Varshavsky,A. and Chen,M.Y. and de Lara,E. and Jon Froehlich and Haehnel,D. and Hightower,J. and LaMarca,A. and Potter,F. and Sohn,T. and Tang,K. and others} } @article {13518, title = {Camera-Based Analysis of Text and Documents: ASurvey}, journal = {International Journal on Document Analysis and Recognition}, volume = {7}, year = {2005}, month = {2005/07//}, pages = {83 - 104}, author = {Liang,Jian and David Doermann and Huiping Li} } @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 {18175, title = {Collusion resistance analysis of multimedia fingerprinting systems}, journal = {IEEE Tran. on Image Processing}, year = {2005}, month = {2005///}, author = {Wang,Z.J. and Wu,M. and Zhao,H.V. and Trappe,W. and Liu,K. J.R} } @conference {13204, title = {Constructing task visibility intervals for a surveillance system}, booktitle = {Proceedings of the third ACM international workshop on Video surveillance \& sensor networks}, series = {VSSN {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {141 - 148}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {One of the goals of a multi-camera surveillance system is to collect useful video clips of objects in the scene. Objects in the collected videos should be unobstructed, in the field of view of the given camera, and meet task-specific resolution requirement. For this purpose, we describe an algorithm that constructs "task visibility intervals", which are tuples of information about what to sense (task-object pairs), when to sense (feasible future temporal intervals to start a task) and how to sense (the camera to use and the corresponding viewing angles and focal length). The algorithm first looks for temporal intervals within which the angular extents of objects overlap each other, causing the object farthest from the given camera to be occluded. Outside these intervals, sub-intervals are then constructed such that feasible camera settings exist for capturing the object. Experimental results are provided to illustrate the system capabilities in constructing such task visibility intervals, followed by scheduling them using a greedy algorithm.}, keywords = {scheduling, sensor}, isbn = {1-59593-242-9}, doi = {10.1145/1099396.1099421}, url = {http://doi.acm.org/10.1145/1099396.1099421}, author = {Lim,Ser-Nam and Mittal,Anurag and Davis, Larry S.} } @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.} } @article {12931, title = {Critical Factors Influencing the Occurrence of Vibrio Cholerae in the Environment of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {71}, year = {2005}, month = {2005/08/01/}, pages = {4645 - 4654}, abstract = {The occurrence of outbreaks of cholera in Africa in 1970 and in Latin America in 1991, mainly in coastal communities, and the appearance of the new serotype Vibrio cholerae O139 in India and subsequently in Bangladesh have stimulated efforts to understand environmental factors influencing the growth and geographic distribution of epidemic Vibrio cholerae serotypes. Because of the severity of recent epidemics, cholera is now being considered by some infectious disease investigators as a {\textquotedblleft}reemerging{\textquotedblright} disease, prompting new work on the ecology of vibrios. Epidemiological and ecological surveillance for cholera has been under way in four rural, geographically separated locations in Bangladesh for the past 4 years, during which both clinical and environmental samples were collected at biweekly intervals. The clinical epidemiology portion of the research has been published (Sack et al., J. Infect. Dis. 187:96-101, 2003). The results of environmental sampling and analysis of the environmental and clinical data have revealed significant correlations of water temperature, water depth, rainfall, conductivity, and copepod counts with the occurrence of cholera toxin-producing bacteria (presumably V. cholerae). The lag periods between increases or decreases in units of factors, such as temperature and salinity, and occurrence of cholera correlate with biological parameters, e.g., plankton population blooms. The new information on the ecology of V. cholerae is proving useful in developing environmental models for the prediction of cholera epidemics.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.71.8.4645-4654.2005}, url = {http://aem.asm.org/content/71/8/4645}, author = {Huq,Anwar and Sack,R. Bradley and Nizam,Azhar and Longini,Ira M. and Nair,G. Balakrish and Ali,Afsar and Morris,J. Glenn and Khan,M. N. Huda and Siddique,A. Kasem and Yunus,Mohammed and Albert,M. John and Sack,David A. and Rita R Colwell} } @conference {17853, title = {Data Redistribution and Remote Method Invocation in Parallel Component Architectures}, booktitle = {Parallel and Distributed Processing Symposium, International}, volume = {1}, year = {2005}, month = {2005///}, pages = {40b - 40b}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {With the increasing availability of high-performance massively parallel computer systems, the prevalence of sophisticated scientific simulation has grown rapidly. The complexity of the scientific models being simulated has also evolved, leading to a variety of coupled multi-physics simulation codes. Such cooperating parallel programs require fundamentally new interaction capabilities, to efficiently exchange parallel data structures and collectively invoke methods across programs. So-called "M?N" research, as part of the Common Component Architecture (CCA) effort, addresses these special and challenging needs, to provide generalized interfaces and tools that support flexible parallel data redistribution and parallel remote method invocation. Using this technology, distinct simulation codes with disparate distributed data decompositions can work together to achieve greater scientific discoveries.}, doi = {http://doi.ieeecomputersociety.org/10.1109/IPDPS.2005.159}, author = {Bertrand,Felipe and Bramley,Randall and Sussman, Alan and Bernholdt,David E. and Kohl,James A. and Larson,Jay W. and Damevski,Kostadin B.} } @conference {14859, title = {Deformation invariant image matching}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/10//}, pages = {1466 -1473 Vol. 2 - 1466 -1473 Vol. 2}, abstract = {We propose a novel framework to build descriptors of local intensity that are invariant to general deformations. In this framework, an image is embedded as a 2D surface in 3D space, with intensity weighted relative to distance in x-y. We show that as this weight increases, geodesic distances on the embedded surface are less affected by image deformations. In the limit, distances are deformation invariant. We use geodesic sampling to get neighborhood samples for interest points, and then use a geodesic-intensity histogram (GIH) as a deformation invariant local descriptor. In addition to its invariance, the new descriptor automatically finds its support region. This means it can safely gather information from a large neighborhood to improve discriminability. Furthermore, we propose a matching method for this descriptor that is invariant to affine lighting changes. We have tested this new descriptor on interest point matching for two data sets, one with synthetic deformation and lighting change, and another with real non-affine deformations. Our method shows promising matching results compared to several other approaches}, keywords = {deformation, deformations;nonaffine, deformations;point, descriptor;geodesic, distances;geodesic, geometry;differential, geometry;image, histogram;image, image, invariant, local, matching;computational, matching;deformation, matching;image, morphing;, sampling;geodesic-intensity}, doi = {10.1109/ICCV.2005.67}, author = {Ling,Haibin and Jacobs, David W.} } @article {15242, title = {On degree constrained shortest paths}, journal = {Algorithms{\textendash}ESA 2005}, year = {2005}, month = {2005///}, pages = {259 - 270}, abstract = {Traditional shortest path problems play a central role in both the design and use of communication networks and have been studied extensively. In this work, we consider a variant of the shortest path problem. The network has two kinds of edges, {\textquotedblleft}actual{\textquotedblright} edges and {\textquotedblleft}potential{\textquotedblright} edges. In addition, each vertex has a degree/interface constraint. We wish to compute a shortest path in the graph that maintains feasibility when we convert the potential edges on the shortest path to actual edges. The central difficulty is when a node has only one free interface, and the unconstrained shortest path chooses two potential edges incident on this node. We first show that this problem can be solved in polynomial time by reducing it to the minimum weighted perfect matching problem. The number of steps taken by this algorithm is O(|E|2 log |E|) for the single-source single-destination case. In other words, for each v we compute the shortest path P v such that converting the potential edges on P v to actual edges, does not violate any degree constraint. We then develop more efficient algorithms by extending Dijkstra{\textquoteright}s shortest path algorithm. The number of steps taken by the latter algorithm is O(|E||V|), even for the single-source all destination case.}, doi = {10.1007/11561071_25}, author = {Khuller, Samir and Lee,K. and Shayman,M.} } @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} } @conference {12279, title = {Differentiated traffic engineering for QoS provisioning}, booktitle = {INFOCOM 2005. 24th Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings IEEE}, volume = {4}, year = {2005}, month = {2005/03//}, pages = {2349 - 2359 vol. 4 - 2349 - 2359 vol. 4}, abstract = {We introduce a new approach for QoS provisioning in packet networks based on the notion of differentiated traffic engineering (DTE). We consider a single AS network capable of source based multi-path routing. We do not require sophisticated queuing or per-class scheduling at individual routers; instead, if a link is used to forward QoS sensitive packets, we maintain its utilization below a threshold. As a consequence, DTE eliminates the need for per-flow (IntServ) or per-class (DiffServ) packet processing tasks such as traffic classification, queueing, shaping, policing and scheduling in the core and hence poses a lower burden on the network management unit. Conversely, DTE utilizes network bandwidth much more efficiently than simple over-provisioning. In this paper, we propose a complete architecture and an algorithmic structure for DTE. We show that our scheme can be formulated as a non-convex optimization problem, and we present an optimal solution framework based on simulated annealing. We present a simulation-based performance evaluation of DTE, and compare our scheme to existing (gradient projection) methods.}, keywords = {based, Computer, differentiated, DiffServ, DTE;, engineering;, evaluation;, link;, links;, management;, multipath, network, networks;, nonconvex, of, optimisation;, OPTIMIZATION, packet, performance, problem;, provisioning;, QoS, QUALITY, routing;, service;, simulation-based, source, Telecommunication, traffic, traffic;}, doi = {10.1109/INFCOM.2005.1498521}, author = {Tabatabaee,V. and Bhattacharjee, Bobby and La,R.J. and Shayman,M.A.} } @inbook {17795, title = {Distributed Algorithms for Dynamic Survivability of Multiagent Systems}, booktitle = {Computational Logic in Multi-Agent SystemsComputational Logic in Multi-Agent Systems}, series = {Lecture Notes in Computer Science}, volume = {3259}, year = {2005}, month = {2005///}, pages = {139 - 144}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Though multiagent systems (MASs) are being increasingly used, few methods exist to ensure survivability of MASs. All existing methods suffer from two flaws. First, a centralized survivability algorithm (CSA) ensures survivability of the MAS {\textendash} unfortunately, if the node on which the CSA exists goes down, the survivability of the MAS is questionable. Second, no mechanism exists to change how the MAS is deployed when external factors trigger a re-evaluation of the survivability of the MAS. In this paper, we present three algorithms to address these two important problems. Our algorithms can be built on top of any CSA. Our algorithms are completely distributed and can handle external triggers to compute a new deployment. We report on experiments assessing the efficiency of these algorithms.}, keywords = {Computer, Science}, isbn = {978-3-540-24010-5}, url = {http://dx.doi.org/10.1007/978-3-540-30200-1_1}, author = {Subrahmanian,V. and Kraus,Sarit and Zhang,Yingqian}, editor = {Dix,J{\"u}rgen and Leite,Jo{\~a}o} } @conference {12342, title = {DSP address optimization using evolutionary algorithms}, booktitle = {Proceedings of the 2005 workshop on Software and compilers for embedded systems}, year = {2005}, month = {2005///}, pages = {91 - 98}, author = {Leventhal,S. and Yuan,L. and Bambha,N. K and Bhattacharyya, Shuvra S. and Qu,G.} } @conference {12283, title = {Efficient geographic routing in multihop wireless networks}, booktitle = {Proceedings of the 6th ACM international symposium on Mobile ad hoc networking and computing}, series = {MobiHoc {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {230 - 241}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose a new link metric called normalized advance (NADV) for geographic routing in multihop wireless networks. NADV selects neighbors with the optimal trade-off between proximity and link cost. Coupled with the local next hop decision in geographic routing, NADV enables an adaptive and efficient cost-aware routing strategy. Depending on the objective or message priority, applications can use the NADV framework to minimize various types of link cost.We present efficient methods for link cost estimation and perform detailed simulations in diverse scenarios. Our results show that NADV outperforms current schemes in many aspects: for example, in high noise environments with frequent packet losses, the use of NADV leads to 81\% higher delivery ratio. When compared to centralized routing under certain settings, geographic routing using NADV finds paths whose cost is close to the optimum.}, keywords = {Geographic routing, Link cost estimation, Routing metric, Wireless multihop networks}, isbn = {1-59593-004-3}, doi = {10.1145/1062689.1062720}, url = {http://doi.acm.org/10.1145/1062689.1062720}, author = {Lee,Seungjoon and Bhattacharjee, Bobby and Banerjee,Suman} } @article {17135, title = {Envisioning help resources for the future information ecology: Toward an enriched sense of help}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {42}, year = {2005}, month = {2005/01/01/}, pages = {n/a-n/a - n/a-n/a}, isbn = {1550-8390}, doi = {10.1002/meet.14504201123}, url = {http://onlinelibrary.wiley.com/doi/10.1002/meet.14504201123/abstract}, author = {Haas,Stephanie W and Brown,Laurie and Denn,Sheila and Locke,David and Shneiderman, Ben} } @conference {14860, title = {On the equivalence of common approaches to lighting insensitive recognition}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/10//}, pages = {1721 -1726 Vol. 2 - 1721 -1726 Vol. 2}, abstract = {Lighting variation is commonly handled by methods invariant to additive and multiplicative changes in image intensity. It has been demonstrated that comparing images using the direction of the gradient can produce broader insensitivity to changes in lighting conditions, even for 3D scenes. We analyze two common approaches to image comparison that are invariant, normalized correlation using small correlation windows, and comparison based on a large set of oriented difference of Gaussian filters. We show analytically that these methods calculate a monotonic (cosine) function of the gradient direction difference and hence are equivalent to the direction of gradient method. Our analysis is supported with experiments on both synthetic and real scenes}, keywords = {3D, conditions;lighting, cosine, difference;image, direction, filters;gradient, function;image, insensitive, intensity;lighting, recognition;image, recognition;lighting, scenes;Gaussian, segmentation;, variation;monotonic}, doi = {10.1109/ICCV.2005.179}, author = {Osadchy,M. and Jacobs, David W. and Lindenbaum,M.} } @article {15297, title = {Evaluating Summaries and Answers: Two Sides of the Same Coin?}, journal = {Intrinsic and Extrinsic Evaluation Measures for Machine Translation and/or Summarization}, year = {2005}, month = {2005///}, pages = {41 - 41}, abstract = {This paper discusses the convergencebetween question answering and multi- document summarization, pointing out implications and opportunities for knowl- edge transfer in both directions. As a case study in one direction, we discuss the recent development of an automatic method for evaluating definition questions based on n-gram overlap, a commonly- used technique in summarization evalua- tion. In the other direction, the move to- wards topic-oriented summaries requires an understanding of relevance and topi- cality, issues which have received atten- tion in the question answering literature. It is our opinion that question answering and multi-document summarization repre- sent two complementary approaches to the same problem of satisfying complex user information needs. Although this points to many exciting opportunities for system- building, here we primarily focus on im- plications for system evaluation. }, author = {Jimmy Lin and Demner-Fushman,D.} } @inbook {16105, title = {Evaluation Methodologies for Visual Analytics}, booktitle = {Illuminating the Path: The Research and Development Agenda for Visual AnalyticsIlluminating the Path: The Research and Development Agenda for Visual Analytics}, year = {2005}, month = {2005///}, pages = {150 - 157}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, keywords = {file-import-09-03-18}, url = {http://nvac.pnl.gov/agenda.stm$\#$book}, author = {Laskowski,S. and Plaisant, Catherine}, editor = {Thomas,James and Cook,Kristin} } @conference {15304, title = {Evaluation of resources for question answering evaluation}, booktitle = {Proceedings of the 28th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {392 - 399}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Controlled and reproducible laboratory experiments, enabled by reusable test collections, represent a well-established methodology in modern information retrieval research. In order to confidently draw conclusions about the performance of different retrieval methods using test collections, their reliability and trustworthiness must first be established. Although such studies have been performed for ad hoc test collections, currently available resources for evaluating question answering systems have not been similarly analyzed. This study evaluates the quality of answer patterns and lists of relevant documents currently employed in automatic question answering evaluation, and concludes that they are not suitable for post-hoc experimentation. These resources, created from runs submitted by TREC QA track participants, do not produce fair and reliable assessments of systems that did not participate in the original evaluations. Potential solutions for addressing this evaluation gap and their shortcomings are discussed.}, keywords = {pooling, Question answering}, isbn = {1-59593-034-5}, doi = {10.1145/1076034.1076102}, url = {http://doi.acm.org/10.1145/1076034.1076102}, author = {Jimmy Lin} } @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 {17157, title = {Extending User Understanding of Federal Statistics in Tables (2000)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {This paper describes progress toward improving user interfaces for US Federal government statistics that are presented in tables. Based on studies of user behaviors and needs related to statistical tables, we describe interfaces to assist diverse users with a range of statistical literacy to explore, find, understand, and use US Federal government statistics.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6473}, author = {Marchionini,Gary and Hert,Carol and Liddy,Liz and Shneiderman, Ben} } @conference {12662, title = {A Factorization Method for Structure from Planar Motion}, booktitle = {Application of Computer Vision, 2005. WACV/MOTIONS {\textquoteright}05 Volume 1. Seventh IEEE Workshops on}, volume = {2}, year = {2005}, month = {2005/01//}, pages = {154 - 159}, abstract = {We propose a factorization method for structure from planar motion using a stationary perspective camera. Compared with [A factorization based algorithm for multi-image projective structure and motion] for general motion, our work has three major differences: a different measurement matrix specialized for planar motion is formed. The measurement matrix has a rank of at most 3, instead of 4; the measurement matrix needs similar scalings, but estimation of fundamental matrices or epipoles is not needed; we have an Euclidean reconstruction instead of a projective reconstruction. The camera is not required to be calibrated. A simple semi-automatic calibration method using vanishing points and lines is sufficient. Experimental results show that the algorithm is accurate and fairly robust to noise and inaccurate calibration.}, doi = {10.1109/ACVMOT.2005.4}, author = {Li,Jian and Chellapa, Rama} } @conference {13553, title = {Fast Camera Motion Estimation for Hand-Devices and Applications}, booktitle = {4th International Conference on Mobile and Ubiquitous Multimedia}, year = {2005}, month = {2005///}, pages = {103 - 108}, abstract = {In this paper we present an efficient motion estimation algorithm for camera-enabled handheld devices, such as mobile phones and PDAs. Compared to general camera motion estimation, the estimation of ego-motion of handheld devices presents unique challenges because most devices are limited in resources (processing power, memory and battery). The algorithm must be lightweight so it can be efficiently embedded and run fast enough to produce smooth seamless translation. Our solution includes a multi-resolution scheme which searches the match from coarse to fine; and optimization of the search space. As a demonstration, we implemented the algorithm on the Symbian based Nokia 3650/6600 camera phone, and explored several interesting applications, including using camera motion for browsing documents and as a pointing device. A cross-platform implementation is also discussed.}, author = {Liu,Xu and David Doermann and Huiping Li} } @conference {13197, title = {Fast illumination-invariant background subtraction using two views: error analysis, sensor placement and applications}, booktitle = {Computer Vision and Pattern Recognition, 2005. CVPR 2005. IEEE Computer Society Conference on}, volume = {1}, year = {2005}, month = {2005/06//}, pages = {1071 - 1078 vol. 1 - 1071 - 1078 vol. 1}, abstract = {Background modeling and subtraction to detect new or moving objects in a scene is an important component of many intelligent video applications. Compared to a single camera, the use of multiple cameras leads to better handling of shadows, specularities and illumination changes due to the utilization of geometric information. Although the result of stereo matching can be used as the feature for detection, it has been shown that the detection process can be made much faster by a simple subtraction of the intensities observed at stereo-generated conjugate pairs in the two views. The methodology however, suffers from false and missed detections due to some geometric considerations. In this paper, we perform a detailed analysis of such errors. Then, we propose a sensor configuration that eliminates false detections. Algorithms are also proposed that effectively eliminate most detection errors due to missed detections, specular reflections and objects being geometrically close to the background. Experiments on several scenes illustrate the utility and enhanced performance of the proposed approach compared to existing techniques.}, keywords = {analysis;, application;, background, cameras;, configuration;, DETECTION, detection;, error, error;, extraction;, false, feature, handling;, illumination-invariance;, image, intelligent, matching;, modeling;, object, placement;, processing;, sensor, sensors;, shadow, stereo, subtraction;, video}, doi = {10.1109/CVPR.2005.155}, author = {Lim,Ser-Nam and Mittal,A. and Davis, Larry S. and Paragios,N.} } @conference {13556, title = {Flattening curved documents in images}, booktitle = {Computer Vision and Pattern Recognition, 2005. CVPR 2005. IEEE Computer Society Conference on}, volume = {2}, year = {2005}, month = {2005/06//}, pages = {338 - 345 vol. 2 - 338 - 345 vol. 2}, abstract = {Compared to scanned images, document pictures captured by camera can suffer from distortions due to perspective and page warping. It is necessary to restore a frontal planar view of the page before other OCR techniques can be applied. In this paper we describe a novel approach for flattening a curved document in a single picture captured by an uncalibrated camera. To our knowledge this is the first reported method able to process general curved documents in images without camera calibration. We propose to model the page surface by a developable surface, and exploit the properties (parallelism and equal line spacing) of the printed textual content on the page to recover the surface shape. Experiments show that the output images are much more OCR friendly than the original ones. While our method is designed to work with any general developable surfaces, it can be adapted for typical special cases including planar pages, scans of thick books, and opened books.}, keywords = {calibration;, camera, character, content;, curved, distortion;, document, document;, image, images;, OCR, optical, page, pictures;, printed, processing;, recognition;, restoration;, scanned, techniques;, textual, warping;}, doi = {10.1109/CVPR.2005.163}, author = {Liang,Jian and DeMenthon,D. and David Doermann} } @article {18216, title = {Forensic analysis of nonlinear collusion attacks for multimedia fingerprinting}, journal = {Image Processing, IEEE Transactions on}, volume = {14}, year = {2005}, month = {2005/05//}, pages = {646 - 661}, abstract = {Digital fingerprinting is a technology for tracing the distribution of multimedia content and protecting them from unauthorized redistribution. Unique identification information is embedded into each distributed copy of multimedia signal and serves as a digital fingerprint. Collusion attack is a cost-effective attack against digital fingerprinting, where colluders combine several copies with the same content but different fingerprints to remove or attenuate the original fingerprints. In this paper, we investigate the average collusion attack and several basic nonlinear collusions on independent Gaussian fingerprints, and study their effectiveness and the impact on the perceptual quality. With unbounded Gaussian fingerprints, perceivable distortion may exist in the fingerprinted copies as well as the copies after the collusion attacks. In order to remove this perceptual distortion, we introduce bounded Gaussian-like fingerprints and study their performance under collusion attacks. We also study several commonly used detection statistics and analyze their performance under collusion attacks. We further propose a preprocessing technique of the extracted fingerprints specifically for collusion scenarios to improve the detection performance.}, keywords = {Automated;Product Labeling;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, bounded Gaussian-like fingerprint;detection statistics;digital fingerprinting;forensic analysis;independent Gaussian fingerprint;multimedia content;multimedia fingerprinting;nonlinear collusion attack;perceptual distortion;perceptual quality;preprocessing, Computer-Assisted;, Computer-Assisted;Models, Statistical;Nonlinear Dynamics;Patents as Topic;Pattern Recognition}, isbn = {1057-7149}, doi = {10.1109/TIP.2005.846035}, author = {Zhao,H.V. and M. Wu and Wang,Z.J. and Liu,K. J.R} } @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} } @article {14616, title = {Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription}, journal = {Journal of VirologyJ. Virol.}, volume = {79}, year = {2005}, month = {2005/06/01/}, pages = {6610 - 6619}, abstract = {We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.}, isbn = {0022-538X, 1098-5514}, doi = {10.1128/JVI.79.11.6610-6619.2005}, url = {http://jvi.asm.org/content/79/11/6610}, author = {Lewinski,M. K and Bisgrove,D. and Shinn,P. and Chen,H. and Hoffmann,C. and Hannenhalli, Sridhar and Verdin,E. and Berry,C. C and Ecker,J. R and Bushman,F. D} } @article {14566, title = {Genome-wide analysis of retroviral DNA integration}, journal = {Nat Rev MicroNat Rev Micro}, volume = {3}, year = {2005}, month = {2005/11//}, pages = {848 - 858}, isbn = {1740-1526}, doi = {10.1038/nrmicro1263}, url = {http://dx.doi.org/10.1038/nrmicro1263}, author = {Bushman,Frederic and Lewinski,Mary and Ciuffi,Angela and Barr,Stephen and Leipzig,Jeremy and Hannenhalli, Sridhar and Hoffmann,Christian} } @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 {14031, title = {High Order Spatial Audio Capture and Binaural Head-Tracked Playback over Headphones with HRTF Cues}, journal = {Proceedings 119th convention of AES}, year = {2005}, month = {2005///}, abstract = {A theory and a system for capturing an audio scene and then rendering it remotely are developed andpresented. The sound capture is performed with a spherical microphone array. The sound field at the location of the array is deduced from the captured sound and is represented using either spherical wave-functions or plane-wave expansions. The sound field representation is then transmitted to a remote location for immediate rendering or stored for later use. The sound renderer, coupled with the head tracker, reconstructs the acoustic field using individualized head-related transfer functions to preserve the perceptual spatial structure of the audio scene. Rigorous error bounds and Nyquist-like sampling criterion for the representation of the sound field are presented and verified. }, author = {Duraiswami, Ramani and Zotkin,Dmitry N and Li,Z. and Grassi,E. and Gumerov, Nail A. and Davis, Larry S.} } @conference {18482, title = {High Order Spatial Audio Capture and Its Binaural Head-Tracked Playback Over Headphones with HRTF Cues}, booktitle = {Audio Engineering Society Convention 119}, year = {2005}, month = {2005///}, abstract = {A theory and a system for capturing an audio scene and then rendering it remotely are developed and presented. The sound capture is performed with a spherical microphone array. The sound field at the location, and in a region of space in the neighborhood, of the array is deduced from the captured sound and represented using either spherical wave-functions or plane-wave expansions. The representation is then transmitted to a remote location for immediate rendering or stored for later reproduction. The sound renderer, coupled with the head tracker, reconstructs the acoustic field using individualized head-related transfer functions to preserve the perceptual spatial structure of the audio scene. Rigorous error bounds and a Nyquist-like sampling criterion for the representation of the sound field are presented and verified.}, author = {Davis, Larry S. and Duraiswami, Ramani and Grassi,E. and Gumerov, Nail A. and Li,Z. and Zotkin,Dmitry N} } @conference {17875, title = {High Performance Communication between Parallel Programs}, booktitle = {Parallel and Distributed Processing Symposium, 2005. Proceedings. 19th IEEE International}, year = {2005}, month = {2005/04//}, pages = {177b- 177b - 177b- 177b}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present algorithms for high performance communication between message-passing parallel programs, and evaluate the algorithms as implemented in InterComm. InterComm is a framework to couple parallel programs in the presence of complex data distributions within a coupled application. Multiple parallel libraries and languages may be used in the different programs of a single coupled application. The ability to couple such programs is required in many emerging application areas, such as complex simulations that model physical phenomena at multiple scales and resolutions, and image data analysis applications. We describe the new algorithms we have developed for computing inter-program communication patterns. We present experimental results showing the performance of various algorithmic tradeoffs, and also compare performance against an earlier system.}, keywords = {Adaptive arrays, Analytical models, Chaotic communication, Computational modeling, Computer science, Data analysis, data distribution, Educational institutions, high performance communication, image data analysis, image resolution, inter-program communication patterns, InterComm, Libraries, Message passing, parallel languages, parallel libraries, parallel programming, parallel programs, performance evaluation, Wind}, isbn = {0-7695-2312-9}, doi = {10.1109/IPDPS.2005.243}, author = {Jae-Yong Lee and Sussman, Alan} } @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} } @article {18163, title = {An interactive and team approach to multimedia design curriculum}, journal = {Signal Processing Magazine, IEEE}, volume = {22}, year = {2005}, month = {2005/11//}, pages = {14 - 19}, abstract = {Over the past decade, increasingly powerful technologies have made it easier to compress, distribute, and store multimedia content. The merger of computing and communications has created a ubiquitous infrastructure that brings digital multimedia closer to the users and opens up tremendous educational and commercial opportunities in multimedia content creation, delivery, rendering, and archiving for millions of users worldwide. Multimedia has become a basic skill demanded by an increasing number of potential jobs for electrical engineering/computer science graduates. In this article, the authors intend to share their experiences and new ways of thinking about curriculum development. It is beneficial for colleagues in the multimedia signal processing areas for use in developing or revising the curriculum to fit the needs and resources of their own programs.}, keywords = {approach;, communication;, courses;, curriculum, curriculum;, design, development;, digital, education;, educational, interactive, learning;, multimedia, multimedia;, processing;, signal, team}, isbn = {1053-5888}, doi = {10.1109/MSP.2005.1550186}, author = {M. Wu and Liu,K. J.R} } @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.} } @conference {18237, title = {Joint uplink and downlink optimization for video conferencing over wireless LAN}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/03//}, pages = {ii/1101 - ii/1104 Vol. 2 - ii/1101 - ii/1104 Vol. 2}, abstract = {A real-time video conferencing framework is proposed for multiple conferencing pairs by jointly considering the uplink and downlink conditions within IEEE 802.11 networks. We formulate this system so as to minimize the maximal end-to-end expected distortion received by all users by selecting the PHY modes and transmission time. Compared with the strategy of individually optimizing uplink and downlink, the proposed framework outperforms by 3.67-8.65 dB for the average received PSNR among all users.}, keywords = {802.11, conferencing, conferencing;, distortion;, end-to-end, expected, IEEE, joint, LAN;, maximal, minimisation;, modes;, multiple, networks;, optimization;, pairs;, PHY, PSNR;, real-time, teleconferencing;, time;, transmission, uplink-downlink, video, wireless}, doi = {10.1109/ICASSP.2005.1415601}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @article {14467, title = {Link Mining for the Semantic Web, Position Statement}, journal = {Proceedings of the Dagstuhl Seminar in Machine Learning for the Semantic Web}, year = {2005}, month = {2005///}, abstract = {A key challenge for data mining is tackling the problem of mining richly structured datasets, where the objectsare linked in some way and we have some ontological information describing the domain. Links among the objects demonstrate certain patterns, which can be helpful for many data mining tasks and are usually hard to capture with traditional statistical models. Our goals are to develop machine learning algorithms which can a) make use of the ontological theory during learning b) learn how to refine, or update the ontological theory, based on learned model and c) do a mix of both. }, author = {Getoor, Lise and Licamele,L.} } @conference {12280, title = {Measurement-based multipath multicast}, booktitle = {INFOCOM 2005. 24th Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings IEEE}, volume = {4}, year = {2005}, month = {2005/03//}, pages = {2803 - 2808 vol. 4 - 2803 - 2808 vol. 4}, abstract = {We propose a measurement-based routing algorithm to load balance intradomain traffic along multiple paths for multiple multicast sources. Multiple paths are established using application-layer overlaying. The proposed algorithm is able to converge under different network models, where each model reflects a different set of assumptions about the multicasting capabilities of the network. The algorithm is derived from simultaneous perturbation stochastic approximation and relies only on noisy estimates from measurements. Simulation results are presented to demonstrate the additional benefits obtained by incrementally increasing the multicasting capabilities.}, keywords = {algorithm;, allocation;, application-layer, approximation, approximation;, balance, communication;, Convergence, convergence;, intradomain, load, measurement-based, methods;, Multicast, multipath, network, numerical, of, overlaying;, perturbation, processes;, resource, Routing, routing;, source;, Stochastic, techniques;, Telecommunication, theory;, traffic;}, doi = {10.1109/INFCOM.2005.1498566}, author = {Guven,T. and La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @article {14821, title = {Mesh saliency}, journal = {ACM transactions on graphics}, volume = {24}, year = {2005}, month = {2005/07//}, pages = {659 - 666}, abstract = {Research over the last decade has built a solid mathematical foundation for representation and analysis of 3D meshes in graphics and geometric modeling. Much of this work however does not explicitly incorporate models of low-level human visual attention. In this paper we introduce the idea of mesh saliency as a measure of regional importance for graphics meshes. Our notion of saliency is inspired by low-level human visual system cues. We define mesh saliency in a scale-dependent manner using a center-surround operator on Gaussian-weighted mean curvatures. We observe that such a definition of mesh saliency is able to capture what most would classify as visually interesting regions on a mesh. The human-perception-inspired importance measure computed by our mesh saliency operator results in more visually pleasing results in processing and viewing of 3D meshes. compared to using a purely geometric measure of shape. such as curvature. We discuss how mesh saliency can be incorporated in graphics applications such as mesh simplification and viewpoint selection and present examples that show visually appealing results from using mesh saliency.}, keywords = {perception, saliency, simplification, viewpoint selection, visual attention}, isbn = {0730-0301}, doi = {10.1145/1073204.1073244}, url = {http://doi.acm.org/10.1145/1073204.1073244}, author = {Lee,Chang Ha and Varshney, Amitabh and Jacobs, David W.} } @conference {12394, title = {Modeling image processing systems with homogeneous parameterized dataflow graphs}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {5}, year = {2005}, month = {2005/03//}, pages = {v/133 - v/136 Vol. 5 - v/133 - v/136 Vol. 5}, abstract = {We describe a new dataflow model called homogeneous parameterized dataflow (HPDF). This form of dynamic dataflow graph takes advantage of the fact that in a large number of image processing applications, data production and consumption rates, though dynamic, are equal across graph edges for any particular iteration, which leads to a homogeneous rate of actor execution, even though data production and consumption values are dynamic and vary across graph edges. We discuss existing dataflow models and formulate in detail the HPDF model. We develop examples of applications that are described naturally in terms of HPDF semantics and present experimental results that demonstrate the efficacy of the HPDF approach.}, keywords = {data consumption, data flow graphs, data production, dynamic dataflow graph, graph edges, homogeneous parameterized dataflow graphs, IMAGE PROCESSING, image processing system modeling, iteration, iterative methods}, doi = {10.1109/ICASSP.2005.1416258}, author = {Sen,Mainak and Bhattacharyya, Shuvra S. and Lv,Tiehan and Wolf,W.} } @conference {15600, title = {A new approach to image fusion based on cokriging}, booktitle = {Information Fusion, 2005 8th International Conference on}, volume = {1}, year = {2005}, month = {2005/07//}, pages = {8 pp. - 8 pp.}, abstract = {We consider the image fusion problem involving remotely sensed data. We introduce cokriging as a method to perform fusion. We investigate the advantages of fusing Hyperion with ALI. This evaluation is performed by comparing the classification of the fused data with that of input images and by calculating well-chosen quantitative fusion quality metrics. We consider the invasive species forecasting system (ISFS) project as our fusion application. The fusion of ALI with Hyperion data is studied using PCA and wavelet-based fusion. We then propose utilizing a geostatistical based interpolation method called cokriging as a new approach for image fusion.}, keywords = {ALI;, analysis;, based, cokriging;, component, data;, forecasting, fusion, fusion;, geophysical, geostatistical, Hyperion, image, Interpolation, interpolation;, invasive, ISFS, method;, metrics;, PCA;, principal, processing;, project;, QUALITY, quantitative, remote, remotely, sensed, sensing;, sensor, sensors;, signal, species, system;, techniques;, transforms;, wavelet, wavelet-based}, doi = {10.1109/ICIF.2005.1591912}, author = {Memarsadeghi,N. and Le Moigne,J. and Mount, Dave and Morisette,J.} } @article {19039, title = {Pioneer: verifying code integrity and enforcing untampered code execution on legacy systems}, journal = {ACM SIGOPS Operating Systems Review}, volume = {39}, year = {2005}, month = {2005}, pages = {1 - 16}, abstract = {We propose a primitive, called Pioneer, as a first step towards verifiable code execution on untrusted legacy hosts. Pioneer does not require any hardware support such as secure co-processors or CPU-architecture extensions. We implement Pioneer on an Intel Pentium IV Xeon processor. Pioneer can be used as a basic building block to build security systems. We demonstrate this by building a kernel rootkit detector.}, keywords = {dynamic root of trust, rootkit detection, self-check-summing code, software-based code attestation, verifiable code execution}, isbn = {0163-5980}, url = {http://doi.acm.org/10.1145/1095809.1095812}, author = {Seshadri, Arvind and Luk, Mark and Elaine Shi and Perrig, Adrian and van Doorn, Leendert and Khosla, Pradeep} } @conference {14522, title = {Plane-wave decomposition analysis for spherical microphone arrays}, booktitle = {IEEE Workshop on Applications of Signal Processing to Audio and Acoustics, 2005}, year = {2005}, month = {2005/10//}, pages = {150 - 153}, publisher = {IEEE}, organization = {IEEE}, abstract = {Spherical microphone arrays have attracted attention for analyzing the sound field in a region and beamforming. The analysis of the recorded sound has been performed in terms of spherical wave-functions, and recently the use of plane-wave expansions has been suggested. We show that the plane-wave basis is intimately related to the spherical wave-functions. Reproduction in terms of both representations satisfies certain band-limit criteria. We provide an error bound that shows that to reproduce the spatial characteristics of a sound of a certain frequency we need to be able to accurately represent sounds of up to a particular order, which establishes a Nyquist-like criterion. The order of the sound field in turn is related to the number of microphones in the array necessary to achieve accurate quadrature on the sphere. These results are illustrated with simulations.}, keywords = {Acoustic propagation, Acoustic scattering, acoustic signal processing, acoustic waves, array signal processing, band-limit criteria, beamforming, Educational institutions, Fourier transforms, Frequency, Laboratories, microphone arrays, Nails, Nyquist criterion, Nyquist-like criterion, Partial differential equations, plane-wave decomposition analysis, sound field analysis, spherical microphone arrays, spherical wave-functions}, isbn = {0-7803-9154-3}, doi = {10.1109/ASPAA.2005.1540191}, author = {Duraiswami, Ramani and Zhiyun Li and Zotkin,Dmitry N and Grassi,E. and Gumerov, Nail A.} } @article {14100, title = {Promoter architecture and response to a positive regulator of archaeal transcription}, journal = {Molecular Microbiology}, volume = {56}, year = {2005}, month = {2005/05/01/}, pages = {625 - 637}, abstract = {The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial-type effectors, especially activators, regulate a eukaryote-like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a {\textquoteleft}one-site{\textquoteright} minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.}, isbn = {1365-2958}, doi = {10.1111/j.1365-2958.2005.04563.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04563.x/abstract}, author = {Ouhammouch,Mohamed and Langham,Geoffrey E and Hausner,Winfried and Simpson,Anjana J. and El-Sayed, Najib M. and Geiduschek,E. Peter} } @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} } @conference {15286, title = {Representation of information needs and the elements of context: A case study in the domain of clinical medicine}, booktitle = {In Proceedings of the ACM SIGIR 2005 Workshop on Information Retrieval in Context (IRiX 2005)}, year = {2005}, month = {2005///}, author = {Jimmy Lin and Fushman,D. D.} } @article {16094, title = {Robotic apparatus and wireless communication system}, volume = {10/085,821}, year = {2005}, month = {2005/05/17/}, abstract = {A robotic apparatus and system adapted to communicate with a wireless sensor. The apparatus may be either physical or virtual in nature and is adapted to communicate physical movements with a wireless sensor. Data received from the sensor and/or robotic apparatus may be reviewed in a real-time mode, or may be saved for review at a later time. In addition, the apparatus may be controlled through an operator that is in local or remote communication with the apparatus. The robotic system may include pre-programmed interactive platforms for enabling communication between a user and the apparatus in a dynamic mode. In addition, the system may allow an operator to program a game/story for use as an interactive platform. Accordingly, the apparatus and system provides a platform for rehabilitative exercise of a patient as well as an entertainment device.}, url = {http://www.google.com/patents?id=5-0VAAAAEBAJ}, author = {Lathan,Corinna E. and Tracey,Michael R. and Vice,Jack M. and Druin, Allison and Plaisant, Catherine} } @conference {14025, title = {A robust and self-reconfigurable design of spherical microphone array for multi-resolution beamforming}, booktitle = {Acoustics, Speech, and Signal Processing, 2005. Proceedings. (ICASSP {\textquoteright}05). IEEE International Conference on}, volume = {4}, year = {2005}, month = {2005/03//}, pages = {iv/1137 - iv/1140 Vol. 4 - iv/1137 - iv/1140 Vol. 4}, abstract = {We describe a robust and self-reconfigurable design of a spherical microphone array for beamforming. Our approach achieves a multi-resolution spherical beamformer with performance that is either optimal in the approximation of desired beampattern or is optimal in the directivity achieved, both robustly. Our implementation converges to the optimal performance quickly while exactly satisfying the specified frequency response and robustness constraint in each iteration step without accumulated round-off errors. The advantage of this design lies in its robustness and self-reconfiguration in microphone array reorganization, such as microphone failure, which is highly desirable in online maintenance and anti-terrorism. Design examples and simulation results are presented.}, keywords = {3D, anti-terrorism;, array, array;, arrays;, audio, beam, beamforming;, beampattern, directivity, Frequency, microphone, multiresolution, omnidirectional, optimisation;, optimization;, processing;, reorganization, response;, robustness;, sampling;, self-reconfigurable, signal, soundfield, spherical, steering;}, doi = {10.1109/ICASSP.2005.1416214}, author = {Zhiyun Li and Duraiswami, Ramani} } @article {12104, title = {ROMER: resilient opportunistic mesh routing for wireless mesh networks}, journal = {Proc. of IEEE WiMesh}, volume = {166}, year = {2005}, month = {2005///}, author = {Yuan,Y. and Yang,H. and Wong,S. H.Y and Lu,S. and Arbaugh, William A.} } @conference {13036, title = {Search-based structured prediction as classification}, booktitle = {NIPS Workshop on Advances in Structured Learning for Text and Speech Processing, Whistler, Canada}, year = {2005}, month = {2005///}, author = {Daum{\'e}, Hal and Langford,J. and Marcu,D.} } @article {13713, title = {A sentence-trimming approach to multi-document summarization}, journal = {Proceedings of DUC2005}, year = {2005}, month = {2005///}, abstract = {We implemented an initial applicationof a sentence-trimming approach (Trim- mer) to the problem of multi-document summarization in the MSE2005 and DUC2005 tasks. Sentence trimming was incorporated into a feature-based summarization system, called Multi- Document Trimmer (MDT), by us- ing sentence trimming as both a pre- processing stage and a feature for sen- tence ranking. We demonstrate that we were able to port Trimmer easily to this new problem. Although the direct im- pact of sentence trimming was minimal compared to other features used in the system, the interaction of the other fea- tures resulted in trimmed sentences ac- counting for nearly half of the selected summary sentences. }, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin and Monz,C. and Schwartz,R.} } @article {17357, title = {Severity and Impact of Computer User Frustration: A Comparison of Student and Workplace Users (2002)}, year = {2005}, month = {2005///}, abstract = {User frustration with information and computing technology is a pervasive 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. Our study of 107 student computer users and 50 workplace computer users shows high levels of frustration and loss of 1/3 to 1/2 of time spent. This paper reports on the incident-specific and user-specific causes of frustration, and they raise frustration severity. It examines the frustration impacts on the daily interactions of the users. The time lost and time to fix problem, and importance of task, strongly correlate with frustration levels for both student and workplace users. Differences between students and workplace users are discussed in the paper.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6496}, author = {Lazar,Jonathan and Jones,Adam and Hackley,Mary and Shneiderman, Ben} } @article {15128, title = {Simulation and Secure Computation-Handling Expected Polynomial-Time Strategies in Simulation-Based Security Proofs}, journal = {Lecture Notes in Computer Science}, volume = {3378}, year = {2005}, month = {2005///}, pages = {128 - 149}, author = {Katz, Jonathan and Lindell,Y.} } @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 {18431, title = {Software process improvement in small organizations: a case study}, journal = {Software, IEEE}, volume = {22}, year = {2005}, month = {2005/12//nov}, pages = {68 - 75}, abstract = {The Capability Maturity Model for software has become a major force in software development process improvement. We looked at the role of process improvement in the context of a small organization. Although the Capability Maturity Model integration is replacing the CMM, we focused on the older CMM. We had to look at more than which CMM key process areas apply to small businesses. Our overall goal was to institute good software development practices, we used the language of the CMM to gain the management{\textquoteright}s cooperation. Applying these practices is essential to managing growth, yet undertaking this effort without prior experience could impede a small company{\textquoteright}s innovative nature. This case study{\textquoteright}s purpose was to investigate the success factors of a software process improvement effort for a small software development organization.}, keywords = {area;, aspects;, capability, CMM, development, improvement;, key, management;, Maturity, model;, organisational, organization;, process, small, software}, isbn = {0740-7459}, doi = {10.1109/MS.2005.162}, author = {Dangle,K.C. and Larsen,P. and Shaw,M. and Zelkowitz, Marvin V} } @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 {12284, title = {Stub Domain DDoS Detection}, year = {2005}, month = {2005///}, institution = {Technical Report of the Department of Computer Science, University of Maryland, College Park}, author = {Kommareddy,C. and Levin,D. and Bhattacharjee, Bobby and La,R.J. and Shayman,M.} } @conference {14531, title = {System for capturing of highorder spatial audio using spherical microphone array and binaural head-tracked playback over headphones with head related transfer function cues}, booktitle = {Proc. 119th convention AES}, year = {2005}, month = {2005///}, author = {Duraiswami, Ramani and Zotkin,Dmitry N and Li,Z. and Grassi,E. and Gumerov, Nail A. and Davis, Larry S.} } @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 {12099, title = {Toward resilient security in wireless sensor networks}, booktitle = {Proceedings of the 6th ACM international symposium on Mobile ad hoc networking and computing}, year = {2005}, month = {2005///}, pages = {34 - 45}, author = {Yang,H. and Ye,F. and Yuan,Y. and Lu,S. and Arbaugh, William A.} } @article {13881, title = {Umd/bbn at mse2005}, journal = {Proceedings of the MSE2005 track of the Association for Computational Linguistics Workshop on Intrinsic and Extrinsic Evaluation Meatures for MT and/or Summarization, Ann Arbor, MI}, year = {2005}, month = {2005///}, abstract = {We implemented an initial applicationof a sentence-trimming approach (Trim- mer) to the problem of multi-document summarization in the MSE2005 task. Sentence trimming was incorporated into a feature-based summarization sys- tem, called Multi-Document Trimmer (MDT), by using sentence trimming as both a pre-processing stage and a fea- ture for sentence ranking. We demon- strate that we were able to port Trimmer easily to this new problem, although the impact of sentence trimming was min- imal compared to other features used in the system. The performance of our sys- tem in the official MSE2005 task was around the middle of the pack (16 out of 27). After some minor bug fixes and a simple correction (dateline removal) we obtained an improvement on a post-hoc run on the test data. }, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin and Schwartz,R.} } @article {15087, title = {Universally composable password-based key exchange}, journal = {Advances in Cryptology{\textendash}Eurocrypt 2005}, year = {2005}, month = {2005///}, pages = {557 - 557}, abstract = {We propose and realize a definition of security for password-based key exchange within the framework of universally composable (UC) security, thus providing security guarantees under arbitrary composition with other protocols. In addition, our definition captures some aspects of the problem that were not adequately addressed by most prior notions. For instance, it does not assume any underlying probability distribution on passwords, nor does it assume independence between passwords chosen by different parties. We also formulate a definition of password-based secure channels, and show that such a definition is achievable given password-based key exchange.Our protocol realizing the new definition of password-based key exchange is in the common reference string model and relies on standard number-theoretic assumptions. The components of our protocol can be instantiated to give a relatively efficient solution which is conceivably usable in practice. We also show that it is impossible to satisfy our definition in the {\textquotedblleft}plain{\textquotedblright} model (e.g., without a common reference string). }, doi = {10.1007/11426639_24}, author = {Canetti,R. and Halevi,S. and Katz, Jonathan and Lindell,Y. and MacKenzie,P.} } @conference {13685, title = {Unwarping Images of Curved Documents Using Global Shape Optimization}, booktitle = {Proc. Fist International Workshop on Camera-based Document Analysis and Recognition}, year = {2005}, month = {2005///}, pages = {25 - 29}, author = {Liang,Jian and DeMenthon,Daniel and David Doermann} } @article {17465, title = {User Frustration with Technology in the Workplace (2004)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {When hard to use computers cause users to become frustrated, it can affect workplace productivity, user mood, and interactions with other co-workers. Previous research has examined the frustration that graduate students and their families face in using computers. To learn more about the causes and effects of user frustration with computers in the workplace, we collected modified time diaries from 50 workplace users, who spent an average of 5.1 hours on the computer. In this experiment, users reported wasting on average, 42-43\% of their time on the computer due to frustrating experiences. The causes of the frustrating experiences, the time lost due to the frustrating experiences, and the effects of the frustrating experiences on the mood of the users are discussed in this paper. Implications for designers, managers, users, information technology staff, and policymakers are discussed.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6515}, author = {Lazar,Jonathan and Jones,Adam and Bessiere,Katie and Ceaparu,Irina and Shneiderman, Ben} } @conference {13687, title = {Using Computer Vision to Detect Web Browser Display Errors}, booktitle = {3rd Web Document Analysis Workshop (on ICDAR 2005)}, year = {2005}, month = {2005/07//}, pages = {5 - 9}, abstract = {As the functionality and complexity of the WWW continues to grow so does the need for WWW quality assurance and testing. Although there have been numerous approaches to automated Web testing, existing techniques analyze primarily textual information, and the final judgment on correctness of layout is via human observation. The motivation of this paper is to employ computer vision techniques to detect Web display errors. To do this, we analyze images of the rendered pages rather than the HTML to discover errors. Our approach includes page segmentation, dynamic matching and outlier identification. We show that the approach successfully detects layout errors in the Opera browser on Microsoft Websites, while minimizing false alarms.}, author = {Liu,Xu and David Doermann} } @conference {14845, title = {Using the inner-distance for classification of articulated shapes}, booktitle = {Computer Vision and Pattern Recognition, 2005. CVPR 2005. IEEE Computer Society Conference on}, volume = {2}, year = {2005}, month = {2005/06//}, pages = {719 - 726 vol. 2 - 719 - 726 vol. 2}, abstract = {We propose using the inner-distance between landmark points to build shape descriptors. The inner-distance is defined as the length of the shortest path between landmark points within the shape silhouette. We show that the inner-distance is articulation insensitive and more effective at capturing complex shapes with part structures than Euclidean distance. To demonstrate this idea, it is used to build a new shape descriptor based on shape contexts. After that, we design a dynamic programming based method for shape matching and comparison. We have tested our approach on a variety of shape databases including an articulated shape dataset, MPEG7 CE-Shape-1, Kimia silhouettes, a Swedish leaf database and a human motion silhouette dataset. In all the experiments, our method demonstrates effective performance compared with other algorithms.}, keywords = {articulated, CE-Shape-1, classification;, database;, databases;, dataset;, descriptor;, dynamic, human, image, inner-distance;, Kimia, landmark, leaf, matching;, MOTION, MPEG7, points;, programming;, SHAPE, silhouette, silhouette;, Swedish, visual}, doi = {10.1109/CVPR.2005.362}, author = {Ling,H. and Jacobs, David W.} } @article {15664, title = {Vision geometry XIII(San Jose CA, 18-19 January 2005)}, journal = {SPIE proceedings series}, year = {2005}, month = {2005///}, author = {Latecki,L.J. and Mount, Dave and Wu,A. Y} } @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.} } @conference {12978, title = {Abstracting workflows: unifying bioinformatics task conceptualization and specification through Semantic Web services}, booktitle = {W3C Workshop on Semantic Web for Life Sciences}, year = {2004}, month = {2004///}, address = {Cambridge, Massachusetts USA}, author = {Hashmi,N. and Lee,S. and Cummings, Michael P.} } @article {14075, title = {Advances in schistosome genomics}, journal = {Trends in Parasitology}, volume = {20}, year = {2004}, month = {2004/04/01/}, pages = {154 - 157}, abstract = {In Spring 2004, the first draft of the 270~Mb genome of Schistosoma mansoni will be released. This sequence is based on the assembly and annotation of a >7.5-fold coverage, shotgun sequencing project. The key stages involved in the international collaborative efforts that have led to the generation of these sequencing data for the parasite S. mansoni are discussed here.}, isbn = {1471-4922}, doi = {16/j.pt.2004.02.002}, url = {http://www.sciencedirect.com/science/article/pii/S1471492204000480}, author = {El-Sayed, Najib M. and Bartholomeu,Daniella and Ivens,Alasdair and Johnston,David A. and LoVerde,Philip T.} } @article {14043, title = {Capture and recreation of higher order 3d sound fields via reciprocity}, journal = {International Conference on Audio Display}, year = {2004}, month = {2004///}, abstract = {We propose a unified and simple approach for capturing andrecreating 3D sound fields by exploring the reciprocity prin- ciple that is satisfied between the two processes. Our ap- proach makes the system easy to build, and practical. Us- ing this approach, we can capture the 3D sound field by a spherical microphone array and recreate it using a spheri- cal loudspeaker array, and ensure that the recreated sound field matches the recorded field up to a high order of spheri- cal harmonics. A design example and simulation results are presented. For some regular or semi-regular microphone layouts, we design an efficient parallel implementation of the multi-directional spherical beamformer by using the ro- tational symmetries of the beampattern and of the spherical microphone array. This can be implemented in either soft- ware or hardware. A simple design example is presented to demonstrate the idea. It can be easily adapted for other regular or semi-regular layouts of microphones. }, author = {Li,Z. and Duraiswami, Ramani and Gumerov, Nail A.} } @conference {12290, title = {The case for a multi-hop wireless local area network}, booktitle = {INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies}, volume = {2}, year = {2004}, month = {2004/03//}, pages = {894 - 905 vol.2 - 894 - 905 vol.2}, abstract = {We propose a multi-hop wireless LAN architecture and demonstrate its benefits to wireless clients. For this architecture, we define implementation paths that allow interoperation with existing wireless LANs which can lead to an incremental deployment of this system. We quantify the performance benefits of the proposed schemes through measurements in realistic wireless LAN environments. We also examine the performance of such multi-hop wireless LANs through detailed simulation studies. Our results show that these multi-hop extensions can significantly improve the wireless access experience (in terms of data throughput, latency, etc.) for clients who enable such mechanisms. More interestingly, when multi-hop extensions are enabled by some of the clients, it also positively impacts the performance at other clients that are completely unaware of these extensions.}, keywords = {access, access;, area, benefits;, client-server, clients;, interoperation;, LAN;, local, multihop, network;, networks;, performance, radio, systems;, wireless}, doi = {10.1109/INFCOM.2004.1356977}, author = {Lee,Seungjoon and Banerjee,S. and Bhattacharjee, Bobby} } @article {14597, title = {CHARACTERIZATION OF Ath17, A QUANTITATIVE TRAIT LOCUS FOR ATHEROSCLEROSIS SUSCEPTIBILITY BETWEEN C57BL/6J AND 129S1/SvImJ; SINGLE-NUCLEOTIDE POLYMORPHISMS HAVE IMPORTANT IMPLICATIONS ON IDENTIFYING ATHEROSCLEROSIS MODIFIER GENES}, journal = {Cardiovascular Pathology}, volume = {13}, year = {2004}, month = {2004/06//May}, pages = {5 - 6}, abstract = {Although identifying quantitative trait loci (QTL) for atherosclerosis susceptibility in experimental murine models has helped us better understand the pathophysiology of atherosclerosis, identifying the genes underlying these QTL has been a slow and difficult process. We are currently in the process of identifying the gene that underlies Ath17, an atherosclerosis-susceptibility QTL we discovered in a (C57BL/6J{\texttimes}129S1/SvImJ)F2 intercross. Ath17 maps to a 6 cM interval region on chromosome 10 (D10Mit31, LOD score 6.6) and contains 46 annotated and 133 predicted genes. We searched the Celera Discovery System database for single nucleotide polymorphisms (SNPs) between C57BL/6J (B6) and 129S1/SvImJ in the Ath17 region and found defined blocks of high and low diversity and one polymorphic region of over 4 Mb surrounded by nonpolymorphic regions. Four of the genes, including the annotated Desrt, in the polymorphic region contained mis-sense mutations. The Desrt coding region contained four mis-sense mutations: B6 lysine to 129 glutamic acid at aa382, B6 asparagine to 129 serine at aa388, B6 threonine to 129 alanine at aa836, and B6 glycine to 129 serine at aa964. In addition, intron 5 of Desrt contained a SNP which co-localized with a putative transcription factor binding site. Desrt is a DNA binding protein, widely expressed in adult tissues, and likely plays a role in cell proliferation, differentiation, and development, making Dsert a strong candidate gene for Ath17. The murine SNP database dramatically reduced the percentage of the murine genome we had to search to find viable candidate genes for Ath17.}, isbn = {1054-8807}, doi = {10.1016/j.carpath.2004.03.010}, url = {http://www.sciencedirect.com/science/article/pii/S1054880704000377}, author = {Ishimori,Naoki and Walsh,Kenneth and Zheng,Xiangqun and Lu,Fu and Hannenhalli, Sridhar and Nusskern,Deborah and Mural,Richard and Paigen,Beverly} } @article {18176, title = {Collusion resistant multimedia fingerprinting: A unified framework}, journal = {Electronic Imaging Symposium: Security, Steganography, and Watermarking of Multimedia Contents VI, San Jose, CA, Proc. of SPIE}, volume = {5306}, year = {2004}, month = {2004///}, pages = {748 - 759}, abstract = {Digital fingerprints are unique labels inserted in different copies of the same content before distribution. Eachdigital fingerprint is assigned to an intended recipient, and can be used to trace the culprits who use their content for unintended purposes. Attacks mounted by multiple users, known as collusion attacks, provide a cost-effective method for attenuating the identifying fingerprint from each colluder, thus collusion poses a real challenge to protect the digital media data and enforce usage policies. This paper examines a few major design methodologies for collusion-resistant fingerprinting of multimedia, and presents a unified framework that helps highlight the common issues and the uniqueness of different fingerprinting techniques. }, author = {Wu,M. and Trappe,W. and Wang,Z.J. and Liu,K. J.R} } @article {18180, title = {Collusion-resistant fingerprinting for multimedia}, journal = {Signal Processing Magazine, IEEE}, volume = {21}, year = {2004}, month = {2004/03//}, pages = {15 - 27}, abstract = {Digital fingerprinting is a technology for enforcing digital rights policies whereby unique labels, known as digital fingerprints, are inserted into content prior to distribution. For multimedia content, fingerprints can be embedded using conventional watermarking techniques that are typically concerned with robustness against a variety of attacks mounted by an individual. These attacks, known as multiuser collusion attacks, provide a cost-effective method for attenuating each of the colluder{\textquoteright}s fingerprints and poses a real threat to protecting media data and enforcing usage policies. In this article, we review some major design methodologies for collusion-resistant fingerprinting of multimedia and highlight common and unique issues of different fingerprinting techniques. It also provides detailed discussions on the two major classes of fingerprinting strategies, namely, orthogonal fingerprinting and correlated fingerprinting.}, keywords = {attacks;, colluder, collusion, collusion-resistant, content;, correlated, data;, digital, fingerprinting;, identification;, multimedia, multiuser, of, orthogonal, policies;, rights, Security, systems;, techniques;, tracing;, watermarking, watermarking;}, isbn = {1053-5888}, doi = {10.1109/MSP.2004.1276103}, author = {M. Wu and Trappe,W. and Wang,Z.J. and Liu,K. J.R} } @conference {13281, title = {Constant-time navigation in four-dimensional nested simplicial meshes}, booktitle = {Shape Modeling Applications, 2004. Proceedings}, year = {2004}, month = {2004/06//}, pages = {221 - 230}, abstract = {We consider a recursive decomposition of a four-dimensional hypercube into a hierarchy of nested 4-dimensional simplexes, that we call pentatopes. The paper presents an algorithm for finding the neighbors of a pentatope along its five tetrahedral faces in constant time. To this aim, we develop a labeling technique for nested pentatopes that enables their identification by using location codes. The constant-time behavior is achieved through bit manipulation operations, thus avoiding traversing the simplicial hierarchy via pointer following. We discuss an application of this representation to multi-resolution representations of four-dimensional scalar fields. Extracting adaptive continuous approximations of the scalar field from such a model requires generating conforming meshes, i.e., meshes in which the pentatopes match along their tetrahedral faces. Our neighbor finding algorithm enables computing face-adjacent pentatopes efficiently.}, keywords = {4-dimensional, adaptive, algorithm;, approximations;, bit, codes;, computational, constant-time, continuous, decomposition;, face-adjacent, faces;, fields;, finding, following;, four-dimensional, generation;, geometry;, hierarchy;, hypercube;, location, manipulation, mesh, meshes;, multiresolution, navigation;, neighbor, nested, operations;, pentatopes;, pointer, recursive, representation;, scalar, simplexes;, simplicial, tetrahedral}, doi = {10.1109/SMI.2004.1314509}, author = {Lee,M. and De Floriani, Leila and Samet, Hanan} } @article {18187, title = {Data hiding in binary image for authentication and annotation}, journal = {Multimedia, IEEE Transactions on}, volume = {6}, year = {2004}, month = {2004/08//}, pages = {528 - 538}, abstract = {This paper proposes a new method to embed data in binary images, including scanned text, figures, and signatures. The method manipulates "flippable" pixels to enforce specific block-based relationship in order to embed a significant amount of data without causing noticeable artifacts. Shuffling is applied before embedding to equalize the uneven embedding capacity from region to region. The hidden data can be extracted without using the original image, and can also be accurately extracted after high quality printing and scanning with the help of a few registration marks. The proposed data embedding method can be used to detect unauthorized use of a digitized signature, and annotate or authenticate binary documents. The paper also presents analysis and discussions on robustness and security issues.}, keywords = {annotation;, authentication;, binary, coding;, data, digital, digitized, document, EMBEDDING, encapsulation;, extraction;, feature, hiding;, image, image;, method;, signature;, unauthorized, user;, watermarking;}, isbn = {1520-9210}, doi = {10.1109/TMM.2004.830814}, author = {M. Wu and Liu,Bede} } @article {14481, title = {Data sciences technology for homeland security information management and knowledge discovery}, journal = {Report of the DHS Workshop Data Sciences, Jointly Released by Sandia National Laboratories and Lawrence Livermore National Laboratory, Alexandria, Va}, year = {2004}, month = {2004///}, author = {Kolda,T. and Brown,D and Corones,J. and Critchlow,T. and Eliassi-Rad,T. and Getoor, Lise and Hendrickson,B. and Kumar, V. and Lambert,D. and Matarazzo,C.} } @article {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 {18200, title = {Distortion management of real-time MPEG-4 video over downlink multicode CDMA networks}, booktitle = {Communications, 2004 IEEE International Conference on}, volume = {5}, year = {2004}, month = {2004/06//}, pages = {3071 - 3075 Vol.5 - 3071 - 3075 Vol.5}, abstract = {In this paper, a protocol is designed to manage source rate/channel coding rate adaptation, code allocation, and power control to transmit real-time MPEG-4 FGS video over downlink multicode CDMA networks. We develop a fast adaptive scheme of distortion management to reduce the overall distortion received by all users subject, to the limited number of codes and maximal transmitted power. Compared with a modified greedy method in literature, our proposed algorithm can reduce the overall system{\textquoteright}s distortion by at least 45\%.}, keywords = {access;, adaptation;, allocation;, CDMA, channel, code, coding, coding;, combined, communication;, compression;, control;, data, distortion, division, downlink, links;, management;, MPEG-4, multicode, multiple, networks;, power, radio, rate, real-time, resource, source, source-channel, video, video;, visual}, doi = {10.1109/ICC.2004.1313096}, author = {Su,Guan-Ming and Han,Zhu and Kwasinski,A. and M. Wu and Liu,K. J.R and Farvardin,N.} } @conference {18201, title = {Dynamic distortion control for 3-D embedded wavelet video over multiuser OFDM networks}, booktitle = {Global Telecommunications Conference, 2004. GLOBECOM {\textquoteright}04. IEEE}, volume = {2}, year = {2004}, month = {2004/12/03/nov}, pages = {650 - 654 Vol.2 - 650 - 654 Vol.2}, abstract = {In this paper, we propose a system to transmit multiple 3D embedded wavelet video programs over downlink multiuser OFDM. We consider the fairness among users and formulate the problem as minimizing the users{\textquoteright} maximal distortion subject to power, rate, and subcarrier constraints. By exploring frequency, time, and multiuser diversity in OFDM and flexibility of the 3D embedded wavelet video codec, the proposed algorithm can achieve fair video qualities among all users. Compared to a scheme similar to the current multiuser OFDM standard (IEEE 802.11a), the proposed scheme outperforms it by 1-5 dB on the worst received PSNR among all users and has much smaller PSNR deviation.}, keywords = {3D, 802.11a;, channels;, codec;, codecs;, communication;, control;, deviation;, distortion, diversity, diversity;, downlink, dynamic, embedded, fairness;, Frequency, IEEE, LAN;, maximal, minimax, minimization;, modulation;, multimedia, multiuser, OFDM, OFDM;, PSNR, rate, reception;, streaming;, systems;, techniques;, theory;, TIME, transforms;, video, video;, wavelet, wireless}, doi = {10.1109/GLOCOM.2004.1378042}, author = {Su,Guan-Ming and Han,Zhu and M. Wu and Liu,K. J.R} } @conference {18202, title = {Dynamic join-exit amortization and scheduling for time-efficient group key agreement}, booktitle = {INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies}, volume = {4}, year = {2004}, month = {2004/03//}, pages = {2617 - 2627 vol.4 - 2617 - 2627 vol.4}, abstract = {We propose a time-efficient contributory key agreement framework for secure communications in dynamic groups. The proposed scheme employs a special join-tree/exit-tree topology in the logical key tree and effectively exploits the efficiency of amortized operations. We derive the optimal parameters and design an activation algorithm for the join and exit trees. We also show that the asymptotic average time cost per user join and leave event is theta;(log (log n)), where n is the group size. Our experiment results on both simulated user activities and the real MBone data have shown that the proposed scheme outperforms the existing tree-based schemes.}, keywords = {agreement;, asymptotic, average, communication;, complexity;, computational, cost;, cryptography;, dynamic, group, join-tree/exit-tree, key, logical, Multicast, network, secure, security;, special, Telecommunication, TIME, time-efficient, topology;, tree;}, doi = {10.1109/INFCOM.2004.1354681}, author = {Mao,Yinian and Sun,Yan and M. Wu and Liu,K. J.R} } @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} } @conference {15313, title = {Fine-grained lexical semantic representations and compositionally-derived events in Mandarin Chinese}, booktitle = {Proceedings of the HLT-NAACL Workshop on Computational Lexical Semantics}, series = {CLS {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {100 - 107}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Current lexical semantic representations for natural language applications view verbs as simple predicates over their arguments. These structures are too coarse-grained to capture many important generalizations about verbal argument structure. In this paper, I specifically defend the following two claims: verbs have rich internal structure expressible in terms of finer-grained primitives of meaning, and at least for some languages, verbal meaning is compositionally derived from these primitive elements. I primarily present evidence from Mandarin Chinese, whose verbal system is very different from that of English. Many empirical facts about the typology of verbs in Mandarin cannot be captured by a "flat" lexical semantic representation. These theoretical results hold important practical consequences for natural language processing applications.}, url = {http://dl.acm.org/citation.cfm?id=1596431.1596445}, author = {Jimmy Lin} } @conference {13220, title = {Flexible layout and optimal cancellation of the orthonormality error for spherical microphone arrays}, booktitle = {Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP {\textquoteright}04). IEEE International Conference on}, volume = {4}, year = {2004}, month = {2004/05//}, pages = {iv-41 - iv-44 vol.4 - iv-41 - iv-44 vol.4}, abstract = {This paper describes an approach to achieving a flexible layout of microphones on the surface of a spherical microphone array for beamforming. Our approach achieves orthonormality of spherical harmonics to higher order for relatively distributed layouts. This gives great flexibility in microphone layout on the spherical surface. One direct advantage is that it makes it much easier to build a real world system, such as those with cable outlets and a mounting base, with minimal effects on the performance. Simulation results are presented.}, keywords = {array, audio, base;, beamforming;, cable, cancellation, correction;, error, flexible, harmonics;, higher, layout;, microphone, microphones;, mounting, optimization;, order, orthonormality, outlets;, processing;, signal, spherical, surface;}, doi = {10.1109/ICASSP.2004.1326758}, author = {Zhiyun Li and Duraiswami, Ramani and Grassi,E. and Davis, Larry S.} } @article {18844, title = {Geometric algorithms for automated design of rotary-platen multi-shot molds}, journal = {Computer-Aided Design}, volume = {36}, year = {2004}, month = {2004/10//}, pages = {1171 - 1187}, abstract = {This paper describes algorithms for automated design of rotary-platen type of multi-shot molds for manufacturing multi-material objects. The approach behind our algorithms works in the following manner. First, we classify the given multi-material object into several basic types based on the relationships among different components in the object. For every basic type, we find a molding sequence based on the precedence constraints resulting due to accessibility and disassembly requirements. Then, starting from the last mold stage, we generate the mold pieces for every mold stage. We expect that algorithms described in this paper will provide the necessary foundations for automating the design of rotary-platen molds.}, keywords = {geometric reasoning, mold design, Multi-shot molds}, isbn = {0010-4485}, doi = {10.1016/j.cad.2003.11.003}, url = {http://www.sciencedirect.com/science/article/pii/S0010448503002331}, author = {Li,Xuejun and Gupta, Satyandra K.} } @article {18648, title = {A global-state-triggered fault injector for distributed system evaluation}, journal = {Parallel and Distributed Systems, IEEE Transactions on}, volume = {15}, year = {2004}, month = {2004/07//}, pages = {593 - 605}, abstract = {Validation of the dependability of distributed systems via fault injection is gaining importance because distributed systems are being increasingly used in environments with high dependability requirements. The fact that distributed systems can fail in subtle ways that depend on the state of multiple parts of the system suggests that a global-state-based fault injection mechanism should be used to validate them. However, global-state-based fault injection is challenging since it is very difficult in practice to maintain the global state of a distributed system at runtime with minimal intrusion into the system execution. We present Loki, a global-state-based fault injector, which has been designed with the goals of low intrusion, high precision, and high flexibility. Loki achieves these goals by utilizing the ideas of partial view of global state, optimistic synchronization, and offline analysis. In Loki, faults are injected based on a partial, view of the global state of the system, and a post-runtime analysis is performed to place events and injections into a single global timeline and to discard experiments with incorrect fault injections. Finally, the experiments with correct fault injections are used to estimate user-specified performance and dependability measures. A flexible measure language has been designed that facilitates the specification of a wide range of measures.}, keywords = {distributed processing, distributed system evaluation, fault tolerant computing, global-state-based fault injection mechanism, Loki, offline clock synchronization, performance evaluation, post-runtime analysis, Synchronisation, system recovery, user-specified performance}, isbn = {1045-9219}, doi = {10.1109/TPDS.2004.14}, author = {Chandra,Ramesh and Lefever,R.M. and Joshi,K.R. and Michel Cukier and Sanders,W. H.} } @article {18220, title = {Group-oriented fingerprinting for multimedia forensics}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2004}, year = {2004}, month = {2004/01//}, pages = {2153 - 2173}, abstract = {Digital fingerprinting of multimedia data involves embedding information in the content signal and offers protection to the digital rights of the content by allowing illegitimate usage of the content to be identified by authorized parties. One potential threat to fingerprinting is collusion, whereby a group of adversaries combine their individual copies in an attempt to remove the underlying fingerprints. Former studies indicate that collusion attacks based on a few dozen independent copies can confound a fingerprinting system that employs orthogonal modulation. However, in practice an adversary is more likely to collude with some users than with other users due to geographic or social circumstances. To take advantage of prior knowledge of the collusion pattern, we propose a two-tier group-oriented fingerprinting scheme where users likely to collude with each other are assigned correlated fingerprints. Additionally, we extend our construction to represent the natural social and geographic hierarchical relationships between users by developing a more flexible tree-structure-based fingerprinting system. We also propose a multistage colluder identification scheme by taking advantage of the hierarchial nature of the fingerprints. We evaluate the performance of the proposed fingerprinting scheme by studying the collusion resistance of a fingerprinting system employing Gaussian-distributed fingerprints. Our results show that the group-oriented fingerprinting system provides the superior collusion resistance over a system employing orthogonal modulation when knowledge of the potential collusion pattern is available.}, keywords = {collusion resistance, group-oriented fingerprinting, multimedia fingerprinting, multimedia forensics, multistage colluder identification}, isbn = {1110-8657}, doi = {10.1155/S1110865704312151}, url = {http://dx.doi.org/10.1155/S1110865704312151}, author = {Wang,Z. Jane and M. Wu and Trappe,Wade and Liu,K. J.R} } @article {15875, title = {iCLEF 2003 at Maryland: Translation selection and document selection}, journal = {Comparative Evaluation of Multilingual Information Access Systems}, year = {2004}, month = {2004///}, pages = {231 - 265}, author = {Dorr, Bonnie J and He,D. and Luo,J. and Oard, Douglas and Schwartz,R. and Wang,J. and Zajic, David} } @inbook {13787, title = {iCLEF 2003 at Maryland: Translation Selection and Document Selection}, booktitle = {Comparative Evaluation of Multilingual Information Access SystemsComparative Evaluation of Multilingual Information Access Systems}, series = {Lecture Notes in Computer Science}, volume = {3237}, year = {2004}, month = {2004///}, pages = {231 - 265}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Maryland performed two sets of experiments for the 2003 Cross-Language Evaluation Forum{\textquoteright}s interactive track, one focused on interactive selection of appropriate translations for query terms, the second focused on interactive selection of relevant documents. Translation selection was supported using possible synonyms discovered through back translation and two techniques for generating KeyWord In Context (KWIC) examples of usage. The results indicate that searchers typically achieved a similar search effectiveness using fewer query iterations when interactive translation selection was available. For document selection, a complete extract of the first 40 words of each news story was compared to a compressed extract generated using an automated parse-and-trim approach that approximates one way in which people can produce headlines. The results indicate that compressed {\textquotedblleft}headlines{\textquotedblright} result in faster assessment, but with a 20\% relative reduction in the F α = 0.8 search effectiveness measure.}, isbn = {978-3-540-24017-4}, url = {http://dx.doi.org/10.1007/978-3-540-30222-3_42}, author = {Dorr, Bonnie J and He,Daqing and Luo,Jun and Oard, Douglas and Schwartz,Richard and Wang,Jianqiang and Zajic, David}, editor = {Peters,Carol and Gonzalo,Julio and Braschler,Martin and Kluck,Michael} } @conference {15842, title = {iCLEF 2004 at Maryland: Summarization design for interactive cross-language question answering}, booktitle = {Proceeding of Cross Language Evaluation Forum (CLEF2004)}, year = {2004}, month = {2004///}, author = {He,D. and Wang,J. and Luo,J. and Oard, Douglas} } @article {15760, title = {Implementation of the regularized structured total least squares algorithms for blind image deblurring}, journal = {Linear Algebra and its Applications}, volume = {391}, year = {2004}, month = {2004/11/01/}, pages = {203 - 221}, abstract = {The structured total least squares (STLS) problem has been introduced to handle problems involving structured matrices corrupted by noise. Often the problem is ill-posed. Recently, regularization has been proposed in the STLS framework to solve ill-posed blind deconvolution problems encountered in image deblurring when both the image and the blurring function have uncertainty. The kernel of the regularized STLS (RSTLS) problem is a least squares problem involving Block{\textendash}Toeplitz{\textendash}Toeplitz{\textendash}Block matrices.In this paper an algorithm is described to solve this problem, based on a particular implementation of the generalized Schur Algorithm (GSA). It is shown that this new implementation improves the computational efficiency of the straightforward implementation of GSA from O(N2.5) to O(N2), where N is the number of pixels in the image. }, keywords = {Block Toeplitz matrix, Displacement rank, Generalized Schur algorithm, Image deblurring, Structured total least squares, Tikhonov regularization}, isbn = {0024-3795}, doi = {10.1016/j.laa.2004.07.006}, url = {http://www.sciencedirect.com/science/article/pii/S0024379504003362}, author = {Mastronardi,N. and Lemmerling,P. and Kalsi,A. and O{\textquoteright}Leary,D. P and Huffel,S. Van} } @article {13227, title = {Improved Multiuser Detectors Employing Genetic Algorithms in a Space-Time Block Coded System, Yinggang Du and Kam Tai Chan}, journal = {Signal}, volume = {2004}, year = {2004}, month = {2004///}, pages = {640 - 648}, author = {Self-Similarity,G.R.U.I. and BenAbdelkader,C. and Cutler,R.G. and Davis, Larry S. and Local,F.R.U. and Global Features,J.H. and Yuen, P.C. and Lai,JH and Li,C.} } @article {15850, title = {Interactive cross-language document selection}, journal = {information retrieval}, volume = {7}, year = {2004}, month = {2004///}, pages = {205 - 228}, author = {Oard, Douglas and Gonzalo,J. and Sanderson,M. and L{\'o}pez-Ostenero,F. and Wang,J.} } @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 {17947, title = {Light Collages: Lighting Design for Effective Visualization}, booktitle = {Proceedings of the conference on Visualization {\textquoteright}04}, series = {VIS {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {281 - 288}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {We introduce Light Collages {\textquestiondown} a lighting design system for effective visualization based on principles of human perception. Artists and illustrators enhance perception of features with lighting that is locally consistent and globally inconsistent. Inspired by these techniques, we design the placement of light sources to convey a greater sense of realism and better perception of shape with globally inconsistent lighting. Our algorithm segments the objects into local surface patches and uses a number of perceptual heuristics, such as highlights, shadows, and silhouettes, to enhance the perception of shape. We show our results on scientific and sculptured datasets.}, keywords = {inconsistent lighting, light placement, lighting design, proximity shadows, scientific illustration, silhouette enhancement}, isbn = {0-7803-8788-0}, doi = {10.1109/VISUAL.2004.62}, url = {http://dx.doi.org/10.1109/VISUAL.2004.62}, author = {Lee,Chang Ha and Hao,Xuejun and Varshney, Amitabh} } @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 {13592, title = {Machine printed text and handwriting identification in noisy document images}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {26}, year = {2004}, month = {2004/03//}, pages = {337 - 353}, abstract = {In this paper, we address the problem of the identification of text in noisy document images. We are especially focused on segmenting and identifying between handwriting and machine printed text because: 1) Handwriting in a document often indicates corrections, additions, or other supplemental information that should be treated differently from the main content and 2) the segmentation and recognition techniques requested for machine printed and handwritten text are significantly different. A novel aspect of our approach is that we treat noise as a separate class and model noise based on selected features. Trained Fisher classifiers are used to identify machine printed text and handwriting from noise and we further exploit context to refine the classification. A Markov Random Field-based (MRF) approach is used to model the geometrical structure of the printed text, handwriting, and noise to rectify misclassifications. Experimental results show that our approach is robust and can significantly improve page segmentation in noisy document collections.}, keywords = {Automated;Reading;Reproducibility of Results;Sensitivity and Specificity;Signal Processing, Computer-Assisted;Information Storage and Retrieval;Models, Computer-Assisted;Pattern Recognition, Computer-Assisted;Stochastic Processes;Subtraction Technique;User-Computer Interface;Writing;, Markov random field;fisher classifiers;handwriting identification;machine printed text;noisy document images;page segmentation;recognition techniques;text identification;Markov processes;document image processing;feature extraction;handwriting recognition, Statistical;Numerical Analysis}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2004.1262324}, author = {Yefeng Zheng and Huiping Li and David Doermann} } @article {15861, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, journal = {Computer Speech \& Language}, volume = {18}, year = {2004}, month = {2004/04//}, pages = {163 - 179}, abstract = {This paper describes the Mandarin{\^a}{\texteuro}{\textquotedblleft}English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English{\^a}{\texteuro}{\textquotedblleft}Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence, this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks {\^a}{\texteuro}{\textquotedblleft} multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {English{\^a}{\texteuro}{\textquotedblleft}Chinese cross-language spoken document retrieval, Multi-scale spoken document retrieval}, isbn = {0885-2308}, doi = {10.1016/j.csl.2003.09.003}, url = {http://www.sciencedirect.com/science/article/pii/S0885230803000524}, author = {Meng,Helen M. and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @conference {12291, title = {Measurement based optimal multi-path routing}, booktitle = {INFOCOM 2004. Twenty-third AnnualJoint Conference of the IEEE Computer and Communications Societies}, volume = {1}, year = {2004}, month = {2004/03//}, pages = {187 - 196}, abstract = {We propose a new architecture for efficient network monitoring and measurements in a traditional IP network. This new architecture enables establishment of multiple paths (tunnels) between source-destination pairs without having to modify the underlying routing protocol(s). Based on the proposed architecture we propose a measurement-based multipath routing algorithm derived from simultaneous perturbation stochastic approximation. The proposed algorithm does not assume that the gradient of analytical cost function is known to the algorithm, but rather relies on noisy estimates from measurements. Using the analytical model presented in the paper we prove the convergence of the algorithm to the optimal solution. Simulation results are presented to demonstrate the advantages of the proposed algorithm under a variety of network scenarios. A comparative study with an existing optimal routing algorithm, MATE, is also provided}, keywords = {algorithm;network, approximation;routing, IP, measurement;network, monitoring;optimization;perturbation, multipath, network;measurement-based, networks;Internet;optimisation;routing, processes;, protocol;IP, protocols;stochastic, Routing, Stochastic}, doi = {10.1109/INFCOM.2004.1354493}, author = {Guven,T. and Kommareddy,C. and La,R.J. and Shayman,M.A. and Bhattacharjee, Bobby} } @conference {13209, title = {Multi-level fast multipole method for thin plate spline evaluation}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {3}, year = {2004}, month = {2004/10//}, pages = {1683 - 1686 Vol. 3 - 1683 - 1686 Vol. 3}, abstract = {Image registration is an important problem in image processing and computer vision. Much recent work in image registration is on matching non-rigid deformations. Thin plate splines are an effective image registration method when the deformation between two images can be modeled as the bending of a thin metal plate on point constraints such that the topology is preserved (non-rigid deformation). However, because evaluating the computed TPS model at all the image pixels is computationally expensive, we need to speed it up. We introduce the use of multi-level fast muitipole method (MLFMM) for this purpose. Our contribution lies in the presentation of a clear and concise MLFMM framework for TPS, which will be useful for future application developments. The achieved speedup using MLFMM is an improvement from O(N2) to O(N log N). We show that the fast evaluation outperforms the brute force method while maintaining acceptable error bound.}, keywords = {(mathematics);, Computer, deformation;, evaluation;, fast, image, MATCHING, matching;, metal, method;, multilevel, multipole, nonrigid, pixel;, plate, plate;, processing;, registration;, resolution;, spline, splines, thin, vision;}, doi = {10.1109/ICIP.2004.1421395}, author = {Zandifar,A. and Lim,S. and Duraiswami, Ramani and Gumerov, Nail A. and Davis, Larry S.} } @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.} } @article {12149, title = {New year{\textquoteright}s resolutions for software quality}, journal = {IEEE Software}, volume = {21}, year = {2004}, month = {2004///}, pages = {12 - 13}, abstract = {In the spirit of making resolutions for betterment in the New Year, ten distinguished individuals in the software quality field offer their recommendations on how organizations can improve software quality In the spirit of making resolutions for betterment in the New Year, ten distinguished individuals in the software quality field offer their recommendations on how organizations can improve software quality.}, author = {Basili, Victor R. and Boehm,B. and Davis,A. and Humphrey,W. S and Leveson,N. and Mead,N. R and Musa,J. D and Parnas,D. L and Pfleeger,S. L and Weyuker,E.} } @article {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 {15097, title = {One-round protocols for two-party authenticated key exchange}, journal = {Applied Cryptography and Network Security}, year = {2004}, month = {2004///}, pages = {220 - 232}, author = {Jeong,I. R and Katz, Jonathan and Lee,D. H} } @article {17798, title = {Optimal models of disjunctive logic programs: semantics, complexity, and computation}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {16}, year = {2004}, month = {2004/04//}, pages = {487 - 503}, abstract = {Almost all semantics for logic programs with negation identify a set, SEM(P), of models of program P, as the intended semantics of P, and any model M in this class is considered a possible meaning of P with regard to the semantics the user has in mind. Thus, for example, in the case of stable models [M. Gelfond et al., (1988)], choice models [D. Sacca et al., (1990)], answer sets [M. Gelfond et al., (1991)], etc., different possible models correspond to different ways of "completing" the incomplete information in the logic program. However, different end-users may have different ideas on which of these different models in SEM(P) is a reasonable one from their point of view. For instance, given SEM(P), user U1 may prefer model M1 isin;SEM(P) to model M2 isin;SEM(P) based on some evaluation criterion that she has. We develop a logic program semantics based on optimal models. This semantics does not add yet another semantics to the logic programming arena - it takes as input an existing semantics SEM(P) and a user-specified objective function Obj, and yields a new semantics Opt(P)_ sube; SEM(P) that realizes the objective function within the framework of preferred models identified already by SEM(P). Thus, the user who may or may not know anything about logic programming has considerable flexibility in making the system reflect her own objectives by building "on top" of existing semantics known to the system. In addition to the declarative semantics, we provide a complete complexity analysis and algorithms to compute optimal models under varied conditions when SEM(P) is the stable model semantics, the minimal models semantics, and the all-models semantics.}, keywords = {complexity;, computational, disjunctive, function;, knowledge, LANGUAGE, Logic, minimal, model, nonmonotonic, objective, optimisation;, OPTIMIZATION, problems;, program, Programming, programming;, reasoning;, representation;, semantics;, stable, user-specified}, isbn = {1041-4347}, doi = {10.1109/TKDE.2004.1269672}, author = {Leone,N. and Scarcello,F. and V.S. Subrahmanian} } @article {12940, title = {Polylysogeny and prophage induction by secondary infection in Vibrio cholerae}, journal = {Environmental Microbiology}, volume = {6}, year = {2004}, month = {2004/07/01/}, pages = {760 - 763}, abstract = {Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (ΦP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, ΦP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6~days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2004.00603.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2004.00603.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Espeland,Eric M. and Lipp,Erin K. and Huq,Anwar and Rita R Colwell} } @article {18018, title = {Reconfigurable optical wireless sensor networks}, journal = {Proceedings of SPIE}, volume = {5237}, year = {2004}, month = {2004/02/06/}, pages = {136 - 146}, abstract = {Optical wireless networks are emerging as a viable, cost effective technology for rapidly deployable broadband sensor communication infrastructures. The use of directional, narrow beam, optical wireless links provides great promise for secure, extremely high data rate communication between fixed or mobile nodes, very suitable for sensor networks in civil and military contexts. The main challenge is to maintain the quality of such networks, as changing atmosphericand platform conditions critically affect their performance. Topology control is used as the means to achieve survivable optical wireless networking under adverse conditions, based on dynamic and autonomous topology reconfiguration. The topology control process involves tracking and acquisition of nodes, assessment of link-state information, collection and distribution of topology data, and the algorithmic solution of an optimal topology. This paper focuses onthe analysis, implementation and evaluation of algorithms and heuristics for selecting the best possible topology in order to optimize a given performance objective while satisfying connectivity constraints. The work done at the physical layer is based on link cost information. A cost measure is defined in terms of bit-error-rate and the heuristics developed seek to form a bi-connected topology which minimizes total network cost. At the network layer a key factor is the traffic matrix, and heuristics were developed in order to minimize congestion, flow-rate or end-to-end delay.}, isbn = {0277786X}, doi = {doi:10.1117/12.511368}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/5237/1/136_1?isAuthorized=no}, author = {Llorca,Jaime and Desai,Aniket and Vishkin, Uzi and Davis,Christopher C. and Milner,Stuart D} } @conference {13208, title = {Recording and reproducing high order surround auditory scenes for mixed and augmented reality}, booktitle = {Mixed and Augmented Reality, 2004. ISMAR 2004. Third IEEE and ACM International Symposium on}, year = {2004}, month = {2004/11//}, pages = {240 - 249}, abstract = {Virtual reality systems are largely based on computer graphics and vision technologies. However, sound also plays an important role in human{\textquoteright}s interaction with the surrounding environment, especially for the visually impaired people. In this paper, we develop the theory of recording and reproducing real-world surround auditory scenes in high orders using specially designed microphone and loudspeaker arrays. It is complementary to vision-based technologies in creating mixed and augmented realities. Design examples and simulations are presented.}, keywords = {array;, audio, auditory, augmented, Computer, graphics;, high, loudspeaker, microphone, mixed, order, processing;, reality, reality;, scene;, signal, surround, system;, technology;, virtual, VISION, vision;}, doi = {10.1109/ISMAR.2004.51}, author = {Zhiyun Li and Duraiswami, Ramani and Davis, Larry S.} } @conference {12298, title = {Scalable resilient media streaming}, booktitle = {Proceedings of the 14th international workshop on Network and operating systems support for digital audio and video}, series = {NOSSDAV {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {4 - 9}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a low-overhead media streaming system, called SRMS (Scalable Resilient Media Streaming) that can be used to scalably deliver streaming data to a large group of receivers. SRMS uses overlay multicast for data distribution. to a large group of users. SRMS leverages a probabilistic loss recovery technique to provide high data delivery guarantees even under large network losses and overlay node failures. The clients in the SRMS system are able to interoperate with existing media streaming servers that use RTP for data transport. One of the interesting features of SRMS is that it can simultaneously support clients with disparate access bandwidths. It enables the necessary bandwidth adaptations using standard Real-time Transport Protocol (RTP) mechanisms, e.g. RTP translators. We have implemented and evaluated the SRMS system in detail on an emulated network as well as on a wide-area testbed with up to 128 clients. Our results show that clients using SRMS achieve high (97\%) data delivery ratios with low overheads (<5\%) even for a very dynamic network (up to five membership changes per minute).}, keywords = {media streaming, Multicast, overlay network, Resilience}, isbn = {1-58113-801-6}, doi = {10.1145/1005847.1005851}, url = {http://doi.acm.org/10.1145/1005847.1005851}, author = {Banerjee,Suman and Lee,Seungjoon and Braud,Ryan and Bhattacharjee, Bobby and Srinivasan, Aravind} } @article {14070, title = {Schistosoma mansoni genome project: an update}, journal = {Parasitology International}, volume = {53}, year = {2004}, month = {2004/06//}, pages = {183 - 192}, abstract = {A schistosome genome project was initiated by the World Health Organization in 1994 with the notion that the best prospects for identifying new targets for drugs, vaccines, and diagnostic development lie in schistosome gene discovery, development of chromosome maps, whole genome sequencing and genome analysis. Schistosoma mansoni has a haploid genome of 270 Mb contained on 8 pairs of chromosomes. It is estimated that the S. mansoni genome contains between 15~000 and 25~000 genes. There are approximately 16~689 ESTs obtained from diverse libraries representing different developmental stages of S. mansoni, deposited in the NCBI EST database. More than half of the deposited sequences correspond to genes of unknown function. Approximately 40-50\% of the sequences form unique clusters, suggesting that approximately 20-25\% of the total schistosome genes have been discovered. Efforts to develop low resolution chromosome maps are in progress. There is a genome sequencing program underway that will provide 3X sequence coverage of the S. mansoni genome that will result in approximately 95\% gene discovery. The genomics era has provided the resources to usher in the era of functional genomics that will involve microarrays to focus on specific metabolic pathways, proteomics to identify relevant proteins and protein-protein interactions to understand critical parasite pathways. Functional genomics is expected to accelerate the development of control and treatment strategies for schistosomiasis.}, keywords = {Chromosome mapping, Gene discovery, Genomics, Schistosoma mansoni}, isbn = {1383-5769}, doi = {16/j.parint.2004.01.009}, url = {http://www.sciencedirect.com/science/article/pii/S1383576904000108}, author = {LoVerde,Philip T. and Hirai,Hirohisa and Merrick,Joseph M and Lee,Norman H and El-Sayed, Najib M.} } @inbook {13324, title = {Selective refinement on nested tetrahedral meshes}, booktitle = {Geometric Modeling for Scientific VisualizationGeometric Modeling for Scientific Visualization}, year = {2004}, month = {2004///}, pages = {329 - 344}, publisher = {Birkh{\"a}user}, organization = {Birkh{\"a}user}, isbn = {9783540401162}, author = {De Floriani, Leila and Lee,M.} } @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} } @article {17657, title = {SESSION 2: STREAMING}, journal = {Proceedings of the 14th International Workshop on Network and Operating Systems Support for Digital Audio and Video: NOSSDAV 2003: June 16-18, 2004, Cork, Ireland}, year = {2004}, month = {2004///}, pages = {3 - 3}, author = {Banerjee,S. and Lee,S. and Braud,R. and Bhattacharjee, Bobby and Srinivasan, Aravind and Chu,Y. and Zhang,H. and Sinha,R. and Papadopoulos,C. and Boustead,P. and others} } @conference {13644, title = {Shot boundary detection based on Image correlation features in video}, booktitle = {TREC-VID: Text Retrieval and Evaluation Conference}, year = {2004}, month = {2004///}, abstract = {This paper introduced a framework of shot boundary detection used by the LAMPLAB, University of Maryland, College Park. It deals with cuts and dissolves detection. Generally, it is based on image correlation features in the videos. The cut detection is based on the so-called 2max ratio criterion in a sequential image buffer. The dissolve detection is based on the skipping image difference and linearity error in a sequential image buffer. We also eliminated the effect of flashlights in our algorithms. We submitted 5 runs to TRECVID 2004. Their run-ids are {\textquotedblleft}D0, D1, {\textellipsis} , D4{\textquotedblright}. They use the same algorithms with different parameter settings. These runs show a tradeoff curve between precision and recall on the testing data of TRECVID 2004.}, author = {Luo,Ming and DeMenthon,D. and David Doermann} } @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} } @conference {13211, title = {A spherical microphone array system for traffic scene analysis}, booktitle = {Intelligent Transportation Systems, 2004. Proceedings. The 7th International IEEE Conference on}, year = {2004}, month = {2004/10//}, pages = {338 - 342}, abstract = {This paper describes a practical spherical microphone array system for traffic auditory scene capture and analysis. Our system uses 60 microphones positioned on the rigid surface of a sphere. We then propose an optimal design of a robust spherical beamformer with minimum white noise gain (WNG) of -6 dB. We test this system in a real-world traffic environment. Some preliminary simulation and experimental results are presented to demonstrate its performance. This system may also find applications in broader areas such as 3D audio, virtual environment, etc.}, keywords = {-6, 3D, analysis;, array, arrays;, audio;, auditory, beamformer;, capture;, dB;, environment;, gain;, microphone, NOISE, noise;, processing;, real, robust, scene, signal, spherical, system;, traffic, traffic;, virtual, white, World}, doi = {10.1109/ITSC.2004.1398921}, author = {Zhiyun Li and Duraiswami, Ramani and Grassi,E. and Davis, Larry S.} } @conference {18787, title = {A STEP TOWARDS AUTOMATED DESIGN OF INDEX-PLATE MULTI-SHOT MOLDS}, year = {2004}, month = {2004/04//}, address = {Lausanne, Switzerland}, abstract = {This paper describes an algorithm for automateddesign of index-plate type of multi-shot molds for manufacturing multi-material objects. This new algorithm is a significant improvement over previous mold design algorithms and it accounts for constraints associated with the index-plate molding process. Our algorithm works in the following manner. First, based on the index-plate process constraints, we determine whether the given multi-material object is moldable by index- plate process by analyzing the geometry of the object. If the object can be molded, then the molding sequence is determined. Finally, the mold pieces. We expect that the algorithm described in this paper will provide the necessary foundations for automating the design of index-plate molds and therefore will help in significantly reducing the mold manufacturing lead-time associated with this type of molds. }, url = {http://www.glue.umd.edu/~skgupta/Publication/TMCE04_Li.pdf}, author = {Li,X. and Gupta,S.K.} } @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} } @conference {13210, title = {Uncalibrated stereo rectification for automatic 3D surveillance}, booktitle = {Image Processing, 2004. ICIP {\textquoteright}04. 2004 International Conference on}, volume = {2}, year = {2004}, month = {2004/10//}, pages = {1357 - 1360 Vol.2 - 1357 - 1360 Vol.2}, abstract = {We describe a stereo rectification method suitable for automatic 3D surveillance. We take advantage of the fact that in a typical urban scene, there is ordinarily a small number of dominant planes. Given two views of the scene, we align a dominant plane in one view with the other. Conjugate epipolar lines between the reference view and plane-aligned image become geometrically identical and can be added to the rectified image pair line by line. Selecting conjugate epipolar lines to cover the whole image is simplified since they are geometrically identical. In addition, the polarities of conjugate epipolar lines are automatically preserved by plane alignment, which simplifies stereo matching.}, keywords = {3D, AUTOMATIC, conjugate, epipolar, image, lines;, matching;, method;, processing;, rectification, scene;, stereo, surveillance;, uncalibrated, urban}, doi = {10.1109/ICIP.2004.1419753}, author = {Lim,S.-N. and Mittal,A. and Davis, Larry S. and Paragios,N.} } @conference {14452, title = {Using the structure of Web sites for automatic segmentation of tables}, booktitle = {Proceedings of the 2004 ACM SIGMOD international conference on Management of data}, series = {SIGMOD {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {119 - 130}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many Web sites, especially those that dynamically generate HTML pages to display the results of a user{\textquoteright}s query, present information in the form of list or tables. Current tools that allow applications to programmatically extract this information rely heavily on user input, often in the form of labeled extracted records. The sheer size and rate of growth of the Web make any solution that relies primarily on user input is infeasible in the long term. Fortunately, many Web sites contain much explicit and implicit structure, both in layout and content, that we can exploit for the purpose of information extraction. This paper describes an approach to automatic extraction and segmentation of records from Web tables. Automatic methods do not require any user input, but rely solely on the layout and content of the Web source. Our approach relies on the common structure of many Web sites, which present information as a list or a table, with a link in each entry leading to a detail page containing additional information about that item. We describe two algorithms that use redundancies in the content of table and detail pages to aid in information extraction. The first algorithm encodes additional information provided by detail pages as constraints and finds the segmentation by solving a constraint satisfaction problem. The second algorithm uses probabilistic inference to find the record segmentation. We show how each approach can exploit the web site structure in a general, domain-independent manner, and we demonstrate the effectiveness of each algorithm on a set of twelve Web sites.}, isbn = {1-58113-859-8}, doi = {10.1145/1007568.1007584}, url = {http://doi.acm.org/10.1145/1007568.1007584}, author = {Lerman,Kristina and Getoor, Lise and Minton,Steven and Knoblock,Craig} } @article {13222, title = {Visibility Planning: Predicting Continuous Period of Unobstructed Views}, journal = {Technical Reports from UMIACS}, year = {2004}, month = {2004/04/19/}, abstract = {To perform surveillance tasks effectively, unobstructed views ofobjects are required e.g. unobstructed video of objects are often needed for gait recognition. As a result, we need to determine intervals for video collection during which a desired object is visible w.r.t. a given sensor. In addition, these intervals are in the future so that the system can effectively plan and schedule sensors for collecting these videos. We describe an approach to determine these visibility intervals. A Kalman filter is first used to predict the trajectories of the objects. The trajectories are converted to polar coordinate representations w.r.t. a given sensor. Trajectories with the same angular displacement w.r.t. the sensor over time can be found by determining intersection points of functions representing these trajectories. Intervals between these intersection points are suitable for video collection. We also address the efficiency issue of finding these intersection points. An obvious brute force approach of $O(N^2)$ exists, where $N$ is the number of objects. This approach suffices when $N$ is small. When $N$ is large, we introduce an optimal segment intersection algorithm of $O(N\log^2N+I)$, $I$ being the number of intersection points. Finally, we model the prediction errors associated with the Kalman filter using a circular object representation. Experimental results that compare the performance of the brute force and the optimal segment intersection algorithms are shown. (UMIACS-TR-2004-22) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1349}, author = {Lim,Ser-Nam and Davis, Larry S. and Wan,Yung-Chun (Justin)} } @article {15656, title = {Vision Geometry XII}, journal = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series}, volume = {5300}, year = {2004}, month = {2004///}, author = {Latecki,L.J. and Mount, Dave and Wu,A. Y} } @article {15663, title = {Vision geometry XII:(San Jose CA, 19-20 January 2004)}, journal = {SPIE proceedings series}, year = {2004}, month = {2004///}, author = {Latecki,L.J. and Mount, Dave and Wu,A. Y} } @article {12189, title = {Visualizations for taxonomic and phylogenetic trees}, journal = {Bioinformatics}, volume = {20}, year = {2004}, month = {2004///}, pages = {2997 - 2997}, author = {Parr,C.S. and Lee,B. and Campbell,D. and Bederson, Benjamin B.} } @conference {15314, title = {What works better for question answering: Stemming or morphological query expansion}, booktitle = {Proceedings of the Information Retrieval for Question Answering (IR4QA) Workshop at SIGIR 2004}, year = {2004}, month = {2004///}, abstract = {How do different information retrieval techniques affect theperformance of document retrieval in the context of question answering? An exploration of this question is our overall re- search goal. In this paper, we specifically examine strategies for coping with morphological variation. This work quanti- tatively compares two different approaches to handling term variation: applying a stemming algorithm at indexing time, and performing morphological query expansion at retrieval time. We discovered that, compared to the no-stemming baseline, stemming results in lower recall, and morphologi- cal expansion yields higher recall. By separately weighting different term variants, we were able to achieve even higher recall, which opens the door to interesting question analy- sis algorithms for sophisticated query generation. Another significant contribution of our work is the development of a reusable question answering test collection to support our experiments. }, author = {Bilotti,M. W and Katz,B. and Jimmy Lin} } @article {14851, title = {Whitening for photometric comparison of smooth surfaces under varying illumination}, journal = {Computer Vision-ECCV 2004}, year = {2004}, month = {2004///}, pages = {217 - 228}, abstract = {We consider the problem of image comparison in order to match smooth surfaces under varying illumination. In a smooth surface nearby surface normals are highly correlated. We model such surfaces as Gaussian processes and derive the resulting statistical characterization of the corresponding images. Supported by this model, we treat the difference between two images, associated with the same surface and different lighting, as colored Gaussian noise, and use the whitening tool from signal detection theory to construct a measure of difference between such images. This also improves comparisons by accentuating the differences between images of different surfaces. At the same time, we prove that no linear filter, including ours, can produce lighting insensitive image comparisons. While our Gaussian assumption is a simplification, the resulting measure functions well for both synthetic and real smooth objects. Thus we improve upon methods for matching images of smooth objects, while providing insight into the performance of such methods. Much prior work has focused on image comparison methods appropriate for highly curved surfaces. We combine our method with one of these, and demonstrate high performance on rough and smooth objects.}, doi = {10.1007/978-3-540-24673-2_18}, author = {Osadchy,M. and Lindenbaum,M. and Jacobs, David W.} } @article {14578, title = {Whole-genome shotgun assembly and comparison of human genome assemblies}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, year = {2004}, month = {2004///}, pages = {1916 - 1916}, author = {Istrail,S. and Sutton,G. G and Florea,L. and Halpern,A. L and Mobarry,C. M and Lippert,R. and Walenz,B. and Shatkay,H. and Dew,I. and Miller,J. R and others} } @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 {12955, title = {A 4-Year Study of the Epidemiology of Vibrio Cholerae in Four Rural Areas of Bangladesh}, journal = {Journal of Infectious DiseasesJ Infect Dis.}, volume = {187}, year = {2003}, month = {2003/01/01/}, pages = {96 - 101}, abstract = {How Vibrio cholerae spreads around the world and what determines its seasonal peaks in endemic areas are not known. These features of cholera have been hypothesized to be primarily the result of environmental factors associated with aquatic habitats that can now be identified. Since 1997, fortnightly surveillance in 4 widely separated geographic locations in Bangladesh has been performed to identify patients with cholera and to collect environmental data. A total of 5670 patients (53\% <5 years of age) have been studied; 14.3\% had cholera (10.4\% due to V. cholerae O1 El Tor, 3.8\% due to O139). Both serogroups were found in all locations; outbreaks were seasonal and often occurred simultaneously. Water-use patterns showed that bathing and washing clothes in tube-well water was significantly protective in two of the sites. These data will be correlated with environmental factors, to develop a model for prediction of cholera outbreaks}, isbn = {0022-1899, 1537-6613}, doi = {10.1086/345865}, url = {http://jid.oxfordjournals.org/content/187/1/96}, author = {Sack,R. Bradley and Siddique,A. Kasem and Longini,Ira M. and Nizam,Azhar and Yunus,Md and M. Sirajul Islam and Morris,Jr and Ali,Afsar and Huq,Anwar and Nair,G. Balakrish and Qadri,Firdausi and Faruque,Shah M. and Sack,David A. and Rita R Colwell} } @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 {13493, title = {AModel-based Line Detection Algorithm in Documents}, booktitle = {ICDAR}, year = {2003}, month = {2003///}, pages = {44 - 48}, author = {Zheng,Y. and Li,H. and David Doermann} } @article {18167, title = {Anti-collusion fingerprinting for multimedia}, journal = {Signal Processing, IEEE Transactions on}, volume = {51}, year = {2003}, month = {2003/04//}, pages = {1069 - 1087}, abstract = {Digital fingerprinting is a technique for identifying users who use multimedia content for unintended purposes, such as redistribution. These fingerprints are typically embedded into the content using watermarking techniques that are designed to be robust to a variety of attacks. A cost-effective attack against such digital fingerprints is collusion, where several differently marked copies of the same content are combined to disrupt the underlying fingerprints. We investigate the problem of designing fingerprints that can withstand collusion and allow for the identification of colluders. We begin by introducing the collusion problem for additive embedding. We then study the effect that averaging collusion has on orthogonal modulation. We introduce a tree-structured detection algorithm for identifying the fingerprints associated with K colluders that requires O(Klog(n/K)) correlations for a group of n users. We next develop a fingerprinting scheme based on code modulation that does not require as many basis signals as orthogonal modulation. We propose a new class of codes, called anti-collusion codes (ACCs), which have the property that the composition of any subset of K or fewer codevectors is unique. Using this property, we can therefore identify groups of K or fewer colluders. We present a construction of binary-valued ACC under the logical AND operation that uses the theory of combinatorial designs and is suitable for both the on-off keying and antipodal form of binary code modulation. In order to accommodate n users, our code construction requires only O( radic;n) orthogonal signals for a given number of colluders. We introduce three different detection strategies that can be used with our ACC for identifying a suspect set of colluders. We demonstrate the performance of our ACC for fingerprinting multimedia and identifying colluders through experiments using Gaussian signals and real images.}, keywords = {(mathematics);, additive, algorithm;, and, anti-collusion, attack;, averaging, binary, code, codes;, codevectors;, coding;, colluders, collusion;, combinatorial, communication;, compression;, correlation;, cost-effective, data, data;, design, DETECTION, detection;, digital, embedding;, fingerprinting;, Gaussian, identification;, image, images;, keying;, logical, mathematics;, Modulation, modulation;, multimedia, multimedia;, of, on-off, operation;, orthogonal, processes;, real, redistribution;, Security, signal, signals;, theory;, tree-structured, TREES, watermarking;}, isbn = {1053-587X}, doi = {10.1109/TSP.2003.809378}, author = {Trappe,W. and M. Wu and Wang,Z.J. and Liu,K. J.R} } @conference {18169, title = {Anti-collusion of group-oriented fingerprinting}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {2}, year = {2003}, month = {2003/07//}, pages = {II - 217-20 vol.2 - II - 217-20 vol.2}, abstract = {Digital fingerprinting of multimedia data involves embedding information in the content, and offers protection to the digital rights of the content by allowing illegitimate usage of the content to be identified by authorized parties. One potential threat to fingerprints is collusion, whereby a group of adversaries combine their individual copies in an attempt to remove the underlying fingerprints. Former studies indicate that collusion attacks based on a few dozen independent copies can confound a fingerprinting system that employs orthogonal modulation. However, since an adversary is more likely to collude with some users than other users, we propose a group-based fingerprinting scheme where users likely to collude with each other are assigned correlated fingerprints. We evaluate the performance of our group-based fingerprints by studying the collusion resistance of a fingerprinting system employing Gaussian distributed fingerprints. We compare the results to those of fingerprinting systems employing orthogonal modulation.}, keywords = {anticollusion, attacks;, collusion, communication;, data;, digital, distributed, distribution;, fingerprinting;, fingerprints;, Gaussian, group-oriented, Internet;, method;, modulation;, multimedia, orthogonal, security;, Telecommunication, watermarking;}, doi = {10.1109/ICME.2003.1221592}, author = {Wang,Z.J. and M. Wu and Trappe,W. and Liu,K. J.R} } @article {13497, title = {AParallel Line Detection Algorithm Based on HMMDecoding}, volume = {LAMP-TR-109,CAR-TR-994,CS-TR-4545,UMIACS-TR-2003-1113}, year = {2003}, month = {2003/12//}, institution = {University of Maryland, College Park}, abstract = {The detection of groups of parallel lines is important in applications such as form processing and text (handwriting) extraciton in rule lined paper. These tasks can be very challenging in degraded documents where the lines are severely broken. In this paper we propose a novel model-based method which incorporates high level context to detect these lines. After preprocessing and skew correction, we use trained Hidden Markov Models (HMM) to locate the optimal positions of all lines simultaneously, based on the Viterbi decoding. The algorithm is trainable, therefore, it can easily be adapted to different application scenarios. The experiments conducted on known form processing and rule line detection show our method is robust, and achieved better results than other widely used line detection methods, such as the Hough transform, projection or vectorization-based methods.}, author = {Yefeng Zheng and Huiping Li and David Doermann} } @conference {14904, title = {Automatic thumbnail cropping and its effectiveness}, booktitle = {Proceedings of the 16th annual ACM symposium on User interface software and technology}, series = {UIST {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {95 - 104}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Thumbnail images provide users of image retrieval and browsing systems with a method for quickly scanning large numbers of images. Recognizing the objects in an image is important in many retrieval tasks, but thumbnails generated by shrinking the original image often render objects illegible. We study the ability of computer vision systems to detect key components of images so that automated cropping, prior to shrinking, can render objects more recognizable. We evaluate automatic cropping techniques 1) based on a general method that detects salient portions of images, and 2) based on automatic face detection. Our user study shows that these methods result in small thumbnails that are substantially more recognizable and easier to find in the context of visual search.}, keywords = {Face detection, image cropping, saliency map, thumbnail, usability study, visual search, zoomable user interfaces}, isbn = {1-58113-636-6}, doi = {10.1145/964696.964707}, url = {http://doi.acm.org/10.1145/964696.964707}, author = {Suh,Bongwon and Ling,Haibin and Bederson, Benjamin B. and Jacobs, David W.} } @conference {12191, title = {Automatic thumbnail cropping and its effectiveness}, booktitle = {Proceedings of the 16th annual ACM symposium on User interface software and technology}, year = {2003}, month = {2003///}, pages = {95 - 104}, author = {Suh,B. and Ling,H. and Bederson, Benjamin B. and Jacobs, David W.} } @conference {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 {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.} } @conference {13527, title = {Content Features for Logical Document Labeling}, booktitle = {Proc. SPIE Conference on Document Recognition and Retrieval X}, year = {2003}, month = {2003///}, pages = {189 - 196}, abstract = {The use of content features extracted from recognized text is valuable in labeling logical elements in documents withoutrigid layout structure, like business letters. This paper discusses a model-based approach to combining content features with other geometrical and presentation features for logical labeling. Models are automatically initialized and adaptively improved using training samples. Satisfactory experimental results are presented. }, author = {Liang,Jian and David Doermann} } @conference {12304, title = {Cooperative peer groups in NICE}, booktitle = {INFOCOM 2003. Twenty-Second Annual Joint Conference of the IEEE Computer and Communications. IEEE Societies}, volume = {2}, year = {2003}, month = {2003///}, pages = {1272 - 1282 vol.2 - 1272 - 1282 vol.2}, abstract = {A distributed scheme for trust inference in peer-to-peer networks is presented. Our work is in context of the NICE system, which is a platform for implementing cooperative applications over the Internet. We describe a technique for efficiently storing user reputation information in a completely decentralized manner, and show how this information can be used to efficiently identify noncooperative users in NICE. We present a simulation based study of our algorithms, in which we show our scheme scales to thousands of users using modest amounts of storage, processing, and bandwidth at any individual node. Lastly, we show that our scheme is robust and can form cooperative groups in systems where the vast majority of users are malicious.}, keywords = {algorithm;, cooperative, decentralized, distributed, identification;, individual, inference, inference;, information, Internet;, malicious, manner;, mechanisms;, networks;, NICE, node;, noncooperative, peer-to-peer, platform;, reputation, retrieval;, storage;, system;, trust, users, users;}, doi = {10.1109/INFCOM.2003.1208963}, author = {Lee,S. and Sherwood,R. and Bhattacharjee, Bobby} } @article {18193, title = {Data hiding in image and video .I. Fundamental issues and solutions}, journal = {Image Processing, IEEE Transactions on}, volume = {12}, year = {2003}, month = {2003/06//}, pages = {685 - 695}, abstract = {We address a number of fundamental issues of data hiding in image and video and propose general solutions to them. We begin with a review of two major types of embedding, based on which we propose a new multilevel embedding framework to allow the amount of extractable data to be adaptive according to the actual noise condition. We then study the issues of hiding multiple bits through a comparison of various modulation and multiplexing techniques. Finally, the nonstationary nature of visual signals leads to highly uneven distribution of embedding capacity and causes difficulty in data hiding. We propose an adaptive solution switching between using constant embedding rate with shuffling and using variable embedding rate with embedded control bits. We verify the effectiveness of our proposed solutions through analysis and simulation.}, keywords = {adaptive, analysis;, bits;, colour, condition;, constant, CONTROL, data, embedded, EMBEDDING, embedding;, encapsulation;, extractable, hiding;, image, Modulation, modulation;, multilevel, multiplexing, multiplexing;, NOISE, nonstationary, processing;, rate;, reviews;, shuffling;, signal, signals;, simulation;, solution;, techniques;, variable, video, visual}, isbn = {1057-7149}, doi = {10.1109/TIP.2003.810588}, author = {M. Wu and Liu,Bede} } @article {18194, title = {Data hiding in image and video .II. Designs and applications}, journal = {Image Processing, IEEE Transactions on}, volume = {12}, year = {2003}, month = {2003/06//}, pages = {696 - 705}, abstract = {For pt. I see ibid., vol.12, no.6, p.685-95 (2003). This paper applies the solutions to the fundamental issues addressed in Part I to specific design problems of embedding data in image and video. We apply multilevel embedding to allow the amount of embedded information that can be reliably extracted to be adaptive with respect to the actual noise conditions. When extending the multilevel embedding to video, we propose strategies for handling uneven embedding capacity from region to region within a frame as well as from frame to frame. We also embed control information to facilitate the accurate extraction of the user data payload and to combat such distortions as frame jitter. The proposed algorithm can be used for a variety of applications such as copy control, access control, robust annotation, and content-based authentication.}, keywords = {access, annotation;, authentication;, capacity;, conditions;, content-based, CONTROL, control;, copy, data, distortions;, EMBEDDING, embedding;, encapsulation;, extraction;, frame, hiding;, image, information;, jitter;, message, multilevel, NOISE, noise;, payload, processing;, robust, signal, uneven, user, video}, isbn = {1057-7149}, doi = {10.1109/TIP.2003.810589}, author = {M. Wu and Yu,H. and Liu,Bede} } @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} } @article {17844, title = {Driving scientific applications by data in distributed environments}, journal = {Computational Science{\textemdash}ICCS 2003}, year = {2003}, month = {2003///}, pages = {713 - 713}, author = {Saltz, J. and Catalyurek,U. and Kurc, T. and Gray,M. and Hastings,S. and Langella,S. and Narayanan,S. and Martino,R. and Bryant,S. and Peszynska,M. and others} } @article {12950, title = {Effect of treatment on the dynamics of circulating hypodermin C in cattle naturally infested with Hypoderma lineatum (Diptera: Oestridae)}, journal = {Veterinary Parasitology}, volume = {113}, year = {2003}, month = {2003/05/01/}, pages = {263 - 272}, abstract = {An antigen capture ELISA, using a murine monoclonal antibody recognising recombinant hypodermin C (rHyC), was used to evaluate the influence of early treatment with eprinomectin (Eprinex{\textregistered}) or fenthion (Spotton{\textregistered}) on the kinetics of circulating hypodermin C in calves naturally infested with Hypoderma lineatum. No viable larvae were collected from treated animals, whereas a variable number of warbles were found in control animals. Treatment provoked a decrease in circulating HyC levels that was significant 9 days post-treatment (p.t.). Circulating antigen levels in the treated cattle remained detectable for approximately 99 days p.t. In contrast, control animals had no detectable antigen at 64 days p.t., 42 days earlier than in the treated animals. These results suggest that larvae were either gradually killed, resulting in slow release of antigen or they were encapsulated, leading to the slow liberation of antigen. Kinetics of circulating HyC did not differ among the two insecticide treatments. Antibodies persisted, in all groups, throughout the 120-day study. These results suggest that the antigen capture ELISA will be useful as a technique for detecting successful treatment of cattle grub infestations and for the detection of new infestations in previously infested cattle.}, keywords = {Capture ELISA, Cattle-arthropoda, Control methods-arthropoda, Eprinomectin, Fenthion, Hypoderma spp.}, isbn = {0304-4017}, doi = {10.1016/S0304-4017(03)00084-0}, url = {http://www.sciencedirect.com/science/article/pii/S0304401703000840}, author = {Douglas D Colwell and Panadero-Fontan,Rosario and L{\'o}pez-Sandez,Ceferino and Parra-Fernandez,Francisco and Paz-Silva,A and S{\'a}nchez-Andrade,Rita and D{\i}́ez-Ba{\~n}os,Pablo} } @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} } @conference {12200, title = {Electronic voting system usability issues}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2003}, month = {2003///}, pages = {145 - 152}, author = {Bederson, Benjamin B. and Lee,B. and Sherman,R.M. and Herrnson,P.S. and Niemi,R.G.} } @conference {18656, title = {An experimental evaluation of correlated network partitions in the Coda distributed file system}, year = {2003}, month = {2003/10//}, pages = {273 - 282}, abstract = {Experimental evaluation is an important way to assess distributed systems, and fault injection is the dominant technique in this area for the evaluation of a system{\textquoteright}s dependability. For distributed systems, network failure is an important fault model. Physical network failures often have far-reaching effects, giving rise to multiple correlated failures as seen by higher-level protocols. This paper presents an experimental evaluation, using the Loki fault injector, which provides insight into the impact that correlated network partitions have on the Coda distributed file system. In this evaluation, Loki created a network partition between two Coda file servers, during which updates were made at each server to the same replicated data volume. Upon repair of the partition, a client requested directory resolution to converge the diverging replicas. At various stages of the resolution, Loki invoked a second correlated network partition, thus allowing us to evaluate its impact on the system{\textquoteright}s correctness, performance, and availability.}, keywords = {client-server systems, Coda distributed file system, correlated network partitions, distributed file systems, experimental evaluation, fault model, Loki fault injector, multiple correlated failures, network failure, Network topology, performance evaluation, replicated data, replicated databases, software fault tolerance, system performance evaluation}, doi = {10.1109/RELDIS.2003.1238077}, author = {Lefever,R.M. and Michel Cukier and Sanders,W. H.} } @conference {15316, title = {Extracting structural paraphrases from aligned monolingual corpora}, booktitle = {Proceedings of the second international workshop on Paraphrasing - Volume 16}, series = {PARAPHRASE {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {57 - 64}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We present an approach for automatically learning paraphrases from aligned monolingual corpora. Our algorithm works by generalizing the syntactic paths between corresponding anchors in aligned sentence pairs. Compared to previous work, structural paraphrases generated by our algorithm tend to be much longer on average, and are capable of capturing long-distance dependencies. In addition to a standalone evaluation of our paraphrases, we also describe a question answering application currently under development that could immensely benefit from automatically-learned structural paraphrases.}, doi = {10.3115/1118984.1118992}, url = {http://dx.doi.org/10.3115/1118984.1118992}, author = {Ibrahim,Ali and Katz,Boris and Jimmy Lin} } @article {15594, title = {A Fast Implementation of the ISOCLUS Algorithm}, journal = {IEEE 2003 International Geoscience and Remote Sensing Symposium}, year = {2003}, month = {2003///}, abstract = {Unsupervised clustering is a fundamental building block in numerous image processing applications. One of the most popular and widely used clustering schemes for remote sensing applications is the ISOCLUS algorithm, which is based on the ISODATA method. The algorithm is given a set of n data points in d-dimensional space, an integer k indicating the initial number of clusters, and a number of additional parameters. The general goal is to compute the coordinates of a set of cluster centers in d-space, such that those centers minimize the mean squared distance from each data point to its nearest center. This clustering algorithm is similar to another well-known clustering method, called k-means. One significant feature of ISOCLUS over k-means is that the actual number of clusters reported might be fewer or more than the number supplied as part of the input. The algorithm uses different heuristics to determine whether to merge lor split clusters. As ISOCLUS can run very slowly, particularly on large data sets, there has been a growing .interest in the remote sensing community in computing it efficiently. We have developed a faster implementation of the ISOCLUS algorithm. Our improvement is based on a recent acceleration to the k-means algorithm of Kanungo, et al. They showed that, by using a kd-tree data structure for storing the data, it is possible to reduce the running time of k-means. We have adapted this method for the ISOCLUS algorithm, and we show that it is possible to achieve essentially the same results as ISOCLUS on large data sets, but with significantly lower running times. This adaptation involves computing a number of cluster statistics that are needed for ISOCLUS but not for k-means. Both the k-means and ISOCLUS algorithms are based on iterative schemes, in which nearest neighbors are calculated until some convergence criterion is satisfied. Each iteration requires that the nearest center for each data point be computed. Naively, this requires O(kn) time, where k denotes the current number of centers. Traditional techniques for accelerating nearest neighbor searching involve storing the k centers in a data structure. However, because of the iterative nature of the algorithm, this data structure would need to be rebuilt with each new iteration. Our approach is to store the data points in a kd-tree data structure. The assignment of points to nearest neighbors is carried out by a filtering process, which successively eliminates centers that can not possibly be the nearest neighbor for a given region of space. This algorithm is significantly faster, because large groups of data points can be assigned to their nearest center in a single operation. Preliminary results on a number of real Landsat datasets show that our revised ISOCLUS-like scheme runs about twice as fast.}, keywords = {algorithms, Cluster Analysis, Data structures, HEURISTIC METHODS, IMAGE PROCESSING, INTEGERS, LANDSAT SATELLITES, MEAN SQUARE VALUES, Remote sensing}, url = {http://ntrs.nasa.gov/search.jsp?R=20030053175}, author = {Memarsadeghi,Nargess and Mount, Dave and Netanyahu,Nathan S. and LeMoigne,Jacqueline} } @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 {12337, title = {Goal-Driven Reconfiguration of Polymorphous Architectures}, journal = {Domain-specific processors: systems, architectures, modeling, and simulation}, volume = {20}, year = {2003}, month = {2003///}, pages = {151 - 151}, author = {Lohani,S. and Bhattacharyya, Shuvra S.} } @article {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 {13244, title = {Image-based pan-tilt camera control in a multi-camera surveillance environment}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {1}, year = {2003}, month = {2003/07//}, pages = {I - 645-8 vol.1 - I - 645-8 vol.1}, abstract = {In automated surveillance systems with multiple cameras, the system must be able to position the cameras accurately. Each camera must be able to pan-tilt such that an object detected in the scene is in a vantage position in the camera{\textquoteright}s image plane and subsequently capture images of that object. Typically, camera calibration is required. We propose an approach that uses only image-based information. Each camera is assigned a pan-tilt zero-position. Position of an object detected in one camera is related to the other cameras by homographies between the zero-positions while different pan-tilt positions of the same camera are related in the form of projective rotations. We then derive that the trajectories in the image plane corresponding to these projective rotations are approximately circular for pan and linear for tilt. The camera control technique is subsequently tested in a working prototype.}, keywords = {automated, camera, cameras;, control;, detection;, environment;, image, image-based, information;, multicamera, object, pan-tilt, position;, processing;, sensors;, Surveillance, surveillance;, systems;, vantage, zero-position;, zero-positions;}, doi = {10.1109/ICME.2003.1221000}, author = {Lim,Ser-Nam and Elgammal,A. and Davis, Larry S.} } @inbook {17237, title = {Innovating the Interaction}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {295 - 295}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, isbn = {978-1-55860-915-0}, author = {Bederson, Benjamin B. and Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben and Hochheiser,H. and Fekete,J. D and Czenvinski,M.} } @article {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 {12300, title = {Intradomain Overlays: Architecture and Applications}, journal = {Technical Reports from UMIACS, UMIACS-TR-2003-70}, year = {2003}, month = {2003/08/01/}, abstract = {We introduce an architecture for {\textquoteleft}{\textquoteleft}Intradomain Overlays{\textquoteright}{\textquoteright}, where a subset of routers within a domain is augmented with a dedicated host. These strategically placed hosts form an overlay network, and we describe a number of applications for such overlays. These applications include efficient network monitoring, policy- and load-based packet re-routing, and network resource accounting. In this paper, we elaborate on the network monitoring application and describe a distributed protocol for monitoring routers within an AS which has been augmented with a few overlay nodes. The routers and other infrastructure are unaware of the overlay nodes, and the monitoring of individual elements is conducted using plain SNMP. We describe techniques for efficiently synthesizing and transporting the monitored SNMP data, and present results using trace data collected from an AS with 400+ routers. Our results show that the overlay-based monitoring reduces overheads by 2--4 orders of magnitude, and thus enables much finer grained monitoring and traffic engineering than is otherwise possible. (UMIACS-TR-2003-70) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1295}, author = {Kommareddy,Christopher and Guven,Tuna and Bhattacharjee, Bobby and La,Richard and Shayman,Mark} } @article {17264, title = {INTRODUCTION TO VOLUME 1, ISSUE 3: WEB NAVIGATION}, journal = {IT\&SOCIETY}, volume = {1}, year = {2003}, month = {2003///}, author = {Shneiderman, Ben and Lazar,J. and IVORY,M.} } @article {12140, title = {Iterative and incremental developments. a brief history}, journal = {Computer}, volume = {36}, year = {2003}, month = {2003/06//}, pages = {47 - 56}, abstract = {Although many view iterative and incremental development as a modern practice, its application dates as far back as the mid-1950s. Prominent software-engineering thought leaders from each succeeding decade supported IID practices, and many large projects used them successfully. These practices may have differed in their details, but all had a common theme-to avoid a single-pass sequential, document-driven, gated-step approach.}, keywords = {agile, and, developments;iterative, engineering;, engineering;software, enhancement;software, incremental, methods;iterative, system;history;software}, isbn = {0018-9162}, doi = {10.1109/MC.2003.1204375}, author = {Larman,C. and Basili, Victor R.} } @inbook {16129, title = {LifeLines: Using Visualization to Enhance Navigation and Analysis of Patient Records}, booktitle = {The Craft of Information VisualizationThe Craft of Information Visualization}, year = {2003}, month = {2003///}, pages = {308 - 312}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, isbn = {978-1-55860-915-0}, url = {http://www.sciencedirect.com/science/article/pii/B978155860915050038X}, author = {Plaisant, Catherine and Mushlin,Richard and Snyder,Aaron and Li,Jia and Heller,Dan and Shneiderman, Ben}, editor = {Bederson, Benjamin B. and Shneiderman, Ben} } @article {13593, title = {Machine Printed Text and Handwriting Identification in Noisy Document Images}, volume = {LAMP-TR-107,CFAR-TR-992,CS-TR-4531,UMIACS-TR-2003-99}, year = {2003}, month = {2003/09//}, institution = {University of Maryland, College Park}, abstract = {In this paper we address the problem of the identification of text in noisy document images. We are especially focused on segmenting and identifying between handwriting and machine printed text because: 1) handwriting in a document often indicates corrections, additions, or other supplemental information that should be treated differently from the main content, and 2) the segmentation and recognition techniques requested for machine printed and handwritten text are significantly different. A novel aspect of our approach is that we treat noise as a separate class and model noise based on selected features. Trained Fisher classifiers are used to identify machine printed text and handwriting from noise, and we further exploit context to refine the classification. AMarkov Random Field (MRF) based approach is used to model the geometrical structure of the printed text, handwriting, and noise to rectify misclassifications. Experimental results show that our approach is robust and can significantly improve page segmentation in noisy document collections.}, author = {Yefeng Zheng and Huiping Li and David Doermann} } @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} } @conference {18857, title = {Manufacturability Analysis of Multi-Material Objects Molded by Rotary Platen Multi-Shot Molding Process}, volume = {2003}, year = {2003}, month = {2003///}, pages = {353 - 365}, publisher = {ASME}, organization = {ASME}, abstract = {This paper describes a systematic approach for manufacturability analysis of multi-material objects molded using rotary platen multi-shot injection molding process. In this paper we first identify potential manufacturability problems that are associated with objects molded by the rotary platen process. Identified problems include infeasibility of molding sequences, unnecessary mold complexity, undesired friction during mold opening and closing, and undesired material flash on finished faces. These problems are unique to multi-material molding and do not occur in traditional injection molding. For each of the above four potential manufacturability problems, this paper also describes geometric algorithms for detecting the potential occurrence of the problem based on the object and mold design, finding its causes, and offering appropriate redesign suggestions. We expect that these algorithms will help in decreasing the product development time and improving the product quality for molded multi-material objects}, isbn = {0-7918-3712-2}, doi = {10.1115/IMECE2003-42442}, url = {http://link.aip.org/link/ASMECP/v2003/i37122/p353/s1\&Agg=doi}, author = {Li,Xuejun and Gupta, Satyandra K.} } @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} } @book {18249, title = {Multimedia Data Hiding}, year = {2003}, month = {2003///}, publisher = {Springer}, organization = {Springer}, abstract = {With the advances of the digital information revolution and the societal changes they have prompted, it has become critical to facilitate secure management of content usage and delivery across communication networks. Data hiding and digital watermarking are promising new technologies for multimedia information protection and rights management. Multimedia Data Hiding addresses the theory, methods, and design of multimedia data hiding and its application to multimedia rights management, information security, and communication. It offers theoretical and practical aspects, and both design and attack problems. Applications discussed include: annotation, tamper detection, copy/access control, fingerprinting, and ownership protection. Countermeasures for attacks on data hiding are discussed, and a chapter assesses attack problems on digital music protection under a unique competitive environment. Topics and features: * Comprehensive and practical coverage of data hiding for various media types, including binary image, grayscale and color images and video, and audio * Provides unique analysis of problems and solutions, such as data hiding in binary signature and generic binary documents, block concealment attacks, and attacks on audio watermarking * Authoritative discussion and analysis of data hiding and effective countermeasures, supported by concrete application examples * Accessible, well-organized progression from the fundamentals to specific approaches to various data-hiding problems This work offers a state-of-the-art presentation covering theoretical, algorithmic, and design topics for digital content/data security protection, and rights management. It is an essential resource for multimedia security researchers and professionals in electrical engineering, computer science, IT, and digital rights management.}, keywords = {computer security, Computers / Computer Engineering, Computers / Computer Science, Computers / Database Management / General, Computers / Information Technology, Computers / Information Theory, Computers / Interactive \& Multimedia, Computers / Networking / General, Computers / Security / Cryptography, Computers / Security / General, Computers / System Administration / Storage \& Retrieval, Data encryption (Computer science), multimedia systems, Technology \& Engineering / Electrical, Technology \& Engineering / Engineering (General)}, isbn = {9780387954264}, author = {M. Wu and Liu,Bede} } @conference {18258, title = {Nonlinear collusion attacks on independent fingerprints for multimedia}, booktitle = {Acoustics, Speech, and Signal Processing, 2003. Proceedings. (ICASSP {\textquoteright}03). 2003 IEEE International Conference on}, volume = {5}, year = {2003}, month = {2003/04//}, pages = {V - 664-7 vol.5 - V - 664-7 vol.5}, abstract = {Digital fingerprinting is a technology for tracing the distribution of multimedia content and protecting them from unauthorized redistribution. Collusion attack is a cost effective attack against digital fingerprinting where several copies with the same content but different fingerprints are combined to remove the original fingerprints. In this paper, we investigate average and nonlinear collusion attacks of independent Gaussian fingerprints and study both their effectiveness and the perceptual quality. We also propose the bounded Gaussian fingerprints to improve the perceptual quality of the fingerprinted copies. We further discuss the tradeoff between the robustness against collusion attacks and the perceptual quality of a fingerprinting system.}, keywords = {attacks;, average, bounded, collusion, computing;, content, copies;, digital, distribution;, fingerprinted, fingerprinting;, fingerprints;, Gaussian, independent, multimedia, nonlinear, perceptual, quality;, robustness;, watermarking;}, doi = {10.1109/ICASSP.2003.1200058}, author = {Zhao,Hong and M. Wu and Wang,Z.J. and Liu,K. J.R} } @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 {18261, title = {Performance of detection statistics under collusion attacks on independent multimedia fingerprints}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {1}, year = {2003}, month = {2003/07//}, pages = {I - 205-8 vol.1 - I - 205-8 vol.1}, abstract = {Digital fingerprinting is a technology for tracing the distribution of multimedia content and protecting them from unauthorized redistribution. Collusion attack is a cost effective attack against digital fingerprinting where several copies with the same content but different fingerprints are combined to remove the original fingerprints. In this paper, we consider average attack and several nonlinear collusion attacks on independent Gaussian based fingerprints, and study the detection performance of several commonly used detection statistics in the literature under collusion attacks. Observing that these detection statistics are not specifically designed for collusion scenarios and do not take into account the characteristics of the newly generated fingerprints under collusion attacks, we propose pre-processing techniques to improve the detection performance of the detection statistics under collusion attacks.}, keywords = {analysis;, attacks;, based, collusion, content;, DETECTION, digital, fingerprint, fingerprinting;, fingerprints;, Gaussian, identification;, independent, multimedia, performance;, preprocessing, processes;, redistribution;, security;, statistical, statistics;, systems;, techniques;, Telecommunication, unauthorized}, doi = {10.1109/ICME.2003.1220890}, author = {Zhao,Hong and M. Wu and Wang,Z.J. and Liu,K. J.R} } @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 {18021, title = {Prefix sums and an application thereof}, volume = {:~09/224,104}, year = {2003}, month = {2003/04/01/}, abstract = {A method for performing prefix sums, by including a prefix sum instruction in the instruction set of a microprocessor. Both general prefix summation, base-zero prefix summation and base-zero suffix summation are included in the scope of the present invention. The prefix sum instruction may be implemented in software, using the instructions of existing instruction sets, or may be implemented in dedicated hardware, for example, as a functional unit of a microprocessor. The hardware implementation is suitable for application to the allocation of computational resources among concurrent tasks. The scope of the present invention includes one such application: guaranteeing conflict-free access to multiple single-ported register files.}, url = {http://www.google.com/patents?id=qCAPAAAAEBAJ}, author = {Vishkin, Uzi}, editor = {Ramot at Tel Aviv University Ltd.} } @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} } @conference {15318, title = {Question answering from the web using knowledge annotation and knowledge mining techniques}, booktitle = {Proceedings of the twelfth international conference on Information and knowledge management}, series = {CIKM {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {116 - 123}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a strategy for answering fact-based natural language questions that is guided by a characterization of real-world user queries. Our approach, implemented in a system called Aranea, extracts answers from the Web using two different techniques: knowledge annotation and knowledge mining. Knowledge annotation is an approach to answering large classes of frequently occurring questions by utilizing semi\-structured and structured Web sources. Knowledge mining is a statistical approach that leverages massive amounts of Web data to overcome many natural language processing challenges. We have integrated these two different paradigms into a question answering system capable of providing users with concise answers that directly address their information needs.}, keywords = {data-redundancy, semistructured data}, isbn = {1-58113-723-0}, doi = {10.1145/956863.956886}, url = {http://doi.acm.org/10.1145/956863.956886}, author = {Jimmy Lin and Katz,Boris} } @article {15322, title = {Question answering techniques for the World Wide Web}, journal = {Tutorial presentation at The 11th Conference of the European Chapter of the Association of Computational Linguistics (EACL-2003)}, year = {2003}, month = {2003///}, abstract = {Question answering systems have become increasingly popular because they deliverusers short, succinct answers instead of overloading them with a large number of irrelevant documents. The vast amount of information readily available on the World Wide Web presents new opportunities and challenges for question answering. In order for question answering systems to benefit from this vast store of useful knowledge, they must cope with large volumes of useless data. Many characteristics of the World Wide Web distinguish Web-based question answering from question answering on closed corpora such as newspaper texts. The Web is vastly larger in size and boasts incredible {\textquotedblleft}data redundancy,{\textquotedblright} which renders it amenable to statistical techniques for answer extraction. A data-driven approach can yield high levels of performance and nicely complements traditional question answering techniques driven by information extraction. In addition to enormous amounts of unstructured text, the Web also contains pockets of structured and semistructured knowledge that can serve as a valuable resource for question answering. By organizing these resources and annotating them with natural language, we can successfully incorporate Web knowledge into question answering systems. This tutorial surveys recent Web-based question answering technology, focusing on two separate paradigms: knowledge mining using statistical tools and knowledge annotation using database concepts. Both approaches can employ a wide spectrum of techniques ranging in linguistic sophistication from simple {\textquotedblleft}bag-of-words{\textquotedblright} treatments to full syntactic parsing. }, author = {Jimmy Lin and Katz,B.} } @article {15019, title = {Recovery of a Digital Image Collection Through the SDSC/UMD/NARA Prototype Persistent Archive}, volume = {UMIACS-TR-2003-105}, year = {2003}, month = {2003/11/25/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The San Diego Supercomputer Center (SDSC), the University of Maryland, and theNational Archives and Records Administration (NARA) are collaborating on building a pilot persistent archive using and extending data grid and digital library technologies. The current prototype consists of node servers at SDSC, University of Maryland, and NARA, connected through the Storage Request Broker (SRB) data grid middleware, and currently holds several terabytes of NARA selected collections. In particular, a historically important image collection that was on the verge of becoming inaccessible was fully restored and ingested into our pilot system. In this report, we describe the methodology behind our approach to fully restore this image collection and the process used to ingest it into the prototype persistent archive. (UMIACS-TR-2003-105) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1321}, author = {Smorul,Mike and JaJa, Joseph F. and McCall,Fritz and Brown,Susan Fitch and Moore,Reagan and Marciano,Richard and Chen,Sheau-Yen and Lopez,Rick and Chadduck,Robert} } @article {12302, title = {Resilient multicast using overlays}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {31}, year = {2003}, month = {2003/06//}, pages = {102 - 113}, abstract = {We introduce PRM (Probabilistic Resilient Multicast): a multicast data recovery scheme that improves data delivery ratios while maintaining low end-to-end latencies. PRM has both a proactive and a reactive component; in this paper we describe how PRM can be used to improve the performance of application-layer multicast protocols, especially when there are high packet losses and host failures. Further, using analytic techniques, we show that PRM can guarantee arbitrarily high data delivery ratios and low latency bounds. As a detailed case study, we show how PRM can be applied to the NICE application-layer multicast protocol. We present detailed simulations of the PRM-enhanced NICE protocol for 10,000 node Internet-like topologies. Simulations show that PRM achieves a high delivery ratio (> 97\%) with a low latency bound (600 ms) for environments with high end-to-end network losses (1-5\%) and high topology change rates (5 changes per second) while incurring very low overheads (< 5\%).}, keywords = {overlay multicast, randomized forwarding, Resilience}, isbn = {0163-5999}, doi = {10.1145/885651.781041}, url = {http://doi.acm.org/10.1145/885651.781041}, author = {Banerjee,Suman and Lee,Seungjoon and Bhattacharjee, Bobby and Srinivasan, Aravind} } @conference {18266, title = {Resistance of orthogonal Gaussian fingerprints to collusion attacks}, booktitle = {Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings. 2003 International Conference on}, volume = {1}, year = {2003}, month = {2003/07//}, pages = {I - 617-20 vol.1 - I - 617-20 vol.1}, abstract = {Digital fingerprinting is a means to offer protection to digital data by which fingerprints embedded in the multimedia are capable of identifying unauthorized use of digital content. A powerful attack that can be employed to reduce this tracing capability is collusion. In this paper, we study the collusion resistance of a fingerprinting system employing Gaussian distributed fingerprints and orthogonal modulation. We propose a likelihood-based approach to estimate the number of colluders, and introduce the thresholding detector for colluder identification. We first analyze the collusion resistance of a system to the average attack by considering the probability of a false negative and the probability of a false positive when identifying colluders. Lower and upper bounds for the maximum number of colluders Kmax are derived. We then show that the detectors are robust to different attacks. We further study different sets of performance criteria.}, keywords = {approach;, attacks;, capability;, collusion, data, data;, digital, distributed, embedded, fingerprinting;, fingerprints;, Gaussian, likelihood-based, modulation;, multimedia, of, orthogonal, probability;, processes;, protection;, Security, systems;, tracing}, doi = {10.1109/ICME.2003.1220993}, author = {Wang,Z.J. and M. Wu and Zhao,Hong and Liu,K. J.R and Trappe,W.} } @conference {13245, title = {Scalable image-based multi-camera visual surveillance system}, booktitle = {Proceedings. IEEE Conference on Advanced Video and Signal Based Surveillance, 2003.}, year = {2003}, month = {2003/07//}, pages = {205 - 212}, abstract = {We describe the design of a scalable and wide coverage visual surveillance system. Scalability (the ability to add and remove cameras easily during system operation with minimal overhead and system degradation) is achieved by utilizing only image-based information for camera control. We show that when a pan-tilt-zoom camera pans and tilts, a given image point moves in a circular and a linear trajectory, respectively. We create a scene model using a plan view of the scene. The scene model makes it easy for us to handle occlusion prediction and schedule video acquisition tasks subject to visibility constraints. We describe a maximum weight matching algorithm to assign cameras to tasks that meet the visibility constraints. The system is illustrated both through simulations and real video from a 6-camera configuration.}, keywords = {ACQUISITION, algorithm;, camera;, constraints;, feature, hidden, image-based, MATCHING, maximum, multi-camera, occlusion, pan-tilt-zoom, PLAN, prediction;, processing;, removal;, scalable, scheduling;, signal, Surveillance, surveillance;, system;, task, video, view;, visibility, visual, weight}, doi = {10.1109/AVSS.2003.1217923}, author = {Lim,Ser-Nam and Davis, Larry S. and Elgammal,A.} } @conference {15846, title = {Searching recorded speech based on the temporal extent of topic labels}, booktitle = {AAAI Spring Symposium on Intelligent Multimedia Knowledge Management}, year = {2003}, month = {2003///}, abstract = {Recorded speech poses unusual challenges for the de- sign of interactive end-user search systems. Automatic speech recognition is sufficiently accurate to support the automated components of interactive search sys- tems in some applications, but finding useful recordings among those nominated by the system can be difficult because listening to audio is time consuming and be- cause recognition errors and speech disfluencies make it difficult to mitigate that effect by skimming automatic transcripts. Support for rapid browsing based on su- pervised learning for automatic classification has shown promise, however, and a segment-then-label framework has emerged as the dominant paradigm for applying that technique to news broadcasts. This paper argues for a more general framework, which we call an activation matrix, that provides a flexible representation for the mapping between labels and time. Three approaches to the generation of activation matrices are briefly de- scribed, with the main focus of the paper then being the use of activation matrices to support search and selec- tion in interactive systems.}, author = {Oard, Douglas and Leuski,A.} } @article {14104, title = {The sequence and analysis of Trypanosoma brucei chromosome II}, journal = {Nucleic acids research}, volume = {31}, year = {2003}, month = {2003///}, pages = {4856 - 4856}, author = {El-Sayed, Najib M. and Ghedin,E. and Song,J. and MacLeod,A. and Bringaud,F. and Larkin,C. and Wanless,D. and Peterson,J. and Hou,L. and Taylor,S. and others} } @article {13249, title = {A Simple and Optimal Energy Surface Reconstruction Algorithm from Volumetric Data}, journal = {Technical Reports from UMIACS}, year = {2003}, month = {2003/02/05/}, abstract = {We describe a new method for building 3D surface meshes from volumetricimages, as are created in Magnetic Resonance Imaging (MRI). The method works by first extracting the contours from the MRI data, and then using modified polygon boolean operations to find difference polygons. The last step is performed by applying a Constrained Delauny Triangulation (CDT) algorithm to build a surface mesh. Since it is based on CDT, the mesh quality is usually very good. Moreover, the resulting triangular surface mesh is the optimal one for surface interpolation. In case of undersampled images, the mesh quality can be improved dramatically by inserting new Steiner points in to the mesh. Thus the mesh can be made suitable for use in scientific computation. Our method has the advantages of combining the generation and optimization of the mesh in one step compared with other methods. These advantages are illustrated. Also UMIACS-TR-2003-11 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1256}, author = {Liu,Kexue and Duraiswami, Ramani and Davis, Larry S.} } @book {14916, title = {Special section on perceptual organization in computer vision}, year = {2003}, month = {2003///}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, author = {Jacobs, David W. and Lindenbaum,M. and August,J. and Zucker,SW and Ben-Shahar,O. and Zucker,SW and Tuytelaars,T. and Turina,A. and Van Gool,L. and Mahamud,S.} } @conference {13650, title = {Sports Video Classification Using HMM}, booktitle = {ICME}, volume = {2}, year = {2003}, month = {2003///}, pages = {345 - 348}, author = {Gilbert,X. and Li,H. and David Doermann} } @conference {18805, title = {A Step Towards Automated Design of Rotary-Platen Multi-Shot Molds}, volume = {2003}, year = {2003}, month = {2003///}, pages = {343 - 354}, publisher = {ASME}, organization = {ASME}, address = {Chicago, Illinois, USA}, abstract = {This paper describes an improved algorithm for automated design of rotary-platen type of multi-shot molds for manufacturing multi-material objects. The algorithm described in this paper accounts for geometric constraints resulting from the rotary-platen process and it can handle significantly more complex interfaces. Our algorithm works in the following manner. First, we classify the multi-material object into several basic types based on the relationships among different single material components in the object. For every basic type, we find a manufacturing sequence based on the precedence constraints resulting due to accessibility and disassembly requirements. Then, starting from the last mold stage, we generate the mold pieces for every mold stage based on the manufacturing sequence. We expect that the algorithm described in this paper will provide the necessary foundations for automating the design of rotary-platen molds and therefore will help in significantly reducing the mold manufacturing lead-time associated with these types of molds.}, isbn = {0-7918-3701-7}, doi = {10.1115/DETC2003/DFM-48168}, url = {http://link.aip.org/link/ASMECP/v2003/i37017a/p343/s1\&Agg=doi}, author = {Li,Xuejun and Gupta, Satyandra K.} } @article {17387, title = {Supporting statistical electronic table usage by citizens}, journal = {Commun. ACM}, volume = {46}, year = {2003}, month = {2003/01//}, pages = {52 - 54}, abstract = {Over 70 agencies at the federal level are charged with collecting data and producing and disseminating statistics. These statistics are used to inform government policy, shape health care initiatives, provide information on the state of the economy, and others. They also have significant impact on the lives of citizens who use the statistics, for example, to determine job opportunities, changes in social security benefits, and quality of life in particular areas. Our digital government project developed several specific technologies to support the location, manipulation, and understanding of a quintessential format for statistical information---the table.}, isbn = {0001-0782}, doi = {10.1145/602421.602449}, url = {http://doi.acm.org/10.1145/602421.602449}, author = {Hert,Carol A. and Liddy,Elizabeth D. and Shneiderman, Ben and Marchionini,Gary} } @article {17809, title = {Temporal probabilistic object bases}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {15}, year = {2003}, month = {2003/08//july}, pages = {921 - 939}, abstract = {There are numerous applications where we have to deal with temporal uncertainty associated with objects. The ability to automatically store and manipulate time, probabilities, and objects is important. We propose a data model and algebra for temporal probabilistic object bases (TPOBs), which allows us to specify the probability with which an event occurs at a given time point. In explicit TPOB-instances, the sets of time points along with their probability intervals are explicitly enumerated. In implicit TPOB-instances, sets of time points are expressed by constraints and their probability intervals by probability distribution functions. Thus, implicit object base instances are succinct representations of explicit ones; they allow for an efficient implementation of algebraic operations, while their explicit counterparts make defining algebraic operations easy. We extend the relational algebra to both explicit and implicit instances and prove that the operations on implicit instances correctly implement their counterpart on explicit instances.}, keywords = {algebra;, algebraic, bases;, constraints;, data, database, database;, databases;, distribution, explicit, functions;, handling;, implicit, instances;, integrity;, intervals;, management;, model;, models;, object, object-oriented, operations;, probabilistic, probability, probability;, relational, temporal, theory;, Uncertainty, uncertainty;}, isbn = {1041-4347}, doi = {10.1109/TKDE.2003.1209009}, author = {Biazzo,V. and Giugno,R. and Lukasiewicz,T. and V.S. Subrahmanian} } @conference {13666, title = {Text Identification in Noisy Document Images Using Markov Random Field}, booktitle = {ICDAR}, year = {2003}, month = {2003///}, pages = {599 - 603}, author = {Zheng,Y. and Li,H. and David Doermann} } @article {14645, title = {Transcriptional regulation of protein complexes and biological pathways}, journal = {Mammalian Genome}, volume = {14}, year = {2003}, month = {2003///}, pages = {611 - 619}, abstract = {The cis-element profile (or cis-profile) of a gene refers to the collection of transcription factor binding sites (TFBS) regulating the transcription of the gene. Underlying the various published studies that attempt to discover cis-elements in the vicinity of co-expressed genes via pattern detection algorithms, there is an implicit assumption that a correlation exists between co-expressed genes and their cis-profiles. In this study, we show that the cis-similarity, defined as the proportion of shared TFBS between two cis-element profiles, is higher for functionally linked interacting proteins as well as for members of a signal transduction pathway. A similar analysis of the enzymes catalyzing the conversion of adjacent substrates to products in a collection of metabolic pathways, did not reveal higher cis-similarity. The analysis is based on three distinct sources of publicly available data, namely, 1) the BIND database of interacting proteins, 2) known interactions in NMDAR protein complex, 3) the apoptosis pathway and nine pathways related to metabolism of cofactors and vitamins all from KEGG. Additionally, we analyze the cis-element profiles of all the genes in the glutamate receptor (GR) sub-complex of NMDAR complex to detect a set of cis-elements that occur adjacent to a majority of the genes. We show that most of the corresponding transcription factors are known to be involved in GR regulation by comparing our findings with the published biomedical literature. In addition, we were able to detect transcripts whose gene products associate with GR by searching for transcripts that share the same regulatory signals as those detected for GR. This suggests a novel computational methodology for constructing high-order gene regulatory models and detecting co-regulated gene products.}, isbn = {0938-8990}, url = {http://dx.doi.org/10.1007/s00335-002-2260-x}, author = {Hannenhalli, Sridhar and Levy,Samuel} } @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 {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.} } @conference {15285, title = {What makes a good answer? The role of context in question answering}, booktitle = {Human-Computer Interaction, Interact {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {25 - 25}, author = {Jimmy Lin and Quan,D. and Sinha,V. and Bakshi,K. and Huynh,D. and Katz,B. and Karger,D. R} } @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 {11915, title = {AD (Attacker Defender) Game}, journal = {Technical Reports from UMIACS, UMIACS-TR-2001-45}, year = {2002}, month = {2002/01/31/}, abstract = {Information Dynamics is a framework for agent-based systems that givesa central position to the role of information, time, and the value of information. We illustrate system design in the Information Dynamics Framework by developing an intelligence game called AD involving attackers, defenders and targets operating in some space of locations. The goal of the attackers is to destroy all targets. Target destruction takes place when the number of attackers in the target{\textquoteright}s neighborhood exceeds the number of defenders in this neighborhood by a value WINNING_DIFFERENCE. The goal of defenders is to prevent attackers from achieving their goal. (Also UMIACS-TR-2001-45) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1142}, author = {Kochut,Andrzej and Agrawala, Ashok K. and Larsen,Ronald L and A. Udaya Shankar} } @article {15541, title = {Algorithmic issues in modeling motion}, journal = {ACM Comput. Surv.}, volume = {34}, year = {2002}, month = {2002/12//}, pages = {550 - 572}, abstract = {This article is a survey of research areas in which motion plays a pivotal role. The aim of the article is to review current approaches to modeling motion together with related data structures and algorithms, and to summarize the challenges that lie ahead in producing a more unified theory of motion representation that would be useful across several disciplines.}, keywords = {computational geometry, Computer vision, mobile networks, modeling, molecular biology, motion modeling, physical simulation, robotoics, spatio-temporal databases}, isbn = {0360-0300}, doi = {10.1145/592642.592647}, url = {http://doi.acm.org/10.1145/592642.592647}, author = {Agarwal,Pankaj K. and Guibas,Leonidas J. and Edelsbrunner,Herbert and Erickson,Jeff and Isard,Michael and Har-Peled,Sariel and Hershberger,John and Jensen,Christian and Kavraki,Lydia and Koehl,Patrice and Lin,Ming and Manocha,Dinesh and Metaxas,Dimitris and Mirtich,Brian and Mount, Dave and Muthukrishnan,S. and Pai,Dinesh and Sacks,Elisha and Snoeyink,Jack and Suri,Subhash and Wolefson,Ouri} } @conference {15307, title = {Annotating the semantic web using natural language}, booktitle = {Proceedings of the 2nd workshop on NLP and XML - Volume 17}, series = {NLPXML {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {1 - 8}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Because the ultimate purpose of the Semantic Web is to help users better locate, organize, and process content, we believe that it should be grounded in the information access method humans are most comfortable with---natural language. However, the Resource Description Framework (RDF), the foundation of the Semantic Web, was designed to be easily processed by computers, not humans. To render RDF more friendly to humans, we propose to augment it with natural language annotations, or metadata written in everyday language. We argue that natural language annotations, parsed into computer-readable representations, are not only intuitive and effective, but can also accelerate the pace with which the Semantic Web is being adopted. We believe that our technology can facilitate a happy marriage between natural language technology and the Semantic Web vision.}, doi = {10.3115/1118808.1118816}, url = {http://dx.doi.org/10.3115/1118808.1118816}, author = {Katz,Boris and Jimmy Lin} } @conference {18166, title = {Anti-collusion codes: multi-user and multimedia perspectives}, booktitle = {Image Processing. 2002. Proceedings. 2002 International Conference on}, volume = {2}, year = {2002}, month = {2002///}, pages = {II-149 - II-152 vol.2 - II-149 - II-152 vol.2}, abstract = {Digital fingerprinting is an effective method to identify users who might try to redistribute multimedia content, such as images and video. These fingerprints are typically embedded into the content using watermarking techniques that are designed to be robust to a variety of attacks. A cheap and effective attack against such digital fingerprints is collusion, where several differently marked copies of the same content are averaged or combined to disrupt the underlying fingerprint. We present a construction of collusion-resistant fingerprints based upon anti-collusion codes (ACC) and binary code modulation. ACC have the property that the composition of any subset of K or fewer codevectors is unique. Using this property, we build fingerprints that allow for the identification of groups of K or less colluders. We present a construction of binary-valued ACC under the logical AND operation using the theory of combinatorial designs. Our code construction requires only Oscr;( radic;n) orthogonal signals to accommodate n users. We demonstrate the performance of our ACC for fingerprinting multimedia by identifying colluders through experiments using real images.}, keywords = {and, anti-collusion, authentication;, binary, code, codes;, coding;, combinatorial, computing;, content;, data, designs;, digital, embedding;, encapsulation;, fingerprinting;, image, images;, logical, mathematics;, message, Modulation, modulation;, multimedia, operation;, performance;, watermarking;}, doi = {10.1109/ICIP.2002.1039909}, author = {Trappe,W. and M. Wu and Liu,K. J.R} } @inbook {16960, title = {An Augmented Visual Query Mechanism for Finding Patterns in Time Series Data}, booktitle = {Flexible Query Answering SystemsFlexible Query Answering Systems}, series = {Lecture Notes in Computer Science}, volume = {2522}, year = {2002}, month = {2002///}, pages = {240 - 250}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Relatively few query tools exist for data exploration and pattern identification in time series data sets. In previous work we introduced Timeboxes . Timeboxes are rectangular, direct-manipulation queries for studying time-series datasets. We demonstrated how Timeboxes can be used to support interactive exploration via dynamic queries, along with overviews of query results and drag-and-drop support for query-by-example. In this paper, we extend our work by introducing Variable Time Timeboxes (VTT). VTTs are a natural generalization of Timeboxes, which permit the specification of queries that allow a degree of uncertainty in the time axis. We carefully motivate the need for these more expressive queries, and demonstrate the utility of our approach on several data sets.}, isbn = {978-3-540-00074-7}, url = {http://dx.doi.org/10.1007/3-540-36109-X_19}, author = {Keogh,Eamonn and Hochheiser,Harry and Shneiderman, Ben}, editor = {Carbonell,Jaime and Siekmann,J{\"o}rg and Andreasen,Troels and Christiansen,Henning and Motro,Amihai and Legind Larsen,Henrik} } @conference {12753, title = {Bayesian methods for face recognition from video}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-4068 -IV-4071 - IV-4068 -IV-4071}, abstract = {Face recognition (FR) from video necessitates simultaneously solving two asks, recognition and tracking. To accommodate the video, a time series state space model is introduced in a Bayesian approach. Given this model, the goal reduces to estimating the posterior distribution of the state vector given the observations up to the present. The Sequential Importance Sampling (SIS) technique is invoked to generate a numerical solution to this model. However, the ultimate goal is to estimate the posterior distribution of the identity of humans for recognition purposes. Presented here are two methods to approximate the above distribution under different experimental scenarios.}, doi = {10.1109/ICASSP.2002.5745551}, author = {Chellapa, Rama and Zhou,Shaohua and Li,Baoxin} } @conference {18179, title = {Collusion-resistant fingerprinting for multimedia}, booktitle = {Acoustics, Speech, and Signal Processing (ICASSP), 2002 IEEE International Conference on}, volume = {4}, year = {2002}, month = {2002/05//}, pages = {IV-3309 -IV-3312 - IV-3309 -IV-3312}, abstract = {Digital fingerprinting is an effective method to identify users who might try to redistribute multimedia content, such as images and video. These fingerprints are typically embedded into the content using watermarking techniques that are designed to be robust to a variety of attacks. A cheap and effective attack against such digital fingerprints is collusion, where several differently marked copies of the same content are averaged or combined to disrupt the underlying fingerprint. In this paper, we study the problem of designing fingerprints that can withstand collusion, yet trace colluders. Since, in antipodal CDMA-type watermarking, the correlation contributions only decrease where watermarks differ, by constructing binary code vectors where any subset of k or fewer of these vectors have unique overlap, we may identify groups of k or less colluders. Our construction of such anti-collusion codes (ACC) uses the theory of combinatorial designs, and for n users requires O( $\#$x221A;n) bits. Further, we explore a block matrix structure for the ACC that reduces the computational complexity for identifying colluders and improves the detection capability when colluders belong to the same subgroup.}, doi = {10.1109/ICASSP.2002.5745361}, author = {Trappe,Wade and M. Wu and Liu,K. J.R} } @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.} } @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.} } @article {13747, title = {Construction of a Chinese-English Verb Lexicon for Embedded Machine Translation in Cross-Language Information Retrieval}, year = {2002}, month = {2002/08//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper addresses the problem of automatic acquisition of lexical knowledge for rapid construction of MT engines for use in multilingual applications. We describe new techniques for large-scale construction of a Chinese-English verb lexicon and we evaluate the coverage and effectiveness of the resulting lexicon for a structured MT approach that is embedded in a cross-language information retrieval system. Leveraging off an existing Chinese conceptual database called HowNet and a large, semantically rich English verb database, we use thematic-role information to create links between Chinese concepts and English classes. We apply the metrics of recall and precision to evaluate the coverage and effectiveness of the linguistic resources. The results of this work indicate that: (1) we are able to obtain reliable Chinese-English entries both with and without pre-existing semantic links between the two languages; (2) if we have pre-existing semantic links, we are able to produce a more robust lexical resource by merging these with our semantically rich English database; (3) In our comparisons with manual lexicon creation, our automatic techniques were shown to achieve 62\% precision, compared to a much lower precision of 10\% for arbitrary assignment of semantic links.}, keywords = {*ACQUISITION, *AUTOMATIC, *CROSS-LANGUAGE INFORMATION RETRIEVAL, *INFORMATION RETRIEVAL, *LEXICAL ACQUISITION, *MACHINE TRANSLATION, *VOCABULARY, Chinese language, CHINESE-ENGLISH LEXICONS, DATA BASES, EMBEDDED MT(MACHINE TRANSLATION) RESOURCES, EMBEDDING, English language, INFORMATION SCIENCE, linguistics, semantics, THEMATIC ROLES}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA459245}, author = {Dorr, Bonnie J and Lin,Dekang and Levow,Gina-Anne} } @article {13748, title = {Construction of a Chinese{\textendash}English Verb Lexicon for Machine Translation and Embedded Multilingual Applications}, journal = {Machine Translation}, volume = {17}, year = {2002}, month = {2002///}, pages = {99 - 137}, abstract = {This paper addresses the problem of automatic acquisition of lexical knowledge for rapid construction of engines for machine translation and embedded multilingual applications. We describe new techniques for large-scale construction of a Chinese{\textendash}English verb lexicon and we evaluate the coverage and effectiveness of the resulting lexicon. Leveraging off an existing Chinese conceptual database called How Net and a large, semantically rich English verb database, we use thematic-role information to create links between Chinese concepts and English classes. We apply the metrics of recall and precision to evaluate the coverage and effectiveness of the linguistic resources. The results of this work indicate that: (a) we are able to obtain reliable Chinese{\textendash}English entries both with and without pre-existing semantic links between the two languages; (b) if we have pre-existing semantic links, we are able to produce a more robust lexical resource by merging these with our semantically rich English database; (c) in our comparisons with manual lexicon creation, our automatic techniques were shown to achieve 62\% precision, compared to a much lower precision of 10\% for arbitrary assignment of semantic links.}, isbn = {0922-6567}, url = {http://dx.doi.org/10.1023/B:COAT.0000010116.83274.c3}, author = {Dorr, Bonnie J and Levow,Gina-Anne and Lin,Dekang} } @article {12958, title = {Detection of Cytotoxin-Hemolysin mRNA in Nonculturable Populations of Environmental and Clinical Vibrio Vulnificus Strains in Artificial Seawater}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {68}, year = {2002}, month = {2002/11/01/}, pages = {5641 - 5646}, abstract = {The objective of this study was to develop a molecular detection method that better estimates the potential risk associated with the presence of Vibrio vulnificus. For that purpose, we applied seminested reverse transcription-PCR (RT-PCR) to viable but nonculturable (VBNC) populations of V. vulnificus and targeted the cytotoxin-hemolysin virulence gene vvhA. Three strains, two environmental, IF Vv10 and IF Vv18, and one clinical, C7184, were used in this study. Artificial seawater, inoculated with mid-log-phase cells, was maintained at 4{\textdegree}C. VBNC cells resulted after 3, 6, and 14 days for C7184, IF Vv18, and IF Vv10, respectively. Our data indicate that seminested RT-PCR is sensitive for the detection of vvhA mRNA in artificial seawater when exclusively nonculturable bacteria are present. This is the first report of the expression of a toxin gene in VBNC V. vulnificus. Moreover, vvhA transcripts were shown to persist in nonculturable populations over a 4.5-month period, with a progressive decline of the signal over time. This result indicates that special attention should be given to the presence of potentially pathogenic VBNC cells in environmental samples when assessing public health risk.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.68.11.5641-5646.2002}, url = {http://aem.asm.org/content/68/11/5641}, author = {Fischer-Le Saux,Marion and Hervio-Heath,Dominique and Loaec,Solen and Rita R Colwell and Pommepuy,Monique} } @article {12959, title = {Effects of Global Climate on Infectious Disease: The Cholera Model}, journal = {Clinical Microbiology ReviewsClin. Microbiol. Rev.}, volume = {15}, year = {2002}, month = {2002/10/01/}, pages = {757 - 770}, abstract = {Recently, the role of the environment and climate in disease dynamics has become a subject of increasing interest to microbiologists, clinicians, epidemiologists, and ecologists. Much of the interest has been stimulated by the growing problems of antibiotic resistance among pathogens, emergence and/or reemergence of infectious diseases worldwide, the potential of bioterrorism, and the debate concerning climate change. Cholera, caused by Vibrio cholerae, lends itself to analyses of the role of climate in infectious disease, coupled to population dynamics of pathogenic microorganisms, for several reasons. First, the disease has a historical context linking it to specific seasons and biogeographical zones. In addition, the population dynamics of V. cholerae in the environment are strongly controlled by environmental factors, such as water temperature, salinity, and the presence of copepods, which are, in turn, controlled by larger-scale climate variability. In this review, the association between plankton and V. cholerae that has been documented over the last 20 years is discussed in support of the hypothesis that cholera shares properties of a vector-borne disease. In addition, a model for environmental transmission of cholera to humans in the context of climate variability is presented. The cholera model provides a template for future research on climate-sensitive diseases, allowing definition of critical parameters and offering a means of developing more sophisticated methods for prediction of disease outbreaks.}, isbn = {0893-8512, 1098-6618}, doi = {10.1128/CMR.15.4.757-770.2002}, url = {http://cmr.asm.org/content/15/4/757}, author = {Lipp,Erin K. and Huq,Anwar and Rita R Colwell} } @article {18385, title = {Empirical findings in agile methods}, journal = {Extreme Programming and Agile Methods{\textemdash}XP/Agile Universe 2002}, year = {2002}, month = {2002///}, pages = {81 - 92}, abstract = {In recent years, the use of, interest in, and controversy about Agile methodologies have realized dramatic growth. Anecdotal evidence is rising regarding the effectiveness of agile methodologies in certain environments and for specified projects. However, collection and analysis of empirical evidence of this effectiveness and classification of appropriate environments for Agile projects has not been conducted. Researchers from four institutions organized an eWorkshop to synchronously and virtually discuss and gather experiences and knowledge from eighteen Agile experts spread across the globe. These experts characterized Agile Methods and communicated experiences using these methods on small to very large teams. They discussed the importance of staffing Agile teams with highly skilled developers. They shared common success factors and identified warning signs of problems in Agile projects. These and other findings and heuristics gathered through this valuable exchange can be useful to researchers and to practitioners as they establish an experience base for better decision making.}, doi = {10.1007/3-540-45672-4_19}, author = {Lindvall,M. and Basili, Victor R. and Boehm,B. and Costa,P. and Dangle,K. and Shull, F. and Tesoriero,R. and Williams,L. and Zelkowitz, Marvin V} } @conference {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} } @article {12752, title = {A generic approach to simultaneous tracking and verification in video}, journal = {Image Processing, IEEE Transactions on}, volume = {11}, year = {2002}, month = {2002/05//}, pages = {530 - 544}, abstract = {A generic approach to simultaneous tracking and verification in video data is presented. The approach is based on posterior density estimation using sequential Monte Carlo methods. Visual tracking, which is in essence a temporal correspondence problem, is solved through probability density propagation, with the density being defined over a proper state space characterizing the object configuration. Verification is realized through hypothesis testing using the estimated posterior density. In its most basic form, verification can be performed as follows. Given a measurement vector Z and two hypotheses H1 and H0, we first estimate posterior probabilities P(H0|Z) and P(H1|Z), and then choose the one with the larger posterior probability as the true hypothesis. Several applications of the approach are illustrated by experiments devised to evaluate its performance. The idea is first tested on synthetic data, and then experiments with real video sequences are presented, illustrating vehicle tracking and verification, human (face) tracking and verification, facial feature tracking, and image sequence stabilization.}, keywords = {approach;, Carlo, configuration;, correspondence, data;, density, density;, estimated, estimation;, evaluation;, extraction;, Face, facial, feature, generic, human, hypothesis, image, measurement, methods;, Monte, object, performance, posterior, probability, probability;, problem;, processing;, propagation;, recognition;, road, sequence, sequences;, sequential, signal, space;, stabilization;, state, synthetic, temporal, testing;, tracking;, vector;, vehicle, vehicles;, verification;, video, visual}, isbn = {1057-7149}, doi = {10.1109/TIP.2002.1006400}, author = {Li,Baoxin and Chellapa, Rama} } @article {16270, title = {Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii}, journal = {Nature}, volume = {419}, year = {2002}, month = {2002/10/03/}, pages = {512 - 519}, abstract = {Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.}, isbn = {0028-0836}, doi = {10.1038/nature01099}, url = {http://www.nature.com/nature/journal/v419/n6906/full/nature01099.html}, author = {Carlton,Jane M. and Angiuoli,Samuel V and Suh,Bernard B. and Kooij,Taco W. and Pertea,Mihaela and Silva,Joana C. and Ermolaeva,Maria D. and Allen,Jonathan E and Jeremy D Selengut and Koo,Hean L. and Peterson,Jeremy D. and Pop, Mihai and Kosack,Daniel S. and Shumway,Martin F. and Bidwell,Shelby L. and Shallom,Shamira J. and Aken,Susan E. van and Riedmuller,Steven B. and Feldblyum,Tamara V. and Cho,Jennifer K. and Quackenbush,John and Sedegah,Martha and Shoaibi,Azadeh and Cummings,Leda M. and Florens,Laurence and Yates,John R. and Raine,J. Dale and Sinden,Robert E. and Harris,Michael A. and Cunningham,Deirdre A. and Preiser,Peter R. and Bergman,Lawrence W. and Vaidya,Akhil B. and Lin,Leo H. van and Janse,Chris J. and Waters,Andrew P. and Smith,Hamilton O. and White,Owen R. and Salzberg,Steven L. and Venter,J. Craig and Fraser,Claire M. and Hoffman,Stephen L. and Gardner,Malcolm J. and Carucci,Daniel J.} } @conference {17178, title = {Getting real about speech: overdue or overhyped?}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {708 - 709}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Speech has recently made headway towards becoming a more mainstream interface modality. For example, there is an increasing number of call center applications, especially in the airline and banking industries. However, speech still has many properties that cause its use to be problematic, such as its inappropriateness in both very quiet and very noisy environments, and the tendency of speech to increase cognitive load. Concerns about such problems are valid; however, they do not explain why the use of speech is so controversial in the HCI community. This panel would like to address the issues underlying the controversy around speech, by discussing the current state of the art, the reasons it is so difficult to build a good speech interface, and how HCI research can contribute to the development of speech interfaces.}, keywords = {cognitive load, social responses, speech interfaces}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506557}, url = {http://doi.acm.org/10.1145/506443.506557}, author = {James,Frankie and Lai,Jennifer and Suhm,Bernhard and Balentine,Bruce and Makhoul,John and Nass,Clifford and Shneiderman, Ben} } @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.} } @article {12386, title = {High-level synthesis of DSP applications using adaptive negative cycle detection}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2002}, year = {2002}, month = {2002/01//}, pages = {893 - 907}, abstract = {The problem of detecting negative weight cycles in a graph is examined in the context of the dynamic graph structures that arise in the process of high level synthesis (HLS). The concept of adaptive negative cycle detection is introduced, in which a graph changes over time and negative cycle detection needs to be done periodically, but not necessarily after every individual change. We present an algorithm for this problem, based on a novel extension of the well-known Bellman-Ford algorithm that allows us to adapt existing cycle information to the modified graph, and show by experiments that our algorithm significantly outperforms previous incremental approaches for dynamic graphs. In terms of applications, the adaptive technique leads to a very fast implementation of Lawlers algorithm for the computation of the maximum cycle mean (MCM) of a graph, especially for a certain form of sparse graph. Such sparseness often occurs in practical circuits and systems, as demonstrated, for example, by the ISCAS 89/93 benchmarks. The application of the adaptive technique to design-space exploration (synthesis) is also demonstrated by developing automated search techniques for scheduling iterative data-flow graphs.}, keywords = {adaptive performance estimation, dynamic graphs, maximum cycle mean, negative cycle detection}, isbn = {1110-8657}, url = {http://dl.acm.org/citation.cfm?id=1283100.1283192}, author = {Chandrachoodan,Nitin and Bhattacharyya, Shuvra S. and Liu,K. J.R} } @article {14091, title = {Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi}, journal = {Molecular and Biochemical Parasitology}, volume = {124}, year = {2002}, month = {2002/09/10/}, pages = {73 - 78}, abstract = {As observed for most eukaryotic cells, trypanosomatids contains non-LTR retrotransposons randomly inserted in the nuclear genome. Autonomous retroelements which, code for their own transposition, have been characterized in Trypanosoma brucei (ingi) and Trypanosoma cruzi (L1Tc), whereas non-autonomous retroelements have only been characterized in T. brucei (RIME). Here, we have characterized in the genome of Trypanosoma cruzi four complete copies of a non-autonomous non-LTR retrotransposon, called NARTc. This 0.26 kb NARTc element has the characteristics of non-LTR retrotransposons: the presence a poly(dA) tail and of a short flanking duplicated motif. Analysis of the Genome Survey Sequence databases indicated that the Trypanosoma cruzi haploid genome contains about 140 NARTc copies and about twice as many L1Tc copies. Interestingly, the NARTc and L1Tc retroelements share, with the Trypanosoma brucei ingi and RIME retrotransposons, a common sequence (the first 45 bp with 91\% identity), whereas the remaining sequences are very divergent. This suggests that these four trypanosome non-LTR retrotransposons were derived from the same common ancester and the sequence of their 5{\textquoteright}-extremity may have a functional role. In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp.}, keywords = {Ingi, L1Tc, Non-LTR retrotransposon, RIME, Trypanosoma brucei, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/S0166-6851(02)00167-6}, url = {http://www.sciencedirect.com/science/article/pii/S0166685102001676}, author = {Bringaud,Fr{\'e}d{\'e}ric and Garc{\'\i}a-P{\'e}rez,Jos{\'e} Luis and Heras,Sara R. and Ghedin,Elodie and El-Sayed, Najib M. and Andersson,Bj{\"o}rn and Baltz,Th{\'e}o and Lopez,Manuel C.} } @article {14624, title = {Identification of transcription factor binding sites in the human genome sequence}, journal = {Mammalian Genome}, volume = {13}, year = {2002}, month = {2002///}, pages = {510 - 514}, abstract = {The identification of transcription factor binding sites (TFBS) is an important initial step in determining the DNA signals that regulate transcription of the genome. We tested the performance of three distinct computational methods for the identification of TFBS applied to the human genome sequence, as judged by their ability to recover the location of experimentally determined, and uniquely mapped, TFBS taken from the TRANSFAC database. These identification methods all attempt to filter the quantity of TFBS identified by aligning positional weight matrices that describe the binding site and employ either (i) a P-value threshold for accepting a site, (ii) an over-representation measure of neighboring sites, or (iii) conservation with the mouse genome and application of P-value thresholds. The results show that the best recognition of TFBS is achieved by combining the identification of TFBS in regions of human{\textendash}mouse conservation and also by applying a high stringency P-value to the TFBS identified in non-coding regions that are not conserved. Additionally, we find that only half of the 481 experimentally mapped sites can be found in sequence regions conserved with mouse, but the predictive power of the binding site identification method is up to threefold higher in the conserved regions.}, isbn = {0938-8990}, url = {http://dx.doi.org/10.1007/s00335-002-2175-6}, author = {Levy,Samuel and Hannenhalli, Sridhar} } @conference {13053, title = {The importance of lexicalized syntax models for natural language generation tasks}, booktitle = {Proc. of INLG}, year = {2002}, month = {2002///}, pages = {9 - 16}, author = {Daum{\'e}, Hal and Knight,K. and Langkilde-Geary,I. and Marcu,D. and Yamada,K.} } @inbook {17604, title = {Improved Approximation Algorithms for the Partial Vertex Cover Problem}, booktitle = {Approximation Algorithms for Combinatorial OptimizationApproximation Algorithms for Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {2462}, year = {2002}, month = {2002///}, pages = {161 - 174}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The partial vertex cover problem is a generalization of the vertex cover problem:given an undirected graph G = ( V,E ) and an integer k , we wish to choose a minimum number of vertices such that at least k edges are covered. Just as for vertex cover, 2-approximation algorithms are known for this problem, and it is of interest to see if we can do better than this.The current-best approximation ratio for partial vertex cover, when parameterized by the maximum degree d of G , is (2 - Θ (1/ d )).We improve on this by presenting a $$ {\l}eft( 2 - \Theta {\l}eft( \tfrac{\l}n {\l}n d {\l}n d \right) \right) $$ -approximation algorithm for partial vertex cover using semidefinite programming, matching the current-best bound for vertex cover. Our algorithmuses a new rounding technique, which involves a delicate probabilistic analysis.}, isbn = {978-3-540-44186-1}, url = {http://dx.doi.org/10.1007/3-540-45753-4_15}, author = {Halperin,Eran and Srinivasan, Aravind}, editor = {Jansen,Klaus and Leonardi,Stefano and Vazirani,Vijay} } @article {12963, title = {In vitro adhesion to human cells by viable but nonculturable Enterococcus faecalis}, journal = {Current microbiology}, volume = {45}, year = {2002}, month = {2002///}, pages = {105 - 110}, abstract = {The ability of viable but nonculturable (VBNC) Enterococcus faecalis to adhere to Caco-2 and Girardi heart cultured cells and to urinary tract epithelial cells (ECs) was studied. Enterococci were harvested during the vegetative growth phase (early exponential and stationary), in the VBNC state, and after recovery of the ability to divide. VBNC bacteria maintained their adherence capability but the efficiency of attachment was reduced by about 50 to 70\%, depending on the target cell employed. The decrease was transient, since enterococci that regained their culturability showed adherence values similar to those observed for actively growing cells. Analysis of the invasive properties of E. faecalis revealed that the VBNC state caused a decrease in the number of bacteria that entered the cultured HEK cells as a result of the reduction in the number of adhering bacteria. These results highlight the importance of studies of the VBNC phenomenon, with respect to both microbial survival in the environment and the impact on human health.}, doi = {10.1007/s00284-001-0089-2}, author = {Pruzzo,C. and Tarsi,R. and Lle{\`o},M. M. and Signoretto,C. and Zampini,M. and Rita R Colwell and Canepari,P.} } @article {18232, title = {Joint coding and embedding for collusion-resistant fingerprinting}, journal = {Proceedings of the European Signal Processing Conference, EUSIPCO}, year = {2002}, month = {2002///}, abstract = {An effective attack against fingerprints for multimedia is collusion,where several differently marked copies of the same content are av- eraged or combined to disrupt the underlying fingerprint. In this paper, we investigate the problem of designing fingerprints that can withstand collusion and allow for the identification of colluders. We begin by introducing the collusion problem for additive embedding, and introduce an efficient detection algorithm for orthogonal mod- ulation that identifies the fingerprints associated with K colluders and requires O(K log(n/K)) correlations for a group of n users. We present a construction of collusion-resistant fingerprints based upon anti-collusion codes (ACC) and binary code modulation. Us- ing ACC, we build fingerprints that identify groups of K or less colluders. We present a construction of binary-valued ACC un- der the logical AND operation using the theory of combinatorial designs. Our code construction requires only O(√n) orthogonal signals to accommodate n users. We demonstrate the performance of our ACC for fingerprinting multimedia and identifying colluders through experiments using Gaussian signals. }, author = {Trappe,W. and Wu,M. and Liu,K. J.R} } @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} } @conference {12107, title = {A light-weight process for capturing and evolving defect reduction experience}, booktitle = {Engineering of Complex Computer Systems, 2002. Proceedings. Eighth IEEE International Conference on}, year = {2002}, month = {2002/12//}, pages = {129 - 132}, abstract = {Selecting technologies for developing software is a crucial activity in software projects. Defect reduction is an example of an area in which software developers have to decide what technologies to use. CeBASE is a NSF funded project that has the role of improving software development by providing decision support on the selection of techniques and tools. The decision support is based on empirical data organized in experience bases and refined into high-level models. Empirical data is collected through various activities, for example through eWorkshops in which experts discuss important issues, and formalized using the lightweight knowledge dust to knowledge pearl process.}, keywords = {bases;experience, CeBASE;NSF, defect, development;software, experience;software, funded, knowledge;software, management;lightweight, management;software, project;decision, projects;software, reduction, reusability;software, reuse;software, support;eWorkshops;experience, tools;, tools;knowledge}, doi = {10.1109/ICECCS.2002.1181505}, author = {Basili, Victor R. and Lindvall,M. and Shull, F.} } @conference {13587, title = {Logical Labeling of Document Images Using Layout Graph Matching with Adaptive Learning}, booktitle = {IAPR Conference on Document Analysis System}, year = {2002}, month = {2002///}, pages = {212 - 223}, abstract = {Logical structure analysis of document images is an important problem in document image understanding. In this paper, we propose a graph matching approach to label logical components on a document page. Our system is able to learn a model for a document class, use this model to label document images through graph matching, and adaptively improve the model with error feed back. We tested our method on journal/proceeding article title pages. The experimental results show promising accuracy, and confirm the ability of adaptive learning.}, author = {Liang,J. and David Doermann} } @article {18240, title = {Methods and apparatus for multi-layer data hiding}, volume = {:~09/427,321}, year = {2002}, month = {2002/09/24/}, abstract = {A data hiding system and method for providing a method of embedding multiple layers of hidden data into multimedia data. First, a media unit of the multimedia data is evaluated to determine an appropriate embedding procedure. Next during a first embedding pass, a ruling layer of primary hidden data is embedded into the media unit. In another embedding pass, a governing layer of secondary hidden data is embedded on top of the ruling layer. The secondary hidden data provides control information for controlling the primary hidden data and the host data. Control information such as error correction data, synchronization data, decoding data, and authentication data is embedded in the governing layer. Embedding schemes such as base domain and spectrum domain embedding are employed.}, url = {http://www.google.com/patents?id=1KYLAAAAEBAJ}, author = {Yu,Hong Heather and M. Wu and Li,Xin and Gelman,Alexander D.}, editor = {Matsushita Electric Industrial Co., Ltd.} } @conference {13317, title = {Multiresolution tetrahedral meshes: an analysis and a comparison}, booktitle = {Shape Modeling International, 2002. Proceedings}, year = {2002}, month = {2002///}, pages = {83 - 91}, abstract = {We deal with the problem of analyzing and visualizing large-size volume data sets. To this aim, we consider multiresolution representations based on a decomposition of the field domain into tetrahedral cells. We compare two types of multiresolution representations that differ on the rule applied to refine an initial coarse mesh: one is based on tetrahedron bisection, and one based on vertex split. The two representations can be viewed as instances of a common multiresolution model, that we call a multiresolution mesh. Encoding data structures for the two representations are briefly described. An experimental comparison on structured volume data sets is presented}, keywords = {(computer, bisection;vertex, cells;tetrahedron, data, generation;rendering, geometry;data, graphics);solid, meshes;rendering;tetrahedral, modelling;, refinement;multiresolution, representations;multiresolution, sets;mesh, split;computational, structures;data, tetrahedral, visualisation;mesh, visualization;experiment;large-size, volume}, doi = {10.1109/SMI.2002.1003532}, author = {Danovaro,E. and De Floriani, Leila and Lee,M. and Samet, Hanan} } @article {14090, title = {A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei}, journal = {Eukaryotic cell}, volume = {1}, year = {2002}, month = {2002///}, pages = {137 - 137}, author = {Bringaud,F. and Biteau,N. and Melville,S. E. and Hez,S. and El-Sayed, Najib M. and Leech,V. and Berriman,M. and Hall,N. and Donelson,J. E and Baltz,T.} } @article {18259, title = {Nonlinear collusion attacks on independent multimedia fingerprints}, journal = {submitted to IEEE Trans. on Image Proc}, year = {2002}, month = {2002///}, author = {Zhao,H. and Wu,M. and Wang,Z.J. and Liu,K. J.R} } @article {15299, title = {Omnibase: Uniform access to heterogeneous data for question answering}, journal = {Natural Language Processing and Information Systems}, year = {2002}, month = {2002///}, pages = {230 - 234}, abstract = {Although the World Wide Web contains a tremendous amount of information, the lack of uniform structure makes finding the right knowledge difficult. A solution is to turn the Web into a {\textquotedblleft}virtual database{\textquotedblright} and to access it through natural language.We built Omnibase, a system that integrates heterogeneous data sources using an object- property-value model. With the help of Omnibase, our Start natural language system can now access numerous heterogeneous data sources on the Web in a uniform manner, and answers millions of user questions with high precision.}, doi = {10.1007/3-540-36271-1_23}, author = {Katz,B. and Felshin,S. and Yuret,D. and Ibrahim,A. and Jimmy Lin and Marton,G. and Jerome McFarland,A. and Temelkuran,B.} } @conference {13618, title = {Page classification through logical labelling}, booktitle = {Pattern Recognition, 2002. Proceedings. 16th International Conference on}, volume = {3}, year = {2002}, month = {2002///}, pages = {477 - 480 vol.3 - 477 - 480 vol.3}, abstract = {We propose an integrated approach to page classification and logical labelling. Layout is represented by a fully connected attributed relational graph that is matched to the graph of an unknown document, achieving classification and labelling simultaneously. By incorporating global constraints in an integrated fashion, ambiguity at the zone level can be reduced, providing robustness to noise and variation. Models are automatically trained from sample documents. Experimental results show promise for the classification and labelling of technical article title pages, and supports the idea of a hierarchical model base.}, keywords = {article, attributed, base;, character, classification;, constraints;, document, document;, experimental, global, graph, graph;, hierarchical, image, images;, labelling;, logical, model, noise;, OCR;, optical, page, pages;, processing;, recognition;, relational, results;, technical, theory;, title, unknown}, doi = {10.1109/ICPR.2002.1047980}, author = {Liang,Jian and David Doermann and Ma,M. and Guo,J. K} } @article {13459, title = {PASSAT: A user-centric planning framework}, journal = {Proceedings of the 3rd International NASA Workshop on Planning and Scheduling for Space}, year = {2002}, month = {2002///}, abstract = {We describe a plan-authoring system called PASSAT (Plan-Authoring System based on Sketches, Advice, and Templates) that combines interactive tools for constructing plans with a suite of automated and mixed-initiative capabilities designed to complement human planning skills. PASSAT is organized around a library of predefined templates that encode task networks describing standard operating procedures and previous cases. Users can select from these templates to apply during plan development, with the system providing various forms of automated assistance. A mixed-initiative plan sketch facility helps users refine outlines for plans to complete solutions, by detecting problems and proposing possible fixes. An advice capability enables user specification of high-level guidelines for plans that the system helps to enforce. Finally, PASSAT includes process facilitation mechanisms designed to help a user track and manage outstanding planning tasks and information requirements, as a means of improving the efficiency and effectiveness of the planning process. PASSAT is designed for applications for which a core of planning knowledge can be captured in predefined action models but where significant user control of the planning process is required. }, author = {Myers,K.L. and Tyson,W.M. and Wolverton,M.J. and Jarvis,P.A. and Lee,T.J. and desJardins, Marie} } @conference {13623, title = {Performance evaluation of object detection algorithms}, booktitle = {Pattern Recognition, 2002. Proceedings. 16th International Conference on}, volume = {3}, year = {2002}, month = {2002///}, pages = {965 - 969 vol.3 - 965 - 969 vol.3}, abstract = {The continuous development of object detection algorithms is ushering in the need for evaluation tools to quantify algorithm performance. In this paper a set of seven metrics are proposed for quantifying different aspects of a detection algorithm{\textquoteright}s performance. The strengths and weaknesses of these metrics are described. They are implemented in the Video Performance Evaluation Resource (ViPER) system and will be used to evaluate algorithms for detecting text, faces, moving people and vehicles. Results for running two previous text-detection algorithms on a common data set are presented.}, keywords = {algorithms;, common, data, DETECTION, detection;, Evaluation, evaluation;, image, object, performance, recognition;, resource, set;, system;, text-detection, video}, doi = {10.1109/ICPR.2002.1048198}, author = {Mariano,V.Y. and Min,Junghye and Park,Jin-Hyeong and Kasturi,R. and Mihalcik,D. and Huiping Li and David Doermann and Drayer,T.} } @article {13009, title = {Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala)}, journal = {Mol Phylogenet Evol}, volume = {23}, year = {2002}, month = {2002/05//}, pages = {288 - 292}, abstract = {Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. These results are consistent with the view of Polyacanthocephala representing an independent class within Acanthocephala.}, doi = {10.1016/S1055-7903(02)00020-9}, author = {Garc{\'\i}a-Varela,M and Cummings, Michael P. and P{\'e}rez-Ponce de Le{\'o}n,G. and Gardner,S. L and Laclette,J. P} } @article {14634, title = {Predicting Transcription Factor Synergism}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {30}, year = {2002}, month = {2002/10/01/}, pages = {4278 - 4284}, abstract = {Transcriptional regulation is mediated by a battery of transcription factor (TF) proteins, that form complexes involving protein{\textendash}protein and protein{\textendash}DNA interactions. Individual TFs bind to their cognate cis-elements or transcription factor-binding sites (TFBS). TFBS are organized on the DNA proximal to the gene in groups confined to a few hundred base pair regions. These groups are referred to as modules. Various modules work together to provide the combinatorial regulation of gene transcription in response to various developmental and environmental conditions. The sets of modules constitute a promoter model. Determining the TFs that preferentially work in concert as part of a module is an essential component of understanding transcriptional regulation. The TFs that act synergistically in such a fashion are likely to have their cis-elements co-localized on the genome at specific distances apart. We exploit this notion to predict TF pairs that are likely to be part of a transcriptional module on the human genome sequence. The computational method is validated statistically, using known interacting pairs extracted from the literature. There are 251 TFBS pairs up to 50 bp apart and 70 TFBS pairs up to 200 bp apart that score higher than any of the known synergistic pairs. Further investigation of 50 pairs randomly selected from each of these two sets using PubMed queries provided additional supporting evidence from the existing biological literature suggesting TF synergism for these novel pairs.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/gkf535}, url = {http://nar.oxfordjournals.org/content/30/19/4278}, author = {Hannenhalli, Sridhar and Levy,Samuel} } @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 {17927, title = {A real-time seamless tiled display system for 3D graphics}, journal = {Immersive Projection Technology Symposium of the IEEE Virtual Reality 2002 Conference (VR2002 IPT)}, year = {2002}, month = {2002///}, abstract = {We outline our seamless tiled display system forinteractive 3D graphics applications that is low-cost, easy to calibrate, scalable, and portable. Our system achieves geometric alignment in software by pre-warping the 3D space in contrast with the current systems that usually achieve this by 2D image pre-warping. Our system accomplishes this through real-time image capture from a digital camcorder, image segmentation, and derivation of the 3D warping matrices for each 3D graphics pipeline that feeds a projector. Our prototype system demonstrates our results on a 2 {\texttimes} 2 tiled array of projectors. }, author = {Li,Z. and Varshney, Amitabh} } @conference {14772, title = {Recompilation for debugging support in a JIT-compiler}, booktitle = {Proceedings of the 2002 ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, series = {PASTE {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {10 - 17}, publisher = {ACM}, organization = {ACM}, address = {Charleston, South Carolina, USA}, abstract = {A static Java compiler converts Java source code into a verifiably secure and compact architecture-neutral intermediate format, called Java byte codes. The Java byte codes can be either interpreted by a Java Virtual Machine or translated into native code by Java Just-In-Time compilers. Static Java compilers embed debug information in the Java class files to be used by the source level debuggers. However, the debug information is generated for architecture independent byte codes and most of the debug information is valid only when the byte codes are interpreted. Translating byte codes into native instructions puts a limitation on the amount of usable debug information that can be used by source level debuggers. In this paper, we present a new technique to generate valid debug information when Just-In-Time compilers are used. Our approach is based on the dynamic recompilation of Java methods by a fast code generator and lazily generates debug information when it is required. We also present three implementations for field watch support in the Java Virtual Machine Debugger Interface to investigate the runtime overhead and code size growth by our approach.}, keywords = {algorithms, debug information, debugging aids, dynamic recompilation, field access watch, java, java virtual machine debugger interface, just-in-time compilation, measurement, performance}, isbn = {1-58113-479-7}, doi = {10.1145/586094.586100}, author = {Tikir, Mustafa M. and Hollingsworth, Jeffrey K and Lueh,Guei-Yuan} } @article {17955, title = {Representing thermal vibrations and uncertainty in molecular surfaces}, journal = {SPIE Conference on Visualization and Data Analysis}, volume = {4665}, year = {2002}, month = {2002///}, pages = {80 - 90}, abstract = {The previous methods to compute smooth molecular surface assumed that each atom in a molecule has a fixedposition without thermal motion or uncertainty. In real world, the position of an atom in a molecule is fuzzy because of its uncertainty in protein structure determination and thermal energy of the atom. In this paper, we propose a method to compute smooth molecular surface for fuzzy atoms. The Gaussian distribution is used for modeling the fuzziness of each atom, and a p-probability sphere is computed for each atom with a certain confidence level. The smooth molecular surface with fuzzy atoms is computed efficiently from extended-radius p-probability spheres. We have implemented a program for visualizing three-dimensional molecular structures including the smooth molecular surface with fuzzy atoms using multi-layered transparent surfaces, where the surface of each layer has a different confidence level and the transparency associated with the confidence level. }, author = {Lee,C. H and Varshney, Amitabh} } @article {18157, title = {A robust error resilient approach for MPEG video transmission over internet}, journal = {Visual Communication and Image Processing, SPIE}, volume = {4671}, year = {2002}, month = {2002///}, pages = {103 - 111}, abstract = {In network delivery of compressed video, packets may be lost if the channel is unreliable. Such losses tend to occur inburst. In this paper, we develop an error resilient video encoding approach to help error concealment at the decoder. We introduce a new block shuffling scheme to isolate erroneous blocks caused by packet losses. And we apply data hiding to add additional protection for motion vectors. The incorporation of these scheme adds little complexity to the standard encoder. Experimental results suggest that our approach can achieve a reasonable quality for packet loss up to 30\% over a wide range of video materials. }, author = {Yin,P. and Wu,M. and Liu,B.} } @article {11913, title = {Rover: scalable location-aware computing}, journal = {Computer}, volume = {35}, year = {2002}, month = {2002/10//}, pages = {46 - 53}, abstract = {All the components necessary for realizing location-aware computing are available in the marketplace today. What has hindered the widespread deployment of location-based systems is the lack of an integration architecture that scales with user populations. The authors have completed the initial implementation of Rover, a system designed to achieve this sort of integration and to automatically tailor information and services to a mobile user{\textquoteright}s location. Their studies have validated Rover{\textquoteright}s underlying software architecture, which achieves system scalability through high-resolution, application-specific resource scheduling at the servers and network. The authors believe that this technology will greatly enhance the user experience in many places, including museums, amusement and theme parks, shopping malls, game fields, offices, and business centers. They designed the system specifically to scale to large user populations and expect its benefits to increase with them.}, keywords = {amusement, application-specific, architecture;, automation;, business, business;, computing;, data, entertainment;, handheld, humanities;, integration, LAN;, location-aware, malls;, mobile, museums;, office, parks;, processing;, resource, Rover;, scalability;, scalable, scheduling;, shopping, software, system, theme, units;, user;, wireless}, isbn = {0018-9162}, doi = {10.1109/MC.2002.1039517}, author = {Banerjee,S. and Agarwal,S. and Kamel,K. and Kochut, A. and Kommareddy,C. and Nadeem,T. and Thakkar,P. and Trinh,Bao and Youssef,A. and Youssef, M. and Larsen,R.L. and Udaya Shankar,A. and Agrawala, Ashok K.} } @conference {13641, title = {Segmentation and Identification of Handwriting in Noisy Documents}, booktitle = {IAPRConference on Document Analysis System}, year = {2002}, month = {2002///}, pages = {95 - 105}, abstract = {In this paper we present an approach to the problem of segmenting and identifying handwritten annotations in noisy document images. In many types of documents such as correspondence, it is not uncommon for handwritten annotations to be added as part of a note, correction, clarification, or instruction, or a signature to appear as an authentication mark. It is important to be able to segment and identify such handwriting so we can 1) locate, interpret and re-trieve them efficiently in large document databases, and 2) use different algo-rithms for printed/handwritten text recognition and signature verification. Our approach consists of two processes: 1) a segmentation process, which divides the text into regions at an appropriate level (character, word, or zone), and 2) a classification process which identifies the segmented regions as handwritten. To determine the approximate region size where classification can be reliably per-formed, we conducted experiments at the character, word and zone level. We found that the reliable results can be achieved at the word level with a classifi-cation accuracy of 97.3\%. The identified handwritten text is further grouped into zones and verified to reduce false alarms. Experiments show our approach is promising and robust.}, author = {Zheng,Y. and Li,H. and David Doermann} } @article {12961, title = {Simple Procedure for Rapid Identification of Vibrio Cholerae from the Aquatic Environment}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {68}, year = {2002}, month = {2002/02/01/}, pages = {995 - 998}, abstract = {Biochemical tests commonly used to screen for Vibrio cholerae in environmental samples were evaluated, and we found that a combination of alkaline peptone enrichment followed by streaking on thiosulfate citrate bile salts sucrose agar and testing for arginine dihydrolase activity and esculin hydrolysis was an effective rapid technique to screen for aquatic environmental V. cholerae. This technique provided 100\% sensitivity and >=70\% specificity.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.68.2.995-998.2002}, url = {http://aem.asm.org/content/68/2/995}, author = {Choopun,Nipa and Louis,Val{\'e}rie and Huq,Anwar and Rita R Colwell} } @conference {15288, title = {The START multimedia information system: Current technology and future directions}, booktitle = {In Proceedings of the International Workshop on Multimedia Information Systems (MIS 2002)}, year = {2002}, month = {2002///}, abstract = {To address the problem of information overload intoday{\textquoteright}s world, we have developed Start, a natural language question answering system that provides users with high-precision multimedia information ac- cess through the use of natural language annota- tions. To address the difficulty of accessing large amounts of heterogeneous data, we have developed Omnibase, which assists Start by integrating struc- tured and semistructured Web databases into a sin- gle, uniformly structured {\textquotedblleft}virtual database.{\textquotedblright} Our ultimate goal is to develop a computer system that acts like a {\textquotedblleft}smart reference librarian,{\textquotedblright} and we be- lieve we have laid a firm foundation for achieving our goal. This paper describes our current implemented system and discusses future research directions. }, author = {Katz,B. and Jimmy Lin and Felshin,S.} } @conference {13667, title = {Text Quality Estimation in Digital Video}, booktitle = {SPIE Conf. on Document Recognition and Information Retrieval}, year = {2002}, month = {2002///}, pages = {232 - 243}, author = {Li,H. and David Doermann} } @inbook {18923, title = {Theoretical and Empirical Aspects of a Planner in a Multi-agent Environment}, booktitle = {Logics in Artificial Intelligence}, series = {Lecture Notes in Computer Science}, volume = {2424}, year = {2002}, month = {2002///}, pages = {173 - 185}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We give the theoretical foundations and empirical evaluation of a planning agent, ashop, performing HTN planning in a multi-agent environment. ashop is based on ASHOP , an agentised version of the original SHOP HTN planning algorithm, and is integrated in the IMPACT multi-agent environment. We ran several experiments involving accessing various distributed, heterogeneous information sources, based on simplified versions of noncombatant evacuation operations, NEO{\textquoteright}s. As a result, we noticed that in such realistic settings the time spent on communication (including network time) is orders of magnitude higher than the actual inference process. This has important consequences for optimisations of such planners. Our main results are: (1) using NEO{\textquoteright}s as new, more realistic benchmarks for planners acting in an agent environment, and (2) a memoization mechanism implemented on top of shop, which improves the overall performance considerably.}, keywords = {Computer science}, isbn = {978-3-540-44190-8}, url = {http://www.springerlink.com/content/10lxp56u3e9k0bdd/abstract/}, author = {Dix,J{\"u}rgen and Munoz-Avila,Hector and Nau, Dana S. and Zhang,Lingling}, editor = {Flesca,Sergio and Greco,Sergio and Ianni,Giovambattista and Leone,Nicola} } @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} } @article {15662, title = {Vision geometry XI(Seattle WA, 7-8 July 2002)}, journal = {SPIE proceedings series}, year = {2002}, month = {2002///}, author = {Latecki,L.J. and Mount, Dave and Wu,A. Y} } @conference {15303, title = {Web question answering: is more always better?}, booktitle = {Proceedings of the 25th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {291 - 298}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a question answering system that is designed to capitalize on the tremendous amount of data that is now available online. Most question answering systems use a wide variety of linguistic resources. We focus instead on the redundancy available in large corpora as an important resource. We use this redundancy to simplify the query rewrites that we need to use, and to support answer mining from returned snippets. Our system performs quite well given the simplicity of the techniques being utilized. Experimental results show that question answering accuracy can be greatly improved by analyzing more and more matching passages. Simple passage ranking and n-gram extraction techniques work well in our system making it efficient to use with many backend retrieval engines.}, isbn = {1-58113-561-0}, doi = {10.1145/564376.564428}, url = {http://doi.acm.org/10.1145/564376.564428}, author = {Dumais,Susan and Banko,Michele and Brill,Eric and Jimmy Lin and Ng,Andrew} } @conference {18765, title = {Web-based innovation alert services to support product design evolution}, year = {2002}, month = {2002///}, abstract = {Technological innovations provide an opportunity toimprove product performance and reduce cost. Therefore, design organizations are interested in monitoring technological innovations. A large number of innovations are announced every year. Monitoring them manually is very time consuming. We are developing web-based innovation-alert services that can be used to monitor and communicate information about innovations relevant to a particular product design. In this paper, we discuss the required infrastructure, relevant design issues, and our approach to developing web-based innovation alert services to support product design evolution. We also describe a prototype innovation monitoring service for computer components and an interactive tool to transform semi-structured web contents into semantic representations in XML. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.198.1039\&rep=rep1\&type=pdf}, author = {Gupta,S.K. and Lin,E. and Lo,A. J. and Xu,C.} } @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} } @conference {12335, title = {Adaptive negative cycle detection in dynamic graphs}, booktitle = {Circuits and Systems, 2001. ISCAS 2001. The 2001 IEEE International Symposium on}, volume = {5}, year = {2001}, month = {2001///}, pages = {163 - 166}, author = {Chandrachoodan,N. and Bhattacharyya, Shuvra S. and Liu,K. J.R} } @article {14067, title = {Analysis of a donor gene region for a variant surface glycoprotein and its expression site in African trypanosomes}, journal = {Nucleic acids research}, volume = {29}, year = {2001}, month = {2001///}, pages = {2012 - 2012}, author = {LaCount,D. J and El-Sayed, Najib M. and Kaul,S. and Wanless,D. and Turner,C. M.R and Donelson,J. E} } @conference {18164, title = {Analysis of attacks on SDMI audio watermarks}, booktitle = {Acoustics, Speech, and Signal Processing, 2001. Proceedings. (ICASSP {\textquoteright}01). 2001 IEEE International Conference on}, volume = {3}, year = {2001}, month = {2001///}, pages = {1369 -1372 vol.3 - 1369 -1372 vol.3}, abstract = {This paper explains and analyzes the successful attacks submitted by the authors on four audio watermark proposals during a 3-week SDMI public challenge. Our analysis points out some weaknesses in the watermark techniques currently under SDMI consideration and suggests directions for further improvement. The paper also discusses the framework and strategies for analyzing the robustness and security of watermarking systems as well as the difficulty, uniqueness, and unrealistic expectations of the attack setup}, keywords = {attacks;watermark, audio, coding;copy, digital, encapsulation;, Initiative;attack, Music, protection;data, SDMI, setup;robustness;security;successful, watermarks;Secure, weaknesses;audio}, doi = {10.1109/ICASSP.2001.941183}, author = {M. Wu and Craver,S. and Felten,E.W. and Liu,B.} } @book {16985, title = {Becoming a Scholar in the Digital Age}, year = {2001}, month = {2001///}, publisher = {National Research Council}, organization = {National Research Council}, keywords = {bibtex-import, digital-library, dlbook}, author = {Duderstadt,James and Arms,William and Messina,Paul and Ellisman,Mark and Atkins,Daniel and Fox,Edward and Shneiderman, Ben and Nissenbaum,Helen and Lederberg,Joshua} } @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 {15872, title = {CLEF experiments at Maryland: Statistical stemming and backoff translation}, journal = {Cross-Language Information Retrieval and Evaluation}, year = {2001}, month = {2001///}, pages = {176 - 187}, author = {Oard, Douglas and Levow,G.A. and Cabezas,C.} } @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} } @article {14607, title = {Enrichment of Regulatory Signals in Conserved Non-Coding Genomic Sequence}, journal = {BioinformaticsBioinformatics}, volume = {17}, year = {2001}, month = {2001/10/01/}, pages = {871 - 877}, abstract = {Motivation: Whole genome shotgun sequencing strategies generate sequence data prior to the application of assembly methodologies that result in contiguous sequence. Sequence reads can be employed to indicate regions of conservation between closely related species for which only one genome has been assembled. Consequently, by using pairwise sequence alignments methods it is possible to identify novel, non-repetitive, conserved segments in non-coding sequence that exist between the assembled human genome and mouse whole genome shotgun sequencing fragments. Conserved non-coding regions identify potentially functional DNA that could be involved in transcriptional regulation.Results: Local sequence alignment methods were applied employing mouse fragments and the assembled human genome. In addition, transcription factor binding sites were detected by aligning their corresponding positional weight matrices to the sequence regions. These methods were applied to a set of transcripts corresponding to 502 genes associated with a variety of different human diseases taken from the Online Mendelian Inheritance in Man database. Using statistical arguments we have shown that conserved non-coding segments contain an enrichment of transcription factor binding sites when compared to the sequence background in which the conserved segments are located. This enrichment of binding sites was not observed in coding sequence. Conserved non-coding segments are not extensively repeated in the genome and therefore their identification provides a rapid means of finding genes with related conserved regions, and consequently potentially related regulatory mechanism. Conserved segments in upstream regions are found to contain binding sites that are co-localized in a manner consistent with experimentally known transcription factor pairwise co-occurrences and afford the identification of novel co-occurring Transcription Factor (TF) pairs. This study provides a methodology and more evidence to suggest that conserved non-coding regions are biologically significant since they contain a statistical enrichment of regulatory signals and pairs of signals that enable the construction of regulatory models for human genes. Contact: samuel.levy@celera.com }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/17.10.871}, url = {http://bioinformatics.oxfordjournals.org/content/17/10/871}, author = {Levy,Samuel and Hannenhalli, Sridhar and Workman,Christopher} } @article {17116, title = {E-tables: Non-specialist use and understanding of statistical data}, journal = {SURFACE, the Syracuse University Research Facility And Collaborative Environment}, year = {2001}, month = {2001///}, pages = {33 - 33}, abstract = {This paper provides a progress report on a project that aims to understand how people think about and understand statistical data presented in tables. The focus is on people who are not statistical specialists. To this end, studies of various user populations were conducted, underlying data enrichment and explanation was investigated, and interactive user interface prototypes were developed and tested.}, author = {Marchionini,G. and Hert,C. and Shneiderman, Ben and Liddy,L.} } @conference {12120, title = {An experience management system for a software engineering research organization}, booktitle = {Software Engineering Workshop, 2001. Proceedings. 26th Annual NASA Goddard}, year = {2001}, month = {2001///}, pages = {29 - 35}, abstract = {Most businesses rely on the fact that their employees possess relevant knowledge and that they can apply it to the task at hand. The problem is that this knowledge is not owned by the organization. It is owned and controlled by its employees. Maintaining an appropriate level of knowledge in the organization is a very important issue. It is, however, not an easy task for most organizations, and it is particularly problematic for software organizations, which are human- and knowledge-intensive. Knowledge management is a relatively new area that has attempted to address these problems. This paper introduces an approach called the "knowledge dust-to-pearls" approach. This approach addresses some of the issues with knowledge management by providing low-barrier mechanisms to "jump start" the experience base. This approach allows the experience base to become more useful more quickly than traditional approaches. This paper describes the approach and gives an example of its use at the Fraunhofer Center for Experimental Software Engineering, Maryland, USA}, keywords = {and, approach;knowledge, base;experience, Center, control;knowledge, data, development, dust-to-pearls, engineering, Engineering;business, engineering;software, experimental, for, Fraunhofer, houses;, knowledge;employee, knowledge;experience, level, maintenance;knowledge, management, management;knowledge, management;software, mechanisms;software, organization;software, organizational, organizations;administrative, organizations;knowledge, organizations;low-barrier, ownership;knowledge-intensive, processing;personnel;research, research, software, system;human-intensive}, doi = {10.1109/SEW.2001.992652}, author = {Basili, Victor R. and Costa,P. and Lindvall,M. and Mendonca,M. and Seaman,C. and Tesoriero,R. and Zelkowitz, Marvin V} } @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 {15319, title = {Gathering knowledge for a question answering system from heterogeneous information sources}, booktitle = {Proceedings of the workshop on Human Language Technology and Knowledge Management - Volume 2001}, series = {HLTKM {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {9:1{\textendash}9:8 - 9:1{\textendash}9:8}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Although vast amounts of information are available electronically today, no effective information access mechanism exists to provide humans with convenient information access. A general, open-domain question answering system is a solution to this problem. We propose an architecture for a collaborative question answering system that contains four primary components: an annotations system for storing knowledge, a ternary expression representation of language, a transformational rule system for handling some complexities of language, and a collaborative mechanism by which ordinary users can contribute new knowledge by teaching the system new information. We have developed a initial prototype, called Webnotator, with which to test these ideas.}, doi = {10.3115/1118220.1118229}, url = {http://dx.doi.org/10.3115/1118220.1118229}, author = {Katz,Boris and Jimmy Lin and Felshin,Sue} } @conference {12139, title = {Implementing the Experience Factory concepts as a set of Experience Bases}, booktitle = {Proc. 13th Int{\textquoteright}l Conf. Software Eng. and Knowledge Eng}, year = {2001}, month = {2001///}, pages = {102 - 109}, abstract = {This talk takes the Experience Factory concept, which was originally developed as organizational support for softwaredevelopment and generalizes it to organizational support for any aspect of a business, e.g., business practices. The Experience Factory supports the evolution of processes and other forms of knowledge, based upon experiences within the organization, and related knowledge gathered from outside the organization. It then discusses how you might design an appropriate experience base for the particular set of organizational needs determined to be of importance. Specific examples are given in developing experience bases for specific organizations and it discusses the Experience Management System (EMS) currently being evolved and how it has been applied. }, author = {Basili, Victor R. and Lindvall,M. and Costa,P.} } @article {17610, title = {Improved Bounds on the Sample Complexity of Learning}, journal = {Journal of Computer and System Sciences}, volume = {62}, year = {2001}, month = {2001/05//}, pages = {516 - 527}, abstract = {We present a new general upper bound on the number of examples required to estimate all of the expectations of a set of random variables uniformly well. The quality of the estimates is measured using a variant of the relative error proposed by Haussler and Pollard. We also show that our bound is within a constant factor of the best possible. Our upper bound implies improved bounds on the sample complexity of learning according to Haussler{\textquoteright}s decision theoretic model.}, keywords = {agnostic learning, empirical process theory, machine learning, PAC learning, sample complexity}, isbn = {0022-0000}, doi = {10.1006/jcss.2000.1741}, url = {http://www.sciencedirect.com/science/article/pii/S0022000000917410}, author = {Li,Yi and Long,Philip M. and Srinivasan, Aravind} } @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.} } @mastersthesis {15323, title = {Indexing and Retrieving Natural Language Using Ternary Expressions}, year = {2001}, month = {2001///}, school = {MASSACHUSETTS INSTITUTE OF TECHNOLOGY}, abstract = {Traditional information retrieval systems based on the "bag-of-words" paradigm can-not completely capture the semantic content of documents. Yet it is impossible with current technology to build a practical information access system that fully ana- lyzes and understands unrestricted natural language. However, if we avoid the most complex and processing-intensive natural language understanding techniques, we can construct a large-scale information access system which is capable of processing unre- stricted text, largely understanding it, and answering natural language queries with high precision. We believe that ternary expressions are the most suitable representa- tional structure for such a system; they are expressive enough for information retrieval purposes, yet amenable to rapid large-scale indexing. }, author = {Lin,J. 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.} } @conference {15899, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, booktitle = {Proceedings of the first international conference on Human language technology research}, series = {HLT {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {1 - 7}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper describes the Mandarin-English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English-Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks -- multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {cross-language, English-Chinese, spoken document retrieval}, doi = {10.3115/1072133.1072202}, url = {http://dx.doi.org/10.3115/1072133.1072202}, author = {Meng,Helen and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @article {18246, title = {Modulation and multiplexing techniques for multimedia data hiding}, journal = {Proc. of SPIE ITcom{\textquoteright}01, SPIE vol}, volume = {4518}, year = {2001}, month = {2001///}, abstract = {Many multimedia data hiding systems demand either multiple bits or multiple sets of data to be embedded. Thispaper examines the modulation and multiplexing techniques for accomplishing the task of extending the basic single- bit embedding to multiple-bit embedding. Amplitude modulo modulation, orthogonal/bi-orthogonal modulation, and TDMA or CDMA type modulation/multiplexing are discussed and compared. Several examples are included to demonstrate the use of such techniques in practical designs. }, author = {Wu,M. and Liu,B.} } @article {17667, title = {The one-inclusion graph algorithm is near-optimal for the prediction model of learning}, journal = {IEEE Transactions on Information Theory}, volume = {47}, year = {2001}, month = {2001/03//}, pages = {1257 - 1261}, abstract = {Haussler, Littlestone and Warmuth (1994) described a general-purpose algorithm for learning according to the prediction model, and proved an upper bound on the probability that their algorithm makes a mistake in terms of the number of examples seen and the Vapnik-Chervonenkis (VC) dimension of the concept class being learned. We show that their bound is within a factor of 1+o(1) of the best possible such bound for any algorithm}, keywords = {Computer science, concept class, general-purpose algorithm, graph theory, learning prediction model, learning systems, near-optimal algorithm, Neural networks, one-inclusion graph algorithm, optimisation, Prediction algorithms, prediction theory, Predictive models, probability, Probability distribution, Upper bound, Vapnik-Chervonenkis dimension, Virtual colonoscopy}, isbn = {0018-9448}, doi = {10.1109/18.915700}, author = {Li,Yi and Long,P. M and Srinivasan, Aravind} } @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} } @article {17820, title = {Probabilistic object bases}, journal = {ACM Trans. Database Syst.}, volume = {26}, year = {2001}, month = {2001/09//}, pages = {264 - 312}, abstract = {Although there are many applications where an object-oriented data model is a good way of representing and querying data, current object database systems are unable to handle objects whose attributes are uncertain. In this article, we extend previous work by Kornatzky and Shimony to develop an algebra to handle object bases with uncertainty. We propose concepts of consistency for such object bases, together with an NP-completeness result, and classes of probabilistic object bases for which consistency is polynomially checkable. In addition, as certain operations involve conjunctions and disjunctions of events, and as the probability of conjunctive and disjunctive events depends both on the probabilities of the primitive events involved as well as on what is known (if anything) about the relationship between the events, we show how all our algebraic operations may be performed under arbitrary probabilistic conjunction and disjunction strategies. We also develop a host of equivalence results in our algebra, which may be used as rewrite rules for query optimization. Last but not least, we have developed a prototype probabilistic object base server on top of ObjectStore. We describe experiments to assess the efficiency of different possible rewrite rules.}, keywords = {consistency, object-oriented database, probabilistic object algebra, probabilistic object base, probability, query language, Query optimization}, isbn = {0362-5915}, doi = {10.1145/502030.502031}, url = {http://doi.acm.org/10.1145/502030.502031}, author = {Eiter,Thomas and Lu,James J. and Lukasiewicz,Thomas and V.S. Subrahmanian} } @article {14635, title = {Promoter prediction in the human genome}, journal = {Bioinformatics}, volume = {17}, year = {2001}, month = {2001/06/01/}, pages = {S90-S96 - S90-S96}, abstract = {Computational prediction of eukaryotic polII promoters has been one of the most elusive problems despite considerable effort devoted to the study. Researchers have looked for various types of signals around the transcriptional start site (TSS), viz. oligo-nucleotide statistics, potential binding sites for core factors, clusters of binding sites, proximity to CpG islands etc.. The proximity of CpG islands to gene starts is now a well established fact, although until recently, it was based on very little genomic data. In this work we explore the possibility of enhancing the promoter prediction accuracy by combining CpG island information with a few other, biologically motivated, seemingly independent signals, that cover most of the known knowledge. We benchmarked the method on a much larger genomic datasets compared to previous studies. We were able to improve slightly upon current prediction accuracy. Furthermore, we observe that CpG islands are the most dominant signals and the other signals do not improve the prediction. This suggests that the computational prediction of promoters for genes with no associated CpG-island (typically having tissue-specific expression) looking only at the immediate neighborhood of the TSS may not even be possible. We suggest some biological experiments and studies to better understand the biology of transcription.}, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/17.suppl_1.S90}, url = {http://bioinformatics.oxfordjournals.org/content/17/suppl_1/S90.short}, author = {Hannenhalli, Sridhar and Levy,S.} } @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 {18265, title = {Reading between the lines: Lessons from the SDMI challenge}, journal = {Proceedings of the 10th USENIX Security Symposium}, year = {2001}, month = {2001///}, pages = {13 - 17}, abstract = {The Secure Digital Music Initiative is a consortium ofparties interested in preventing piracy of digital music, and to this end they are developing architectures for con- tent protection on untrusted platforms. SDMI recently held a challenge to test the strength of four watermark- ing technologies, and two other security technologies. No documentation explained the implementations of the technologies, and neither watermark embedding nor de- tecting software was directly accessible to challenge par- ticipants. We nevertheless accepted the challenge, and explored the inner workings of the technologies. We re- port on our results here. }, author = {Craver,S.A. and Wu,M. and Liu,B. and Stubblefield,A. and Swartzlander,B. and Wallach,D.S. and Dean,D. and Felten,E.W.} } @conference {15592, title = {Robust matching of wavelet features for sub-pixel registration of Landsat data}, booktitle = {Geoscience and Remote Sensing Symposium, 2001. IGARSS {\textquoteright}01. IEEE 2001 International}, volume = {2}, year = {2001}, month = {2001///}, pages = {706 -708 vol.2 - 706 -708 vol.2}, abstract = {For many Earth and space science applications, automatic geo-registration at sub-pixel accuracy has become a necessity. In this work, we are focusing on building an operational system, which will provide a sub-pixel accuracy registration of Landsat-5 and Landsat-7 data. The input to our registration method consists of scenes that have been geometrically and radiometrically corrected. Such preprocessed scenes are then geo-registered relative to a database of Landsat chips. The method assumes a transformation composed of a rotation and a translation, and utilizes rotation- and translation-invariant wavelets to extract image features that are matched using statistically robust feature matching and a partial Hausdorff distance metric. The registration process is described and results on four Landsat input scenes of the Washington, D.C., area are presented}, keywords = {Feature extraction, geo-registration, geophysical measurement technique, geophysical signal processing, geophysical techniques, Hausdorff distance metric, image registration, infrared, IR, land surface, Landsat, Landsat-5, Landsat-7, multispectral remote sensing, robust feature matching, robust matching, sub pixel registration, subpixel accuracy, terrain mapping, visible, wavelet feature, wavelet method, Wavelet transforms}, doi = {10.1109/IGARSS.2001.976609}, author = {Le Moigne,J. and Netanyahu,N. S and Masek,J. G and Mount, Dave and Goward, S.N.} } @article {15296, title = {The role of a natural language conversational interface in online sales: A case study}, journal = {International Journal of Speech Technology}, volume = {4}, year = {2001}, month = {2001///}, pages = {285 - 295}, abstract = {This paper describes the evaluation of a natural language dialog-based navigation system (HappyAssistant) that helps users access e-commerce sites to find relevant information about products and services. The prototype system leverages technologies in natural language processing and human-computer interaction to create a faster and more intuitive way of interacting with websites, especially for less experienced users. The result of a comparative study shows that users prefer the natural language-enabled navigation two to one over the menu driven navigation. In addition, the study confirmed the efficiency of using natural language dialog in terms of the number of clicks and the amount of time required to obtain the relevant information. In the case study, as compared to the menu driven system, the average number of clicks used in the natural language system was reduced by 63.2\% and the average time was reduced by 33.3\%.}, doi = {10.1023/A:1011316909641}, author = {Chai,J. and Jimmy Lin and Zadrozny,W. and Ye,Y. and Stys-Budzikowska,M. and Horvath,V. and Kambhatla,N. and Wolf,C.} } @article {18271, title = {Rotation, scale, and translation resilient public watermarking for images using a log-polar fourier transform}, year = {2001}, month = {2001/08/28/}, abstract = {A method for detecting a watermark signal in digital image data. The detecting method includes the steps of: computing a log-polar Fourier transform of the image data to obtain a log-polar Fourier spectrum; projecting the log-polar Fourier spectrum down to a lower dimensional space to obtain an extracted signal; comparing the extracted signal to a target watermark signal; and declaring the presence or absence of the target watermark signal in the image data based on the comparison. Also provided is a method for inserting a watermark signal in digital image data to obtain a watermarked image. The inserting method includes the steps of: computing a log-polar Fourier transform of the image data to obtain a log-polar Fourier spectrum; projecting the log-polar Fourier spectrum down to a lower dimensional space to obtain an extracted signal; modifying the extracted signal such that it is similar to a target watermark; performing a one-to-many mapping of the modified signal back to...}, url = {http://www.google.com/patents?id=v4AIAAAAEBAJ}, author = {Bloom,Jeffrey A. and Cox,Ingemar J. and Miller,Matthew L. and M. Wu and Lin,Ching-Yung and Lui,Yui Man}, editor = {Signafy, Inc.} } @article {18272, title = {Rotation, scale, and translation resilient watermarking for images}, journal = {Image Processing, IEEE Transactions on}, volume = {10}, year = {2001}, month = {2001/05//}, pages = {767 - 782}, abstract = {Many electronic watermarks for still images and video content are sensitive to geometric distortions. For example, simple rotation, scaling, and/or translation (RST) of an image can prevent blind detection of a public watermark. In this paper, we propose a watermarking algorithm that is robust to RST distortions. The watermark is embedded into a one-dimensional (1-D) signal obtained by taking the Fourier transform of the image, resampling the Fourier magnitudes into log-polar coordinates, and then summing a function of those magnitudes along the log-radius axis. Rotation of the image results in a cyclical shift of the extracted signal. Scaling of the image results in amplification of the extracted signal, and translation of the image has no effect on the extracted signal. We can therefore compensate for rotation with a simple search, and compensate for scaling by using the correlation coefficient as the detection measure. False positive results on a database of 10 000 images are reported. Robustness results on a database of 2000 images are described. It is shown that the watermark is robust to rotation, scale, and translation. In addition, we describe tests examining the watermarks resistance to cropping and JPEG compression}, keywords = {axis;one-dimensional, coding;security, coefficient;cropping;cyclical, compression;RST, coordinates;log-radius, data;, detection;correlation, distortions;blind, distortions;images;log-polar, encapsulation;image, Fourier, images;translation, magnitudes;Fourier, measure;geometric, of, protection;data, resilient, shift;detection, signal;public, transform;JPEG, transforms;copy, watermark;resampling;rotation;scale;search;still, watermarking;video;Fourier}, isbn = {1057-7149}, doi = {10.1109/83.918569}, author = {Lin,C.-Y. and Wu,M. and Bloom,J.A. and Cox,I.J. and Miller,M.L. and Lui,Y.M.} } @conference {16156, title = {Therapeutic play with a storytelling robot}, booktitle = {CHI {\textquoteright}01 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {27 - 28}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We are developing a prototype storytelling robot for use with children in rehabilitation. Children can remotely control a furry robot by using a variety of body sensors adapted to their disability or rehabilitation goal. We believe this robot can motivate children and help them reach their therapy goals through therapeutic play, either by exercising muscles or joints (e.g. for physically challenged children) or by reflecting on the stories (e.g. for children with developmental disabilities). To develop this technology we use an innovative design methodology involving children as design partners.}, keywords = {children, design process, rehabilitation, robot, therapeutic play, user interface}, isbn = {1-58113-340-5}, doi = {10.1145/634067.634088}, url = {http://doi.acm.org/10.1145/634067.634088}, author = {Lathan,Corinna and Vice,Jack Maxwell and Tracey,Michael and Plaisant, Catherine and Druin, Allison and Edward,Kris and Montemayor,Jaime} } @conference {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 {15658, title = {Vision Geometry X}, booktitle = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series}, volume = {4476}, year = {2001}, month = {2001///}, author = {Latecki,L.J. and Mount, Dave and Wu,A. Y and Melter,R.A.} } @article {18291, title = {Watermarking scheme for image authentication}, year = {2001}, month = {2001/09/04/}, abstract = {A digital watermarking process whereby an invisible watermark inserted into a host image is utilized to determine whether or not the image has been altered and, if so, where in the image such alteration occurred. The watermarking method includes the steps of providing a look-up table containing a plurality of coefficients and corresponding values; transforming the image into a plurality of blocks, wherein each block contains coefficients matching coefficients in the look-up table; and embedding the watermark in the image by performing the following substeps for at least some of the blocks: First, a coefficient is selected for insertion of a marking value representative of a corresponding portion of the watermark. Next, the value of the selected coefficient to used to identify a corresponding value in the look-up table. Finally, the identified coefficient is left unchanged if the corresponding value is the same as the marking value, and is changed if the corresponding value is...}, url = {http://www.google.com/patents?id=BmoIAAAAEBAJ}, author = {M. Wu and Liu,Bede}, editor = {The Trustees of the University of Princeton} } @article {17945, title = {Web-based interactive design of freeform motions}, journal = {Proceedings of the ASME 2001 Design Engineering Technical Conferences and Computers and Information in Engineering Conference}, year = {2001}, month = {2001///}, author = {Li,ST and Ge,Q. J and Varshney, Amitabh} } @conference {18292, title = {What can we reasonably expect from watermarks?}, booktitle = {Applications of Signal Processing to Audio and Acoustics, 2001 IEEE Workshop on the}, year = {2001}, month = {2001///}, pages = {223 - 226}, abstract = {Digital watermarking has been positioned as a solution to copyright protection of digital music, and some doubt exists about its ability to perform in this regard. A survey of watermarking applications assesses the technology{\textquoteright}s potential for copy protection, as well as other digital audio applications}, keywords = {applications;audio, applications;digital, audio, coding;copy, data;, databases;music, hashing;steganography;watermarking, music;digital, of, protection;copyright, protection;copyright;music;security, protection;digital, watermarking;copy, watermarking;forensic, watermarking;music}, doi = {10.1109/ASPAA.2001.969583}, author = {Craver,S.A. and M. Wu and Liu,B.} } @article {13510, title = {Automatic Text Detection and Tracking in Digital Video}, journal = {IEEE Transactions on Image Processing - Special Issue on Image and Video Processing for Digital Libraries}, volume = {9}, year = {2000}, month = {2000/01//}, pages = {147 - 156}, abstract = {Text that appears in a scene or is graphically added to video can provide an important supplemental source of index information as well as clues for decoding the video{\textquoteright}s structure and for classification. In this work, we present algorithms for detecting and tracking text in digital video. Our system implements a scale-space feature extractor that feeds an artificial neural processor to detect text blocks. Our text tracking scheme consists of two modules: a sum of squared difference (SSD) based module to find the initial position and a contour-based module to refine the position. Experiments conducted with a variety of video sources show that our scheme can detect and track text robustly.}, author = {Li,H. and David Doermann and Kia,O.} } @conference {13512, title = {AVideo Text Detection System Based on Automated Training}, booktitle = {ICPR}, volume = {2}, year = {2000}, month = {2000///}, pages = {223 - 226}, author = {Li,H. and David Doermann} } @inbook {13732, title = {Building a Chinese-English Mapping Between Verb Concepts for Multilingual Applications}, booktitle = {Envisioning Machine Translation in the Information FutureEnvisioning Machine Translation in the Information Future}, series = {Lecture Notes in Computer Science}, volume = {1934}, year = {2000}, month = {2000///}, pages = {345 - 363}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper addresses the problem of building conceptual resources for multilingual applications. We describe new techniques for large-scale construction of a Chinese-English lexicon for verbs, using thematic-role information to create links between Chinese and English conceptual information. We then present an approach to compensating for gaps in the existing resources. The resulting lexicon is used for multilingual applications such as machine translation and cross-language information retrieval.}, isbn = {978-3-540-41117-8}, url = {http://dx.doi.org/10.1007/3-540-39965-8_1}, author = {Dorr, Bonnie J and Levow,Gina-Anne and Lin,Dekang}, editor = {White,John} } @article {13737, title = {Chinese-English Semantic Resource Construction}, year = {2000}, month = {2000/06//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We describe an approach to large-scale construction of a semantic lexicon for Chinese verbs. We leverage off of three existing resources-- a classification of English verbs called EVCA (English Verbs Classes and Alternations), a Chinese conceptual database called HowNet, and a large-machine readable dictionary called Optilex. The resulting lexicon is used for determining appropriate word senses in applications such as machine translation and cross-language information retrieval.}, keywords = {*CHINESE LANGUAGE, *ENGLISH LANGUAGE, *LEXICONS, *SEMANTICS, *VERBS, *WORD SENSES, *WORDS(LANGUAGE), classification, CONCEPTS, CONSTRUCTION, Dictionaries, INFORMATION SCIENCE, linguistics, VERB CLASSES, Vocabulary}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458703}, author = {Dorr, Bonnie J and Levow,Gina-Anne and Lin,Dekang and Thomas,Scott} } @conference {15287, title = {Comparative Evaluation of a Natural Language Dialog Based System and a Menu-Driven System for Information Access: A Case Study}, booktitle = {In Proceedings of the International Conference on Multimedia Information Retrieval (RIAO 2000)}, year = {2000}, month = {2000///}, abstract = {This paper describes the evaluation of a natural language dialog based navigation system (HappyAssistant) thathelps users access e-commerce sites to find relevant information about products and services. The prototype system leverages technologies in natural language processing and human computer interaction to create a faster and more intuitive way of interacting with websites, especially for the less experienced users. The result of a comparative study shows that users prefer the natural language enabled navigation two to one over the menu driven navigation. In addition, the study confirmed the efficiency of using natural language dialog in terms of the number of clicks and the amount of time required to obtain the relevant information. In the case study, comparing to the menu driven system, the average number of clicks used in the natural language system was reduced by 63.2\% and the average time was reduced by 33.3\%. }, author = {Chai,J. and Jimmy Lin and Zadrozny,W. and Ye,Y. and Budzikowska,M. and Horvath,V. and Kambhatla,N. and Wolf,C.} } @book {12848, title = {A compositional approach to statecharts semantics}, volume = {25}, year = {2000}, month = {2000///}, publisher = {ACM}, organization = {ACM}, author = {L\{\"u}ttgen,G. and Von Der Beeck,M. and Cleaveland, Rance} } @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.} } @article {13749, title = {Construction of Chinese-English Semantic Hierarchy for Information Retrieval}, year = {2000}, month = {2000///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper describes an approach to large-scale construction of a semantic hierarchyfor Chinese verbs. Leveraging off of an existing Chinese conceptual databased called HowNet and a Levin-based Egnlish verb classification, we use thematic-role information to create links between Chinese concepts and English classes. The resulting hierarchy is used for multilingual lexicons in an English-Chinese cross-language information retrieval application. We demonstrate a structured syntax interface that exploits this large-scale hierarchy and its linages to WordNet for English-Chinese cross-language information re- trieval. }, author = {Levow,G.A. and Dorr, Bonnie J and Lin,D.} } @article {14879, title = {Convexity in Perceptual Completion}, journal = {KLUWER INTERNATIONAL SERIES IN ENGINEERING AND COMPUTER SCIENCE}, year = {2000}, month = {2000///}, pages = {73 - 90}, author = {Liu,Z. and Jacobs, David W. and Basri,R.} } @conference {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} } @conference {18192, title = {Data hiding in digital binary image}, booktitle = {Multimedia and Expo, 2000. ICME 2000. 2000 IEEE International Conference on}, volume = {1}, year = {2000}, month = {2000///}, pages = {393 -396 vol.1 - 393 -396 vol.1}, abstract = {This paper proposes a new method to embed data in binary images, including scanned text, figures and signatures. The method manipulates ldquo;flippable rdquo; pixels and uses shuffling to embed a significant amount of data without causing noticeable artifacts. The extraction of the hidden data does not require the original image. Potential applications include detecting unauthorized use of a digitized signature and authenticating binary documents}, keywords = {authentication;data, binary, data;, document, encapsulation;image, hiding;digital, image;digital, of, pixels;multimedia;scanned, processing;multimedia, signature;flippable, systems;security, text;shuffling;data, watermarking;digitized}, doi = {10.1109/ICME.2000.869623}, author = {M. Wu and Tang,E. and Lin, B.} } @conference {18636, title = {Dynamic node management and measure estimation in a state-driven fault injector}, year = {2000}, month = {2000///}, pages = {248 - 261}, abstract = {Validation of distributed systems using fault injectionis difficult because of their inherent complexity, lack of a global clock, and lack of an easily accessible notion of a global state. To address these challenges, the Loki fault injector injects faults based on a partial view of the global state of a distributed system, and performs a post-runtime analysis using an off-line clock synchronization algorithm to determine whether the faults were properly injected. In this paper, we first describe an enhanced runtime architecture for the Loki fault injector and then present a new method for obtaining measures in Loki. The enhanced runtime allows dynamic entry and exit of nodes in the system. It also offers more efficient multicast of notification messages and more efficient communication between state machines on the same host, and is more scalable than the previous runtime. We then detail a new and flexible method for obtaining a wide range of performance and dependability measures in Loki. }, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/00CHA01.pdf}, author = {Chandra,R. and Michel Cukier and Lefever,R. and Sanders,W. and others} } @conference {16164, title = {Evaluation challenges for a Federation of heterogeneous information providers: the case of NASA{\textquoteright}s Earth Science Information Partnerships}, booktitle = {Enabling Technologies: Infrastructure for Collaborative Enterprises, 2000. (WET ICE 2000). Proeedings. IEEE 9th International Workshops on}, year = {2000}, month = {2000///}, pages = {130 - 135}, abstract = {NASA{\textquoteright}s Earth Science Information Partnership Federation is an experiment funded to assess the ability of a group of widely heterogeneous earth science data or service providers to self organize and provide improved and affordable access to an expanding earth science user community. As it is self-organizing, the Federation is mandated to set in place an evaluation methodology and collect metrics reflecting the outcomes and benefits of the Federation. This paper describes the challenges of organizing such a federated partnership self-evaluation and discusses the issues encountered during the metrics definition phase of the early data collection. Our experience indicates that a large number of metrics will be needed to fully represent the activities and strengths of all partners, but because of the heterogeneity of the ESIPs the qualitative data (comments accompanying the metric data and success stories) becomes the most useful information. Other lessons learned included the absolute need for online browsing tools to accompany data collection tools. Finally, our experience confirms the effect of evaluation as an agent of change, the best example being the high level of collaboration among the ESIPs which can be in part attributed to the initial identification of collaboration as one of the important evaluation factors of the Federation}, keywords = {Browsing, collection;heterogeneous, computing;groupware;, data;online, Earth, Federation;data, information, NASA{\textquoteright}s, Partnership, Science, systems;geophysics, tools;geographic}, doi = {10.1109/ENABL.2000.883717}, author = {Plaisant, Catherine and Komlodi,A. and Lindsay,F.} } @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} } @conference {17156, title = {Extending understanding of federal statistics in tables}, booktitle = {Proceedings of the 2000 annual national conference on Digital government research}, series = {dg.o {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {1 - 7}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {This paper describes progress toward improving user interfaces for US Federal government statistics that are presented in tables. Based on studies of user behaviors and needs related to statistical tables, we describe interfaces to assist diverse users with a range of statistical literacy to explore, find, understand, and use US Federal government statistics.}, keywords = {data exploration, dynamic queries, Statistics, tablular data, User interfaces}, url = {http://dl.acm.org/citation.cfm?id=1123075.1123079}, author = {Marchionini,Gary and Hert,Carol and Liddy,Liz and Shneiderman, Ben} } @article {16161, title = {Facilitating data exploration with query previews: A study of user performance and preference}, journal = {Behaviour \& Information Technology}, volume = {19}, year = {2000}, month = {2000///}, pages = {393 - 403}, abstract = {Networked and local data exploration systems that use command languages, menus, or form fill-in interfaces rarely give users an indication of the distribution of data. This often leads users to waste time, posing queries that have zero-hit or mega-hit results. Query previews are a novel visual approach for browsing databases. Query previews supply users with data distribution information for selected attributes of the database, and give continuous feedback about the size of the result set as the query is being formed. Subsequent refinements might be necessary to narrow the search. As there is a risk that query previews are an additional step, leading to a more complex and slow search process, a within-subjects empirical study was ran with 12 subjects who used interfaces with and without query previews and with minimized network delays. Even with 12 subjects and minimized network delays statistically significant differences were found, showing that query previews could speed up performance 1.6 to 2.1 times and lead to higher user satisfaction.Networked and local data exploration systems that use command languages, menus, or form fill-in interfaces rarely give users an indication of the distribution of data. This often leads users to waste time, posing queries that have zero-hit or mega-hit results. Query previews are a novel visual approach for browsing databases. Query previews supply users with data distribution information for selected attributes of the database, and give continuous feedback about the size of the result set as the query is being formed. Subsequent refinements might be necessary to narrow the search. As there is a risk that query previews are an additional step, leading to a more complex and slow search process, a within-subjects empirical study was ran with 12 subjects who used interfaces with and without query previews and with minimized network delays. Even with 12 subjects and minimized network delays statistically significant differences were found, showing that query previews could speed up performance 1.6 to 2.1 times and lead to higher user satisfaction. }, isbn = {0144-929X}, doi = {10.1080/014492900750052651}, url = {http://www.tandfonline.com/doi/abs/10.1080/014492900750052651}, author = {Tanin,Egemen and Lotem,Amnon and Haddadin,Ihab and Shneiderman, Ben and Plaisant, Catherine and Slaughter,Laura} } @article {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 {18960, title = {The genome sequence of Drosophila melanogaster}, journal = {Science}, volume = {287}, year = {2000}, month = {2000///}, pages = {2185 - 2185}, abstract = {The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the \~{}120-megabase euchromatic portion of theDrosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes \~{}13,600 genes, somewhat fewer than the smaller Caenorhabditis elegansgenome, but with comparable functional diversity.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.287.5461.2185}, url = {http://www.sciencemag.org/content/287/5461/2185}, author = {Adams,M.D. and Celniker,S.E. and Holt,R.A. and Evans,C.A. and Gocayne,J.D. and Amanatides,P.G. and Scherer,S.E. and Li,P.W. and Hoskins,R.A. and Galle,R.F. and others} } @conference {15591, title = {Geo-registration of Landsat data by robust matching of wavelet features}, booktitle = {Geoscience and Remote Sensing Symposium, 2000. Proceedings. IGARSS 2000. IEEE 2000 International}, volume = {4}, year = {2000}, month = {2000///}, pages = {1610 -1612 vol.4 - 1610 -1612 vol.4}, abstract = {The goal of our project is to build an operational system, which will provide a sub-pixel accuracy registration of Landsat-5 and Landsat-7 data. Integrated within an automated mass processing/analysis system for Landsat data (REALM), the input to our registration method consists of scenes that have been geometrically and radiometrically corrected, as well as pre-processed for the detection of clouds and cloud shadows. Such pre-processed scenes are then geo-registered relative to a database of Landsat chips. This paper describes our registration process, including the use of a database of landmark chips, a feature extraction performed by an overcomplete wavelet representation, and feature matching using statistically robust techniques. Knowing the approximate longitudes and latitudes of the four corners of the scene, a subset of chips which represent landmarks included in the scene are extracted from the database. For each of these selected landmark chips, a corresponding window is extracted from the scene, and each chip-window pair is registered using our robust wavelet feature matching. First results and future directions are presented in the paper}, keywords = {atmospheric techniques, automated mass processing/analysis system, chip-window pair, cloud shadows, Clouds, Feature extraction, feature matching, geo-registration, geometrically corrected scene, geophysical signal processing, Image matching, image registration, landmark chips, Landsat chips, Landsat data, Landsat-5 data, Landsat-7 data, overcomplete wavelet representation, pre-processed scenes, radiometrically corrected scene, REALM, Remote sensing, robust matching, robust wavelet feature matching, scenes, statistically robust techniques, sub-pixel accuracy registration, wavelet features, Wavelet transforms, window}, doi = {10.1109/IGARSS.2000.857287}, author = {Le Moigne,J. and Netanyahu,N. S and Masek,J. G and Mount, Dave and Goward,S. and Honzak,M.} } @article {13809, title = {Large-Scale Construction of a Chinese-English Semantic Hierarchy}, year = {2000}, month = {2000/04//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper addresses the problem of building conceptual resources for multilingual applications. We describe new techniques for large-scale construction of a semantic hierarchy for Chinese verbs, using thematic-role information to create links between Chinese concepts and English classes. We then present an approach to compensating for gaps in the existing resources. The resulting hierarchy is used for a multilingual lexicon for Chinese-English machine translation and cross-language information retrieval applications.}, keywords = {*CHINESE VERBS, *HIERARCHIES, *SEMANTICS, CHINA, CROSS CORRELATION, Information retrieval, INFORMATION SCIENCE, LANGUAGE, LEXICONS, linguistics, Machine translation, MULTILINGUAL, operations research, SYSTEMS APPROACH}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458682}, author = {Dorr, Bonnie J and Levow,Gina-Anne and Lin,Dekang} } @conference {18678, title = {Loki: a state-driven fault injector for distributed systems}, year = {2000}, month = {2000///}, pages = {237 - 242}, abstract = {Distributed applications can fail in subtle ways that depend on the state of multiple parts of a system. This complicates the validation of such systems via fault injection, since it suggests that faults should be injected based on the global state of the system. In Loki, fault injection is performed based on a partial view of the global state of a distributed system, i.e. faults injected in one node of the system can depend on the state of other nodes. Once faults are injected, a post-runtime analysis, using off-line clock synchronization, is used to place events and injections on a single global timeline and to determine whether the intended faults were properly injected. Finally, experiments containing successful fault injections are used to estimate the specified measures. In addition to briefly reviewing the concepts behind Loki and its organization, we detail Loki{\textquoteright}s user interface. In particular, we describe the graphical user interfaces for specifying state machines and faults, for executing a campaign and for verifying whether the faults were properly injected}, keywords = {campaign execution, computer testing, distributed applications failure, distributed processing, distributed system validation, Fault diagnosis, fault event placement, fault specification, global system state, global timeline, Graphical user interfaces, Loki, off-line clock synchronization, post-runtime analysis, specified measures estimation, state machine specification, state-driven fault injection, Synchronisation}, doi = {10.1109/ICDSN.2000.857544}, author = {Chandra,R. and Lefever,R.M. and Michel Cukier and Sanders,W. H.} } @inbook {14236, title = {New Eyes for Shape and Motion Estimation}, booktitle = {Biologically Motivated Computer VisionBiologically Motivated Computer Vision}, series = {Lecture Notes in Computer Science}, volume = {1811}, year = {2000}, month = {2000///}, pages = {23 - 47}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Motivated by the full field of view of insect eyes and their fast and accurate estimation of egomotion, we constructed a system of cameras to take advantage of the full field of view (FOV) constraints that insects use. In this paper, we develop a new ego-motion algorithm for a rigidly mounted set of cameras undergoing arbitrary rigid motion. This egomotion algorithm combines the unambiguous components of the motion computed by each separate camera. We prove that the cyclotorsion is resistant to errors and show this empirically. We show how to calibrate the system with two novel algorithms, one using secondary cameras and one using self calibration. Given this system calibration, the new 3D motion algorithm first computes the rotation and then the 3D translation. We apply this algorithm to a camera system constructed with four rigidly mounted synchronized cameras pointing in various directions and present motion estimation results at www.cfar.umd.edu/ pbaker/argus.html.}, isbn = {978-3-540-67560-0}, url = {http://dx.doi.org/10.1007/3-540-45482-9_12}, author = {Baker,Patrick and Pless,Robert and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Lee,Seong-Whan and B{\"u}lthoff,Heinrich and Poggio,Tomaso} } @article {17676, title = {A new relative perturbation theorem for singular subspaces}, journal = {Linear Algebra and its Applications}, volume = {313}, year = {2000}, month = {2000/07/01/}, pages = {41 - 51}, abstract = {This note addresses the sensitivity of singular subspaces of a matrix under relative perturbations. It employs a new technique of separating a multiplicative perturbation D into two components: one is the distance of a scalar multiple of D to the nearest unitary matrix Q and the other is the distance of Q to the identity. Consequently, the new bounds reflect the intrinsic differences in how left and right multiplicative perturbations affect left and right singular subspaces.}, keywords = {Multiplicative perturbation, Relative gap, Relative perturbation theory, Singular subspace}, isbn = {0024-3795}, doi = {10.1016/S0024-3795(00)00074-4}, url = {http://www.sciencedirect.com/science/article/pii/S0024379500000744}, author = {Li,Ren-Cang and Stewart, G.W.} } @article {14900, title = {Perceptual Completion Behind Occluders: The Role of Convexity}, journal = {Perceptual Organization for Artificial Vision Systems}, year = {2000}, month = {2000///}, pages = {73 - 90}, abstract = {An important problem in perceptual organization is to determine whether two image regions belong to the same object. In this chapter, we consider the situation when two image regions potentially group into a single object behind a common occluder. We study the extent to which two image regions are grouped more strongly than two other image regions. Existing theories in both human and computer vision have mainly emphasized the role of good continuation. Namely, the shorter and smoother the completing contours are between two image regions, the stronger the grouping will be. In contrast, Jacobs [3] has proposed a theory that considers relative positions and orientations of two image regions. For instance, the theory predicts that two image regions that can be linked by convex completing contours are grouped more strongly than those that can only be linked by concave completing contours, even though the completing contours are identical in shape. We present, in addition to our previous work (Liu, Jacobs, and Basri, 1999), human psychophysical evidence that concurs with the predictions of this theory and suggests an important role of convexity in perceptual grouping.}, doi = {10.1007/978-1-4615-4413-5_6}, author = {Liu,Z. and Jacobs, David W. and Basri,R.} } @article {13011, title = {Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences}, journal = {J Mol Evol}, volume = {50}, year = {2000}, month = {2000/06//}, pages = {532 - 540}, abstract = {Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala.}, author = {Garc{\'\i}a-Varela,M and P{\'e}rez-Ponce de Le{\'o}n,G. and de la Torre,P and Cummings, Michael P. and Sarma,SS and Laclette,J. P} } @article {12363, title = {Resynchronization for multiprocessor DSP systems}, journal = {Circuits and Systems I: Fundamental Theory and Applications, IEEE Transactions on}, volume = {47}, year = {2000}, month = {2000///}, pages = {1597 - 1609}, author = {Bhattacharyya, Shuvra S. and Sriram,S. and Lee,E. A} } @conference {15311, title = {REXTOR: a system for generating relations from natural language}, booktitle = {Proceedings of the ACL-2000 workshop on Recent advances in natural language processing and information retrieval: held in conjunction with the 38th Annual Meeting of the Association for Computational Linguistics - Volume 11}, series = {RANLPIR {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {67 - 77}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper argues that a finite-state language model with a ternary expression representation is currently the most practical and suitable bridge between natural language processing and information retrieval. Despite the theoretical computational inadequacies of finite-state grammars, they are very cost effective (in time and space requirements) and adequate for practical purposes. The ternary expressions that we use are not only linguistically-motivated, but also amenable to rapid large-scale indexing. REXTOR (Relations EXtracTOR) is an implementation of this model; in one uniform framework, the system provides two separate grammars for extracting arbitrary patterns of text and building ternary expressions from them. These content representational structures serve as the input to our ternary expressions indexer. This approach to natural language information retrieval promises to significantly raise the performance of current systems.}, doi = {10.3115/1117755.1117764}, url = {http://dx.doi.org/10.3115/1117755.1117764}, author = {Katz,Boris and Jimmy Lin} } @article {18270, title = {Rotation, scale, and translation resilient public watermarking for images}, journal = {PROC SPIE INT SOC OPT ENG}, volume = {3971}, year = {2000}, month = {2000///}, pages = {90 - 98}, abstract = {Many electronic watermarks for still images and video content are sensitive to geometric distortions. For example,simple rotation, scaling, and/or translation (RST) of an image can prevent detection of a public watermark. In this paper, we propose a watermarking algorithm that is robust to RST distortions. The watermark is embedded into a 1-dimensional signal obtained by first taking the Fourier transform of the image, resampling the Fourier magnitudes into log-polar coordinates, and then summing a function of those magnitudes along the log-radius axis. If the image is rotated, the resulting signal is cyclically shifted. If it is scaled, the signal is multiplied by some value. And if the image is translated, the signal is unaffected. We can therefore compensate for rotation with a simple search, and for scaling by using the correlation coefficient for the detection metric. False positive results on a database of 10,000 images are reported. Robustness results on a database of 2,000 images are described. It is shown that the watermark is robust to rotation, scale and translation. In addition, the algorithm shows resistance to cropping. }, author = {Lin,C.Y. and Wu,M. and Bloom,J.A. and Cox,I.J. and Miller,M.L. and Lui,Y.M.} } @article {12808, title = {A semantic theory for heterogeneous system design}, journal = {FST TCS 2000: Foundations of Software Technology and Theoretical Computer Science}, year = {2000}, month = {2000///}, pages = {312 - 324}, author = {Cleaveland, Rance and L\{\"u}ttgen,G.} } @conference {16163, title = {A storytelling robot for pediatric rehabilitation}, booktitle = {Proceedings of the fourth international ACM conference on Assistive technologies}, series = {Assets {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {50 - 55}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {children, design process, rehabilitation, robot, therapeutic play, user interface}, isbn = {1-58113-313-8}, doi = {10.1145/354324.354338}, url = {http://doi.acm.org/10.1145/354324.354338}, author = {Plaisant, Catherine and Druin, Allison and Lathan,Corinna and Dakhane,Kapil and Edwards,Kris and Vice,Jack Maxwell and Montemayor,Jaime} } @conference {13654, title = {Superresolution-based enhancement of text in digital video}, booktitle = {Pattern Recognition, 2000. Proceedings. 15th International Conference on}, volume = {1}, year = {2000}, month = {2000///}, pages = {847 -850 vol.1 - 847 -850 vol.1}, abstract = {We present a superresolution-based text enhancement scheme to improve optical character recognition (OCR) and readability of text in digital video. The quality of video text is degraded by factors such as low resolution, antialiasing, clutter and blurring. We use the fact that the same text string often exists in consecutive frames to explore the temporal information and enhance the text image. For graphic text, we register text blocks to subpixel accuracy and fuse them to a new block with high resolution and a cleaner background. We use a projection onto convex sets based method to deblur scene text to improve readability. Experimental results show our scheme can improve OCR for graphic text and readability for scene text significantly}, keywords = {accuracy;superresolution-based, antialiasing;blurring;clutter;digital, based, character, convex, Enhancement, enhancement;image, information;text, method;readability;subpixel, onto, recognition;, resolution;image, resolution;projection, scheme;temporal, sequences;optical, sets, string;video, text, text;geometry;image, text;low, video;graphic}, doi = {10.1109/ICPR.2000.905546}, author = {Huiping Li and David Doermann} } @article {15858, title = {Textual data mining to support science and technology management}, journal = {Journal of Intelligent Information Systems}, volume = {15}, year = {2000}, month = {2000///}, pages = {99 - 119}, author = {Losiewicz,P. and Oard, Douglas and Kostoff,R.N.} } @conference {18289, title = {Video transcoding by reducing spatial resolution}, booktitle = {Image Processing, 2000. Proceedings. 2000 International Conference on}, volume = {1}, year = {2000}, month = {2000///}, pages = {972 -975 vol.1 - 972 -975 vol.1}, abstract = {In network delivery of digital video, if the bandwidth required for a video is not available, the video has to be recoded at a reduced bit rate. It is highly desirable that the transcoding is carried out in real time while maintaining reasonable image quality. In this paper, we propose a fast approach to derive from an MPEG stream a new MPEG stream with half the spatial resolution. For the downsized video, we first generate from the original compressed video an improved estimate of the motion vectors. We then propose a compressed domain approach with data hiding to produce DCT residues by an open-loop method. The computational complexity is significantly lower than a number of previous approaches. Simulation suggests that our approach produces reasonable image quality}, keywords = {approach;computational, coding;, coding;video, complexity;data, compression;data, cosine, DCT, delivery;open-loop, domain, encapsulation;discrete, estimation;network, estimation;transform, hiding;digital, method;spatial, quality;motion, reduction;video, residues;MPEG, resolution, resolution;motion, stream;compressed, transcoding;computational, transforms;image, vectors, video;downsized, video;image}, doi = {10.1109/ICIP.2000.901123}, author = {Yin,Peng and M. Wu and Liu,Bede} } @article {15661, title = {Vision geometry IX:(San Diego CA, 30-31 July 2000)}, journal = {SPIE proceedings series}, year = {2000}, month = {2000///}, author = {Latecki,L.J. and Mount, Dave and Wu,A. Y} } @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} } @conference {15376, title = {Advances in spherical harmonic device modeling: calibration and nanoscale electron dynamics}, booktitle = {Simulation of Semiconductor Processes and Devices, 1999. SISPAD {\textquoteright}99. 1999 International Conference on}, year = {1999}, month = {1999///}, pages = {167 - 170}, abstract = {Improvements in the Spherical Harmonic (SH) method for solving Boltzmann Transport Equation (BTE) are presented. The simulation results provide the same physical detail as analytical band Monte Carlo (MC) calculations, and are obtained approximately a thousand times faster. A new physical model for surface scattering has also been developed. As a result, the SHBTE model achieves calibration for a complete process of I-V characteristics and substrate current consistently for the first time}, keywords = {Boltzmann, characteristics;SHBTE, current;surface, device, dynamics;spherical, electron, equation;calibration;semiconductor, equation;I-V, harmonic, model;substrate, models;surface, scattering;, scattering;Boltzmann, simulation;calibration;nanoscale, transport}, doi = {10.1109/SISPAD.1999.799287}, author = {Lin,Chung-Kai and Goldsman,N. and Mayergoyz, Issak D and Aronowitz,S. and Belova,N.} } @article {16954, title = {Agents vs. direct manipulation: what{\textquoteright}s best to disentangle the Web?}, journal = {Computer Networks: The International Journal of Computer and Telecommunications Networking}, volume = {31}, year = {1999}, month = {1999/05//}, pages = {1765 - 1767}, isbn = {1389-1286}, url = {http://dl.acm.org/citation.cfm?id=313009.313142}, author = {S{\'a}nchez,J. Alfredo and Etzioni,Oren and Kautz,Henry and Lieberman,Henry and Shneiderman, Ben} } @conference {16955, title = {Agents vs. direct manipulation: what{\textquoteright}s best to disentangle the Web?}, booktitle = {Proceedings of the eighth international conference on World Wide Web}, year = {1999}, month = {1999///}, author = {S{\'a}nchez,J.A. and Etzioni,O. and Kautz,H. and Lieberman,H. and Shneiderman, Ben} } @conference {18170, title = {Attacks on digital watermarks}, booktitle = {Signals, Systems, and Computers, 1999. Conference Record of the Thirty-Third Asilomar Conference on}, volume = {2}, year = {1999}, month = {1999/10//}, pages = {1508 -1512 vol.2 - 1508 -1512 vol.2}, abstract = {Two methods for attacking watermarks in images and videos have been proposed. The first attack is to remove robust watermarks by iterative block dropping and concealment. Our study suggests that the block size chosen by a robust watermark embedding system should be large enough to circumventing concealment based attacks. The second attacking method is to forge valid watermarks for authentication systems based on fragile-watermarking. Double watermarking is then proposed as one possible countermeasure.}, keywords = {attacks;copy, Authentication, authentication;video, based, block, coding;, coding;iterative, control;digital, countermeasure;fragile-watermarking;images;iterative, dropping;ownership, EMBEDDING, forging;copyright;image, methods;message, protection;robust, removal;videos;watermarks, size;concealment, system;robust, systems;block, watermark, watermarking, watermarks, watermarks;double}, doi = {10.1109/ACSSC.1999.832001}, author = {M. Wu and Liu,Bede} } @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} } @conference {17080, title = {Developing the next generation of Earth science data systems: the Global Land Cover Facility}, booktitle = {Geoscience and Remote Sensing Symposium, 1999. IGARSS {\textquoteright}99 Proceedings. IEEE 1999 International}, volume = {1}, year = {1999}, month = {1999///}, pages = {616-618 vol.1 - 616-618 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {A recent initiative by NASA has resulted in the formation of a federation of Earth science data partners. These Earth Science Information Partners (ESIPs) have been tasked with creating novel Earth science data products and services as well as distributing new and existing data sets to the Earth science community and the general public. The University of Maryland established its ESIP activities with the creation of the Global Land Cover Facility (GLCF). This joint effort of the Institute for Advanced Computer Studies (UMIACS) and the Department of Geography has developed an operational data archiving and distribution system aimed at advancing current land cover research efforts. The success of the GLCF is tied closely to assessing user needs as well. As the timely delivery of data products to the research community. This paper discusses the development and implementation of a web-based interface that allows users to query the authors{\textquoteright} data holdings and perform user requested processing tasks on demand. The GLCF takes advantage of a scaleable, high performance computing architecture for the manipulation of very large remote sensing data sets and the rapid spatial indexing of multiple format data types. The user interface has been developed with the cooperation of the Human-Computer Interaction Laboratory (HCIL) and demonstrates advances in spatial and temporal querying tools as well as the ability to overlay multiple raster and vector data sets. Their work provides one perspective concerning how critical earth science data may be handled in the near future by a coalition of distributed data centers}, keywords = {Computer architecture, data archiving, data distribution system, Data systems, Distributed computing, Earth science data products, Earth science data system, ESIP, geographic information system, geographic information systems, Geography, geophysical measurement technique, geophysical signal processing, geophysical techniques, Geoscience, GIS, GLCF, Global Land Cover Facility, High performance computing, Indexing, information service, Information services, Institute for Advanced Computer Studies, land cover, NASA, next generation, PACS, Remote sensing, terrain mapping, UMIACS, University of Maryland, User interfaces, web-based interface}, isbn = {0-7803-5207-6}, doi = {10.1109/IGARSS.1999.773583}, author = {Lindsay,F.E. and Townshend,J.R.G. and JaJa, Joseph F. and Humphries,J. and Plaisant, Catherine and Shneiderman, Ben} } @conference {18198, title = {Digital watermarking using shuffling}, booktitle = {Image Processing, 1999. ICIP 99. Proceedings. 1999 International Conference on}, volume = {1}, year = {1999}, month = {1999///}, pages = {291 -295 vol.1 - 291 -295 vol.1}, abstract = {This paper applies shuffling to digital watermarking and data hiding. The data embedding capacity in the multimedia source generally varies significantly from one part of the source to another. Sequential embedding is very sensitive to noise which may cause synchronization problem; the common but conservative solution via partitioning an image into large segments and embedding only one bit per segment is wasteful of the data embedding capacity. This paper shows how random shuffling can be used to equalize the uneven distribution of embedding capacity. The effectiveness of random shuffling is demonstrated by analysis and experiments}, keywords = {coding;, data, embeddin;data, encapsulation;document, hiding;digital, image, processing;image, shuffling;shuffling;synchronization;data, source;random, watermarking;multimedia}, doi = {10.1109/ICIP.1999.821616}, author = {M. Wu and Liu,B.} } @article {15614, title = {Efficient algorithms for robust feature matching}, journal = {Pattern Recognition}, volume = {32}, year = {1999}, month = {1999///}, pages = {17 - 38}, abstract = {One of the basic building blocks in any point-based registration scheme involves matching feature points that areextracted from a sensed image to their counterparts in a reference image. This leads to the fundamental problem of point matching: Given two sets of points, find the (affine) transformation that transforms one point set so that its distance from the other point set is minimized. Because of measurement errors and the presence of outlying data points, it is important that the distance measure between the two point sets be robust to these effects. We measure distances using the partial Hausdorff distance. Point matching can be a computationally intensive task, and a number of theoretical and applied approaches have been proposed for solving this problem. In this paper, we present two algorithmic approaches to the point matching problem, in an attempt to reduce its computational complexity, while still providing a guarantee of the quality of the final match. Our first method is an approximation algorithm, which is loosely based on a branch-and- bound approach due to Huttenlocher and Rucklidge, (Technical Report 1321, Dept. of Computer Science, Cornell University, Ithaca, 1992; Proc. IEEE Conf. on Computer vision and Pattern Recognition, New York, 1993, pp. 705{\textemdash}706). We show that by varying the approximation error bounds, it is possible to achieve a tradeoff between the quality of the match and the running time of the algorithm. Our second method involves a Monte Carlo method for accelerating the search process used in the first algorithm. This algorithm operates within the framework of a branch-and-bound procedure, but employs point-to-point alignments to accelerate the search. We show that this combination retains many of the strengths of branch-and-bound search, but provides significantly faster search times by exploiting alignments. With high probability, this method succeeds in finding an approximately optimal match. We demonstrate the algorithms{\textquoteright} performances on both synthetically generated data points and actual satellite images. }, author = {Mount, Dave and Netanyahu,N. S and Le Moigne,J.} } @conference {15386, title = {Gate leakage current simulation by Boltzmann transport equation and its dependence on the gate oxide thickness}, booktitle = {Simulation of Semiconductor Processes and Devices, 1999. SISPAD {\textquoteright}99. 1999 International Conference on}, year = {1999}, month = {1999///}, pages = {247 - 250}, abstract = {As device dimensions shrink toward 0.1 mu;m, gate oxides are becoming so thin that MOSFET gate leakage current and oxide degradation are becoming limiting issues. We provide a more rigorous way to calculate gate leakage current. To achieve this we build upon the Spherical Harmonic Method of modeling, which deterministically solves the Boltzmann equation for an entire device. The method gives the distribution function and is 1000 times faster than MC. Once the distribution function is calculated, the tunneling probability is derived from the first principle WKB method. The barrier lowering effect is accounted for by the method of image charges. We calculate gate leakage current as a function of DC bias. The thermionic and tunneling components are compared at different DC bias points. The dependence of gate leakage current on gate oxide thickness is simulated}, keywords = {30, angstrom;60, angstrom;Boltzmann, Bias, calculations;leakage, charges;spherical, component;tunneling, current, currents;semiconductor, dependence;method, dependence;MOSFET;barrier, device, effect;distribution, equation;DC, equation;MOSFET;WKB, function;first, harmonic, image, leakage, lowering, method, method;gate, model;thermionic, models;tunnelling;, of, oxide, principle, probability;Boltzmann, simulation;gate, thickness, transport, WKB}, doi = {10.1109/SISPAD.1999.799307}, author = {Han,Zhiyi and Lin,Chung-Kai and Goldsman,N. and Mayergoyz, Issak D and Yu,S. and Stettler,M.} } @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.} } @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 {18862, title = {Nano-to-millimeter scale integrated systems}, journal = {Components and Packaging Technologies, IEEE Transactions on}, volume = {22}, year = {1999}, month = {1999/06//}, pages = {338 - 343}, abstract = {Over the last several years various industries have been developing nano, micro, and millimeter scale technologies, which have resulted in components ranging from quantum transistors, to widely commercialized integrated circuits, to microelectromechanical sensors. A common emphasis of these fabrication industries has been on the integration of different functions in miniaturized systems; however, the technology currently used to realize these systems is monolithic. A unique class of hybrid technology systems is Integrated nano to millimeter (In2m) systems. An In2m system typically has components spanning multiple sizes, diverse technology domains, and mixtures of electrical, mechanical, thermal, chemical, fluidic, and biological functions}, keywords = {fabrication technology, In2m, integrated nano to millimeter system, micromechanical devices, nanotechnology}, isbn = {1521-3331}, doi = {10.1109/6144.774758}, author = {Last,H.R. and Deeds,M. and Garvick,D. and Kavetsky,R. and Sandborn,P. A. and Magrab,E. B. and Gupta,S.K.} } @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} } @book {14913, title = {Perceptual Organization in Computer Vision}, year = {1999}, month = {1999///}, publisher = {Academic Press}, organization = {Academic Press}, author = {Boyer,K.L. and Sarkar,S. and Feldman,J. and Granlund,G. and Horaud,R. and Hutchinson,S. and Jacobs, David W. and Kak,A. and Lowe,D. and Malik,J.} } @article {12790, title = {A practical approach to implementing real-time semantics}, journal = {Annals of Software Engineering}, volume = {7}, year = {1999}, month = {1999///}, pages = {127 - 155}, author = {Bhat,G. and Cleaveland, Rance and L\{\"u}ttgen,G.} } @article {13465, title = {Reports on the AAAI Fall Symposia}, journal = {AI Magazine}, volume = {20}, year = {1999}, month = {1999/09/15/}, pages = {87 - 87}, abstract = {The Association for the Advancement of Artificial Intelligence (AAAI) held its 1998 Fall Symposium Series on 23 to 25 October at the Omni Rosen Hotel in Orlando, Florida. This article contains summaries of seven of the symposia that were conducted: (1) Cognitive Robotics; (2) Distributed, Continual Planning; (3) Emotional and Intelligent: The Tangled Knot of Cognition; (4) Integrated Planning for Autonomous Agent Architectures; (5) Planning with Partially Observable Markov Decision Processes; (6) Reasoning with Visual and Diagrammatic Representations; and (7) Robotics and Biology: Developing Connections.}, isbn = {0738-4602}, doi = {10.1609/aimag.v20i3.1470}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1470}, author = {De Giacomo,Giuseppe and desJardins, Marie and Canamero,Dolores and Wasson,Glenn and Littman,Michael and Allwein,Gerard and Marriott,Kim and Meyer,Bernd and Webb,Barbara and Consi,Tom} } @article {14911, title = {The role of convexity in perceptual completion: beyond good continuation}, journal = {Vision Research}, volume = {39}, year = {1999}, month = {1999/12//}, pages = {4244 - 4257}, abstract = {Since the seminal work of the Gestalt psychologists, there has been great interest in understanding what factors determine the perceptual organization of images. While the Gestaltists demonstrated the significance of grouping cues such as similarity, proximity and good continuation, it has not been well understood whether their catalog of grouping cues is complete {\textemdash} in part due to the paucity of effective methodologies for examining the significance of various grouping cues. We describe a novel, objective method to study perceptual grouping of planar regions separated by an occluder. We demonstrate that the stronger the grouping between two such regions, the harder it will be to resolve their relative stereoscopic depth. We use this new method to call into question many existing theories of perceptual completion (Ullman, S. (1976). Biological Cybernetics, 25, 1{\textendash}6; Shashua, A., \& Ullman, S. (1988). 2nd International Conference on Computer Vision (pp. 321{\textendash}327); Parent, P., \& Zucker, S. (1989). IEEE Transactions on Pattern Analysis and Machine Intelligence, 11, 823{\textendash}839; Kellman, P. J., \& Shipley, T. F. (1991). Cognitive psychology, Liveright, New York; Heitger, R., \& von der Heydt, R. (1993). A computational model of neural contour processing, figure-ground segregation and illusory contours. In Internal Conference Computer Vision (pp. 32{\textendash}40); Mumford, D. (1994). Algebraic geometry and its applications, Springer, New York; Williams, L. R., \& Jacobs, D .W. (1997). Neural Computation, 9, 837{\textendash}858) that are based on Gestalt grouping cues by demonstrating that convexity plays a strong role in perceptual completion. In some cases convexity dominates the effects of the well known Gestalt cue of good continuation. While convexity has been known to play a role in figure/ground segmentation (Rubin, 1927; Kanizsa \& Gerbino, 1976), this is the first demonstration of its importance in perceptual completion.}, keywords = {Amodal completion, Convexity, Good continuation, Grouping, Stereoscopic depth}, isbn = {0042-6989}, doi = {10.1016/S0042-6989(99)00141-8}, url = {http://www.sciencedirect.com/science/article/pii/S0042698999001418}, author = {Liu,Zili and Jacobs, David W. and Basri,Ronen} } @conference {12774, title = {Statecharts via process algebra}, booktitle = {CONCUR{\textquoteright}99: concurrency theory: 10th International Conference, Eindhoven, the Netherlands, August 24-27, 1999: proceedings}, year = {1999}, month = {1999///}, pages = {399 - 399}, author = {Liittgen,G. and Cleaveland, Rance} } @article {12321, title = {Synthesis of embedded software from synchronous dataflow specifications}, journal = {The Journal of VLSI Signal Processing}, volume = {21}, year = {1999}, month = {1999///}, pages = {151 - 166}, author = {Bhattacharyya, Shuvra S. and Murthy,P. K and Lee,E. A} } @conference {13662, title = {Text Enhancement in Digital Video}, booktitle = {Proceedings of SPIE - Conference on Document Recognition and Retrieval VI}, year = {1999}, month = {1999/01//}, pages = {2 - 9}, author = {Li,H. and Kia,O. and David Doermann} } @conference {13663, title = {Text enhancement in digital video using multiple frame integration}, booktitle = {Proceedings of the seventh ACM international conference on Multimedia (Part 1)}, series = {MULTIMEDIA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {19 - 22}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper a multiple frame based technique to enhance text in digital video is presented. After extracting a reference text block, we use an image matching technique to find the corresponding text blocks in consecutive frames. We register these text blocks to subpixel levels by using image interpolation techniques to improve both correspondence and text resolution. The registered text blocks are averaged to obtain a new text block with a clean background and a higher resolution. Experiments conducted on several video sequences show that our enhancement scheme can improve the accuracy of commercial off-the-shelf OCR considerably.}, isbn = {1-58113-151-8}, doi = {10.1145/319463.319466}, url = {http://doi.acm.org/10.1145/319463.319466}, author = {Huiping Li and David Doermann} } @article {15660, title = {Vision geometry VIII(Denver CO, 19-20 July 1999)}, journal = {SPIE proceedings series}, year = {1999}, month = {1999///}, author = {Latecki,L.J. and Melter,R.A. and Mount, Dave and Wu,A. Y} } @conference {18162, title = {An algorithm for wipe detection}, booktitle = {Image Processing, 1998. ICIP 98. Proceedings. 1998 International Conference on}, volume = {1}, year = {1998}, month = {1998/10//}, pages = {893 -897 vol.1 - 893 -897 vol.1}, abstract = {The detection of transitions between shots in video programs is an important first step in analyzing video content. The wipe is a frequently used transitional form between shots. Wipe detection is more involved than the detection of abrupt and other gradual transitions because a wipe may take various patterns and because of the difficulty in discriminating a wipe from object and camera motion. In this paper, we propose an algorithm for detecting wipes using both structural and statistical information. The algorithm can effectively detect most wipes used in current TV programs. It uses the DC sequence which can be easily extracted from the MPEG stream without full decompression}, keywords = {algorithm;image, analysis;video, content;video, DC, DETECTION, detection;statistical, domain;object, information;structural, information;video, motion;compressed, motion;shot, processing;, programs;camera, programs;wipe, sequence;MPEG, sequences;signal, signal, stream;TV, transitions}, doi = {10.1109/ICIP.1998.723664}, author = {M. Wu and Wolf,W. and Liu,B.} } @conference {13507, title = {Automatic Identification of Text In Digital Video Key Frames}, booktitle = {Proceedings of International Conference on Pattern Recognition}, year = {1998}, month = {1998///}, pages = {129 - 132}, abstract = {Scene and graphic text can provide important supplemental index information in video sequences. In this paper we address the problem automatically identifying text regions in digital video key frames. The text contained in video frames is typically very noisy because it is aliased and/or digitized at a much lower resolution than typical document images, making identification, extraction and recognition difficult. The proposed method is based on the use of a hybrid wavelet/neural network segmenter on a series of overlapping small windows to classify regions which contain text. To detect text over a wide range of font sizes, the method is applied to a pyramid of images and the regions identified at each level are integrated.}, author = {Li,H. and David Doermann} } @article {13509, title = {Automatic Text Detection and Tracking in Digital Video}, volume = {LAMP-TR-028,CFAR-TR-900,CS-TR-3962}, year = {1998}, month = {1998/12//}, institution = {University of Maryland, College Park}, abstract = {Text which either appears in a scene or is graphically added to video can provide an important supplemental source of index information as well as clues for decoding the video{\textquoteright}s structure and for classification. In this paper we present algorithms for detecting and tracking text components that appear within digital video frames. Our system implements a scale-space feature extractor that feeds an artificial neural processor to extract textual regions and track their movement over time. The extracted regions can then be used as input to an appropriate Optical Character Recognition system which produces indexible keywords.}, author = {Li,H. and David Doermann and Kia,O.} } @conference {13511, title = {Automatic Text Tracking In Digital Videos}, booktitle = {Proceedings of IEEE 1998 Workshop on Multimedia Signal Processing}, year = {1998}, month = {1998///}, pages = {21 - 26}, abstract = {We address the problem of automatically tracking moving text in digital videos. Our scheme consists of two separate processes: monitoring which detects the new text line entering a frame, and tracking which uses prediction techniques to reconcile the text from frame to frame. Temporal consistency allows one to monitor periodically and reduce the computation complexity. The tracking process uses a rapid prediction/search scheme to update the position of the text blocks between frames. We provide details of the implementation and results for text moving in the scene and text which moves as a result of camera motion.}, author = {Li,H. and David Doermann} } @article {17001, title = {Browsing Unix Directories With Dynamic Queries: An Evaluation of Three Information Display Techniques}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {We designed, implemented, and evaluated an innovative concept fordynamic queries which involves the direct manipulation of small databases. Our domain was directories in a Unix file system. Dynamic queries allow users to formulate queries and explore the databases with graphical widgets, such as sliders and buttons, without requiring them to have any knowledge about the underlying structure of the database query languages, or command language syntax. Three interfaces for presenting directories were developed and tested with eighteen subjects in a within-subject design. The results of the formative evaluation yielded some useful guidelines for software designers. (Also cross-referenced as CAR-TR-605) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/379}, author = {Liao,Holmes and Osada,Masakazu 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 {16191, title = {Data object and label placement for information abundant visualizations}, booktitle = {Proceedings of the 1998 workshop on New paradigms in information visualization and manipulation}, series = {NPIV {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {41 - 48}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {control panel, data object placement, Information Visualization, label placement, metrics, timelines, visual feedback}, isbn = {1-58113-179-8}, doi = {10.1145/324332.324341}, url = {http://doi.acm.org/10.1145/324332.324341}, author = {Li,Jia and Plaisant, Catherine and Shneiderman, Ben} } @article {13668, title = {The detection of duplicates in document image databases}, journal = {Image and Vision Computing}, volume = {16}, year = {1998}, month = {1998/08/24/}, pages = {907 - 920}, abstract = {Document imaging technology has developed to the point where it is not uncommon for organizations to scan large numbers of documents into databases with little or no index information. This may be done for archival purposes with an index as simple as a case number, or with the ultimate goal of automatically extracting index information for content-based queries. Maintaining the integrity of such a database is difficult, however, especially in a distributed environment where copies of the same documents may be scanned at different times.In this paper we present a novel approach to detecting duplicate documents in very large databases using only features extracted from the image. The method is based on a robust {\textquoteleft}signature{\textquoteright} extracted from each document image which is used to index into a table of previously processed documents. The system is able to deal with differences between scanned document instances such resolution, skew and image quality. The approach has a number of advantages over OCR or other recognition-based methods including speed and robustness to imaging distortions. To justify the approach and demonstrate its scalability, we have developed a simulator which allows us to change parameters of the system and examine performance while processing millions of document signatures. A complete system has been implemented and tested on a collection of technical articles and memos. }, keywords = {Document image databases, Document indexing, Duplicate detection, Shape coding}, isbn = {0262-8856}, doi = {10.1016/S0262-8856(98)00054-7}, url = {http://www.sciencedirect.com/science/article/pii/S0262885698000547}, author = {David Doermann and Huiping Li and Kia,Omid} } @conference {17094, title = {Distance learning: is it the end of education as most of us know it?}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {86 - 87}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {distance learning, education, Internet, Web}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286542}, url = {http://doi.acm.org/10.1145/286498.286542}, author = {Laurillard,Diana and Preece,Jenny and Shneiderman, Ben and Neal,Lisa and W{\ae}rn,Yvonne} } @article {15367, title = {Extension of Spherical Harmonic Method to RF Transient Regime}, journal = {Simulation of semiconductor processes and devices 1998: SISPAD 98}, year = {1998}, month = {1998///}, pages = {42 - 42}, abstract = {The space and time dependent electron Boltzmann transport equation (BTE)is solved sclf-consistently with the Poisson and transient hole current-continuity equation. A transient Spherical Harmonic expansion method is used to solve the BTE. By this method we can efficiently solve the BTE in the RF regime to observe how the complete distribution function responds to a rapid transient. Calculations on a BJT, which give the time dependent distribution function over a large energy range 0-3eV, throughout the device, as well as average quantities, require only 40 minutes CPU time on an Alpha workstation. }, author = {Lin,C. K. and Goldsman,N. and Chang,C. H. and Mayergoyz, Issak D and Aronowitz,S. and Dong,J. and Belova,N.} } @article {16178, title = {Facilitating Network Data Exploration with Query Previews: A Study of User Performance and Preference}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {Current network data exploration systems which use command languages (e.g.SQL) or form fill-in interfaces fail to give users an indication of the distribution of data items. This leads many users to waste time posing queries which have zero-hit or mega-hit result sets. Query previewing is a novel visual approach for browsing huge networked information warehouses. Query previews supply data distribution information about the database that is being searched and give continuous feedback about the size of the result set for the query as it is being formed. Our within-subjects empirical comparison studied 12 subjects using a form fill-in interface with and without query previews. We found statistically significant differences showing that query previews sped up performance 1.6 to 2.1 times and led to higher subjective satisfaction. (Also cross-referenced as UMIACS-98-14) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/488}, author = {Tanin,Egemen and Lotem,Amnon and Haddadin,Ihab and Shneiderman, Ben and Plaisant, Catherine and Slaughter,Laura} } @article {15362, title = {Hydrodynamic Device Simulation with New State Variables Specially Chosen a Block Gummel Iterative Approach}, journal = {VLSI DESIGN}, volume = {6}, year = {1998}, month = {1998///}, pages = {191 - 195}, abstract = {A new numerical formulation for solving the hydrodynamic model of semiconductor devicesis presented. Themethod is based on using new variables to transform the conventional hydrodynamic equations into forms which facilitatenumerical evaluation with a block Gum- mel approach. To demonstrate the new method, we apply it to model a 0.35 wn 2-D LDD MOSFET, where robust convergence properties are observed. }, author = {Liang,W. and Kerr,D. C. and Goldsman,N. and Mayergoyz, Issak D} } @conference {15635, title = {Improved algorithms for robust point pattern matching and applications to image registration}, booktitle = {Proceedings of the fourteenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {155 - 164}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-973-4}, doi = {10.1145/276884.276902}, url = {http://doi.acm.org/10.1145/276884.276902}, author = {Mount, Dave and Netanyahu,Nathan S. and LeMoigne,Jacqueline} } @article {16182, title = {Incorporating String Search in a Hypertext System:User Interface and Signature File Design Issues}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {Hypertext systems provide an appealing mechanism forinformally browsing databases by traversing selectable links. However, in many fact finding situations string search is an effective complement to browsing. This paper describes the application of the signature file method to achieve rapid and convenient string search in small personal computer hypertext environments. The method has been implemented in a prototype, as well as in a commercial product. Performance data for search times and storage space are presented from a commercial hypertext database. User interface issues are then discussed. Experience with the string search interface indicates that it was used sucessfully by novice users. (Also cross-referenced as CAR-TR-448) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/359}, author = {Faloutsos,Christos and Lee,Raymond and Plaisant, Catherine and Shneiderman, Ben} } @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 {16190, title = {LifeLines: using visualization to enhance navigation and analysis of patient records}, journal = {In Proceedings of the 1998 American Medical Informatic Association Annual Fall SymposiumProc AMIA Symp}, year = {1998}, month = {1998///}, pages = {76 - 80}, abstract = {LifeLines provide a general visualization environment for personal histories. We explore its use for clinical patient records. A Java user interface is described, which presents a one-screen overview of a computerized patient record using timelines. Problems, diagnoses, test results or medications can be represented as dots or horizontal lines. Zooming provides more details; line color and thickness illustrate relationships or significance. The visual display acts as a giant menu, giving direct access to the data.}, isbn = {1531-605X}, author = {Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben} } @article {17281, title = {LifeLines: using visualization to enhance navigation and analysis of patient records.}, journal = {Proceedings of the AMIA Symposium}, year = {1998}, month = {1998///}, pages = {76 - 80}, abstract = {LifeLines provide a general visualization environment for personal histories. We explore its use for clinical patient records. A Java user interface is described, which presents a one-screen overview of a computerized patient record using timelines. Problems, diagnoses, test results or medications can be represented as dots or horizontal lines. Zooming provides more details; line color and thickness illustrate relationships or significance. The visual display acts as a giant menu, giving direct access to the data.}, isbn = {1531-605X}, author = {Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben} } @inbook {17618, title = {Low-bandwidth routing and electrical power networks}, booktitle = {Automata, Languages and ProgrammingAutomata, Languages and Programming}, series = {Lecture Notes in Computer Science}, volume = {1443}, year = {1998}, month = {1998///}, pages = {604 - 615}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Given a graph G and a (multi-)set of pairs of vertices in it, the classical NP-hard maximum edge-disjoint-paths problem (MDP) is to connect as many of the given pairs as possible using pairwise edge-disjoint paths in G . We study a relative of this problem: we have a network with fixed link capacities that may have to service large demands when necessary. In particular, individual demands are allowed to exceed capacities, and thus flows for some request pairs necessarily have to be split into different flow-paths. This is the framework for computational problems arising from: (i) electrical power networks due to the proposed deregulation of the electric utility industry in the USA, and (ii) applications such as real-time Internet services (e.g., telephone, fax, video). We show that these problems come in a few variants, some efficiently solvable and many NP -hard; we also present approximation algorithms for many of the NP -hard variants presented. Some of our approximation algorithms benefit from certain improved tail estimates that we derive; the latter also yield improved approximations for a family of packing integer programs.}, isbn = {978-3-540-64781-2}, url = {http://dx.doi.org/10.1007/BFb0055088}, author = {Cook,Doug and Faber,Vance and Marathe,Madhav and Srinivasan, Aravind and Sussmann,Yoram}, editor = {Larsen,Kim and Skyum,Sven and Winskel,Glynn} } @article {14988, title = {Models and high-performance algorithms for global BRDF retrieval}, journal = {Computational Science Engineering, IEEE}, volume = {5}, year = {1998}, month = {1998/12//oct}, pages = {16 - 29}, abstract = {The authors describe three models for retrieving information related to the scattering of light on the Earth{\textquoteright}s surface. Using these models, they{\textquoteright}ve developed algorithms for the IBM SP2 that efficiently retrieve this information}, keywords = {algorithms;, BRDF, Earth, geomorphology;, geophysical, global, high-performance, IBM, information, light, machines;, models;, Parallel, processing;, reflectivity;, retrieval, retrieval;, scattering;, signal, SP2;, surface;}, isbn = {1070-9924}, doi = {10.1109/99.735892}, author = {Zengyan Zhang and Kalluri, SNV and JaJa, Joseph F. and Liang,Shunlin and Townshend,J.R.G.} } @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} } @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 {12778, title = {Probabilistic resource failure in real-time process algebra}, journal = {CONCUR{\textquoteright}98 Concurrency Theory}, year = {1998}, month = {1998///}, pages = {465 - 472}, author = {Philippou,A. and Cleaveland, Rance and Lee,I. and Smolka,S. and Sokolsky,O.} } @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 {18723, title = {The Solution Structure and Dynamics of the Pleckstrin Homology Domain of G Protein-coupled Receptor Kinase 2 (β-Adrenergic Receptor Kinase 1) A BINDING PARTNER OF Gβγ SUBUNITS}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, volume = {273}, year = {1998}, month = {1998/01/30/}, pages = {2835 - 2843}, abstract = {The solution structure of an extended pleckstrin homology (PH) domain from the β-adrenergic receptor kinase is obtained by high resolution NMR. The structure establishes that the β-adrenergic receptor kinase extended PH domain has the same fold and topology as other PH domains, and there are several unique features, most notably an extended C-terminal α-helix that behaves as a molten helix, and a surface charge polarity that is extensively modified by positive residues in the extended α-helix and the C terminus. These observations complement biochemical evidence that the C-terminal portion of this PH domain participates in protein-protein interactions with Gβγ subunits. This suggests that the C-terminal segment of the PH domain may function to mediate protein-protein interactions with the targets of PH domains.}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.273.5.2835}, url = {http://www.jbc.org/content/273/5/2835}, author = {Fushman, David and Najmabadi-Haske,Taraneh and Cahill,Sean and Zheng,Jie and LeVine,Harry and Cowburn,David} } @conference {13665, title = {Text Extraction and Recognition in Digital Video}, booktitle = {Proceedings of Third IAPRWorkshop on Document Analysis Systems}, year = {1998}, month = {1998///}, pages = {119 - 128}, author = {Li,H. and David Doermann and Kia,O.} } @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} } @conference {16189, title = {Visualizing medical records with LifeLines}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {28 - 29}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {healthcare, History, medical record, overview, timeline, Visualization}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286513}, url = {http://doi.acm.org/10.1145/286498.286513}, author = {Plaisant, Catherine and Heller,Daniel and Li,Jia and Shneiderman, Ben and Mushlin,Rich and Karat,John} } @conference {18290, title = {Watermarking for image authentication}, booktitle = {Image Processing, 1998. ICIP 98. Proceedings. 1998 International Conference on}, volume = {2}, year = {1998}, month = {1998/10//}, pages = {437 -441 vol.2 - 437 -441 vol.2}, abstract = {A data embedding method is proposed for image authentication based on table look-up in frequency domain. A visually meaningful watermark and a set of simple features are embedded invisibly in the marked image, which can be stored in the compressed form. The scheme can detect and localize alterations of the original image, such as the tampering of images exported from a digital camera}, keywords = {alterations, analysis;image, analysis;message, authentication;image, authentication;table, camera;frequency, coding;image, colour, compression;frequency-domain, detection;alterations, domain;image, EMBEDDING, image, image;compressed, image;ownership, localisation;color, look-up;watermarking;data, lookup;, method;digital, protection;table, storage;data, tampering;marked}, doi = {10.1109/ICIP.1998.723413}, author = {M. Wu and Liu,Bede} } @conference {17269, title = {Is the Web really different from everything else?}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {92 - 93}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {design, user experience, World Wide Web}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286545}, url = {http://doi.acm.org/10.1145/286498.286545}, author = {Shneiderman, Ben and Nielsen,Jakob and Butler,Scott and Levi,Michael and Conrad,Frederick} } @article {15369, title = {2-D MOSFET modeling including surface effects and impact ionization by self-consistent solution of the Boltzmann, Poisson, and hole-continuity equations}, journal = {Electron Devices, IEEE Transactions on}, volume = {44}, year = {1997}, month = {1997/02//}, pages = {257 - 267}, abstract = {We present a new two-dimensional (2-D) MOSFET simulation method achieved by directly solving the Boltzmann transport equation for electrons, the hole-current continuity equation, and the Poisson equation self-consistently. The spherical harmonic method is used for the solution of the Boltzmann equation. The solution directly gives the electron distribution function, electrostatic potential, and the hole concentration for the entire 2-D MOSFET. Average quantities such as electron concentration and electron temperature are obtained directly from the integration of the distribution function. The collision integral is formulated to arbitrarily high spherical harmonic order, and new collision terms are included that incorporate effects of surface scattering and electron-hole pair recombination/generation. I-V characteristics, which agree with experiment, are calculated directly from the distribution function for an LDD submicron MOSFET. Electron-hole pair generation due to impact ionization is also included by direct application of the collision integral. The calculations are efficient enough for day-to-day engineering design on workstation-type computers}, keywords = {2D, characteristics;LDD, concentration;electron, concentration;hole-continuity, density;electron-hole, density;impact, device, distribution, effects;surface, equation;collision, equation;I-V, equation;MOSFET;electron, equations;impact, equations;semiconductor, function;electron, generation;electron-hole, harmonic, integral;electron, ionisation;integral, ionization;self-consistent, method;Boltzmann, method;surface, modeling;Boltzmann, models;surface, MOSFET, MOSFET;Poisson, pair, potential;hole, recombination;electrostatic, recombination;hole, scattering;, scattering;two-dimensional, simulation, solution;spherical, submicron, temperature;electron-hole, transport}, isbn = {0018-9383}, doi = {10.1109/16.557713}, author = {Liang,Wenchao and Goldsman,N. and Mayergoyz, Issak D and Oldiges,P.J.} } @article {12771, title = {An algebraic theory of multiple clocks}, journal = {CONCUR{\textquoteright}97: Concurrency Theory}, year = {1997}, month = {1997///}, pages = {166 - 180}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Mendler,M.} } @article {12336, title = {APGAN and RPMC: Complementary heuristics for translating DSP block diagrams into efficient software implementations}, journal = {Design Automation for Embedded Systems}, volume = {2}, year = {1997}, month = {1997///}, pages = {33 - 60}, author = {Bhattacharyya, Shuvra S. and Murthy,P. K and Lee,E. A} } @conference {17554, title = {Approximating hyper-rectangles: learning and pseudo-random sets}, booktitle = {Proceedings of the twenty-ninth annual ACM symposium on Theory of computing}, series = {STOC {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {314 - 323}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {approximations of distributions, derandomization, explicit constructions, machine learning, multiple-instance learning, PAC learning, pseudorandomness, Ramsey graphs, random graphs, rectangles, sample complexity}, isbn = {0-89791-888-6}, doi = {10.1145/258533.258611}, url = {http://doi.acm.org/10.1145/258533.258611}, author = {Auer,Peter and Long,Philip M. and Srinivasan, Aravind} } @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.} } @conference {15693, title = {Challenges in sending large radiology images over military communications channels}, booktitle = {Proceedings of SPIE}, volume = {3035}, year = {1997}, month = {1997///}, pages = {230 - 230}, author = {Cleary,K.R. and Levine,B.A. and Norton,G.S. and Mundur,P.V.} } @article {18377, title = {Comments on "Towards a framework for software measurement validation"}, journal = {Software Engineering, IEEE Transactions on}, volume = {23}, year = {1997}, month = {1997/03//}, pages = {187 - 189}, abstract = {A view of software measurement that disagrees with the model presented by Kitchenham, Pfleeger, and Fenton (1995), is given. Whereas Kitchenham et al. argue that properties used to define measures should not constrain the scale type of measures, the authors contend that that is an inappropriate restriction. In addition, a misinterpretation of Weyuker{\textquoteright}s (1988) properties is noted.}, keywords = {measurement, metrics;, software, testing;program, validation;program, verification;software}, isbn = {0098-5589}, doi = {10.1109/32.585506}, author = {Morasca,S. and Briand,L.C. and Basili, Victor R. and Weyuker,E.J. and Zelkowitz, Marvin V and Kitchenham,B. and Lawrence Pfleeger,S. and Fenton,N.} } @conference {13523, title = {Compressed Domain video indexing techniques using DCT and motion vector information in MPEG video}, booktitle = {Proceedings of SPIE - conference on Storage and Retrieval for Image and Video Databases V}, year = {1997}, month = {1997///}, pages = {200 - 211}, abstract = {Development of various multimedia applications hinges on the availability of fast and e cient storage, brows-ing, indexing, and retrieval techniques. Given that video is typically stored e ciently in a compressed format, if we can analyze the compressed representation directly, we can avoid the costly overhead of decompressing and operating at the pixel level. Compressed domain parsing of video has been presented in earlier work where a video clip is divided into shots, subshots, and scenes. In this paper, we describe key frame selection, feature extraction, and indexing and retrieval techniques that are directly applicable to MPEG compressed video. We develop a frame-type independent representation of the various types of frames present in an MPEG video in which all frames can be considered equivalent. Features are derived from the available DCT, macroblock, and motion vector information and mapped to a low-dimensional space where they can be accessed with standard database techniques. The spatial information is used as primary index while the temporal information is used to enhance the robustness of the system during the retrieval process. The techniques presented enable fast archiv- ing, indexing, and retrieval of video. Our operational prototype typically takes a fraction of a second to retrieve similar video scenes from our database, with over 95\% success. }, author = {Kobla,V. and David Doermann and Lin,K-I. and Faloutsos,C.} } @conference {13669, title = {The Detection of Duplicates in Document Image Databases}, booktitle = {ICDAR}, year = {1997}, month = {1997///}, pages = {314 - 318}, 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 Li,H. and Kia,O.} } @article {12791, title = {Dynamic priorities for modeling real-time}, journal = {Proc. of the Formal Description Techniques and Protocol Specification, Testing and Verification (FORTE X/PSTV XVII{\textquoteright}97)}, year = {1997}, month = {1997///}, pages = {321 - 336}, author = {Bhat,G. and Cleaveland, Rance and L\{\"u}ttgen,G.} } @article {18382, title = {Editorial: Evaluation and assessment in software engineering}, journal = {Information and Software Technology}, volume = {39}, year = {1997}, month = {1997///}, author = {Kitchenham,B. and Brereton,P. and Budgen,D. and Linkman,S. and Almstrum,V. L and Pfleeger,S. L and Zelkowitz, Marvin V and Wallace,D.} } @conference {15598, title = {Efficient algorithms for robust feature matching}, booktitle = {Image Registration Workshop Proceedings}, year = {1997}, month = {1997///}, publisher = {NASA}, organization = {NASA}, abstract = {One of the basic building blocks in any point-based registration scheme involves matching feature points that are extracted from the sensed image to their counterparts in the reference image. This leads to the fundamental problem of point matching: given two sets of points, find the affine transformation that transforms one point set so that its distance from the other point set is minimized. Because of measurement errors and the presence of outlying data points, it is important that the distance measure between two point sets be robust to these effects. We measure distances using the generalized Hausdorff distance. Point matching can be a computationally intensive task, and there have been a number of algorithms and approaches proposed for solving this problem both theoretical and applied. We present two approaches to the point matching problem, in an attempt to reduce the computational complexity of the problem, while still providing guarantees on the quality of the final match. Our first method is an approximation algorithm, which is loosely based on a branch-and-bound approach due to Huttenlocher and Rucklidge. We show that by varying the approximation error bounds, it is possible to achieve a tradeoff between the quality of the match and the running time of the algorithm. Our second method involves a Monte Carlo method for accelerating the search process used in the first algorithm. With high probability this method succeeds in finding an approximately optimal match. We establish the efficiency of our approaches empirically.}, author = {Mount, Dave and Netanyahu,N. S and Le Moigne,J.} } @article {14966, title = {Fast algorithms for estimating aerosol optical depth and correcting thematic mapper imagery}, journal = {The Journal of Supercomputing}, volume = {10}, year = {1997}, month = {1997///}, pages = {315 - 329}, abstract = {Remotely sensed images collected by satellites are usually contaminated by the effects of atmospheric particles through the absorption and scattering of radiation from the earth{\textquoteright}s surface. The objective of atmospheric correction is to retrieve the surface reflectance from remotely sensed imagery by removing the atmospheric effects, which is usually performed in two steps. First, the optical characteristics of the atmosphere are estimated and then the remotely sensed imagery is corrected by inversion procedures that derive the surface reflectance. In this paper we introduce an efficient algorithm to estimate the optical characteristics of the Thematic Mapper imagery and to remove the atmospheric effects from it. Our algorithm introduces a set of techniques to significantly improve the quality of the retrieved images. We pay particular attention to the computational efficiency of the algorithm, thereby allowing us to correct large TM images quickly. We also provide a parallel implementation of our algorithm and show its portability and scalability on three parallel machines.}, doi = {10.1007/BF00227861}, author = {Fallah-Adl,H. and JaJa, Joseph F. and Liang, S.} } @article {12385, title = {Joint minimization of code and data for synchronous dataflow programs}, journal = {Formal Methods in System Design}, volume = {11}, year = {1997}, month = {1997///}, pages = {41 - 70}, author = {Murthy,P. K and Bhattacharyya, Shuvra S. and Lee,E. A} } @article {12366, title = {Optimizing synchronization in multiprocessor DSP systems}, journal = {Signal Processing, IEEE Transactions on}, volume = {45}, year = {1997}, month = {1997///}, pages = {1605 - 1618}, author = {Bhattacharyya, Shuvra S. and Sriram,S. and Lee,E. A} } @inbook {11921, title = {Regulation of Cable Television}, booktitle = {The Froehlich/Kent Encyclopedia of Telecommunications: Volume 15-Radio Astronomy to Submarine Cable SystemsThe Froehlich/Kent Encyclopedia of Telecommunications: Volume 15-Radio Astronomy to Submarine Cable Systems}, volume = {15}, year = {1997}, month = {1997///}, pages = {84 - 84}, author = {Agrawala, Ashok K. and CILINGIROGLU,A. and Lee,S.} } @article {17472, title = {User Interfaces for a Complex Robotic Task: A Comparison of Tiles vs. Overlapped Windows}, journal = {Institute for Systems Research Technical Reports}, year = {1997}, month = {1997///}, abstract = {High complexity tasks, such as remote teleoperation of robotic vehicles, often require multiple windows. For these complex tasks, the windows necessary for task completion, may occupy more area than available on a single visual display unit (VDU). Since the focus of the robotic task constantly changes, modular control panels that can be opened, closed, and moved on the screen are invaluable to the operator. This study describes a specific robotic task and the need for a multi window interface that can be easily manipulated. This paper examines two multi-window management strategies: tiled (fixed size) and arbitrary overlap. Multi-window searches were performed using the two management styles and they were compared on the basis of search completion time and error rates. Results with 35 novice users showed faster completion times for the tiled management strategy than for the arbitrary overlap strategy. Over factors such as the number of windows available, the number of displayed windows workload of opening or closing windows, and effect of learning are discussed.}, keywords = {Human computer interaction, overlapped, Systems Integration Methodology, tiled, user interface design, window management}, url = {http://drum.lib.umd.edu/handle/1903/5874}, author = {Lane,J. Corde and Kuester,Steven P and Shneiderman, Ben} } @conference {15040, title = {The vegetation canopy lidar mission}, booktitle = {Proceedings of Land Satellite Information in the Next Decade, II: Sources and Applications. Bethesda (MD): American Society of Photogrammetry and Remote Sensing}, year = {1997}, month = {1997///}, pages = {100 - 112}, abstract = {The Vegetation Canopy Lidar (VCL) is the first selected mission of NASA{\textquoteright}s new EarthSystem Science Pathfinder program. The principal goal of VCL is the characterization of the three-dimensional structure of the earth; in particular, canopy vertical and horizontal structure and land surface topography. Its primary science objectives are: landcover characterization for terrestrial ecosystem modeling, monitoring and prediction; landcover characterization for climate modeling and prediction; and, production of a global reference data set of topographic spot heights and transects. VCL will provide unique data sets for understanding important environ- mental issues including climatic change and variability, biotic erosion and sustainable landuse, and will dramatically improve our estimation of global biomass and carbon stocks, fractional forest cover, forest extent and condition. It will also provide canopy data critical for biodiversity, natural hazard, and climate studies. Scheduled for launch in early 2000, VCL is an active lidar remote sensing system consisting of a five-beam instrument with 25 m contiguous along track resolution. The five beams are in a circular configuration 8 km across and each beam traces a separate ground track spaced 2 km apart, eventually producing 2 km coverage between 65{\textdegree} N and S. VCL{\textquoteright}s core measurement objectives are: (1) canopy top heights; (2) vertical distribution of intercepted surfaces (e.g. leaves and branches); and, (3) ground surface topographic elevations. These measurements are used to derive a variety of science data products including canopy heights, canopy vertical distribution, and ground elevations gridded monthly at 1{\textdegree} resolution and every 6 months at 2 km resolution, as well as a 2 km fractional forest cover product. }, author = {Dubayah, R. and Blair,J. B. and Bufton,J. L. and Clark,D. B. and JaJa, Joseph F. and Knox,R. and Luthcke,S. B. and Prince,S. and Weishampel,J.} } @conference {13500, title = {Archiving, indexing, and retrieval of video in compressed domain}, booktitle = {SPIEConference on Multimedia Storage and Archiving Systems}, volume = {2916}, year = {1996}, month = {1996///}, pages = {78 - 89}, author = {Kobla,V. and David Doermann and Lin,K-I.} } @book {15378, title = {Basic Electric Circuit Theory: A One-Semester Text}, year = {1996}, month = {1996///}, publisher = {Academic Press}, organization = {Academic Press}, abstract = {This is the only book on the market that has been conceived and deliberately written as a one-semester text on basic electric circuit theory. As such, this book employs a novel approach to the exposition of the material in which phasors and ac steady-state analysis are introduced at the beginning. This allows one to use phasors in the discussion of transients excited by ac sources, which makes the presentation of transients more comprehensive and meaningful. Furthermore, the machinery of phasors paves the road to the introduction of transfer functions, which are then used in the analysis of transients and the discussion of Bode plots and filters. Another salient feature of the text is the consolidation into one chapter of the material concerned with dependent sources and operational amplifiers. Dependent sources are introduced as linear models for transistors on the basis of small signal analysis. In the text, PSpice simulations are prominently featured to reinforce the basic material and understanding of circuit analysis.Key Features* Designed as a comprehensive one-semester text in basic circuit theory* Features early introduction of phasors and ac steady-state analysis* Covers the application of phasors and ac steady-state analysis* Consolidates the material on dependent sources and operational amplifiers* Places emphasis on connections between circuit theory and other areas in electrical engineering* Includes PSpice tutorials and examples* Introduces the design of active filters* Includes problems at the end of every chapter* Priced well below similar books designed for year-long courses}, keywords = {Electric circuits, Technology \& Engineering / Electrical}, isbn = {9780124808652}, author = {Mayergoyz, Issak D and Lawson,Wes} } @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 {12844, title = {The Concurrency Factory: A development environment for concurrent systems}, booktitle = {Computer Aided Verification}, year = {1996}, month = {1996///}, pages = {398 - 401}, author = {Cleaveland, Rance and Lewis,P. and Smolka,S. and Sokolsky,O.} } @conference {14956, title = {Efficient algorithms for estimating atmospheric parameters for surface reflectance retrieval}, booktitle = {Parallel Processing, 1996., Proceedings of the 1996 International Conference on}, volume = {2}, year = {1996}, month = {1996/08//}, pages = {132 -141 vol.2 - 132 -141 vol.2}, abstract = {The objective of atmospheric correction is to retrieve the surface reflectance from remotely sensed imagery by removing the atmospheric effects. We introduce an efficient algorithm to estimate the optical characteristics of the TM imagery and to remove the atmospheric effects from it. Our algorithm introduces a set of techniques to significantly improve the quality of the retrieved images. We pay a particular attention to the computational efficiency of the algorithm thereby allowing us to correct large TM images quite fast. We also provide a parallel implementation of our algorithm and show its portability and scalability on several parallel machines}, keywords = {Atmospheric, correction;atmospheric, effects;atmospheric, imagery;scalability;surface, parameters;portability;remotely, reconstruction;photoreflectance;remote, reflectance, reflectance;surface, retrieval;image, sensed, sensing;}, doi = {10.1109/ICPP.1996.537392}, author = {Fallah-Adl,H. and JaJa, Joseph F. and Liang,Shunlin} } @article {18438, title = {The empirical investigation of Perspective-Based Reading}, journal = {Empirical Software Engineering}, volume = {1}, year = {1996}, month = {1996///}, pages = {133 - 164}, abstract = {We consider reading techniques a fundamental means of achieving high quality software. Due to the lack of research in this area, we are experimenting with the application and comparison of various reading techniques. This paper deals with our experiences with a family of reading techniques known as Perspective-Based Reading (PBR), and its application to requirements documents. The goal of PBR is to provide operational scenarios where members of a review team read a document from a particular perspective, e.g., tester, developer, user. Our assumption is that the combination of different perspectives provides better coverage of the document, i.e., uncovers a wider range of defects, than the same number of readers using their usual technique.}, keywords = {Computer, Science}, isbn = {1382-3256}, url = {http://dx.doi.org/10.1007/BF00368702}, author = {Basili, Victor R. and Green,Scott and Laitenberger,Oliver and Lanubile,Filippo and Shull, Forrest and S{\o}rumg{\r a}rd,Sivert and Zelkowitz, Marvin V} } @article {12994, title = {Evolutionary biology of parasitic platyhelminths: The role of molecular phylogenetics}, journal = {Parasitol Today}, volume = {12}, year = {1996}, month = {1996/02//}, pages = {66 - 71}, abstract = {As our appreciation of the diversity within the flatworms has grown, so too has our curiosity about the ways in which these varied creatures are related to one another. In particular, the parasitic groups (trematodes, cestodes and monogeneans have been the focus of enquiry. Until recently, morphology, anatomy and life histories have provided the raw data for building hypotheses on relationships. Now, ultrastructural evidence, and most recently, molecular data from nucleic acid sequences, have been brought to bear on the topic. Here, David Blair, Andr{\'e}s Campos, Michael Cummings and Juan Pedro Laclette discuss the ways in which molecular data, in particular, are helping us recognize the various lineages of flatworms.}, author = {Blair,D and Campos,A. and Cummings, Michael P. and Laclette,J. P} } @article {14967, title = {Fast algorithms for removing atmospheric effects from satellite images}, journal = {Computational Science Engineering, IEEE}, volume = {3}, year = {1996}, month = {1996///summer}, pages = {66 - 77}, abstract = {The varied features of the earth{\textquoteright}s surface each reflect sunlight and other wavelengths of solar radiation in a highly specific way. This principle provides the foundation for the science of satellite based remote sensing. A vexing problem confronting remote sensing researchers, however, is that the reflected radiation observed from remote locations is significantly contaminated by atmospheric particles. These aerosols and molecules scatter and absorb the solar photons reflected by the surface in such a way that only part of the surface radiation can be detected by a sensor. The article discusses the removal of atmospheric effects due to scattering and absorption, ie., atmospheric correction. Atmospheric correction algorithms basically consist of two major steps. First, the optical characteristics of the atmosphere are estimated. Various quantities related to the atmospheric correction can then be computed by radiative transfer algorithms, given the atmospheric optical properties. Second, the remotely sensed imagery is corrected by inversion procedures that derive the surface reflectance. We focus on the second step, describing our work on improving the computational efficiency of the existing atmospheric correction algorithms. We discuss a known atmospheric correction algorithm and then introduce a substantially more efficient version which we have devised. We have also developed a parallel implementation of our algorithm}, keywords = {algorithms;reflectivity;remote, Atmospheric, based, computing;image, correction;atmospheric, effects;atmospheric, efficiency;inversion, enhancement;parallel, imagery;satellite, images;solar, implementation;reflected, particles;computational, photons;surface, procedures;parallel, radiation;atmospheric, radiation;remote, reflectance;atmospheric, remote, research;remotely, sensed, sensing, sensing;, sensing;satellite, techniques;geophysics}, isbn = {1070-9924}, doi = {10.1109/99.503316}, author = {Fallah-Adl,H. and JaJa, Joseph F. and Liang, S. and Townshend,J. and Kaufman,Y.J.} } @article {13555, title = {Feature Normalization for Video Indexing and Retrieval}, volume = {LAMP-TR-003,CFAR-TR-847,CS-TR-3732}, year = {1996}, month = {1996/11//}, institution = {University of Maryland, College Park}, abstract = {Fast and efficient storage, browsing, indexing, and retrieval of video is necessary for the development of various multimedia database applications. Given that video is typically stored efficiently in a compressed format, if we can analyze the compressed representation directly, we can avoid the costly overhead of decompressing and operating at the pixel level. Compressed domain parsing of video has been presented in earlier work where key frames are identified for shots, subshots, and scenes. In this paper, we describe key frame selection, feature extraction, indexing, and retrieval techniques that are directly applicable to MPEG-compressed video. We develop a frame-type independent representation of the various types of frames present in an MPEG video in which all frames can be considered equivalent. Features are derived from the available DCT, macroblock, and motion vector information and mapped to a low-dimensional space where they can be accessed using standard database techniques. The spatial information is used as primary index while the temporal information is used to enhance the robustness of the system during the retrieval process. The techniques presented enable fast archiving, indexing, and retrieval of video. Our operational prototype typically takes a fraction of a second to retrieve similar video scenes from our database, with over 95\&$\#$x0025; success.}, author = {Kobla,Vikrant and David Doermann and Lin,King-Ip (David) and Faloutsos,Christos} } @article {18703, title = {Identification of the Binding Site for Acidic Phospholipids on the PH Domain of Dynamin: Implications for Stimulation of GTPase Activity}, journal = {Journal of Molecular Biology}, volume = {255}, year = {1996}, month = {1996/01/12/}, pages = {14 - 21}, abstract = {It has recently been suggested that pleckstrin homology (PH) domains bind specifically to phospholipids, with phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) being most strongly bound. This observation suggests that PH domains may be responsible for membrane association of proteins in which they occur. Further, this membrane association may be regulated by enzymes that modify lipid head groups to which PH domains may bind. We have studied the binding of phospholipids to the PH domain of human dynamin, a 100 kDa GTPase that is involved in the initial stages of endocytosis. We describe a rapid method for screening PH domain/ligand interactions that gives precise binding constants. We confirm that PtdIns(4,5)P2can bind to dynamin PH domain, although not in an aggregated state. Using NMR spectroscopy, we have mapped a specific site on the surface of dynamin PH domain of which binding of gIns(1,4,5)P3(the head-group skeleton of PtdIns(4,5)P2) occurs. The relative affinity of acidic phospholipids for dynamin PH domain correlates with their ability to activate the GTPase of dynamin. We propose, therefore, that the interaction of these phospholipids with dynamin is likely to occurviathe PH domain. Given the fact that PH domains are often found in pro- teins associated with GTPase activity, or in guanine nucleotide exchange factors, we suggest that one role of PH domains may be to couple phosphatidylinositol signalling to GTP hydrolysis.}, keywords = {Fluorescence, ligand binding, NMR, PH domain, phospholipid}, isbn = {0022-2836}, doi = {10.1006/jmbi.1996.0002}, url = {http://www.sciencedirect.com/science/article/pii/S0022283696900029}, author = {Zheng,Jie and Cahill,Sean M. and Lemmon,Mark A. and Fushman, David and Schlessinger,Joseph and Cowburn,David} } @inbook {13005, title = {Inferring phylogenies from DNA sequence data: The effects of sampling}, booktitle = {New Uses for New PhylogeniesNew Uses for New Phylogenies}, year = {1996}, month = {1996///}, pages = {103 - 115}, publisher = {Oxford University Press}, organization = {Oxford University Press}, author = {Otto,S. P and Cummings, Michael P. and Wakeley,J.}, editor = {Harvey,PH and Leigh Brown,AJ and Maynard Smith,J and Nee,S} } @article {12785, title = {Modeling and verifying distributed systems using priorities: A case study}, journal = {Software - Concepts and Tools}, volume = {17}, year = {1996}, month = {1996///}, pages = {50 - 62}, author = {Cleaveland, Rance and Natarajan,V. and Sims,S. and Luettgen,G.} } @article {14568, title = {Positional sequencing by hybridization}, journal = {Computer applications in the biosciences : CABIOS}, volume = {12}, year = {1996}, month = {1996/02/01/}, pages = {19 - 24}, abstract = {Sequencing by hybridization (SBH) is a promising alternative to the classical DNA sequencing approaches. However, the resolving power of SBH is rather low: with 64kb sequencing chips, unknown DNA fragments only as long as 200 bp can be reconstructed in a single SBH experiment. To improve the resolving power of SBH, positional SBH (PSBH) has recently been suggested; this allows (with additional experimental work) approximate positions of every l-tuple in a target DNA fragment to be measured. We study the positional Eulerian path problem motivated by PSBH. The input to the positional eulerian path problem is an Eulerian graph G( V, E) in which every edge has an associated range of integers and the problem is to find an Eulerian path el, {\textellipsis}, e|E| in G such that the range of ei, contains i. We show that the positional Eulerian path problem is NP-complete even when the maximum out-degree (in-degree) of any vertex in the graph is 2. On a positive note we present polynomial algorithms to solve a special case of PSBH (bounded PSBH), where the range of the allowed positions for any edge is bounded by a constant (it corresponds to accurate experimental measurements of positions in PSBH). Moreover, if the positions of every l-tuple in an unknown DNA fragment of length n are measured with O(log n) error, then our algorithm runs in polynomial time. We also present an estimate of the resolving power of PSBH for a more realistic case when positions are measured with Θ(n) error.}, doi = {10.1093/bioinformatics/12.1.19}, url = {http://bioinformatics.oxfordjournals.org/content/12/1/19.abstract}, author = {Hannenhalli, Sridhar and Feldman,William and Lewis,Herbert F. and Skiena,Steven S. and Pevzner,Pavel A.} } @article {12824, title = {Priorities for modeling and verifying distributed systems}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {1996}, month = {1996///}, pages = {278 - 297}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Natarajan,V. and Sims,S.} } @article {12804, title = {A process algebra with distributed priorities}, journal = {CONCUR{\textquoteright}96: Concurrency Theory}, year = {1996}, month = {1996///}, pages = {34 - 49}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Natarajan,V.} } @book {12332, title = {Software synthesis from dataflow graphs}, year = {1996}, month = {1996///}, publisher = {Springer}, organization = {Springer}, author = {Bhattacharyya, Shuvra S. and Murthy,P. K and Lee,E. A} } @inbook {14272, title = {Video representations}, booktitle = {Recent Developments in Computer Vision}, series = {Lecture Notes in Computer Science}, volume = {1035}, year = {1996}, month = {1996///}, pages = {33 - 41}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, isbn = {978-3-540-60793-9}, url = {http://dx.doi.org/10.1007/3-540-60793-5_60}, author = {Bolle,Ruud and Aloimonos, J. and Ferm{\"u}ller, Cornelia}, editor = {Li,Stan and Mital,Dinesh and Teoh,Eam and Wang,Han} } @article {14406, title = {The COLLAGE/KHOROS link: Planning for image processing tasks}, journal = {Integrated Planning Applications}, year = {1995}, month = {1995///}, pages = {67 - 76}, author = {Lansky,A. and Friedman,M. and Getoor, Lise and Schmidler,S. and Short Jr,N.} } @book {13756, title = {Development of interlingual lexical conceptual structures with syntactic markers for machine translation}, year = {1995}, month = {1995///}, publisher = {University of Maryland}, organization = {University of Maryland}, abstract = {This document reports on research conducted at the University of Mary-land for the Korean/English Machine Translation (MT) project. Our pri- mary objective was to develop an interlingual representation based on lexical conceptual structure (LCS) and to examine the relation between this repre- sentation and a set of linguistically motivated semantic classes. We view the work of the past year as a critical step toward achieving our goal of building a generator: the classification of LCS{\textquoteright}s into a semantic hierarchy provides a systematic mapping between semantic knowledge about verbs and their surface syntactic structures. We have focused on several areas in support of our objectives: (1) inves- tigation of morphological structure including distinctions between Korean and English; (2) porting a fast, message-passing parser to Korean (and to the IBM PC); (3) study of free word order and development of the associ- ated processing algorithm; (4) investigation of the aspectual dimension as it impacts morphology, syntax, and lexical semantics; (5) investigation of the relation between semantic classes and syntactic structure; (6) develop- ment of theta-role and lexical-semantic templates through lexical acquisition techniques; (7) definition a mapping between KR concepts and interlingual representations; (8) formalization of the lexical conceptual structure }, author = {Dorr, Bonnie J and Lee,J. and Voss,C. and Suh,S.} } @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.} } @conference {14955, title = {Efficient Algorithms for Atmospheric Correction of Remotely Sensed Data}, booktitle = {Supercomputing, 1995. Proceedings of the IEEE/ACM SC95 Conference}, year = {1995}, month = {1995///}, pages = {12 - 12}, abstract = {Remotely sensed imagery has been used for developing and validating various studies regarding land cover dynamics. However, the large amounts of imagery collected by the satellites are largely contaminated by the effects of atmospheric particles. The objective of atmospheric correction is to retrieve the surface reflectance from remotely sensed imagery by removing the atmospheric effects. We introduce a number of computational techniques that lead to a substantial speedup of an atmospheric correction algorithm based on using look-up tables. Excluding I/O time, the previous known implementation processes one pixel at a time and requires about 2.63 seconds per pixel on a SPARC-10 machine, while our implementation is based on processing the whole image and takes about 4-20 microseconds per pixel on the same machine. We also develop a parallel version of our algorithm that is scalable in terms of both computation and I/O. Experimental results obtained show that a Thematic Mapper (TM) image (36 MB per band, 5 bands need to be corrected) can be handled in less than 4.3 minutes on a 32-node CM-5 machine, including I/O time.}, keywords = {Atmospheric, AVHRR;, computing;, correction;, high, I/O;, Parallel, performance, processing;, remote, scalable, sensing;, TM;}, doi = {10.1109/SUPERC.1995.242453}, author = {Fallah-Adl,H. and JaJa, Joseph F. and Liang,Shunlin and Kaufman,Y.J. and Townshend,J.} } @article {13762, title = {Efficient parsing for Korean and English: A parameterized message-passing approach}, journal = {Computational Linguistics}, volume = {21}, year = {1995}, month = {1995///}, pages = {255 - 263}, author = {Dorr, Bonnie J and Lee,J. and Lin,D. and Suh,S.} } @article {12384, title = {Generating compact code from dataflow specifications of multirate signal processing algorithms}, journal = {Circuits and Systems I: Fundamental Theory and Applications, IEEE Transactions on}, volume = {42}, year = {1995}, month = {1995///}, pages = {138 - 150}, author = {Bhattacharyya, Shuvra S. and Buck,J. T and Ha,S. and Lee,E. A} } @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 {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.} } @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 {14409, title = {Scope and abstraction: Two criteria for localized planning}, journal = {INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {14}, year = {1995}, month = {1995///}, pages = {1612 - 1619}, abstract = {Localization is a general-purpose representational technique for partitioning a problem intosubproblems. A localized problem-solver searches several smaller search spaces, one for each subproblem. Unlike most methods of partitioning, however, localization allows for subprob- lems that overlap i.e. multiple search spaces may be involved in constructing shared pieces of the overall plan. In this paper we focus on two criteria for forming localizations: scope and abstraction. We describe a method for automatically generating such localizations and provide empirical results that contrast their use in an o ce-building construction domain. }, author = {Lansky,A. L and Getoor, Lise} } @article {14786, title = {Techniques for performance measurement of parallel programs}, journal = {Parallel computers: theory and practice}, year = {1995}, month = {1995///}, pages = {225 - 240}, author = {Hollingsworth, Jeffrey K and Lumpp, J. E and Miller, B. P} } @inbook {14644, title = {Towards a computational theory of genome rearrangements}, booktitle = {Computer Science TodayComputer Science Today}, series = {Lecture Notes in Computer Science}, volume = {1000}, year = {1995}, month = {1995///}, pages = {184 - 202}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Analysis of genome rearrangements in molecular biology started in the late 1930{\textquoteright}s, when Dobzhansky and Sturtevant published a milestone paper presenting a rearrangement scenario with 17 inversions for the species of Drosophila. However, until recently there were no computer science results allowing a biologist to analyze genome rearrangements. The paper describes combinatorial problems motivated by genome rearrangements, surveys recently developed algorithms for genomic sequence comparison and presents applications of these algorithms to analyze rearrangements in herpes viruses, plant organelles, and mammalian chromosomes.}, isbn = {978-3-540-60105-0}, url = {http://dx.doi.org/10.1007/BFb0015244}, author = {Hannenhalli, Sridhar and Pevzner,Pavel}, editor = {van Leeuwen,Jan} } @article {14153, title = {Use of linear algebra kernels to build an efficient finite element solver}, journal = {Parallel Computing}, volume = {21}, year = {1995}, month = {1995/01//}, pages = {161 - 173}, abstract = {For scientific codes to achieve good performance on computers with hierarchical memories, it is necessary that the ratio of memory references to arithmetic operations be low. In this paper, we show that Level 3 BLAS linear algebra kernels can be used to satisfy this requirement to produce an efficient implementation of a parallel finite element solver on a shared memory parallel computer with a fast cache memory.}, keywords = {Cache memory, finite element, hp-version, Level 3 BLAS, Parallel algorithm, shared memory multiprocessor}, isbn = {0167-8191}, doi = {16/0167-8191(94)00030-E}, url = {http://www.sciencedirect.com/science/article/pii/016781919400030E}, author = {Elman, Howard and Lee,Dennis K. -Y.} } @article {15043, title = {Using synthetic perturbations and statistical screening to assay shared-memory programs}, journal = {Information processing letters}, volume = {54}, year = {1995}, month = {1995///}, pages = {147 - 153}, author = {Snelick,R. and JaJa, Joseph F. and Kacker,R. and Lyon,G.} } @article {18964, title = {An Atlas of Drosophila Genes: Sequences and Molecular Features}, journal = {Journal of Heredity}, volume = {85}, year = {1994}, month = {1994///}, pages = {495 - 496}, author = {Maroni,G. and Mount, Stephen M. and Cavener,DR and Cavener,BA and Sharp,PM and Lloyd,AT and Schaeffer,SW} } @conference {16987, title = {Beyond accuracy, reliability, and efficiency: criteria for a good computer system}, booktitle = {Conference companion on Human factors in computing systems}, series = {CHI {\textquoteright}94}, year = {1994}, month = {1994///}, pages = {195 - 198}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-651-4}, doi = {10.1145/259963.260253}, url = {http://doi.acm.org/10.1145/259963.260253}, author = {Friedman,Batya and Levenson,Nancy and Shneiderman, Ben and Suchman,Lucy and Winograd,Terry} } @book {19353, title = {Fault tolerant system design}, year = {1994}, month = {1994}, pages = {440}, publisher = {McGraw-Hill}, organization = {McGraw-Hill}, abstract = {This book presents a comprehensive exploration of the practical issues, tested techniques, and accepted theory for developing fault tolerant systems. It is a ready reference to work already done in the field, with new approaches devised by the authors.}, keywords = {Computers / Intelligence (AI) \& Semantics, Computers / Programming Languages / General, Computers / Software Development \& Engineering / Systems Analysis \& Design, Reference / General, Technology \& Engineering / Engineering (General)}, isbn = {9780070375154}, author = {Levi,Shem-Tov and Agrawala, Ashok K.} } @article {18319, title = {Human Emotion Recognition From Motion Using A Radial Basis Function Network Architecture}, journal = {University Of Maryland}, year = {1994}, month = {1994///}, author = {Mark,R. and Yaser,Y. and Larry,D.} } @article {12380, title = {Looped schedules for dataflow descriptions of multirate signal processing algorithms}, journal = {Formal Methods in System Design}, volume = {5}, year = {1994}, month = {1994///}, pages = {183 - 205}, author = {Bhattacharyya, Shuvra S. and Lee,E. A} } @article {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 {13711, title = {A paradigm for non-head-driven parsing: Parameterized message-passing}, journal = {Proceedings of the International Conference on New Methods in Language Processing, Manchester, UK}, year = {1994}, month = {1994///}, author = {Dorr, Bonnie J and Lin,D. and Lee,J. and Suh,S.} } @article {18055, title = {Pattern matching in a digitized image}, journal = {Algorithmica}, volume = {12}, year = {1994}, month = {1994///}, pages = {375 - 408}, author = {Landau,G. M and Vishkin, Uzi} } @proceedings {15797, title = {Regularization by Truncated Total Least Squares}, year = {1994}, month = {1994///}, pages = {250 - 254}, publisher = {SIAM Press}, address = {Philadelphia}, author = {Fierro,Richardo and Golub, Gene H. and Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.}, editor = {Lewis,J.G.} } @inbook {15798, title = {Regularization of Ill-Posed Problems in Image Restoration}, booktitle = {Proceedings of the Fifth SIAM Conference on Applied Linear AlgebraProceedings of the Fifth SIAM Conference on Applied Linear Algebra}, year = {1994}, month = {1994///}, pages = {102 - 105}, publisher = {SIAM Press}, organization = {SIAM Press}, address = {Philadelphia}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Lewis,J.G.} } @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.} } @inbook {15809, title = {Some Themes in Gene H.Golub{\textquoteright}s Work on Iterative Methods}, booktitle = {Recent Advances in Iterative MethodsRecent Advances in Iterative Methods}, volume = {60}, year = {1994}, month = {1994///}, pages = {1 - 11}, publisher = {Springer-Verlag IMA Volumes in Mathematics and Its Applications}, organization = {Springer-Verlag IMA Volumes in Mathematics and Its Applications}, address = {New York}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Golub, Gene H. and Greenbaum,Anne and Luskin,Mitchell} } @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.} } @article {15828, title = {URV ESPRIT for tracking time-varying signals}, journal = {Signal Processing, IEEE Transactions on}, volume = {42}, year = {1994}, month = {1994/12//}, pages = {3441 - 3448}, abstract = {ESPRIT is an algorithm for determining the fixed directions of arrival of a set of narrowband signals at an array of sensors. Unfortunately, its computational burden makes it unsuitable for real time processing of signals with time-varying directions of arrival. The authors develop a new implementation of ESPRIT that has potential for real time processing. It is based on a rank-revealing URV decomposition, rather than the eigendecomposition or singular value decomposition used in previous ESPRIT algorithms. The authors demonstrate its performance on simulated data representing both constant and time-varying signals. They find that the URV-based ESPRIT algorithm is effective for estimating time-varying directions-of-arrival at considerable computational savings over the SVD-based algorithm}, keywords = {arrival;narrowband, decomposition;real, directions, ESPRIT;fixed, estimation;real-time, of, processing;time-varying, signals;performance;rank-revealing, signals;tracking;direction-of-arrival, systems;time-varying, systems;tracking;, TIME, URV}, isbn = {1053-587X}, doi = {10.1109/78.340778}, author = {Liu,K. J.R and O{\textquoteright}Leary, Dianne P. and Stewart, G.W. and Wu,Y.-J.J.} } @conference {15713, title = {An adaptive ESPRIT based on URV decomposition}, booktitle = {Acoustics, Speech, and Signal Processing, 1993. ICASSP-93., 1993 IEEE International Conference on}, volume = {4}, year = {1993}, month = {1993/04//}, pages = {37 -40 vol.4 - 37 -40 vol.4}, abstract = {ESPRIT is an algorithm for determining the fixed directions of arrival of a set of narrowband signals at an array of sensors. Its computational burden makes it unsuitable for real-time processing of signals with time-varying directions of arrival. The authors develop a new implementation of ESPRIT that has potential for real-time processing. It is based on a rank-revealing URV decomposition, rather than the eigendecomposition or singular value decomposition (SVD) used in previous ESPRIT algorithms. Its performance is demonstrated on simulated data representing both constant and time-varying signals. It is shown that the URV-based ESPRIT algorithm is effective for estimating time-varying directions-of-arrival at considerable computational savings over the SVD-based algorithm.<>}, keywords = {algorithm;array, complexity;parameter, decomposition;real-time, ESPRIT, estimation;real-time, filters;array, of, processing;adaptive, processing;computational, savings;performance;rank-revealing, sensors;computational, signal, systems;, systems;time-varying, URV, URV-based}, doi = {10.1109/ICASSP.1993.319588}, author = {Liu,K. J.R and O{\textquoteright}Leary, Dianne P. and Stewart, G.W. and Wu,Y.-J.J.} } @article {16956, title = {Alpha Slider: Searching Textual Lists with Sliders}, journal = {Institute for Systems Research Technical Reports}, year = {1993}, month = {1993///}, abstract = {AlphaSlider is a query interface that uses a direct manipulation slider to select words, phrases, or names from an existing list. This paper introduces a prototype of AlphaSlider, describes the design issues, reports on an experimental evaluation, and offers directions for further research. The experiment tested 24 subjects selecting items from lists of 40, 80, 160, and 320 entries. Mean selection times only doubled with the 8-fold increase in list length. Users quickly accommodated to this selection method.}, keywords = {direct manipulation, Human-computer interaction, keyboard data entry, sliders, Systems Integration, touchscreen}, url = {http://drum.lib.umd.edu/handle/1903/5397}, author = {Osada,M. and Liao,Holmes and Shneiderman, Ben} } @article {16957, title = {Alphaslider: Development and Evaluation of Text Retrieval Methods Using Sliders}, journal = {Ninth Symposium on Human Interface}, year = {1993}, month = {1993///}, pages = {91 - 94}, abstract = {AlphaSlider is a query interface that uses a direct manipulation slider to select words, phrases, or names from an existing list. This paper introduces a prototype of AlphaSlider, describes the design issues, reports on an experimental evaluation, and offers directions for further research. The experiment tested 24 subjects selecting items from lists of 40, 80, 160, and 320 entries. Mean selection times only doubled with the 8-fold increase in list length. Users quickly accommodated to this selection method.}, author = {Osada,M. and Liao,H. and Shneiderman, Ben} } @conference {17000, title = {Browsing Unix directories with dynamic queries: An analytical and experimental evaluation}, booktitle = {Proc. Ninth Japanese Symp. Human Interface}, year = {1993}, month = {1993///}, pages = {95 - 98}, abstract = {We designed, implemented, and evaluated an innovative concept for dynamic queries which involves the direct manipulation of small databases. Our domain was directories in a Unix file system. Dynamic queries allow users to formulate queries and explore the databases with graphical widgets, such as sliders and buttons, without requiring them to have any knowledge about the underlying structure of the database query languages, or command language syntax. Three interfaces for presenting directories were developed and tested with eighteen subjects in a within-subject design. The results of the formative evaluation yielded some useful guidelines for software designers.}, author = {Liao,H. and Osada,M. and Shneiderman, Ben} } @article {17003, title = {Building HCI partnerships and infrastructure}, journal = {Behaviour \& Information Technology}, volume = {12}, year = {1993}, month = {1993///}, pages = {130 - 135}, abstract = {As policymakers and technology planners respond to the growing activity in human?computer interaction, a broad perspective may be helpful. This article offers a top-down view of current activities and suggests opportunities and challenges for the continued growth of HCI. Partnerships among universities, corporations, government agencies, and professional societies are proposed. Infrastructure needs to support this new discipline are outlined.Abstract As policymakers and technology planners respond to the growing activity in human?computer interaction, a broad perspective may be helpful. This article offers a top-down view of current activities and suggests opportunities and challenges for the continued growth of HCI. Partnerships among universities, corporations, government agencies, and professional societies are proposed. Infrastructure needs to support this new discipline are outlined. }, isbn = {0144-929X}, doi = {10.1080/01449299308924373}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449299308924373}, author = {Shneiderman, Ben and LEWIS,CLAYTON} } @article {17004, title = {Building Partnerships and Infrastructure}, journal = {Communications of the ACM}, volume = {32}, year = {1993}, month = {1993///}, pages = {9 - 23}, abstract = {As policymakers and technology planners respond to the growingactivity in human-computer interaction, a broad perspective may be helpful. This article offers a top-down view of current activities and suggests opportunities and challenges for the continued growth of HCI. Partnerships among universities, corporations, government agencies, and professional societies are proposed. Infrastructure needs to support this new discipline are outlined. }, author = {Shneiderman, Ben and Lewis,C.} } @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} } @conference {16219, title = {Facilitating Data Exploration: Dynamic Queries On A Health Statistics Map}, booktitle = {Proc. of the Government Statistics Section, Annual Meeting of the American Statistical Assoc. Conf. Proc, pg}, year = {1993}, month = {1993///}, pages = {18 - 23}, abstract = {: Users with no specialized computer training are often discouraged by the complex syntax of query languages and the output of long tables of alphanumerical values. The Human-Computer Interaction Laboratory has recently developed the concept of dynamic queries which allows user control of animated visual displays of information. Experiments with our first applications have shown that dynamic queries can help reveal trends or global properties as well as assist users in answering specific questions. We present a new application developed with the National Center for Health Statistics and running on a simple PC. A thematic map of the United States is animated by adjusting sliders displayed on the side of the map. A time slider illustrates time trends. The other sliders control the filtering out of areas of the map according to parameters such as demographics. Detailed data about a particular area is obtained by clicking directly on its location on the map. We have received encouraging fe...}, author = {Plaisant, Catherine and Laboratory,Human-computer Interaction} } @article {12365, title = {Scheduling synchronous dataflow graphs for efficient looping}, journal = {The Journal of VLSI Signal Processing}, volume = {6}, year = {1993}, month = {1993///}, pages = {271 - 288}, author = {Bhattacharyya, Shuvra S. and Lee,E. A} } @article {18997, title = {Species-specific signals for the splicing of a short Drosophila intron in vitro.}, journal = {Molecular and Cellular BiologyMol. Cell. Biol.}, volume = {13}, year = {1993}, month = {1993/02/01/}, pages = {1104 - 1118}, abstract = {The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3{\textquoteright} splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5{\textquoteright} splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species.}, isbn = {0270-7306, 1098-5549}, doi = {10.1128/MCB.13.2.1104}, url = {http://mcb.asm.org/content/13/2/1104}, author = {Guo,M. and Lo,P. C. and Mount, Stephen M.} } @conference {18065, title = {Two dimensional pattern matching in a digitized image}, booktitle = {Combinatorial Pattern Matching}, year = {1993}, month = {1993///}, pages = {134 - 151}, author = {Landau,G. and Vishkin, Uzi} } @conference {15044, title = {Using Synthetic-Perturbation Techniques for Tuning Shared Memory Programs}, booktitle = {Parallel Processing, 1993. ICPP 1993. International Conference on}, volume = {2}, year = {1993}, month = {1993/08//}, pages = {2 - 10}, abstract = {The Synthetic-Perturbation Tuning (SPT) methodology is base d on compirical approach that introduces artificial delays into the MIMD program and captures the effects of such delays by using the modrn branch statistics called design of experiments.}, doi = {10.1109/ICPP.1993.184}, author = {Snelick,Robert and JaJa, Joseph F. and Kacker,Raghu and Lyon,Gordon} } @conference {16976, title = {Anthropomorphism: from Eliza to Terminator 2}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, series = {CHI {\textquoteright}92}, year = {1992}, month = {1992///}, pages = {67 - 70}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-513-5}, doi = {10.1145/142750.142760}, url = {http://doi.acm.org/10.1145/142750.142760}, author = {Don,Abbe and Brennan,Susan and Laurel,Brenda and Shneiderman, Ben} } @article {13734, title = {Building a lexicon for machine translation: use of corpora for aspectual classification of verbs}, year = {1992}, month = {1992///}, institution = {University of Maryland at College Park}, address = {College Park, MD, USA}, author = {Dorr, Bonnie J and Lee,Ki} } @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 {16231, title = {The effects of time delays on a telepathology user interface.}, journal = {Proceedings of the Annual Symposium on Computer Application in Medical CareProc Annu Symp Comput Appl Med Care}, year = {1992}, month = {1992///}, pages = {256 - 260}, abstract = {Telepathology enables a pathologist to examine physically distant tissue samples by microscope operation over a communication link. Communication links can impose time delays which cause difficulties in controlling the remote device. Such difficulties were found in a microscope teleoperation system. Since the user interface is critical to pathologist{\textquoteright}s acceptance of telepathology, we redesigned the user interface for this system, built two different versions (a keypad whose movement commands operated by specifying a start command followed by a stop command and a trackball interface whose movement commands were incremental and directly proportional to the rotation of the trackball). We then conducted a pilot study to determine the effect of time delays on the new user interfaces. In our experiment, the keypad was the faster interface when the time delay is short. There was no evidence to favor either the keypad or trackball when the time delay was longer. Inexperienced participants benefitted by allowing them to move long distances over the microscope slide by dragging the field-of-view indicator on the touchscreen control panel. The experiment suggests that changes could be made to the trackball interface which would improve its performance.}, isbn = {0195-4210}, author = {Carr,D. and Hasegawa,H. and Lemmon,D. and Plaisant, Catherine} } @article {18075, title = {Efficient pattern matching with scaling}, journal = {Journal of Algorithms}, volume = {13}, year = {1992}, month = {1992///}, pages = {2 - 32}, author = {Amir, A. and Landau,G. M and Vishkin, Uzi} } @book {16924, title = {A formative evaluation of three interfaces for browsing directories using dynamic queries}, year = {1992}, month = {1992///}, publisher = {University of Maryland, Center for Automation Research, Computer Vision Laboratory}, organization = {University of Maryland, Center for Automation Research, Computer Vision Laboratory}, author = {Liao,H.S. and Osada,M. and Shneiderman, Ben} } @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 {15050, title = {VLSI Implementation of Real-Time Parallel DCT/DST Lattice Structures for Video}, volume = {ISR-TR-1992-34}, year = {1992}, month = {1992///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The alternate use [1] of the discrete cosine transform (DCT) and the discrete sine transform (DST) can achieve a higher data compression rate and less block effect in image processing. A parallel lattice structure that can dually generate the 1-D DCT and DST is proposed. We also develop a fully-pipelined 2-D DCT lattice architecture that consists of two 1-D DCT/DST arrays without transposition. Both architectures are ideally suited for VLSI implementation because they are modular, regular, and have only local interconnections. the VLSI implementation of the lattice module using the distributed arithmetic approach is described. This realization of the lattice module using 2 um CMOS technology can achieve an 80Mb/s data rate.}, keywords = {Parallel architectures, Signal processing, Systems Integration, VLSI architectures}, url = {http://drum.lib.umd.edu/handle/1903/5216}, author = {Chiu,Ching-Te and Kolagotla,Ravi K. and Liu,K. J. Ray and JaJa, Joseph F.} } @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 {11929, title = {Computer based systems engineering workshop}, journal = {Software Engineering Education}, year = {1991}, month = {1991///}, pages = {149 - 163}, abstract = {Modern computer based systems are complex multi-systems consisting of many connected individual subsystems; each one of them is typically also a multicomputer system. The subsystems in a multi-system can be either geographically distributed or locally connected systems. Typical examples of computer based systems are medical systems, process control systems, communications systems, weapon systems and large information systems.The development of these complex systems requires the establishment of a new engineering discipline in its own right, Computer Based Systems Engineering {\textemdash} CBSE. The definition of the discipline, its current and future practice and the ways to establish and promote it were discussed in an international IEEE workshop held in Neve-Ilan, Israel in May 1990. The major conclusion of the workshop was that CBSE should be established as a new field in its own right. To achieve this goal, the workshop participants recommended that the IEEE Computer Society shall set up a task force for the promotion of the field, the establishment of CBSE Institutes and the development of the educational framework of CBSE. The paper describes the major findings of the workshop that led to these conclusions and recommendations. }, author = {Lavi,J. and Agrawala, Ashok K. and Buhr,R. and Jackson,K. and Jackson,M. and Lang,B.} } @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.} } @article {17510, title = {Window control strategies for hypertext traversal: An empirical study}, journal = {Proc. 29th Annual ACM DC Technical Symposium}, year = {1991}, month = {1991///}, abstract = {Nowadays, larger and higher resolution screens supporting multiple windows are widely available. They are often used to traverse hypertext databases for fact retrieval, education or casual browsing. This paper describes a study comparing two methods of window control strategies for article placement in four, equal sized and tiled windows (By tiled we mean non-overlapping, non-movable and non-resizable windows, which together cover the entire screen.) The first placement strategy - Automatic Panning (A P) - was controlled by the system software and the second placement strategy - User Controlled Placement (UCP) - trasferred control to the users. The task required subjects to answer questions about the content of a hypertext. Statistical analysis shows that subjective preference was significantly higher and amount of backtracking was significantly lower for the user controlled placement. Speed differences did not prove to be significant, although there was consistent tendency favoring the automatic pa nning strategy.}, author = {Lifshitz,J. and Shneiderman, Ben} } @article {18083, title = {[31] Fast alignment of DNA and protein sequences}, journal = {Methods in Enzymology}, volume = {183}, year = {1990}, month = {1990///}, pages = {487 - 502}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @article {18972, title = {Drosophila melanogaster genes for U1 snRNA variants and their expression during development}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {18}, year = {1990}, month = {1990/01/01/}, pages = {6971 - 6979}, abstract = {We have cloned and characterized a complete set of seven U1-related sequences from Drosophila melanogaster. These sequences are located at the three cytogenetic loci 21D, 82E, and 95C. Three of these sequences have been previously studied: one U1 gene at 21D which encodes the prototype U1 sequence (U1a), one U1 gene at 82E which encodes a U1 variant with a single nucleotide substitution (1Mb), and a pseudogene at 82E. The four previously uncharacterized genes are another U1b gene at 82E, two additional U1 a genes at 95C, and a U1 gene at 95C which encodes a new variant (U1c) with a distinct single nucleotide change relative to U1a. Three blocks of 5' flanking sequence similarity are common to all six full length genes. Using specific primer extension assays, we have observed that the 1Mb RNA is expressed in Drosophila Kc cells and is associated with snRNP proteins, suggesting that the U1b-contalning snRNP particles are able to participate in the process of premRNA splicing. We have also examined the expression throughout Drosophila development of the two U1 variants relative to the prototype sequence. The U1c variant is undetectable by our methods, while the U1b variant exhibits a primarily embryonic pattern reminiscent of the expression of certain U1 variants in sea urchin, Xenopus, and mouse.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/18.23.6971}, url = {http://nar.oxfordjournals.org/content/18/23/6971}, author = {Lo,Partick C. H. and Mount, Stephen M.} } @article {18084, title = {Fast alignment of DNA and protein sequences}, journal = {Methods in enzymology}, volume = {183}, year = {1990}, month = {1990///}, pages = {487 - 502}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @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} } @article {14791, title = {IPS-2: the second generation of a parallel program measurement system}, journal = {IEEE Transactions on Parallel and Distributed Systems}, volume = {1}, year = {1990}, month = {1990/04//}, pages = {206 - 217}, abstract = {IPS, a performance measurement system for parallel and distributed programs, is currently running on its second implementation. IPS{\textquoteright}s model of parallel programs uses knowledge about the semantics of a program{\textquoteright}s structure to provide two important features. First, IPS provides a large amount of performance data about the execution of a parallel program, and this information is organized so that access to it is easy and intuitive. Secondly, IPS provides performance analysis techniques that help to guide the programmer automatically to the location of program bottlenecks. The first implementation of IPS was a testbed for the basic design concepts, providing experience with a hierarchical program and measurement model, interactive program analysis, and automatic guidance techniques. It was built on the Charlotte distributed operating system. The second implementation, IPS-2, extends the basic system with new instrumentation techniques, an interactive and graphical user interface, and new automatic guidance analysis techniques. This implementation runs on 4.3BSD UNIX systems, on the VAX, DECstation, Sun 4, and Sequent Symmetry multiprocessor}, keywords = {4.3BSD UNIX systems, automatic guidance techniques, Automatic testing, Charlotte distributed operating system, CPA, DECstation, design concepts, distributed programs, graphical user interface, Graphical user interfaces, Instruments, interactive program analysis, IPS-2, measurement, message systems, network operating systems, Operating systems, parallel program measurement system, parallel programming, parallel programs, Performance analysis, performance analysis techniques, performance evaluation, performance measurement system, Power system modeling, program bottlenecks, program diagnostics, Programming profession, semantics, Sequent Symmetry multiprocessor, shared-memory systems, software tools, Springs, Sun, Sun 4, Unix, VAX}, isbn = {1045-9219}, doi = {10.1109/71.80132}, author = {Miller, B. P and Clark, M. and Hollingsworth, Jeffrey K and Kierstead, S. and Lim,S. -S and Torzewski, T.} } @article {19001, title = {Structure and expression of the Drosophila melanogaster gene for the U1 small nuclear ribonucleoprotein particle 70K protein.}, journal = {Molecular and Cellular BiologyMol. Cell. Biol.}, volume = {10}, year = {1990}, month = {1990/06/01/}, pages = {2492 - 2502}, abstract = {A genomic clone encoding the Drosophila U1 small nuclear ribonucleoprotein particle 70K protein was isolated by hybridization with a human U1 small nuclear ribonucleoprotein particle 70K protein cDNA. Southern blot and in situ hybridizations showed that this U1 70K gene is unique in the Drosophila genome, residing at cytological position 27D1,2. Polyadenylated transcripts of 1.9 and 3.1 kilobases were observed. While the 1.9-kilobase mRNA is always more abundant, the ratio of these two transcripts is developmentally regulated. Analysis of cDNA and genomic sequences indicated that these two RNAs encode an identical protein with a predicted molecular weight of 52,879. Comparison of the U1 70K proteins predicted from Drosophila, human, and Xenopus cDNAs revealed 68\% amino acid identity in the most amino-terminal 214 amino acids, which include a sequence motif common to many proteins which bind RNA. The carboxy-terminal half is less well conserved but is highly charged and contains distinctive arginine-rich regions in all three species. These arginine-rich regions contain stretches of arginine-serine dipeptides like those found in transformer, transformer-2, and suppressor-of-white-apricot proteins, all of which have been identified as regulators of mRNA splicing in Drosophila melanogaster.}, isbn = {0270-7306, 1098-5549}, doi = {10.1128/MCB.10.6.2492}, url = {http://mcb.asm.org/content/10/6/2492}, author = {Mancebo,R. and Lo,P. C. and Mount, Stephen M.} } @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} } @article {18085, title = {Fast parallel and serial approximate string matching* 1}, journal = {Journal of Algorithms}, volume = {10}, year = {1989}, month = {1989///}, pages = {157 - 169}, author = {Landau,G. M and Vishkin, Uzi} } @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 {12344, title = {Gabriel: A design environment for DSP}, journal = {Acoustics, Speech and Signal Processing, IEEE Transactions on}, volume = {37}, year = {1989}, month = {1989///}, pages = {1751 - 1762}, author = {Lee,E. A and Ho,W. H and Goei,E. E and Bier,J. C and Bhattacharyya, Shuvra S.} } @article {18092, title = {Fast string matching with k differences.}, journal = {J. COMP. SYST. SCI.}, volume = {37}, year = {1988}, month = {1988///}, pages = {63 - 78}, author = {Landau,G. M and Vishkin, Uzi} } @article {18093, title = {Fast string matching with k differences* 1,* 2}, journal = {Journal of Computer and System Sciences}, volume = {37}, year = {1988}, month = {1988///}, pages = {63 - 78}, author = {Landau,G. M and Vishkin, Uzi} } @article {18091, title = {Locating alignments with k differences for nucleotide and amino acid sequences}, journal = {Computer applications in the biosciences: CABIOS}, volume = {4}, year = {1988}, month = {1988///}, pages = {19 - 19}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @article {18098, title = {Parallel construction of a suffix tree with applications}, journal = {Algorithmica}, volume = {3}, year = {1988}, month = {1988///}, pages = {347 - 365}, author = {Apostolico,A. and Iliopoulos,C. and Landau,G. M and Schieber,B. and Vishkin, Uzi} } @article {18101, title = {An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences*}, journal = {Journal of theoretical biology}, volume = {126}, year = {1987}, month = {1987///}, pages = {483 - 490}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @article {16965, title = {An evaluation of jump-ahead techniques in menu selection}, journal = {Behaviour \& Information Technology}, volume = {6}, year = {1987}, month = {1987///}, pages = {97 - 108}, abstract = {Menu selection systems provide a means of selecting operations and retrieving information which requires little training and reduces the need for memorizing complex command sequences. However, a major disadvantage of many menu selection systems is that experienced users cannot traverse the menu tree significantly faster than novices. A common solution to this problem is to provide the menu selection system with a jump-ahead capability.The purpose of this research was to evaluate two jump-ahead methods (type-ahead and direct-access). In the type-ahead method the user anticipates a selection on each of several successive menus and enters as many selections at one time as desired. In the direct-access method, each menu frame is assigned a unique name which the user must enter to locate it. Thirty-two students were given training on an information retrieval system for college course information and were required to learn the two jump-ahead methods in a counterbalanced design. The direct-access method resulted in fewer traversals to learn the system, lower error rates, and reduced learning time. The subjective impressions, obtained from post-experiment questionnaires and oral comments, indicated that the direct-access jump-ahead method was also preferred in a frequently used menu selection system. }, isbn = {0144-929X}, doi = {10.1080/01449298708901820}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449298708901820}, author = {Laverson,Alan and Norman,Kent and Shneiderman, Ben} } @article {18103, title = {Parallel construction of a suffix tree}, journal = {Automata, Languages and Programming}, year = {1987}, month = {1987///}, pages = {314 - 325}, author = {Landau,G. and Schieber,B. and Vishkin, Uzi} } @article {17511, title = {Window control strategies for on-line text traversal}, journal = {Department of Computer Science and Human Computer Interaction Laboratory, University of Maryland, College Park, MD (correspondence with B. Schneiderman)}, year = {1987}, month = {1987///}, abstract = {Larger and higher resolution screens that support multiple windows are now widely available. They are often used to traverse hypertext databases for fact retrieval, education or casual browsing. This paper introduces window control strategies that we implemented, describes their cognitive complexity, and characterizes the tasks that users might encounter. An infomal usage by dozens of visitors and a usability test with four subjects performing information search tasks revealed the limitations of several strategies and guided us to select user control of article placement in a tiled non-overlapping multiple window display.}, author = {Lifshitz,K. and Shneiderman, Ben} } @article {18108, title = {Efficient Parallel and Serial String Matching}, journal = {Computer Science Department Technical Report}, volume = {221}, year = {1986}, month = {1986///}, author = {Landau,G. M and Vishkin, Uzi} } @article {18107, title = {An efficient string matching algorithm with k differences for nudeotide and amino acid sequences}, journal = {Nucleic acids research}, volume = {14}, year = {1986}, month = {1986///}, pages = {31 - 31}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @article {18109, title = {Efficient string matching with k mismatches}, journal = {Theoretical Computer Science}, volume = {43}, year = {1986}, month = {1986///}, pages = {239 - 249}, author = {Landau,G. M and Vishkin, Uzi} } @conference {18110, title = {Introducing efficient parallelism into approximate string matching and a new serial algorithm}, booktitle = {Proceedings of the eighteenth annual ACM symposium on Theory of computing}, year = {1986}, month = {1986///}, pages = {220 - 230}, author = {Landau,G. M and Vishkin, Uzi} } @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 {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.} } @conference {18121, title = {Efficient string matching in the presence of errors}, booktitle = {Foundations of Computer Science, 1985., 26th Annual Symposium on}, year = {1985}, month = {1985///}, pages = {126 - 136}, author = {Landau,G. M and Vishkin, Uzi} } @article {16968, title = {An experimental comparison of tabular and graphic data presentation}, journal = {International Journal of Man-Machine Studies}, volume = {20}, year = {1984}, month = {1984/06//}, pages = {545 - 566}, abstract = {We present the results of our experiment designed to test the hypothesis that more usable information can be conveyed using a combination of graphical and tabular data then by using either form alone. Our independent variables were memory (recall and non-recall) and form (tables, graphs, or both). Comprehension was measured with a multiple choice exam consisting of three types of questions (retrieve, compare, or compare/calculate answers). Both non-recall and tabular treatments significantly increased comprehension. Combinations of graphs and tables produced slower but more accurate performance. An executive should use the form with which he/she is most familiar and comfortable.}, isbn = {0020-7373}, doi = {10.1016/S0020-7373(84)80029-2}, url = {http://www.sciencedirect.com/science/article/pii/S0020737384800292}, author = {Powers,Matthew and Lashley,Conda and Sanchez,Pamela and Shneiderman, Ben} } @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 {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 {19002, title = {Structure and function of small ribonucleoproteins from eukaryotic cells}, journal = {Princess Takamatsu symposiaInt. Symp. Princess Takamatsu Cancer Res. Fund}, volume = {12}, year = {1982}, month = {1982///}, pages = {101 - 107}, abstract = {Autoantibodies from patients with systemic lupus erythematosus and other related diseases have been used to identify and study small RNA-protein complexes from mammalian cells. Properties of three previously described and several new classes of small ribonucleoproteins (RNPs) are reviewed. The sequence of Drosophila U1 RNA reveals that the region proposed to pair with 5{\textquoteright} splice junctions is conserved, while that proposed to interact with 3{\textquoteright} junctions diverges; this forces some revision of the model for U1 small nuclear (sn)RNP participation in hnRNA splicing. Further characterization of the Ro and La small RNPs has shown that the Ro small cytoplasmic (sc)RNPs are a subclass of La RNPs. Both tRNA and 5S rRNA precursors are at least transiently associated with the La protein. This raises the possibility that the La protein may be an RNA polymerase III transcription factor.}, keywords = {Antigen-Antibody Complex, Autoantibodies, HUMANS, Lupus Erythematosus, Systemic, Nucleoproteins, Ribonucleoproteins, RNA Polymerase III, Transcription, Genetic}, url = {http://www.ncbi.nlm.nih.gov/pubmed/7166547}, author = {Steitz,J. A. and Berg,C and Gottlieb,E. and Hardin,J A and Hashimoto,C and Hendrick,J P and Hinterberger,M. and Krikeles,M and Lerner,M R and Mount, Stephen M.} } @article {18397, title = {Implementation of language enhancements}, journal = {Computer Languages}, volume = {6}, year = {1981}, month = {1981///}, pages = {139 - 153}, abstract = {Data abstractions have been proposed as a means to enhance program modularity. The implementation of such new features to an existing language is typically handled by either rewriting large portions of an existing compiler or by using a preprocessor to translate the extensions into the standard language. The first technique is expensive to implement while the latter is usually slow and clumsy to use. In this paper a data abstraction addition to PL 1 is described and a hybrid implementation is given. A minimal set of primitive features are added to the compiler and the other extensions are added via an internal macro processor that expands the new syntax into the existing language.}, keywords = {Compiler design, Data abstraction, Language extensions, specifications}, isbn = {0096-0551}, doi = {10.1016/0096-0551(81)90026-6}, url = {http://www.sciencedirect.com/science/article/pii/0096055181900266}, author = {Zelkowitz, Marvin V and Lyle,James R.} } @article {18967, title = {Are snRNPs involved in splicing?}, journal = {Nature}, volume = {283}, year = {1980}, month = {1980/01/10/}, pages = {220 - 224}, abstract = {Discrete, stable small RNA molecules are found in the nuclei of cells from a wide variety of eukaryotic organisms. Many of these small nuclear RNA (snRNA) species, which range in size from about 90 to 220 nucleotides, have been well-characterised biochemically, and some sequenced. However, their function has remained obscure. The most abundant snRNA species exist as a closely related set of RNA{\textendash}protein complexes called small nuclear ribonucleoproteins (snRNPs). snRNPs are the antigens recognised by antibodies from some patients with lupus erythematosus (LE), an autoimmune rheumatic disease. Anti-RNP antibodies from lupus sera selectively precipitate snRNP species containing Ula7 and Ulb9 RNAs from mouse Ehrlich ascites cell nuclei, whereas anti-Sm antibodies bind these snRNPs and four others containing U2, U4, US and U6 RNAs. Both antibody systems precipitate the same seven prominent nuclear proteins (molecular weight 12,000{\textendash}32,000). All molecules of the snRNAs U1, U2, U4, U5 and U6 appear to exist in the form of antigenic snRNPs9. The particles sediment at about 10S and each probably contains a single snRNA molecule. Indirect immunofluorescence studies using anti-RNP and anti-Sm sera confirm the nuclear (but non-nucleolar) location of the antigenic snRNPs. Here we present several lines of evidence that suggest a direct involvement of snRNPs in the splicing of hnRNA. Most intriguing is the observation that the nucleotide sequence at the 5' end of U1 RNA exhibits extensive complementarity to those across splice junctions in hnRNA molecules.}, doi = {10.1038/283220a0}, url = {http://www.nature.com/nature/journal/v283/n5743/abs/283220a0.html}, author = {Lerner,Michael R. and Boyle,John A. and Mount, Stephen M. and Wolin,Sandra L. and Steitz,Joan A.} } @article {18396, title = {Implementation of a Capability-Based Data Abstraction}, journal = {Software Engineering, IEEE Transactions on}, volume = {SE-4}, year = {1978}, month = {1978/01//}, pages = {56 - 64}, abstract = {One important feature in programming language design is an appropriate data definitional facility. Criteria now recognized as important are the concepts of information hiding and data abstraction. The problem, however, is to embed these ideas into languages. Although including these ideas has often led to the design of a new language, that is not always necessary. Such facilities may be added to languages like PL/1 or Pascal. This report discusses the inclusion of such facilities within one such PL/1 compiler. While the resulting system does not have the optimal set of protection features, it does have several advantages: the base language is known to a large class of programmers, there are many such compilers already written, and the system achieves almost as much protection as is needed.}, keywords = {Data abstraction; Pascal, PL/1; infonnation hiding; pointer variables;}, isbn = {0098-5589}, doi = {10.1109/TSE.1978.231466}, author = {Zelkowitz, Marvin V and Larsen,H.J.} } @conference {17321, title = {Personality and programming: Time-sharing vs. batch preference}, booktitle = {Proceedings of the 1978 annual conference - Volume 2}, series = {ACM {\textquoteright}78}, year = {1978}, month = {1978///}, pages = {561 - 569}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Only within the past ten years has some attention been given to psychological concerns of human-machine interface. A review of the literature in this area reveals that personality has received the least attention, but interest is growing. If critical personality factors can be isolated and associated with particular programming tasks, such information could be a useful tool for education as well as management. The hypothesis of this exploratory study was that two personality dimensions, assertiveness and locus of control, influence a programmer{\textquoteright}s choice of batch or interactive processing for program development. Locus of control relates to the perception an individual has of his/her influence over events. Assertiveness allows an individual expression in a manner that fully communicates personal desires without infringing upon the rights of others. These two dimensions and the programmer{\textquoteright}s preference for batch or interactive mode were studied through a questionnaire survey of experienced programmers.}, keywords = {Assertive/passive, batch processing, Locus of control, Personality, Programming, Psychology, Time sharing}, isbn = {0-89791-000-1}, doi = {10.1145/800178.810092}, url = {http://doi.acm.org/10.1145/800178.810092}, author = {Lee,Jeanne M. and Shneiderman, Ben} } @conference {18387, title = {Error checking with pointer variables}, booktitle = {Proceedings of the 1976 annual conference}, series = {ACM {\textquoteright}76}, year = {1976}, month = {1976///}, pages = {391 - 395}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The use of pointer variables in a programming language often results in a difficult class of errors to detect. Pointers may point to storage that no longer is allocated, or storage may be allocated as one data type and accessed as another. This report describes the implementation of pointers in the PLUM PL/1 compiler such that all error conditions are detected. In addition, preliminary tests with PLUM seem to indicate that the total checking of pointers is not as expensive an operation as it first appears.}, doi = {10.1145/800191.805623}, url = {http://doi.acm.org/10.1145/800191.805623}, author = {Zelkowitz, Marvin V and McMullin,Paul R. and Merkel,Keith R. and Larsen,Howard J.} }