@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 {19706, title = {Surveying the Accessibility of Mobile Touchscreen Games for Persons with Motor Impairments: A Preliminary Analysis}, journal = {terpconnect.umd.edu}, year = {Submitted}, abstract = {ABSTRACT Touchscreen devices have rapidly become one of the most pervasive video game platforms in the world and, in turn, an integral part of popular culture; however, little work exists on comprehensively examining their accessibility. In this poster paper, we ...}, url = {http://terpconnect.umd.edu/~leahkf/pubs/ASSETS2013-TouchscreenGames.pdf}, author = {Kim, Y and Sutreja, N and Jon Froehlich and Findlater, L} } @article {20283, title = {A Metagenomic Approach to Evaluating Surface Water Quality in Haiti}, journal = {International Journal of Environmental Research and Public Health}, volume = {1542}, year = {2018}, month = {Jan-10-2018}, pages = {2211}, abstract = {The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30309013}, author = {Roy, Monika and Arnaud, Jean and Jasmin, Paul and Hamner, Steve and Hasan, Nur and Rita R Colwell and Ford, Timothy} } @article {20314, title = {Beyond cost-effectiveness: Using systems analysis for infectious disease preparedness}, journal = {Vaccine}, volume = {35}, year = {2017}, month = {Jan-01-2017}, pages = {A46 - A49}, abstract = {Until the recent outbreaks, Ebola vaccines ranked low in decision makers{\textquoteright} priority lists based on cost-effectiveness analysis and (or) corporate profitability. Despite a relatively small number of Ebola-related cases and deaths (compared to other causes), Ebola vaccines suddenly leapt to highest priority among international health agencies and vaccine developers. Clearly, earlier cost-effectiveness analyses badly missed some factors affecting real world decisions. Multi-criteria systems analysis can improve evaluation and prioritization of vaccine development and also of many other health policy and investment decisions. Neither cost-effectiveness nor cost-benefit analysis can capture important aspects of problems such as Ebola or the emerging threat of Zika, especially issues of inequality and disparity{\textemdash}issues that dominate the planning of many global health and economic organizations. Cost-benefit analysis requires assumptions about the specific value of life{\textemdash}an idea objectionable to many analysts and policy makers. Additionally, standard cost-effectiveness calculations cannot generally capture effects on people uninfected with Ebola for example, but nevertheless affected through such factors as contagion, herd immunity, and fear of dread disease, reduction of travel and commerce, and even the hope of disease eradication. Using SMART Vaccines, we demonstrate how systems analysis can visibly include important {\textquotedblleft}other factors{\textquotedblright} and more usefully guide decision making and beneficially alter priority setting processes.}, issn = {0264410X}, doi = {10.1016/j.vaccine.2016.08.090}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0264410X16309501}, author = {Phelps, Charles and Madhavan, Guruprasad and Rappuoli, Rino and Rita R Colwell and Fineberg, Harvey} } @article {20448, title = {A Bioinformatics 3D Cellular Morphotyping Strategy for Assessing Biomaterial Scaffold Niches}, journal = {ACS Biomaterials Science \& Engineering}, volume = {3}, year = {2017}, month = {Sep-10-2017}, pages = {2302 - 2313}, issn = {2373-9878}, doi = {10.1021/acsbiomaterials.7b00473}, url = {http://pubs.acs.org/doi/10.1021/acsbiomaterials.7b00473http://pubs.acs.org/doi/pdf/10.1021/acsbiomaterials.7b00473}, author = {Florczyk, Stephen J. and Simon, Mylene and Juba, Derek and Pine, P. Scott and Sarkar, Sumona and Chen, Desu and Baker, Paula J. and Bodhak, Subhadip and Cardone, Antonio and Brady, Mary C. and Bajcsy, Peter and Simon, Carl G.} } @article {20310, title = {Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources}, journal = {BMC Genomics}, year = {2017}, month = {Jan-12-2017}, abstract = {BACKGROUND: The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition systems, specifically Sit and aerobactin, have yet to be determined for Salmonella spp. In a recent study, Salmonella enterica strains isolated from different food sources were sequenced on the Illumina MiSeq platform and found to harbor the incompatibility group (Inc) FIB plasmid. In this study, we examined sequence diversity and the contribution of factors encoded on the IncFIB plasmid to the virulence of S. enterica. RESULTS: Whole genome sequences of seven S. enterica isolates were compared to genomes of serovars of S. enterica isolated from food, animal, and human sources. SeqSero analysis predicted that six strains were serovar Typhimurium and one was Heidelberg. Among the S. Typhimurium strains, single nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that five of the isolates clustered as a single monophyletic S. Typhimurium subclade, while one of the other strains branched with S. Typhimurium from a bovine source. DNA sequence based phylogenetic diversity analyses showed that the IncFIB plasmid-encoded Sit and aerobactin iron acquisition systems are conserved among bacterial species including S. enterica. The IncFIB plasmid was transferred to an IncFIB plasmid deficient strain of S. enterica by conjugation. The transconjugant SE819::IncFIB persisted in human intestinal epithelial (Caco-2) cells at a higher rate than the recipient SE819. Genes of the Sit and aerobactin operons in the IncFIB plasmid were differentially expressed in iron-rich and iron-depleted growth media. CONCLUSIONS: Minimal sequence diversity was detected in the Sit and aerobactin operons in the IncFIB plasmids present among different bacterial species, including foodborne Salmonella strains. IncFIB plasmid encoded factors play a role during infection under low-iron conditions in host cells.}, doi = {10.1186/s12864-017-3954-5}, url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3954-5}, author = {Khajanchi, Bijay K. and Hasan, Nur A. and Choi, Seon Young and Han, Jing and Zhao, Shaohua and Rita R Colwell and Cerniglia, Carl E. and Foley, Steven L.} } @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.} } @proceedings {20156, title = {Deep-learning-assisted visualization for live-cell images}, year = {2017}, month = {09/2017}, publisher = {IEEE}, address = {Beijing, China}, abstract = {Analyzing live-cell images is particularly challenging because cells move at the same time they undergo systematic changes. Visually inspecting live-cell images therefore involves simultaneously tracking individual cells and detecting relevant spatio-temporal changes. The high cognitive burden of such a complex task makes this kind of analysis inefficient and error-prone. In this paper we describe a deep-learning-assisted visualization based on automatically derived high-level features to identify target cell changes in live-cell images. Applying a novel user-mediated color assignment scheme that maps abstract features into corresponding colors, we create color-based visual annotations that facilitate visual reasoning and analysis of complex time varying live-cell imagery datasets. The visual representations can be used to study temporal changes in cells, such as the morphological changes in cell at various stages of life cycle.}, keywords = {deep learning, live-cell images, Visualization}, author = {Hsueh-Chien Cheng and Cardone, Antonio and Krokos, Eric and Stoica, Bogdan and Faden, Alan and Varshney, Amitabh} } @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.} } @conference {20065, title = {3D Cellular Morphotyping of Scaffold Niches}, booktitle = {2016 32nd Southern Biomedical Engineering Conference (SBEC)}, year = {2016}, publisher = {IEEE}, organization = {IEEE}, author = {Florczyk, Stephen J and Simon, Mylene and Juba, Derek and Pine, P Scott and Sarkar, Sumona and Chen, Desu and Baker, Paula J and Bodhak, Subhadip and Cardone, Antonio and Brady, Mary and others} } @article {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 {20336, title = {Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed infection leading to necrotizing fasciitis}, journal = {Proceedings of the National Academy of Sciences}, volume = {11312161268}, year = {2016}, month = {Jul-01-2017}, pages = {722 - 727}, abstract = {Necrotizing fasciitis (NF) caused by flesh-eating bacteria is associated with high case fatality. In an earlier study, we reported infection of an immunocompetent individual with multiple strains of Aeromonas hydrophila (NF1{\textendash}NF4), the latter three constituted a clonal group whereas NF1 was phylogenetically distinct. To understand the complex interactions of these strains in NF pathophysiology, a mouse model was used, whereby either single or mixed A. hydrophila strains were injected intramuscularly. NF2, which harbors exotoxin A (exoA) gene, was highly virulent when injected alone, but its virulence was attenuated in the presence of NF1 (exoA-minus). NF1 alone, although not lethal to animals, became highly virulent when combined with NF2, its virulence augmented by cis-exoA expression when injected alone in mice. Based on metagenomics and microbiological analyses, it was found that, in mixed infection, NF1 selectively disseminated to mouse peripheral organs, whereas the other strains (NF2, NF3, and NF4) were confined to the injection site and eventually cleared. In vitro studies showed NF2 to be more effectively phagocytized and killed by macrophages than NF1. NF1 inhibited growth of NF2 on solid media, but ExoA of NF2 augmented virulence of NF1 and the presence of NF1 facilitated clearance of NF2 from animals either by enhanced priming of host immune system or direct killing via a contact-dependent mechanism.}, issn = {0027-8424}, doi = {10.1073/pnas.1523817113}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1523817113}, author = {Ponnusamy, Duraisamy and Kozlova, Elena V. and Sha, Jian and Erova, Tatiana E. and Azar, Sasha R. and Fitts, Eric C. and Kirtley, Michelle L. and Tiner, Bethany L. and Andersson, Jourdan A. and Grim, Christopher J. and Isom, Richard P. and Hasan, Nur A. and Rita R Colwell and Chopra, Ashok K.} } @article {20331, title = {In Plain View: A Transparent Systems Approach for Enhancing Health Policy Decisions}, year = {2016}, month = {07/2016}, url = {https://www.nae.edu/19582/Bridge/155266/155393.aspx}, author = {Guru Madhavan and Charles E. Phelps and Rita R Colwell and Rino Rappuoli and Harvey V. Fineberg} } @article {20321, title = {Modeling Sustainability: Population, Inequality, Consumption, and Bidirectional Coupling of the Earth and Human Systems}, journal = {National Science Review}, year = {2016}, month = {Nov-12-2016}, pages = {nww081}, abstract = {Over the last two centuries, the impact of the Human System has grown dramatically, becoming strongly dominant within the Earth System in many different ways. Consumption, inequality, and population have increased extremely fast, especially since about 1950, threatening to overwhelm the many critical functions and ecosystems of the Earth System. Changes in the Earth System, in turn, have important feedback effects on the Human System, with costly and potentially serious consequences. However, current models do not incorporate these critical feedbacks. We argue that in order to understand the dynamics of either system, Earth System Models must be coupled with Human System Models through bidirectional couplings representing the positive, negative, and delayed feedbacks that exist in the real systems. In particular, key Human System variables, such as demographics, inequality, economic growth, and migration, are not coupled with the Earth System but are instead driven by exogenous estimates, such as United Nations population projections. This makes current models likely to miss important feedbacks in the real Earth{\textendash}Human system, especially those that may result in unexpected or counterintuitive outcomes, and thus requiring different policy interventions from current models. The importance and imminence of sustainability challenges, the dominant role of the Human System in the Earth System, and the essential roles the Earth System plays for the Human System, all call for collaboration of natural scientists, social scientists, and engineers in multidisciplinary research and modeling to develop coupled Earth{\textendash}Human system models for devising effective science-based policies and measures to benefit current and future generations.}, issn = {2095-5138}, doi = {10.1093/nsr/nww081}, url = {https://academic.oup.com/nsr/article-lookup/doi/10.1093/nsr/nww081}, author = {Motesharrei, Safa and Rivas, Jorge and Kalnay, Eugenia and Asrar, Ghassem R. and Busalacchi, Antonio J. and Cahalan, Robert F. and Cane, Mark A. and Rita R Colwell and Feng, Kuishuang and Franklin, Rachel S. and Hubacek, Klaus and Miralles-Wilhelm, Fernando and Miyoshi, Takemasa and Ruth, Matthias and Sagdeev, Roald and Shirmohammadi, Adel and Shukla, Jagadish and Srebric, Jelena and Yakovenko, Victor M. and Zeng, Ning} } @article {20337, title = {Environmental Surveillance for Toxigenic Vibrio cholerae in Surface Waters of Haiti}, journal = {The American Journal of Tropical Medicine and Hygiene}, volume = {92}, year = {2015}, month = {Jul-01-2015}, pages = {118 - 125}, abstract = {Epidemic cholera was reported in Haiti in 2010, with no information available on the occurrence or geographic distribution of toxigenic Vibrio cholerae in Haitian waters. In a series of field visits conducted in Haiti between 2011 and 2013, water and plankton samples were collected at 19 sites. Vibrio cholerae was detected using culture, polymerase chain reaction, and direct viable count methods (DFA-DVC). Cholera toxin genes were detected by polymerase chain reaction in broth enrichments of samples collected in all visits except March 2012. Toxigenic V. cholerae was isolated from river water in 2011 and 2013. Whole genome sequencing revealed that these isolates were a match to the outbreak strain. The DFA-DVC tests were positive for V. cholerae O1 in plankton samples collected from multiple sites. Results of this survey show that toxigenic V. cholerae could be recovered from surface waters in Haiti more than 2 years after the onset of the epidemic.}, issn = {0002-9637}, doi = {10.4269/ajtmh.13-0601}, url = {http://www.ajtmh.org/content/journals/10.4269/ajtmh.13-0601}, author = {Hill, Vincent R. and Humphrys, Michael S. and Kahler, Amy M. and Boncy, Jacques and Tarr, Cheryl L. and Huq, Anwar and Chen, Arlene and Katz, Lee S. and Mull, Bonnie J. and Derado, Gordana and Haley, Bradd J. and Freeman, Nicole and Rita R Colwell and Turnsek, Maryann} } @article {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 {20360, title = {Validation of high throughput sequencing and microbial forensics applications}, journal = {Investigative Genetics}, volume = {5}, year = {2014}, month = {Jan-01-2014}, pages = {9}, abstract = {High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.}, issn = {2041-2223}, doi = {10.1186/2041-2223-5-9}, url = {http://investigativegenetics.biomedcentral.com/articles/10.1186/2041-2223-5-9}, author = {Budowle, Bruce and Connell, Nancy D and Bielecka-Oder, Anna and Rita R Colwell and Corbett, Cindi R and Fletcher, Jacqueline and Forsman, Mats and Kadavy, Dana R and Markotic, Alemka and Morse, Stephen A and Murch, Randall S and Sajantila, Antti and Schmedes, Sarah E and Ternus, Krista L and Turner, Stephen D and Minot, Samuel} } @article {20366, title = {Viewing Marine Bacteria, Their Activity and Response to Environmental Drivers from Orbit}, journal = {Microbial Ecology}, year = {2014}, month = {Jan-04-2014}, pages = {489 - 500}, abstract = {Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.}, issn = {0095-3628}, doi = {10.1007/s00248-013-0363-4}, url = {http://link.springer.com/10.1007/s00248-013-0363-4}, author = {Grimes, D. Jay and Ford, Tim E. and Rita R Colwell and Baker-Austin, Craig and Martinez-Urtaza, Jaime and Subramaniam, Ajit and Capone, Douglas G.} } @conference {19214, title = {Age-Related Differences in Performance with Touchscreens Compared to Traditional Mouse Input}, booktitle = {CHI 2013 To Appear}, year = {2013}, month = {2013}, abstract = {Despite the apparent popularity of touch screen for older adults, little is known about the psychomotor performance of these devices. We compare performance between older adults and younger adults in four desktop and touchscreen tasks: pointing, dragging, crossing and steering. On the touchscreen, we also examine pinch zoom. Our results show that while older adults were significantly slower than younger adults in general, the touchscreen reduced the performance gap relative to the desktop and mouse. Indeed, the touchscreen resulted in a significant movement time reduction of 35\% over the mouse for older adults, compared to only 16\% for younger adults. Error rates also decreased. }, author = {Findlater,L. and Jon Froehlich and Fattal, K. and Wobbrock,J.O. and Dastyar, T.} } @article {19704, title = {Bear-with-me: an embodied prototype to explore tangible two-way exchanges of emotional language}, journal = {CHI{\textquoteright}13 Extended Abstracts on Human Factors in Computing Systems}, year = {2013}, month = {2013/00/01}, abstract = {Abstract Given the busy day-to-day schedule of families and couples, communication between loved ones is often limited to text-messaging, email, or phone calls. These forms of communication do not allow for more tangible modes of intimate expression like hugging. ...}, url = {http://dl.acm.org/citation.cfm?id=2468537}, author = {Fong, A and Ashktorab, Z and Jon Froehlich} } @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 {19701, title = {Exploring early designs for teaching anatomy and physiology to children using wearable e-textiles}, journal = {IDC {\textquoteright}13 Proceedings of the 12th International Conference on Interaction Design and Children}, year = {2013}, month = {2013/00/24}, pages = {577 - 580}, publisher = {The New SchoolACM}, address = {New York, New York, USA}, abstract = {Abstract Unlike external body parts, organs are invisible and untouchable, making it difficult for children to learn their size, position, and function. Traditionally, human anatomy (body form) and physiology (body function) are taught using a mixture of techniques from ...}, isbn = {9781450319188}, doi = {10.1145/2485760.2485869}, url = {http://dl.acm.org/citation.cfm?doid=2485760.2485869}, author = {Norooz, Leyla and Jon Froehlich} } @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 {20380, title = {Fostering advances in interdisciplinary climate science}, journal = {Proceedings of the National Academy of Sciences}, year = {2013}, month = {Feb-02-2015}, pages = {3653 - 3656}, issn = {0027-8424}, doi = {10.1073/pnas.1301104110}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1301104110}, author = {Shaman, J. and Solomon, S. and Rita R Colwell and Field, C. B.} } @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 {19703, title = {An Initial Study of Automatic Curb Ramp Detection with Crowdsourced Verification Using Google Street View Images}, journal = {First AAAI Conference on Human Computation and Crowdsourcing}, year = {2013}, month = {2013/00/11}, abstract = {In our previous research, we examined whether minimally trained crowd workers could find, categorize, and assess sidewalk accessibility problems using Google Street View (GSV) images. This poster paper presents a first step towards combining automated methods ( e.g., machine vision-based curb ramp detectors) in concert with human computation to improve the overall scalability of our approach.}, url = {http://www.aaai.org/ocs/index.php/HCOMP/HCOMP13/paper/view/7507}, author = {Hara, Kotaro and Sun, Jin and Chazan, Jonah and Jacobs, David and Jon Froehlich} } @conference {19213, title = {Mind the Theoretical Gap: Interpreting, Using, and Developing Behavioral Theory in HCI Research}, booktitle = {CHI 2013 To Appear}, year = {2013}, month = {2013}, author = {Hekler, E. B. and Klasnja,P. and Jon Froehlich and Buman, M. P.} } @article {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 {19666, title = {Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures}, journal = {Science}, volume = {342}, year = {2013}, month = {2013/11/29/}, pages = {1100 - 1104}, abstract = {Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.Don{\textquoteright}t Ape Protein Variation Changes in DNA and messenger RNA (mRNA) expression levels have been used to estimate evolutionary changes between species. However protein expression levels may better reflect selection on divergent and constrained phenotypes. Khan et al. (p. 1100, published online 17 October; see the Perspective by Vogel) measured the differences among and within species between mRNA expression and protein levels in humans, chimpanzees, and rhesus macaques, identifying protein transcripts that seem to be under lineage-specific constraint between humans and chimpanzees. }, isbn = {0036-8075, 1095-9203}, url = {http://www.sciencemag.org/content/342/6162/1100}, author = {Zia Khan and Ford, Michael J. and Cusanovich, Darren A. and Mitrano, Amy and Pritchard, Jonathan K. and Gilad, Yoav} } @article {20377, title = {A water marker monitored by satellites to predict seasonal endemic cholera}, journal = {Remote Sensing Letters}, volume = {4472741982394456}, year = {2013}, month = {Jan-08-2013}, pages = {822 - 831}, abstract = {The ability to predict an occurrence of cholera, a water-related disease, offers a significant public health advantage. Satellite-based estimates of chlorophyll, a surrogate for plankton abundance, have been linked to cholera incidence. However, cholera bacteria can survive under a variety of coastal ecological conditions, thus constraining the predictive ability of the chlorophyll, since it provides only an estimate of greenness of seawater. Here, a new remote-sensing-based index is proposed: Satellite Water Marker (SWM), which estimates the condition of coastal water, based on observed variability in the difference between blue (412 nm) and green (555 nm) wavelengths that can be related to seasonal cholera incidence. The index is bounded between physically separable wavelengths for relatively clear (blue) and turbid (green) water. Using SWM, prediction of cholera with reasonable accuracy, at least two months in advance, can potentially be achieved in the endemic coastal regions. }, issn = {2150-704X}, doi = {10.1080/2150704X.2013.802097}, url = {http://www.tandfonline.com/doi/abs/10.1080/2150704X.2013.802097}, author = {Jutla, Antarpreet and Akanda, Ali Shafqat and Huq, Anwar and Faruque, Abu Syed Golam and Rita R Colwell and Islam, Shafiqul} } @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 {19028, title = {Cloud Data Protection for the Masses}, journal = {Computer}, volume = {45}, year = {2012}, month = {2012}, pages = {39 - 45}, abstract = {Offering strong data protection to cloud users while enabling rich applications is a challenging task. Researchers explore a new cloud platform architecture called Data Protection as a Service, which dramatically reduces the per-application development effort required to offer data protection, while still allowing rapid development and maintenance.}, keywords = {Cloud computing, cloud data protection, cloud platform architecture, cloud users, Maintenance, rapid development, security of data, strong data protection}, isbn = {0018-9162}, author = {Song,D. and Elaine Shi and Fischer, I. and Shankar,U.} } @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.} } @inbook {18698, title = {Determining Protein Dynamics from 15N Relaxation Data by Using DYNAMICS}, booktitle = {Protein NMR Techniques}, series = {Methods in Molecular Biology}, volume = {831}, year = {2012}, month = {2012///}, pages = {485 - 511}, publisher = {Humana Press}, organization = {Humana Press}, abstract = {Motions are essential for protein function, and knowledge of protein dynamics is a key to our understanding the mechanisms underlying protein folding and stability, ligand recognition, allostery, and catalysis. In the last two decades, NMR relaxation measurements have become a powerful tool for characterizing backbone and side chain dynamics in complex biological macromolecules such as proteins and nucleic acids. Accurate analysis of the experimental data in terms of motional parameters is an essential prerequisite for developing physical models of motions to paint an adequate picture of protein dynamics. Here, I describe in detail how to use the software package DYNAMICS that was developed for accurate characterization of the overall tumbling and local dynamics in a protein from nuclear spin-relaxation rates measured by NMR. Step-by-step instructions are provided and illustrated through an analysis of 15 N relaxation data for protein G.}, keywords = {Biomedical and Life Sciences}, isbn = {978-1-61779-480-3}, url = {http://www.springerlink.com/content/q667p0k138058103/abstract/}, author = {Fushman, David}, editor = {Shekhtman,Alexander and Burz,David S. and Walker,John M.} } @article {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 {19231, title = {Duking it out at the smartphone mobile app mapping API corral: Apple, Google, and the competition}, booktitle = {1st ACM SIGSPATIAL International Workshop on Mobile Geographic Information Systems (MobiGIS 2012)}, year = {2012}, month = {11/2012}, address = {Redondo Beach, California}, abstract = {The recent introduction of the Apple iPhone 5 and the accompanying iOS6 software environment which, among other changes, replaced the use of the Google Maps API in iOS5 by Apple{\textquoteright}s own Maps API, has led to significant changes in the user experience with apps that make use of maps and has resulted in closer scrutiny of mapping applications on mobile devices. Many of these changes in the user experience deal with the quality of the data that is being produced and presented to the user, and has led to a wide ranging discussion of data quality and the seeming lack of quality assurance policies and protocols by Apple. These are widely documented in web postings. However, equally important are significant changes in the manner in which the data is presented to the user, but, surprisingly, not much attention has been paid to this aspect of the user experience which is somewhat analogous to the concept of the {\textquotedblleft}last mile{\textquotedblright} when discussing the bandwidth of communications networks and its associated costs. The changes in the presentation and in the amount of data that are presented to the user on the Apple mapping platform, with an emphasis on mobile devices with a small form factor such as smartphones, are tabulated and compared along with other mapping platforms such as the iOS apps of ESRI, MapQuest, and OpenSeaMap (using the open source map data of OpenStreetMap), as well as Bing Maps and Nokia Maps for which no iOS app exists and thus the corresponding mobile web versions are used. }, author = {Samet, Hanan and Fruin, B.C and Nutanong,S.} } @inbook {19634, title = {Efficient Password Authenticated Key Exchange via Oblivious Transfer}, booktitle = {Public Key Cryptography {\textendash} PKC 2012}, series = {Lecture Notes in Computer Science}, year = {2012}, month = {2012/01/01/}, pages = {449 - 466}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We present a new framework for constructing efficient password authenticated key exchange (PAKE) protocols based on oblivious transfer (OT). Using this framework, we obtain: an efficient and simple UC-secure PAKE protocol that is secure against adaptive corruptions without erasures. efficient and simple PAKE protocols under the Computational Diffie-Hellman (CDH) assumption and the hardness of factoring. (Previous efficient constructions rely on hash proof systems, which appears to be inherently limited to decisional assumptions.) All of our constructions assume a common reference string (CRS) but do not rely on random oracles.}, keywords = {adaptive security, Algorithm Analysis and Problem Complexity, Computer Communication Networks, Data Encryption, Discrete Mathematics in Computer Science, Management of Computing and Information Systems, oblivious transfer, Password Authenticated Key Exchange, search assumptions, Systems and Data Security, UC security}, isbn = {978-3-642-30056-1, 978-3-642-30057-8}, url = {http://link.springer.com/chapter/10.1007/978-3-642-30057-8_27}, author = {Canetti, Ran and Dana Dachman-Soled and Vaikuntanathan, Vinod and Wee, Hoeteck}, editor = {Fischlin, Marc and Buchmann, Johannes and Manulis, Mark} } @article {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 {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 {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 {18540, title = {Lithium: Event-Driven Network Control}, volume = {GT-CS-12-03}, year = {2012}, month = {2012///}, institution = {Georgia Institute of Technology}, abstract = {This paper introduces event-driven network control, a network control framework that makes networks easier to manage by automating many tasks that must currently be performed by manually modifying low-level, distributed, and complex device configuration. We identify four policy domains that inherently capture many events: time, user, history, and traffic flow. We then present Lithium, an event-driven network control framework that can implement policies expressed using these domains. Lithium can support policies that automatically react to a wide range of events, from fluctuations in traffic volumes to changes in the time of day. Lithium allows network operators to specify networkwide policies in terms of a high-level, event-driven policy model, as opposed to configuring individual network devices with low-level commands. To show that Lithium is practical, general, and applicable in different types of network scenarios, we have deployed Lithium in both a campus network and a home network and used it to implement more flexible and dynamic network policies. We also perform evaluations to show that Lithium introduces negligible overhead beyond a conventional OpenFlow-based control framework.}, url = {http://hdl.handle.net/1853/43377}, author = {Kim,H. and Voellmy,A. and Burnett,S. and Feamster, Nick and Clark,R.} } @article {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 {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.} } @conference {15650, title = {Polytope approximation and the Mahler volume}, booktitle = {Proceedings of the Twenty-Third Annual ACM-SIAM Symposium on Discrete Algorithms}, series = {SODA {\textquoteright}12}, year = {2012}, month = {2012///}, pages = {29 - 42}, publisher = {SIAM}, organization = {SIAM}, abstract = {The problem of approximating convex bodies by polytopes is an important and well studied problem. Given a convex body K in Rd, the objective is to minimize the number of vertices (alternatively, the number of facets) of an approximating polytope for a given Hausdorff error ε. Results to date have been of two types. The first type assumes that K is smooth, and bounds hold in the limit as ε tends to zero. The second type requires no such assumptions. The latter type includes the well known results of Dudley (1974) and Bronshteyn and Ivanov (1976), which show that in spaces of fixed dimension, O((diam(K)/ε)(d-1)/2) vertices (alt., facets) suffice. Our results are of this latter type. In our first result, under the assumption that the width of the body in any direction is at least ε, we strengthen the above bound to [EQUATION]. This is never worse than the previous bound (by more than logarithmic factors) and may be significantly better for skinny bodies. Our analysis exploits an interesting analogy with a classical concept from the theory of convexity, called the Mahler volume. This is a dimensionless quantity that involves the product of the volumes of a convex body and its polar dual. In our second result, we apply the same machinery to improve upon the best known bounds for answering ε-approximate polytope membership queries. Given a convex polytope P defined as the intersection of halfspaces, such a query determines whether a query point q lies inside or outside P, but may return either answer if q{\textquoteright}s distance from P{\textquoteright}s boundary is at most ε. We show that, without increasing storage, it is possible to reduce the best known search times for ε-approximate polytope membership significantly. This further implies improvements to the best known search times for approximate nearest neighbor searching in spaces of fixed dimension.}, url = {http://dl.acm.org/citation.cfm?id=2095116.2095119}, author = {Arya,Sunil and da Fonseca,Guilherme D. and Mount, Dave} } @article {19254, title = {Prototyping scalable digital signal processing systems for radio astronomy using dataflow models}, journal = {Radio Science}, volume = {47}, year = {2012}, month = {2012}, pages = {n/a - n/a}, abstract = {There is a growing trend toward using high-level tools for design and implementation of radio astronomy digital signal processing (DSP) systems. Such tools, for example, those from the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER), are usually platform-specific, and lack high-level, platform-independent, portable, scalable application specifications. This limits the designer{\textquoteright}s ability to experiment with designs at a high-level of abstraction and early in the development cycle. We address some of these issues using a model-based design approach employing dataflow models. We demonstrate this approach by applying it to the design of a tunable digital downconverter (TDD) used for narrow-bandwidth spectroscopy. Our design is targeted toward an FPGA platform, called theInterconnect Break-out Board (IBOB), that is available from the CASPER. We use the term TDD to refer to a digital downconverter for which the decimation factor and center frequency can be reconfigured without the need for regenerating the hardware code. Such a design is currently not available in the CASPER DSP library. The work presented in this paper focuses on two aspects. First, we introduce and demonstrate a dataflow-based design approach using thedataflow interchange format (DIF) tool for high-level application specification, and we integrate this approach with the CASPER tool flow. Secondly, we explore the trade-off between the flexibility of TDD designs and the low hardware cost of fixed-configuration digital downconverter (FDD) designs that use the available CASPER DSP library. We further explore this trade-off in the context of a two-stage downconversion scheme employing a combination of TDD or FDD designs.}, keywords = {dataflow models, digital downconverter, Digital signal processing, model-based design, radio astronomy, rapid prototyping}, isbn = {1944-799X}, url = {http://onlinelibrary.wiley.com/doi/10.1029/2011RS004924/abstract}, author = {Sane, N. and Ford, J. and Harris, A. I. and Bhattacharyya, Shuvra S.} } @article {19458, title = {Refactoring Network Infrastructure to Improve Manageability: A Case Study of Home Networking}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {42}, year = {2012}, month = {2012/06//}, pages = {54 - 61}, abstract = {Managing a home network is challenging because the underlying infrastructure is so complex. Existing interfaces either hide or expose the network{\textquoteright}s underlying complexity, but in both cases, the information that is shown does not necessarily allow a user to complete desired tasks. Recent advances in software defined networking, however, permit a redesign of the underlying network and protocols, potentially allowing designers to move complexity further from the user and, in some cases, eliminating it entirely. In this paper, we explore whether the choices of what to make visible to the user in the design of today{\textquoteright}s home network infrastructure, performance, and policies make sense. We also examine whether new capabilities for refactoring the network infrastructure - changing the underlying system without compromising existing functionality - should cause us to revisit some of these choices. Our work represents a case study of how co-designing an interface and its underlying infrastructure could ultimately improve interfaces for that infrastructure.}, keywords = {home networking, management, Monitoring, software defined networking}, isbn = {0146-4833}, url = {http://doi.acm.org/10.1145/2317307.2317318}, author = {Marshini Chetty and Feamster, Nick} } @inbook {18597, title = {Re-wiring Activity of Malicious Networks}, booktitle = {Passive and Active MeasurementPassive and Active Measurement}, series = {Lecture Notes in Computer Science}, volume = {7192}, year = {2012}, month = {2012///}, pages = {116 - 125}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper studies the AS-level re-wiring dynamics (changes in the connectivity) of malicious networks. Anecdotal evidence suggests that some malicious ASes that are primarily involved in nefarious activities on the Internet, were sequentially de-peered by providers before their final cut-off (as occurred in the well-publicized cases of Atrivo/Intercage). We present the first systematic study of the re-wiring dynamics of malicious ASes. We tracked the ASes that were listed by Hostexploit over the last two years and compared their AS-level re-wiring dynamics with non-reported ASes. Using a publicly available dataset of Customer-Provider (CP) relations in the Internet{\textquoteright}s AS graph, we studied how interconnection between autonomous systems evolves, both for ASes that provide connectivity for attackers and ASes that were not reported as malicious. We find that malicious networks are more aggressive both in forming links with providers and changing their upstream connectivity than other ASes. Our results indicate that the re-wiring dynamics of the networks that host attacks are stable over time, despite the evolving nature of the attacks themselves, which suggests that existing defense mechanisms could benefit from incorporating these features.}, keywords = {Computer science}, isbn = {978-3-642-28536-3}, url = {http://www.springerlink.com/content/95vn833728404877/abstract/}, author = {Konte,Maria and Feamster, Nick}, editor = {Taft,Nina and Ricciato,Fabio} } @article {18712, title = {Rpn1 and Rpn2 coordinate ubiquitin processing factors at the proteasome}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, year = {2012}, month = {2012/02/08/}, abstract = {Substrates tagged with (poly)ubiquitin for degradation can be targeted directly to the 26S proteasome where they are proteolysed. Independently, ubiquitin-conjugates may also be delivered by bivalent shuttles. The majority of shuttles attach to the proteasome through a ubiquitin-like domain (UBL) while anchoring cargo at a C-terminal polyubiquitin-binding domain(s). We found that two shuttles of this class, Rad23 and Dsk2, dock at two different receptors embedded within a single subunit of the 19S proteasome regulatory particle (RP), Rpn1. Their association/dissociation constants and affinities for Rpn1 are similar. In contrast, another UBL-containing protein, the deubiquitinase Ubp6, is also anchored by Rpn1, yet dissociates slower, thus behaving as a sometimes proteasome subunit distinct from transiently-associated shuttles. Two neighboring subunits, Rpn10 and Rpn13, show a marked preference for polyubiquitin over UBLs. Rpn10 attaches to the central solenoid portion of Rpn1 although this association is stabilized by the presence of a third subunit, Rpn2. Rpn13 binds directly to the C-terminal portion of Rpn2. These intrinsic polyubiquitin receptors may compete with substrate shuttles for their polyubiquitin-conjugates, thereby aiding release of the emptied shuttles. By binding multiple ubiquitin-processing factors simultaneously, Rpn1 is uniquely suited to coordinate substrate recruitment, deubiquitination, and movement towards the catalytic core. The broad range of affinities for ubiquitin, ubiquitin-like, and non-ubiquitin signals by adjacent yet non-overlapping sites all within the Base illustrates a hub of activity that coordinates the intricate relay of substrates within the proteasome, and consequently influences substrate residency time and commitment to degradation.}, keywords = {deubiquitination, Proteasome, solenoid, Surface plasmon resonance (SPR), ubiquitin, Ubiquitin-dependent protease}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.M111.316323}, url = {http://www.jbc.org/content/early/2012/02/08/jbc.M111.316323}, author = {Rosenzweig,Rina and Bronner,Vered and Zhang,Daoning and Fushman, David and Glickman,Michael H.} } @article {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} } @article {19132, title = {Structure, function and diversity of the healthy human microbiome}, journal = {Nature}, volume = {486}, year = {2012}, month = {2012}, pages = {207 - 214}, abstract = {Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat{\textquoteright}s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81{\textendash}99\% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.}, author = {Huttenhower, C. and Gevers, D. and Knight,R. and Abubucker, S. and Badger, J.H. and Chinwalla, A.T. and Creasy, H.H. and Earl, A.M. and Fitzgerald, M.G. and Fulton, R.S. and others} } @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 {14398, title = {TACI: Taxonomy-Aware Catalog Integration}, journal = {IEEE Transactions on Knowledge and Data Engineering (TKDE)}, year = {2012}, month = {2012///}, abstract = {A fundamental data integration task faced by online commercial portals and commerce search engines is the integration of products coming from multiple providers to their product catalogs. In this scenario, the commercial portal has its own taxonomy (the {\textquotedblleft}master taxonomy{\textquotedblright}), while each data provider organizes its products into a different taxonomy (the {\textquotedblleft}provider taxonomy{\textquotedblright}). In this paper, we consider the problem of categorizing products from the data providers into the master taxonomy, while making use of the provider taxonomy information. Our approach is based on a taxonomy-aware processing step that adjusts the results of a text-based classifier to ensure that products that are close together in the provider taxonomy remain close in the master taxonomy. We formulate this intuition as a structured prediction optimization problem. To the best of our knowledge, this is the first approach that leverages the structure of taxonomies in order to enhance catalog integration. We propose algorithms that are scalable and thus applicable to the large datasets that are typical on the Web. We evaluate our algorithms on real-world data and we show that taxonomy-aware classification provides a significant improvement over existing approaches.}, author = {Papadimitriou,P. and Tsaparas,P. and Fuxman,A. and Getoor, Lise} } @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 {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 {19181, title = {Ability-based design: Concept, principles and examples}, journal = {ACM Transactions on Accessible Computing (TACCESS)}, volume = {3}, year = {2011}, month = {2011}, author = {Wobbrock,J.O. and Kane,S.K. and Gajos,K.Z. and Harada,S. and Jon Froehlich} } @conference {14192, title = {Active scene recognition with vision and language}, booktitle = {2011 IEEE International Conference on Computer Vision (ICCV)}, year = {2011}, month = {2011/11/06/13}, pages = {810 - 817}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a novel approach to utilizing high level knowledge for the problem of scene recognition in an active vision framework, which we call active scene recognition. In traditional approaches, high level knowledge is used in the post-processing to combine the outputs of the object detectors to achieve better classification performance. In contrast, the proposed approach employs high level knowledge actively by implementing an interaction between a reasoning module and a sensory module (Figure 1). Following this paradigm, we implemented an active scene recognizer and evaluated it with a dataset of 20 scenes and 100+ objects. We also extended it to the analysis of dynamic scenes for activity recognition with attributes. Experiments demonstrate the effectiveness of the active paradigm in introducing attention and additional constraints into the sensing process.}, keywords = {accuracy, active scene recognition, classification performance, Cognition, Computer vision, Detectors, Equations, high level knowledge utilization, HUMANS, image classification, inference mechanisms, object detectors, Object recognition, reasoning module, sensing process, sensory module, support vector machines, Training}, isbn = {978-1-4577-1101-5}, doi = {10.1109/ICCV.2011.6126320}, author = {Yu,Xiaodong and Ferm{\"u}ller, Cornelia and Ching Lik Teo and Yezhou Yang and Aloimonos, J.} } @article {19279, title = {Analysis of SystemC actor networks for efficient synthesis}, journal = {ACM Trans. Embed. Comput. Syst.}, volume = {10}, year = {2011}, month = {2011}, pages = {18:1 - 18:34}, abstract = {Applications in the signal processing domain are often modeled by dataflow graphs. Due to heterogeneous complexity requirements, these graphs contain both dynamic and static dataflow actors. In previous work, we presented a generalized clustering approach for these heterogeneous dataflow graphs in the presence of unbounded buffers. This clustering approach allows the application of static scheduling methodologies for static parts of an application during embedded software generation for multiprocessor systems. It systematically exploits the predictability and efficiency of the static dataflow model to obtain latency and throughput improvements. In this article, we present a generalization of this clustering technique to dataflow graphs with bounded buffers, therefore enabling synthesis for embedded systems without dynamic memory allocation. Furthermore, a case study is given to demonstrate the performance benefits of the approach.}, keywords = {actor-oriented design, clustering, Dataflow analysis, scheduling}, isbn = {1539-9087}, url = {http://doi.acm.org/10.1145/1880050.1880054}, author = {Falk, Joachim and Zebelein, Christian and Keinert, Joachim and Haubelt, Christian and Teich, Juergen and Bhattacharyya, Shuvra S.} } @article {15616, title = {Approximate polytope membership queries}, journal = {Proceedings of 43rd Annual ACM Symposium on Theory of Computing}, year = {2011}, month = {2011///}, pages = {579 - 586}, abstract = {We consider an approximate version of a fundamental geo-metric search problem, polytope membership queries. Given a convex polytope P in Rd, presented as the intersection of halfspaces, the objective is to preprocess P so that, given a query point q, it is possible to determine efficiently whether q lies inside P subject to an error bound ε. Previous solutions to this problem were based on straight- forward applications of classic polytope approximation tech- niques by Dudley (1974) and Bentley et al. (1982). The former yields minimum storage, and the latter yields con- stant query time. A space-time tradeoff can be obtained by interpolating between the two. We present the first sig- nificant improvements to this tradeoff. For example, using the same storage as Dudley, we reduce the query time from O(1/ε (d-1)/2 ) to O(1/ε (d-1)/4 ). Our approach is based on a very simple algorithm. Both lower bounds and upper bounds on the performance of the algorithm are presented. To establish the relevance of our results, we introduce a reduction from approximate nearest neighbor searching to approximate polytope membership queries. We show that our tradeoff provides significant improvements to the best known space-time tradeoffs for approximate nearest neigh- bor searching. Furthermore, this is achieved with construc- tions that are much simpler than existing methods }, author = {Arya,S. and da Fonseca,G. D and Mount, Dave} } @article {18547, title = {Architecting for innovation}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011///}, pages = {24 - 36}, abstract = {We argue that the biggest problem with the current Internet architecture is not a particular functional deficiency, but its inability to accommodate innovation. To address this problem we propose a minimal architectural "framework" in which comprehensive architectures can reside. The proposed Framework for Internet Innovation (FII) --- which is derived from the simple observation that network interfaces should be extensible and abstract --- allows for a diversity of architectures to coexist, communicate, and evolve. We demonstrate FII{\textquoteright}s ability to accommodate diversity and evolution with a detailed examination of how information flows through the architecture and with a skeleton implementation of the relevant interfaces.}, keywords = {diversity, Evolution, innovation, internet architecture}, isbn = {0146-4833}, doi = {10.1145/2002250.2002256}, url = {http://doi.acm.org/10.1145/2002250.2002256}, author = {Koponen,Teemu and Shenker,Scott and Balakrishnan,Hari and Feamster, Nick and Ganichev,Igor and Ghodsi,Ali and Godfrey,P. Brighten and McKeown,Nick and Parulkar,Guru and Raghavan,Barath and Rexford,Jennifer and Arianfar,Somaya and Kuptsov,Dmitriy} } @conference {13069, title = {AVSS 2011 demo session: A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Advanced Video and Signal-Based Surveillance (AVSS), 2011 8th IEEE International Conference on}, year = {2011}, month = {2011/09/30/2}, pages = {527 - 528}, abstract = {We introduce to the surveillance community the VIRAT Video Dataset[1], which is a new large-scale surveillance video dataset designed to assess the performance of event recognition algorithms in realistic scenes1.}, doi = {10.1109/AVSS.2011.6027400}, author = {Oh,Sangmin and Hoogs,Anthony and Perera,Amitha and Cuntoor,Naresh and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,Saurajit and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,Eran and Wang,Xiaoyang and Ji,Qiang and Reddy,Kishore and Shah,Mubarak and Vondrick,Carl and Pirsiavash,Hamed and Ramanan,Deva and Yuen,Jenny and Torralba,Antonio and Song,Bi and Fong,Anesco and Roy-Chowdhury,Amit and Desai,Mita} } @article {16247, title = {Bacillus Anthracis Comparative Genome Analysis in Support of the Amerithrax Investigation}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {108}, year = {2011}, month = {2011/03/22/}, pages = {5027 - 5032}, abstract = {Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on microbial genotyping schemes based on a small portion of a genome sequence. Amerithrax, the investigation into the anthrax letter attacks, applied high-resolution whole-genome sequencing and comparative genomics to identify key genetic features of the letters{\textquoteright} Bacillus anthracis Ames strain. During systematic microbiological analysis of the spore material from the letters, we identified a number of morphological variants based on phenotypic characteristics and the ability to sporulate. The genomes of these morphological variants were sequenced and compared with that of the B. anthracis Ames ancestor, the progenitor of all B. anthracis Ames strains. Through comparative genomics, we identified four distinct loci with verifiable genetic mutations. Three of the four mutations could be directly linked to sporulation pathways in B. anthracis and more specifically to the regulation of the phosphorylation state of Spo0F, a key regulatory protein in the initiation of the sporulation cascade, thus linking phenotype to genotype. None of these variant genotypes were identified in single-colony environmental B. anthracis Ames isolates associated with the investigation. These genotypes were identified only in B. anthracis morphotypes isolated from the letters, indicating that the variants were not prevalent in the environment, not even the environments associated with the investigation. This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.1016657108}, url = {http://www.pnas.org/content/108/12/5027}, author = {Rasko,David A and Worsham,Patricia L and Abshire,Terry G and Stanley,Scott T and Bannan,Jason D and Wilson,Mark R and Langham,Richard J and Decker,R. Scott and Jiang,Lingxia and Read,Timothy D. and Phillippy,Adam M and Salzberg,Steven L. and Pop, Mihai and Van Ert,Matthew N and Kenefic,Leo J and Keim,Paul S and Fraser-Liggett,Claire M and Ravel,Jacques} } @conference {13067, title = {Birdlets: Subordinate categorization using volumetric primitives and pose-normalized appearance}, booktitle = {Computer Vision (ICCV), 2011 IEEE International Conference on}, year = {2011}, month = {2011/11//}, pages = {161 - 168}, abstract = {Subordinate-level categorization typically rests on establishing salient distinctions between part-level characteristics of objects, in contrast to basic-level categorization, where the presence or absence of parts is determinative. We develop an approach for subordinate categorization in vision, focusing on an avian domain due to the fine-grained structure of the category taxonomy for this domain. We explore a pose-normalized appearance model based on a volumetric poselet scheme. The variation in shape and appearance properties of these parts across a taxonomy provides the cues needed for subordinate categorization. Training pose detectors requires a relatively large amount of training data per category when done from scratch; using a subordinate-level approach, we exploit a pose classifier trained at the basic-level, and extract part appearance and shape information to build subordinate-level models. Our model associates the underlying image pattern parameters used for detection with corresponding volumetric part location, scale and orientation parameters. These parameters implicitly define a mapping from the image pixels into a pose-normalized appearance space, removing view and pose dependencies, facilitating fine-grained categorization from relatively few training examples.}, keywords = {appearance, Birdlets;category, categorization;subordinate-level, detection;pose, detectors;pose-normalized, distinctions;shape, estimation;, extraction;pose, extraction;subordinate-level, information, model;salient, models;volumetric, pixels;part, poselet, primitives;computer, resolution;information, retrieval;object, scheme;volumetric, taxonomy;computer, vision;image}, doi = {10.1109/ICCV.2011.6126238}, author = {Farrell,R. and Oza,O. and Zhang,Ning and Morariu,V.I. and Darrell,T. and Davis, Larry S.} } @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} } @article {18510, title = {Broadband internet performance: A view from the gateway}, journal = {SIGCOMM-Computer Communication Review}, volume = {41}, year = {2011}, month = {2011///}, pages = {134 - 134}, abstract = {We present the first study of network access link performance mea-sured directly from home gateway devices. Policymakers, ISPs, and users are increasingly interested in studying the performance of Internet access links. Because of many confounding factors in a home network or on end hosts, however, thoroughly understanding access network performance requires deploying measurement in- frastructure in users{\textquoteright} homes as gateway devices. In conjunction with the Federal Communication Commission{\textquoteright}s study of broad- band Internet access in the United States, we study the throughput and latency of network access links using longitudinal measure- ments from nearly 4,000 gateway devices across 8 ISPs from a de- ployment of over 4,200 devices. We study the performance users achieve and how various factors ranging from the user{\textquoteright}s choice of modem to the ISP{\textquoteright}s traffic shaping policies can affect performance. Our study yields many important findings about the characteristics of existing access networks. Our findings also provide insights into the ways that access network performance should be measured and presented to users, which can help inform ongoing broader efforts to benchmark the performance of access networks. }, author = {Sundaresan,S. and de Donato,W. and Feamster, Nick and Teixeira,R. and Crawford,S. and Pescap{\`e},A.} } @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 {14326, title = {CHI 2011 sustainability community invited panel: challenges ahead}, booktitle = {2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {73 - 76}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {As part of a new CHI Sustainability Community, focused on environmental sustainability, this panel will discuss specific ways in which HCI research will be critical in finding solutions to this global challenge. While research to date has primarily focused on the end consumer, the panel will be challenged with enlarging the discussion to include the designer as a target user and to consider interfaces and interactions that support sustainable design and sustainable manufacturing, as well as sustainable consumption. Specifically, to make real progress, we seek to enumerate ways that HCI needs to grow, as well as to find ways that can help more HCI researchers to become involved.}, keywords = {design, Environment, sustainability; community, user behavior}, doi = {10.1145/1979482.1979484}, url = {http://doi.acm.org/10.1145/1979482.1979484}, author = {Khan,Azam and Bartram,Lyn and Blevis,Eli and DiSalvo,Carl and Jon Froehlich and Kurtenbach,Gordon} } @article {12869, title = {Clonal transmission, dual peak, and off-season cholera in Bangladesh}, journal = {Infection Ecology \& Epidemiology}, volume = {1}, year = {2011}, month = {08/2011}, abstract = {Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March{\textendash}May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March{\textendash}May and September{\textendash}November) pattern in the city of Dhaka that is bordered by a heavily polluted freshwater river system and flood embankment. In August 2007, extreme flooding was accompanied by an unusually severe diarrhea outbreak in Dhaka that resulted in a record high illness. This study was aimed to understand the unusual outbreak and if it was related to the circulation of a new V. cholerae clone. Nineteen V. cholerae isolated during the peak of the 2007 outbreak were subjected to extensive phenotypic and molecular analyses, including multi-locus genetic screening by polymerase chain reaction (PCR), sequence-typing of the ctxB gene, and pulsed-field gel electrophoresis (PFGE). Factors associated with the unusual incidence of cholera were determined and analysis of the disease severity was done. Overall, microbiological and molecular data confirmed that the hypervirulent V. cholerae was O1 biotype El Tor (ET) that possessed cholera toxin (CT) of the classical biotype. The PFGE (NotI) and dendrogram clustering confirmed that the strains were clonal and related to the pre-2007 variant ET from Dhaka and Matlab and resembled one of two distinct clones of the variant ET confirmed to be present in the estuarine ecosystem of Bangladesh. Results of the analyses of both diarrheal case data for three consecutive years (2006{\textendash}2008) and regional hydroclimatology over three decades (1980{\textendash}2009) clearly indicate that the pattern of cholera occurring in Dhaka, and not seen at other endemic sites, was associated with flood waters transmitting the infectious clone circulating via the fecal-oral route during and between the dual seasonal cholera peaks in Dhaka. Circular river systems and flood embankment likely facilitate transmission of infectious V. cholerae throughout the year that leads to both sudden and off-season outbreaks in the densely populated urban ecosystem of Dhaka. Clonal recycling of hybrid El Tor with increasing virulence in a changing climate and in a region with a growing urban population represents a serious public health concern for Bangladesh.}, doi = {10.3402/iee.v1i0.7273}, author = {Alam,M. and Islam,A. and Bhuiyan,N. A. and Rahim,N. and Hossain,A. and Khan,G. Y. and Ahmed,D. and Watanabe,H. and Izumiya,H. and Faruque,A. S. G. and Rita R Colwell} } @article {19442, title = {Communicating with Caps: Managing Usage Caps in Home Networks}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011/08//}, pages = {470 - 471}, abstract = {As Internet service providers increasingly implement and impose "usage caps", consumers need better ways to help them understand and control how devices in the home use up the available network resources or available capacity. Towards this goal, we will demonstrate a system that allows users to monitor and manage their usage caps. The system uses the BISMark firmware running on network gateways to collect usage statistics and report them to a logically centralized controller, which displays usage information. The controller allows users to specify policies about how different people, devices, and applications should consume the usage cap; it implements and enforces these policies via a secure OpenFlow control channel to each gateway device. The demonstration will show various use cases, such as limiting the usage of a particular application, visualizing usage statistics, and allowing users within a single household to "trade" caps with one another.}, keywords = {home network, openflow, usage cap}, isbn = {0146-4833}, url = {http://doi.acm.org/10.1145/2043164.2018526}, author = {Kim, Hyojoon and Sundaresan, Srikanth and Marshini Chetty and Feamster, Nick and Edwards, W. Keith} } @article {18557, title = {Communicating with caps: managing usage caps in home networks}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {41}, year = {2011}, month = {2011/08//}, pages = {470 - 471}, abstract = {As Internet service providers increasingly implement and impose "usage caps", consumers need better ways to help them understand and control how devices in the home use up the available network resources or available capacity. Towards this goal, we will demonstrate a system that allows users to monitor and manage their usage caps. The system uses the BISMark firmware running on network gateways to collect usage statistics and report them to a logically centralized controller, which displays usage information. The controller allows users to specify policies about how different people, devices, and applications should consume the usage cap; it implements and enforces these policies via a secure OpenFlow control channel to each gateway device. The demonstration will show various use cases, such as limiting the usage of a particular application, visualizing usage statistics, and allowing users within a single household to "trade" caps with one another.}, keywords = {home network, openflow, usage cap}, isbn = {0146-4833}, doi = {10.1145/2043164.2018526}, url = {http://doi.acm.org/10.1145/2043164.2018526}, author = {Kim,Hyojoon and Sundaresan,Srikanth and Marshini Chetty and Feamster, Nick and Edwards,W. Keith} } @conference {12401, title = {Comparing values and sentiment using Mechanical Turk}, booktitle = {Proceedings of the 2011 iConference}, series = {iConference {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {783 - 784}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Human values can help to explain people{\textquoteright}s sentiment toward current events. In this experiment, we compare people{\textquoteright}s values with their agreement or disagreement with paragraphs that were classified as either supporting or opposing a specific topic. We found that five value types have statistically significant agreement (p<0.001) for both the supporting and opposing paragraphs, in opposite directions. We hope to use these paragraph ratings to train an automatic text classifier to agree or disagree with paragraphs based on a specific value profile.}, keywords = {human values, sentiment analysis, text classification}, isbn = {978-1-4503-0121-3}, doi = {10.1145/1940761.1940903}, url = {http://doi.acm.org/10.1145/1940761.1940903}, author = {Templeton,Thomas Clay and Fleischmann,Kenneth R. and Jordan Boyd-Graber} } @conference {14183, title = {A Corpus-Guided Framework for Robotic Visual Perception}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, author = {Teo,C.L. and Yang, Y. and Daum{\'e}, Hal and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @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} } @inbook {14676, title = {Directed Symbolic Execution}, booktitle = {Static AnalysisStatic Analysis}, series = {Lecture Notes in Computer Science}, volume = {6887}, year = {2011}, month = {2011///}, pages = {95 - 111}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper, we study the problem of automatically finding program executions that reach a particular target line. This problem arises in many debugging scenarios; for example, a developer may want to confirm that a bug reported by a static analysis tool on a particular line is a true positive. We propose two new directed symbolic execution strategies that aim to solve this problem: shortest-distance symbolic execution (SDSE) uses a distance metric in an interprocedural control flow graph to guide symbolic execution toward a particular target; and call-chain-backward symbolic execution (CCBSE) iteratively runs forward symbolic execution, starting in the function containing the target line, and then jumping backward up the call chain until it finds a feasible path from the start of the program. We also propose a hybrid strategy, Mix-CCBSE, which alternates CCBSE with another (forward) search strategy. We compare these three with several existing strategies from the literature on a suite of six GNU Coreutils programs. We find that SDSE performs extremely well in many cases but may fail badly. CCBSE also performs quite well, but imposes additional overhead that sometimes makes it slower than SDSE. Considering all our benchmarks together, Mix-CCBSE performed best on average, combining to good effect the features of its constituent components.}, isbn = {978-3-642-23701-0}, url = {http://dx.doi.org/10.1007/978-3-642-23702-7_11}, author = {Ma,Kin-Keung and Yit Phang,Khoo and Foster, Jeffrey S. and Hicks, Michael W.}, editor = {Yahav,Eran} } @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.} } @conference {19024, title = {Do You Know Where Your Data Are? Secure Data Capsules for Deployable Data Protection}, year = {2011}, month = {2011}, url = {http://static.usenix.org/event/hotos11/tech/final_files/ManiatisAkhawe.pdf}, author = {Maniatis, P. and Akhawe, D. and Fall,K. and Elaine Shi and McCamant, S. and Song,D.} } @conference {14315, title = {Dynamic inference of static types for ruby}, booktitle = {Proceedings of the 38th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {459 - 472}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {There have been several efforts to bring static type inference to object-oriented dynamic languages such as Ruby, Python, and Perl. In our experience, however, such type inference systems are extremely difficult to develop, because dynamic languages are typically complex, poorly specified, and include features, such as eval and reflection, that are hard to analyze. In this paper, we introduce constraint-based dynamic type inference, a technique that infers static types based on dynamic program executions. In our approach, we wrap each run-time value to associate it with a type variable, and the wrapper generates constraints on this type variable when the wrapped value is used. This technique avoids many of the often overly conservative approximations of static tools, as constraints are generated based on how values are used during actual program runs. Using wrappers is also easy to implement, since we need only write a constraint resolution algorithm and a transformation to introduce the wrappers. The best part is that we can eat our cake, too: our algorithm will infer sound types as long as it observes every path through each method body---note that the number of such paths may be dramatically smaller than the number of paths through the program as a whole. We have developed Rubydust, an implementation of our algorithm for Ruby. Rubydust takes advantage of Ruby{\textquoteright}s dynamic features to implement wrappers as a language library. We applied Rubydust to a number of small programs and found it to be both easy to use and useful: Rubydust discovered 1 real type error, and all other inferred types were correct and readable.}, keywords = {dynamic languages, dynamic type inference, ruby, static types}, isbn = {978-1-4503-0490-0}, doi = {10.1145/1926385.1926437}, url = {http://doi.acm.org/10.1145/1926385.1926437}, author = {An,Jong-hoon (David) and Chaudhuri,Avik and Foster, Jeffrey S. and Hicks, Michael W.} } @article {15751, title = {Euclidean distance matrix completion problems}, journal = {Optimization Methods and Software}, year = {2011}, month = {2011///}, pages = {1 - 23}, abstract = {A Euclidean distance matrix (EDM) is one in which the (i, j) entry specifies the squared distance between particle i and particle j. Given a partially specified symmetric matrix A with zero diagonal, the Euclidean distance matrix completion problem (EDMCP) is to determine the unspecified entries to make A an EDM. We survey three different approaches to solving the EDMCP. We advocate expressing the EDMCP as a non-convex optimization problem using the particle positions as variables and solving using a modified Newton or quasi-Newton method. To avoid local minima, we develop a randomized initialization technique that involves a nonlinear version of the classical multidimensional scaling, and a dimensionality relaxation scheme with optional weighting. Our experiments show that the method easily solves the artificial problems introduced by Mor{\'e} and Wu. It also solves the 12 much more difficult protein fragment problems introduced by Hendrickson, and the six larger protein problems introduced by Grooms, Lewis and Trosset.A Euclidean distance matrix (EDM) is one in which the (i, j) entry specifies the squared distance between particle i and particle j. Given a partially specified symmetric matrix A with zero diagonal, the Euclidean distance matrix completion problem (EDMCP) is to determine the unspecified entries to make A an EDM. We survey three different approaches to solving the EDMCP. We advocate expressing the EDMCP as a non-convex optimization problem using the particle positions as variables and solving using a modified Newton or quasi-Newton method. To avoid local minima, we develop a randomized initialization technique that involves a nonlinear version of the classical multidimensional scaling, and a dimensionality relaxation scheme with optional weighting. Our experiments show that the method easily solves the artificial problems introduced by Mor{\'e} and Wu. It also solves the 12 much more difficult protein fragment problems introduced by Hendrickson, and the six larger protein problems introduced by Grooms, Lewis and Trosset. }, isbn = {1055-6788}, doi = {10.1080/10556788.2011.643888}, url = {http://www.tandfonline.com/doi/abs/10.1080/10556788.2011.643888}, author = {Fang,Haw-ren and O{\textquoteright}Leary, Dianne P.} } @article {14690, title = {Evaluating Dynamic Software Update Safety Using Systematic Testing}, journal = {IEEE Transactions on Software Engineering}, volume = {PP}, year = {2011}, pages = {1 - 1}, abstract = {Dynamic software updating (DSU) systems patch programs on the fly without incurring downtime. To avoid failures due to the updating process itself, many DSU systems employ timing restrictions. However, timing restrictions are theoretically imperfect, and their practical effectiveness is an open question. This paper presents the first significant empirical evaluation of three popular timing restrictions: activeness safety (AS), which prevents updates to active functions; con-freeness safety (CFS), which only allows modifications to active functions when doing so is provably type-safe; and manual identification of the event-handling loops during which an update may occur. We evaluated these timing restrictions using a series of DSU patches to three programs: OpenSSH, vsftpd, and ngIRCd. We systematically applied updates at each distinct update point reached during execution of a suite of system tests for these programs to determine which updates pass and which fail. We found that all three timing restrictions prevented most failures, but only manual identification allowed none. Further, although CFS and AS allowed many more update points, manual identification still supported updates with minimal delay. Finally, we found that manual identification required the least developer effort. Overall, we conclude that manual identification is most effective.}, keywords = {and serviceability, Availability, Computer Systems Organization, Delay, Manuals, Performance of Systems, reliability, Safety, servers, software, software engineering, Test execution, Testing and Debugging}, isbn = {0098-5589}, doi = {10.1109/TSE.2011.101}, author = {Hayden,C. and Smith,E. and Hardisty,E. and Hicks, Michael W. and Foster, Jeffrey S.} } @article {14329, title = {Every bit has a cost}, journal = {XRDS}, volume = {17}, year = {2011}, month = {2011/06//}, pages = {5 - 5}, isbn = {1528-4972}, doi = {10.1145/1961678.1961695}, url = {http://doi.acm.org/10.1145/1961678.1961695}, author = {Jon Froehlich} } @article {19191, title = {Every bit has a cost}, journal = {XRDS}, volume = {17}, year = {2011}, month = {2011}, pages = {5 - 5}, isbn = {1528-4972}, url = {http://doi.acm.org/10.1145/1961678.1961695}, author = {Jon Froehlich} } @article {18526, title = {The Evolution of Network Configuration: A Tale of Two Campuses}, journal = {Networks}, volume = {7}, year = {2011}, month = {2011///}, pages = {18 - 18}, abstract = {Studying network configuration evolution can improve our under- standing of the evolving complexity of networks and can be helpful in making network configuration less error-prone. Unfortunately, the nature of changes that operators make to network configuration is poorly understood. Towards improving our understanding, we examine and analyze five years of router, switch, and firewall con- figurations from two large campus networks using the logs from version control systems used to store the configurations. We study how network configuration is distributed across different network operations tasks and how the configuration for each task evolves over time, for different types of devices and for different loca- tions in the network. To understand the trends of how configura- tion evolves over time, we study the extent to which configuration for various tasks are added, modified, or deleted. We also study whether certain devices experience configuration changes more fre- quently than others, as well as whether configuration changes tend to focus on specific portions of the configuration (or on specific tasks). We also investigate when network operators make configu- ration changes of various types. Our results concerning configura- tion changes can help the designers of configuration languages un- derstand which aspects of configuration might be more automated or tested more rigorously and may ultimately help improve config- uration languages.}, author = {Kim,H. and Benson,T. and Akella,A. and Feamster, Nick} } @article {15752, title = {Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {79}, year = {2011}, month = {2011/07/01/}, pages = {2268 - 2281}, abstract = {We present and evaluate a rigid-body, deterministic, molecular docking method, called ELMDOCK, that relies solely on the three-dimensional structure of the individual components and the overall rotational diffusion tensor of the complex, obtained from nuclear spin-relaxation measurements. We also introduce a docking method, called ELMPATIDOCK, derived from ELMDOCK and based on the new concept of combining the shape-related restraints from rotational diffusion with those from residual dipolar couplings, along with ambiguous contact/interface-related restraints obtained from chemical shift perturbations. ELMDOCK and ELMPATIDOCK use two novel approximations of the molecular rotational diffusion tensor that allow computationally efficient docking. We show that these approximations are accurate enough to properly dock the two components of a complex without the need to recompute the diffusion tensor at each iteration step. We analyze the accuracy, robustness, and efficiency of these methods using synthetic relaxation data for a large variety of protein-protein complexes. We also test our method on three protein systems for which the structure of the complex and experimental relaxation data are available, and analyze the effect of flexible unstructured tails on the outcome of docking. Additionally, we describe a method for integrating the new approximation methods into the existing docking approaches that use the rotational diffusion tensor as a restraint. The results show that the proposed docking method is robust against experimental errors in the relaxation data or structural rearrangements upon complex formation and is computationally more efficient than current methods. The developed approximations are accurate enough to be used in structure refinement protocols. Proteins 2011; {\textcopyright} 2011 Wiley-Liss, Inc.}, keywords = {diffusion-guided molecular assembly, ellipsoid model, ELM, PATI, protein complexes, residual dipolar couplings, rigid-body docking}, isbn = {1097-0134}, doi = {10.1002/prot.23053}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.23053/full}, author = {Berlin,Konstantin and O{\textquoteright}Leary, Dianne P. and Fushman, David} } @conference {17184, title = {HCI for peace: from idealism to concrete steps}, booktitle = {PART 2 {\textemdash}{\textemdash}{\textemdash}{\textendash} Proceedings of the 2011 annual conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {613 - 616}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This panel will contribute diverse perspectives on the use of computer technology to promote peace and prevent armed conflict. These perspectives include: the use of social media to promote democracy and citizen participation, the role of computers in helping people communicate across division lines in zones of conflict, how persuasive technology can promote peace, and how interaction design can play a role in post-conflict reconciliation.}, keywords = {cyprus, peace, persuasive technology, post-conflict reconciliation, social media, value sensitive design, war}, doi = {10.1145/1979482.1979493}, url = {http://doi.acm.org/10.1145/1979482.1979493}, author = {Hourcade,Juan Pablo and Bullock-Rest,Natasha E. and Friedman,Batya and Nelson,Mark and Shneiderman, Ben and Zaphiris,Panayiotis} } @conference {19452, title = {Helping Users Shop for ISPs with Internet Nutrition Labels}, booktitle = {ACM SIGCOMM Workshop on Home Networks {\textquoteright}11}, series = {HomeNets {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {13 - 18}, publisher = {ACM}, organization = {ACM}, abstract = {When purchasing home broadband access from Internet service providers (ISPs), users must decide which service plans are most appropriate for their needs. Today, ISPs advertise their available service plans using only generic upload and download speeds. Unfortunately, these metrics do not always accurately reflect the varying performance that home users will experience for a wide range of applications. In this paper, we propose that each ISP service plan carry a "nutrition label" that conveys more comprehensive information about network metrics along many dimensions, including various aspects of throughput, latency, loss rate, and jitter. We first justify why these metrics should form the basis of a network nutrition label. Then, we demonstrate that current plans that are superficially similar with respect to advertised download rates may have different performance according to the label metrics. We close with a discussion of the challenges involved in presenting a nutrition label to users in a way that is both accurate and easy to understand.}, keywords = {access networks, benchmarking, bismark, broadband networks, gateway measurements}, isbn = {978-1-4503-0798-7}, url = {http://doi.acm.org/10.1145/2018567.2018571}, author = {Sundaresan, Srikanth and Feamster, Nick and Teixeira, Renata and Tang, Anthony and Edwards, W. Keith and Grinter, Rebecca E. and Marshini Chetty and de Donato, Walter} } @article {13942, title = {A Hierarchical Algorithm for Fast Debye Summation with Applications to Small Angle Scattering}, journal = {Technical Reports from UMIACS}, year = {2011}, month = {2011/09/01/}, abstract = {Debye summation, which involves the summation of sinc functions of distances between all pair of atoms in three dimensional space, arises in computations performed in crystallography, small/wide angle X-ray scattering (SAXS/WAXS) and small angle neutron scattering (SANS). Direct evaluation of Debye summation has quadratic complexity, which results in computational bottleneck when determining crystal properties, or running structure refinement protocols that involve SAXS or SANS, even for moderately sized molecules. We present a fast approximation algorithm that efficiently computes the summation to any prescribed accuracy epsilon in linear time. The algorithm is similar to the fast multipole method (FMM), and is based on a hierarchical spatial decomposition of the molecule coupled with local harmonic expansions and translation of these expansions. An even more efficient implementation is possible when the scattering profile is all that is required, as in small angle scattering reconstruction (SAS) of macromolecules. We examine the relationship of the proposed algorithm to existing approximate methods for profile computations, and provide detailed description of the algorithm, including error bounds and algorithms for stable computation of the translation operators. Our theoretical and computational results show orders of magnitude improvement in computation complexity over existing methods, while maintaining prescribed accuracy.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/11857}, author = {Gumerov, Nail A. and Berlin,Konstantin and Fushman, David and Duraiswami, Ramani} } @article {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} } @conference {13073, title = {Image ranking and retrieval based on multi-attribute queries}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {801 - 808}, abstract = {We propose a novel approach for ranking and retrieval of images based on multi-attribute queries. Existing image retrieval methods train separate classifiers for each word and heuristically combine their outputs for retrieving multiword queries. Moreover, these approaches also ignore the interdependencies among the query terms. In contrast, we propose a principled approach for multi-attribute retrieval which explicitly models the correlations that are present between the attributes. Given a multi-attribute query, we also utilize other attributes in the vocabulary which are not present in the query, for ranking/retrieval. Furthermore, we integrate ranking and retrieval within the same formulation, by posing them as structured prediction problems. Extensive experimental evaluation on the Labeled Faces in the Wild(LFW), FaceTracer and PASCAL VOC datasets show that our approach significantly outperforms several state-of-the-art ranking and retrieval methods.}, keywords = {datasets;image, datasets;PASCAL, faces, FaceTracer, in, methods;labeled, queries;image, ranking;image, retrieval, retrieval;, the, VOC, wild;multiattribute}, doi = {10.1109/CVPR.2011.5995329}, author = {Siddiquie,B. and Feris,R.S. and Davis, Larry S.} } @article {16043, title = {Improved Identification and Visualization of Emergency Department Patient Visits}, journal = {Annals of Emergency Medicine}, volume = {58}, year = {2011}, month = {2011///}, pages = {S309 - S309}, author = {Hettinger,AZ and Rackoff,A. and Wongsuphasawat,K. and Cheng,H. and Fairbanks,RJ and Plaisant, Catherine and Smith,M. S} } @article {18579, title = {Instrumenting home networks}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {41}, year = {2011}, month = {2011///}, pages = {84 - 89}, abstract = {In managing and troubleshooting home networks, one of the challenges is in knowing what is actually happening. Availability of a record of events that occurred on the home network before trouble appeared would go a long way toward addressing that challenge. In this position/work-in-progress paper, we consider requirements for a general-purpose logging facility for home networks. Such a facility, if properly designed, would potentially have other uses. We describe several such uses and discuss requirements to be considered in the design of a logging platform that would be widely supported and accepted. We also report on our initial deployment of such a facility.}, keywords = {home network management, home network troubleshooting}, isbn = {0146-4833}, doi = {10.1145/1925861.1925875}, url = {http://doi.acm.org/10.1145/1925861.1925875}, author = {Calvert,Kenneth L. and Edwards,W. Keith and Feamster, Nick and Grinter,Rebecca E. and Deng,Ye and Zhou,Xuzi} } @conference {14226, title = {Language Models for Semantic Extraction and Filtering in Video Action Recognition}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011/08/24/}, abstract = {The paper addresses the following issues: (a) how to represent semantic information from natural language so that a vision model can utilize it? (b) how to extract the salient textual information relevant to vision? For a given domain, we present a new model of semantic extraction that takes into account word relatedness as well as word disambiguation in order to apply to a vision model. We automatically process the text transcripts and perform syntactic analysis to extract dependency relations. We then perform semantic extraction on the output to filter semantic entities related to actions. The resulting data are used to populate a matrix of co-occurrences utilized by the vision processing modules. Results show that explicitly modeling the co-occurrence of actions and tools significantly improved performance.}, url = {https://www.aaai.org/ocs/index.php/WS/AAAIW11/paper/viewPaper/3919}, author = {Tzoukermann,Evelyne and Neumann, Jan and Kosecka,Jana and Ferm{\"u}ller, Cornelia and Perera,Ian and Ferraro,Frank and Sapp,Ben and Chaudhry,Rizwan and Singh,Gautam} } @conference {13074, title = {A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {3153 - 3160}, abstract = {We introduce a new large-scale video dataset designed to assess the performance of diverse visual event recognition algorithms with a focus on continuous visual event recognition (CVER) in outdoor areas with wide coverage. Previous datasets for action recognition are unrealistic for real-world surveillance because they consist of short clips showing one action by one individual [15, 8]. Datasets have been developed for movies [11] and sports [12], but, these actions and scene conditions do not apply effectively to surveillance videos. Our dataset consists of many outdoor scenes with actions occurring naturally by non-actors in continuously captured videos of the real world. The dataset includes large numbers of instances for 23 event types distributed throughout 29 hours of video. This data is accompanied by detailed annotations which include both moving object tracks and event examples, which will provide solid basis for large-scale evaluation. Additionally, we propose different types of evaluation modes for visual recognition tasks and evaluation metrics along with our preliminary experimental results. We believe that this dataset will stimulate diverse aspects of computer vision research and help us to advance the CVER tasks in the years ahead.}, keywords = {algorithm;evaluation, CVER, databases;, databases;video, dataset;moving, event, metrics;large-scale, object, recognition, recognition;diverse, recognition;video, scenes;surveillance, surveillance;visual, tasks;computer, tracks;outdoor, video, video;computer, vision;continuous, vision;image, visual}, doi = {10.1109/CVPR.2011.5995586}, author = {Oh,Sangmin and Hoogs, A. and Perera,A. and Cuntoor, N. and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,S. and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,E. and Wang,Xioyang and Ji,Qiang and Reddy,K. and Shah,M. and Vondrick,C. and Pirsiavash,H. and Ramanan,D. and Yuen,J. and Torralba,A. and Song,Bi and Fong,A. and Roy-Chowdhury, A. and Desai,M.} } @article {14705, title = {LOCKSMITH: Practical static race detection for C}, journal = {ACM Trans. Program. Lang. Syst.}, volume = {33}, year = {2011}, month = {2011/01//}, pages = {3:1{\textendash}3:55 - 3:1{\textendash}3:55}, abstract = {Locksmith is a static analysis tool for automatically detecting data races in C programs. In this article, we describe each of Locksmith{\textquoteright}s component analyses precisely, and present systematic measurements that isolate interesting trade-offs between precision and efficiency in each analysis. Using a benchmark suite comprising stand-alone applications and Linux device drivers totaling more than 200,000 lines of code, we found that a simple no-worklist strategy yielded the most efficient interprocedural dataflow analysis; that our sharing analysis was able to determine that most locations are thread-local, and therefore need not be protected by locks; that modeling C structs and void pointers precisely is key to both precision and efficiency; and that context sensitivity yields a much more precise analysis, though with decreased scalability. Put together, our results illuminate some of the key engineering challenges in building Locksmith and data race detection analyses in particular, and constraint-based program analyses in general.}, keywords = {context sensitivity, contextual effects, correlation inference, Data race, locksmith, race detection, sharing analysis, static analysis}, isbn = {0164-0925}, doi = {10.1145/1889997.1890000}, url = {http://doi.acm.org/10.1145/1889997.1890000}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. 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 {12406, title = {Modeling diverse standpoints in text classification: learning to be human by modeling human values}, booktitle = {Proceedings of the 2011 iConference}, series = {iConference {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {672 - 673}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {An annotator{\textquoteright}s classification of a text not only tells us something about the intent of the text{\textquoteright}s author, it also tells us something about the annotator{\textquoteright}s standpoint. To understand authorial intent, we can consider all of these diverse standpoints, as well as the extent to which the annotators{\textquoteright} standpoints affect their perceptions of authorial intent. To model human behavior, it is important to model humans{\textquoteright} unique standpoints. Human values play an especially important role in determining human behavior and how people perceive the world around them, so any effort to model human behavior and perception can benefit from an effort to understand and model human values. Instead of training humans to obscure their standpoints and act like computers, we should teach computers to have standpoints of their own.}, keywords = {diversity, framing theory, machine learning, standpoint epistemology, value sensitive computing}, isbn = {978-1-4503-0121-3}, doi = {10.1145/1940761.1940863}, url = {http://doi.acm.org/10.1145/1940761.1940863}, author = {Fleischmann,Kenneth R. and Templeton,Thomas Clay and Jordan Boyd-Graber} } @article {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 {14709, title = {MultiOtter: Multiprocess Symbolic Execution}, journal = {Technical Reports of the Computer Science Department}, year = {2011}, month = {2011///}, abstract = {Symbolic execution can be an effective technique for exploring large numbers of program paths, but it has generally been applied to programs running in isolation, whose inputs are files or command-line arguments. Programs that take inputs from other programs---servers, for example---have been beyond the reach of symbolic execution. To address this, we developed a multiprocess symbolic executor called MultiOtter, along with an implementation of many of the POSIX functions, such as socket and select, that interactive programs usually rely on. However, that is just a first step. Next, we must determine what symbolic inputs to feed to an interactive program to make multiprocess symbolic execution effective. Providing completely unconstrained symbolic values causes symbolic execution to spend too much time exploring uninteresting paths, such as paths to handle invalid inputs. MultiOtter allows us to generate inputs that conform to a context-free grammar, similar to previous work, but it also enables new input generation capabilities because we can now run arbitrary programs concurrently with the program being studied. As examples, we symbolically executed a key-value store server, redis, and an FTP server, vsftpd, each with a variety of inputs, including symbolic versions of tests from redis{\textquoteright}s test suite and wget as a client for vsftpd. We report the coverage provided by symbolic execution with various forms of symbolic input, showing that different testing goals require different degrees of symbolic inputs.}, author = {Turpie,J. and Reisner,E. and Foster, Jeffrey S. and Hicks, Michael W.} } @conference {13461, title = {Playing to Program: Towards an Intelligent Programming Tutor for RUR-PLE}, booktitle = {Second AAAI Symposium on Educational Advances in Artificial Intelligence}, year = {2011}, month = {2011/04/08/}, abstract = {Intelligent tutoring systems (ITSs) provide students with a one-on-one tutor, allowing them to work at their own pace, and helping them to focus on their weaker areas. The RUR1{\textendash}Python Learning Environment (RUR-PLE), a game-like virtual environment to help students learn to program, provides an interface for students to write their own Python code and visualize the code execution (Roberge 2005). RUR-PLE provides a fixed sequence of learning lessons for students to explore. We are extending RUR-PLE to develop the Playing to Program (PtP) ITS, which consists of three components: (1) a Bayesian student model that tracks student competence, (2) a diagnosis module that provides tailored feedback to students, and (3) a problem selection module that guides the student{\textquoteright}s learning process. In this paper, we summarize RUR-PLE and the PtP design, and describe an ongoing user study to evaluate the predictive accuracy of our student modeling approach.}, url = {http://www.aaai.org/ocs/index.php/EAAI/EAAI11/paper/viewPaper/3497}, author = {desJardins, Marie and Ciavolino,Amy and Deloatch,Robert and Feasley,Eliana} } @article {18521, title = {Practical Data-Leak Prevention for Legacy Applications in Enterprise Networks}, volume = {GT-CS-11-01}, year = {2011}, month = {2011///}, institution = {Georgia Institute of Technology}, abstract = {Organizations must control where private information spreads; this problem is referred to in the industry as data leak prevention. Commercial solutions for DLP are based on scanning content; these impose high overhead and are easily evaded. Research solutions for this problem, information flow control, require rewriting applications or running a custom operating system, which makes these approaches difficult to deploy. They also typically enforce information flow control on a single host, not across a network, making it difficult to implement an information flow control policy for a network of machines. This paper presents Pedigree, which enforces information flow control across a network for legacy applications. Pedigree allows enterprise administrators and users to associate a label with each file and process; a small, trusted module on the host uses these labels to determine whether two processes on the same host can communicate. When a process attempts to communicate across the network, Pedigree tracks these information flows and enforces information flow control either at end-hosts or at a network switch. Pedigree allows users and operators to specify network-wide information flow policies rather than having to specify and implement policies for each host. Enforcing information flow policies in the network allows Pedigree to operate in networks with heterogeneous devices and operating systems. We present the design and implementation of Pedigree, show that it can prevent data leaks, and investigate its feasibility and usability in common environments.}, url = {http://hdl.handle.net/1853/36612}, author = {Mundada,Y. and Ramachandran,A. and Tariq,M.B. and Feamster, Nick} } @conference {13336, title = {The PR-star octree: a spatio-topological data structure for tetrahedral meshes}, booktitle = {Proceedings of the 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {92 - 101}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose the PR-star octree as a combined spatial data structure for performing efficient topological queries on tetrahedral meshes. The PR-star octree augments the Point Region octree (PR Octree) with a list of tetrahedra incident to its indexed vertices, i.e. those in the star of its vertices. Thus, each leaf node encodes the minimal amount of information necessary to locally reconstruct the topological connectivity of its indexed elements. This provides the flexibility to efficiently construct the optimal data structure to solve the task at hand using a fraction of the memory required for a corresponding data structure on the global tetrahedral mesh. Due to the spatial locality of successive queries in typical GIS applications, the construction costs of these runtime data structures are amortized over multiple accesses while processing each node. We demonstrate the advantages of the PR-star octree representation in several typical GIS applications, including detection of the domain boundaries, computation of local curvature estimates and mesh simplification.}, isbn = {978-1-4503-1031-4}, doi = {10.1145/2093973.2093987}, url = {http://doi.acm.org/10.1145/2093973.2093987}, author = {Weiss,Kenneth and De Floriani, Leila and Fellegara,Riccardo and Velloso,Marcelo} } @article {17920, title = {A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing}, journal = {Graphical Models}, volume = {73}, year = {2011}, month = {2011/09//}, pages = {231 - 242}, abstract = {In recent years, we have witnessed a striking increase in research concerning how to describe a meshed surface. These descriptors are commonly used to encode mesh properties or guide mesh processing, not to augment existing computations by replication. In this work, we first define a robust surface descriptor based on a local height field representation, and present a transformation via the extraction of Zernike moments. Unlike previous work, our local surface descriptor is innately rotationally invariant. Second, equipped with this novel descriptor, we present SAMPLE {\textendash} similarity augmented mesh processing using local exemplars {\textendash} a method which uses feature neighbourhoods to propagate mesh processing done in one part of the mesh, the local exemplar, to many others. Finally, we show that SAMPLE can be used in a number of applications, such as detail transfer and parameterization.}, keywords = {Local descriptors, Non-local mesh processing, shape analysis, Similarity processing}, isbn = {1524-0703}, doi = {10.1016/j.gmod.2011.05.002}, url = {http://www.sciencedirect.com/science/article/pii/S1524070311000166}, author = {Maximo, A. and Patro,R. and Varshney, Amitabh and Farias, R.} } @article {18535, title = {SilverLine: Data and Network Isolation for Cloud Services}, journal = {2nd USENIX Workshop on Hot Topics in Cloud Computing}, year = {2011}, month = {2011///}, abstract = {Although cloud computing service providers offer op-portunities for improving the administration, reliability, and maintenance of hosted services, they also concen- trate network resources and data in a small number of cloud service providers. The concentration of data and resources also entails various associated risks, including sharing the underlying infrastructure with unknown (and untrusted) tenants and relying on the availability and se- curity of the underlying infrastructure itself. These se- curity risks represent some of the most significant bar- riers to the adoption of cloud-based services. To begin tackling these risks, a cloud hosting infrastructure should provide strong guarantees for resource and data isolation. This paper examines data and network isolation prob- lems with today{\textquoteright}s cloud hosting infrastructures and pro- poses SilverLine, a collection of techniques to improve data and network isolation for a cloud tenants{\textquoteright} service. }, author = {Mundada,Y. and Ramachandran,A. and Feamster, Nick} } @conference {12413, title = {Simulating Audiences: Automating Analysis of Values, Attitudes, and Sentiment}, booktitle = {Privacy, Security, Risk and Trust (PASSAT), 2011 IEEE Third International Conference on and 2011 IEEE Third International Confernece on Social Computing (SocialCom)}, year = {2011}, month = {2011/10/09/11}, pages = {734 - 737}, publisher = {IEEE}, organization = {IEEE}, abstract = {Current events such as the Park51 Project in downtown Manhattan create "critical discourse moments," explosions of discourse around a topic that can be exploited for data gathering. Policymakers have a need to understand the dynamics of public discussion in real time. Human values, which are cognitively related to attitudes and serve as reference points in moral argument, are important indicators of what{\textquoteright}s at stake in a public controversy. This work shows that it is possible to link values data with reader behavior to infer values implicit in a topical corpus, and that it is possible to automate this process using machine learning.}, keywords = {audience simulation, behavioural sciences computing, crowdsourcing, Educational institutions, human values, HUMANS, learning (artificial intelligence), machine learning, moral argument, natural language processing, Park51 project, Presses, public controversy, public discussion, Security, social sciences computing, support vector machines, Weaving}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.238}, author = {Templeton,T.C. and Fleischmann,K.R. and Jordan Boyd-Graber} } @conference {18599, title = {Spam or ham?: characterizing and detecting fraudulent "not spam" reports in web mail systems}, booktitle = {Proceedings of the 8th Annual Collaboration, Electronic messaging, Anti-Abuse and Spam Conference}, series = {CEAS {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {210 - 219}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Web mail providers rely on users to "vote" to quickly and col-laboratively identify spam messages. Unfortunately, spammers have begun to use bots to control large collections of compromised Web mail accounts not just to send spam, but also to vote "not spam" on incoming spam emails in an attempt to thwart collaborative filtering. We call this practice a vote gaming attack. This attack confuses spam filters, since it causes spam messages to be mislabeled as legitimate; thus, spammer IP addresses can continue sending spam for longer. In this paper, we introduce the vote gaming attack and study the extent of these attacks in practice, using four months of email voting data from a large Web mail provider. We develop a model for vote gaming attacks, explain why existing detection mechanisms cannot detect them, and develop a new, scalable clustering-based detection method that identifies compromised accounts that engage in vote-gaming attacks. Our method detected 1.1 million potentially compromised accounts with only a 0.17\% false positive rate, which is nearly 10 times more effective than existing clustering methods used to detect bots that send spam from compromised Web mail accounts.}, isbn = {978-1-4503-0788-8}, doi = {10.1145/2030376.2030401}, url = {http://doi.acm.org/10.1145/2030376.2030401}, author = {Ramachandran,Anirudh and Dasgupta,Anirban and Feamster, Nick and Weinberger,Kilian} } @article {12442, title = {Special Issue on Video Analysis on Resource-Limited Systems}, journal = {IEEE Transactions on Circuits and Systems for Video Technology}, volume = {21}, year = {2011}, month = {2011/10//}, pages = {1349 - 1352}, abstract = {The 17 papers in this special issue focus on resource-limited systems.}, keywords = {computational complexity, Image Enhancement, Special issues and sections, Video compression}, isbn = {1051-8215}, doi = {10.1109/TCSVT.2011.2165795}, author = {Chellapa, Rama and Cavallaro, A. and Wu,Y. and Shan, C. and Fu, Y. and Pulli, K.} } @conference {14736, title = {State transfer for clear and efficient runtime updates}, booktitle = {2011 IEEE 27th International Conference on Data Engineering Workshops (ICDEW)}, year = {2011}, month = {2011/04/11/16}, pages = {179 - 184}, publisher = {IEEE}, organization = {IEEE}, abstract = {Dynamic software updating (DSU), the practice of updating software while it executes, is a lively area of research. The DSU approach most prominent in both commercial and research systems is in-place updating, in which patches containing program modifications are loaded into a running process. However, in-place updating suffers from several problems: it requires complex tool support, it may adversely affect the performance of normal execution, it requires challenging reasoning to understand the behavior of an updated program, and it requires extra effort to modify program state to be compatible with an update. This paper presents preliminary work investigating the potential for state transfer updating to address these problems. State transfer updates work by launching a new process running the updated program version and transferring program state from the running process to the updated version. In this paper, we describe the use and implementation of Ekiden, a new state transfer updating library for C/C++ programs. Ekiden seeks to redress the difficulties of in-place updating, and we report on our experience updating VSFTPD using Ekiden. This initial experience suggests that state transfer provides the availability benefits of in-place DSU approaches while addressing many of their shortcomings.}, keywords = {C++ language, C++ program, Cognition, complex tool support, dynamic software updating, efficient runtime update, in-place DSU approach, Libraries, Operating systems, program modification, Program processors, program transfer, program version, Runtime, servers, software libraries, Software maintenance, state transfer update, Steady-state, updating library, VSFTPD}, isbn = {978-1-4244-9195-7}, doi = {10.1109/ICDEW.2011.5767632}, author = {Hayden,C.M. and Smith,E. K and Hicks, Michael W. and Foster, Jeffrey S.} } @article {18720, title = {Structure and recognition of polyubiquitin chains of different lengths and linkage}, journal = {F1000 Biology ReportsF1000 Biol Rep}, volume = {3}, year = {2011}, month = {2011/12/01/}, abstract = {The polyubiquitin signal is post-translationally attached to a large number of proteins, often directing formation of macromolecular complexes resulting in the translocation, assembly or degradation of the attached protein. Recent structural and functional studies reveal general mechanisms by which different architectures and length of the signal are distinguished.}, isbn = {1757-594X}, doi = {10.3410/B3-26}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229271/}, author = {Fushman, David and Wilkinson,Keith D.} } @article {19118, title = {Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral}, journal = {Electronic Journal of Biotechnology}, volume = {14}, year = {2011}, month = {2011}, pages = {8 - 9}, author = {Lopez, J.V. and Ledger, A. and Santiago-V{\'a}zquez, L.Z. and Pop, Mihai and Sommer, D.D. and Ranzer, L.K. and Feldman, R.A. and Russell, G.K.} } @article {18543, title = {A survey of virtual LAN usage in campus networks}, journal = {Communications Magazine, IEEE}, volume = {49}, year = {2011}, month = {2011/07//}, pages = {98 - 103}, abstract = {VLANs are widely used in today{\textquoteright}s enterprise networks to improve Ethernet scalability and support network policies. However, manuals and textbooks offer very little information about how VLANs are actually used in practice. Through discussions with network administrators and analysis of configuration data, we describe how three university campuses and one academic department use VLANs to achieve a variety of goals. We argue that VLANs are ill-suited to some of these goals (e.g., VLANs are often used to realize access control policies, but constrain the types of policies that can be expressed). Furthermore, the use of VLANs leads to significant complexity in the configuration of network devices.}, keywords = {academic department, campus network, educational computing, Educational institutions, Ethernet scalability, Local area networks, network policy support, university campus, virtual LAN usage, VLAN}, isbn = {0163-6804}, doi = {10.1109/MCOM.2011.5936161}, author = {Yu,Minlan and Rexford,J. and Sun,Xin and Rao,Sanjay and Feamster, Nick} } @inbook {12458, title = {Tracking and Identification via Object Reflectance Using a Hyperspectral Video Camera}, booktitle = {Machine Vision Beyond Visible SpectrumMachine Vision Beyond Visible Spectrum}, series = {Augmented Vision and Reality}, volume = {1}, year = {2011}, month = {2011///}, pages = {201 - 219}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and particle filters to simultaneously track and identify an object based on its reflectance spectra is proposed. By exploiting high-resolution spectral features in the visible and near-infrared regimes, the framework is able to track objects that appear featureless to the human eye. For example, we demonstrate that near-IR spectra of human skin can also be used to distinguish different people in a video sequence. These capabilities are illustrated using experiments conducted on real hyperspectral video data.}, isbn = {978-3-642-11568-4}, url = {http://dx.doi.org/10.1007/978-3-642-11568-4_9}, author = {Nguyen,Hien Van and Banerjee,Amit and Burlina,Philippe and Broadwater,Joshua and Chellapa, Rama}, editor = {Hammoud,Riad and Fan,Guoliang and McMillan,Robert W. W. and Ikeuchi,Katsushi and Hammoud,Riad I. and Wolff,Lawrence B.} } @conference {14274, title = {Visual Scene Interpretation as a Dialogue between Vision and Language}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011/08/24/}, abstract = {We present a framework for semantic visual scene interpretation in a system with vision and language. In this framework the system consists of two modules, a language module and a vision module that communicate with each other in a form of a dialogue to actively interpret the scene. The language module is responsible for obtaining domain knowledge from linguistic resources and reasoning on the basis of this knowledge and the visual input. It iteratively creates questions that amount to an attention mechanism for the vision module which in turn shifts its focus to selected parts of the scene and applies selective segmentation and feature extraction. As a formalism for optimizing this dialogue we use information theory. We demonstrate the framework on the problem of recognizing a static scene from its objects and show preliminary results for the problem of human activity recognition from video. Experiments demonstrate the effectiveness of the active paradigm in introducing attention and additional constraints into the sensing process.}, url = {http://www.aaai.org/ocs/index.php/WS/AAAIW11/paper/viewPaper/3989}, author = {Yu,Xiaodong and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {18614, title = {Wide-area routing dynamics of malicious networks}, booktitle = {Proceedings of the ACM SIGCOMM 2011 conference}, series = {SIGCOMM {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {432 - 433}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper studies the routing dynamics of malicious networks. We characterize the routing behavior of malicious networks on both short and long timescales. We find that malicious networks more consistently advertise prefixes with short durations and long inter- arrival times; over longer timescales, we find that malicious ASes connect with more upstream providers than legitimate ASes, and they also change upstream providers more frequently.}, keywords = {BGP, Security, spam}, isbn = {978-1-4503-0797-0}, doi = {10.1145/2018436.2018505}, url = {http://doi.acm.org/10.1145/2018436.2018505}, author = {Konte,Maria and Feamster, Nick} } @article {15262, title = {Achieving anonymity via clustering}, journal = {ACM Trans. Algorithms}, volume = {6}, year = {2010}, month = {2010/07//}, pages = {49:1{\textendash}49:19 - 49:1{\textendash}49:19}, abstract = {Publishing data for analysis from a table containing personal records, while maintaining individual privacy, is a problem of increasing importance today. The traditional approach of deidentifying records is to remove identifying fields such as social security number, name, etc. However, recent research has shown that a large fraction of the U.S. population can be identified using nonkey attributes (called quasi-identifiers) such as date of birth, gender, and zip code. The k-anonymity model protects privacy via requiring that nonkey attributes that leak information are suppressed or generalized so that, for every record in the modified table, there are at least k-1 other records having exactly the same values for quasi-identifiers. We propose a new method for anonymizing data records, where quasi-identifiers of data records are first clustered and then cluster centers are published. To ensure privacy of the data records, we impose the constraint that each cluster must contain no fewer than a prespecified number of data records. This technique is more general since we have a much larger choice for cluster centers than k-anonymity. In many cases, it lets us release a lot more information without compromising privacy. We also provide constant factor approximation algorithms to come up with such a clustering. This is the first set of algorithms for the anonymization problem where the performance is independent of the anonymity parameter k. We further observe that a few outlier points can significantly increase the cost of anonymization. Hence, we extend our algorithms to allow an ε fraction of points to remain unclustered, that is, deleted from the anonymized publication. Thus, by not releasing a small fraction of the database records, we can ensure that the data published for analysis has less distortion and hence is more useful. Our approximation algorithms for new clustering objectives are of independent interest and could be applicable in other clustering scenarios as well.}, keywords = {anonymity, Approximation algorithms, clustering, privacy}, isbn = {1549-6325}, doi = {10.1145/1798596.1798602}, url = {http://doi.acm.org/10.1145/1798596.1798602}, author = {Aggarwal,Gagan and Panigrahy,Rina and Feder,Tom{\'a}s and Thomas,Dilys and Kenthapadi,Krishnaram and Khuller, Samir and Zhu,An} } @article {14660, title = {Adapting Scrum to Managing a Research Group}, journal = {Technical Reports of the Computer Science Department}, year = {2010}, month = {2010/09/18/undef}, abstract = {Score is an adaptation of the Scrum agile software development methodology to the task of managing Ph.D. students in an academic research group. This paper describes Score, conceived in October 2006, and our experience using it. We have found that Score enables us---faculty and students---to be more efficient and thereby more productive, and enhances the cohesion of our research group.}, author = {Hicks, Michael W. and Foster, Jeffrey S.} } @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 {15564, title = {Approximate range searching: The absolute model}, journal = {Computational Geometry}, volume = {43}, year = {2010}, month = {2010/05//}, pages = {434 - 444}, abstract = {Range searching is a well known problem in the area of geometric data structures. We consider this problem in the context of approximation, where an approximation parameter ε \> 0 is provided. Most prior work on this problem has focused on the case of relative errors, where each range shape R is bounded, and points within distance ε . diam ( R ) of the range{\textquoteright}s boundary may or may not be included. We consider a different approximation model, called the absolute model, in which points within distance ε of the range{\textquoteright}s boundary may or may not be included, regardless of the diameter of the range. We consider range spaces consisting of halfspaces, Euclidean balls, simplices, axis-aligned rectangles, and general convex bodies. We consider a variety of problem formulations, including range searching under general commutative semigroups, idempotent semigroups, groups, and range emptiness. We show how idempotence can be used to improve not only approximate, but also exact halfspace range searching. Our data structures are much simpler than both their exact and relative model counterparts, and so are amenable to efficient implementation.}, keywords = {Absolute model, approximation, Halfbox quadtree, Idempotence, Range searching}, isbn = {0925-7721}, doi = {10.1016/j.comgeo.2008.09.009}, url = {http://www.sciencedirect.com/science/article/pii/S0925772109000844}, author = {da Fonseca,Guilherme D. and Mount, Dave} } @article {15566, title = {Approximation algorithm for the kinetic robust K-center problem}, journal = {Computational Geometry}, volume = {43}, year = {2010}, month = {2010/08//}, pages = {572 - 586}, abstract = {Two complications frequently arise in real-world applications, motion and the contamination of data by outliers. We consider a fundamental clustering problem, the k-center problem, within the context of these two issues. We are given a finite point set S of size n and an integer k. In the standard k-center problem, the objective is to compute a set of k center points to minimize the maximum distance from any point of S to its closest center, or equivalently, the smallest radius such that S can be covered by k disks of this radius. In the discrete k-center problem the disk centers are drawn from the points of S, and in the absolute k-center problem the disk centers are unrestricted.We generalize this problem in two ways. First, we assume that points are in continuous motion, and the objective is to maintain a solution over time. Second, we assume that some given robustness parameter 0 \< t ⩽ 1 is given, and the objective is to compute the smallest radius such that there exist k disks of this radius that cover at least ⌈ t n ⌉ points of S. We present a kinetic data structure (in the KDS framework) that maintains a ( 3 + ε ) -approximation for the robust discrete k-center problem and a ( 4 + ε ) -approximation for the robust absolute k-center problem, both under the assumption that k is a constant. We also improve on a previous 8-approximation for the non-robust discrete kinetic k-center problem, for arbitrary k, and show that our data structure achieves a ( 4 + ε ) -approximation. All these results hold in any metric space of constant doubling dimension, which includes Euclidean space of constant dimension. }, keywords = {Approximation algorithms, clustering, kinetic data structures, robust statistics}, isbn = {0925-7721}, doi = {10.1016/j.comgeo.2010.01.001}, url = {http://www.sciencedirect.com/science/article/pii/S0925772110000027}, author = {Friedler,Sorelle A. and Mount, Dave} } @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} } @article {14201, title = {Better Flow Estimation from Color Images-Volume 2007, Article ID 53912, 9 pages}, journal = {EURASIP Journal on Advances in Signal Processing}, volume = {2007}, year = {2010}, month = {2010///}, author = {Ji,H. and Ferm{\"u}ller, Cornelia} } @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} } @article {18553, title = {Building a fast, virtualized data plane with programmable hardware}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {40}, year = {2010}, month = {2010/01//}, pages = {75 - 82}, abstract = {Network virtualization allows many networks to share the same underlying physical topology; this technology has offered promise both for experimentation and for hosting multiple networks on a single shared physical infrastructure. Much attention has focused on virtualizing the network control plane, but, ultimately, a limiting factor in the deployment of these virtual networks is data-plane performance: Virtual networks must ultimately forward packets at rates that are comparable to native, hardware-based approaches. Aside from proprietary solutions from vendors, hardware support for virtualized data planes is limited. The advent of open, programmable network hardware promises flexibility, speed, and resource isolation, but, unfortunately, hardware does not naturally lend itself to virtualization. We leverage emerging trends in programmable hardware to design a flexible, hardware-based data plane for virtual networks. We present the design, implementation, and preliminary evaluation of this hardware-based data plane and show how the proposed design can support many virtual networks without compromising performance or isolation.}, keywords = {netfpga, network virtualization}, isbn = {0146-4833}, doi = {10.1145/1672308.1672323}, url = {http://doi.acm.org/10.1145/1672308.1672323}, author = {Anwer,Muhammad Bilal and Feamster, Nick} } @conference {18932, title = {Building an IT Taxonomy with Co-occurrence Analysis, Hierarchical Clustering, and Multidimensional Scaling}, year = {2010}, month = {2010///}, abstract = {Different information technologies (ITs) are related in complex ways. How can the relationships among a large number of ITs be described and analyzed in a representative, dynamic, and scalable way? In this study, we employed co-occurrence analysis to explore the relationships among 50 information technologies discussed in six magazines over ten years (1998-2007). Using hierarchical clustering and multidimensional scaling, we have found that the similarities of the technologies can be depicted in hierarchies and two-dimensional plots, and that similar technologies can be classified into meaningful categories. The results imply reasonable validity of our approach for understanding technology relationships and building an IT taxonomy. The methodology that we offer not only helps IT practitioners and researchers make sense of numerous technologies in the iField but also bridges two related but thus far largely separate research streams in iSchools - information management and IT management.}, url = {https://www.ideals.illinois.edu/handle/2142/14918}, author = {Tsui,C. and Wang,P. and Fleischmann,K.R. and Sayeed,A. B. and Weinberg, Amy} } @conference {13905, title = {Children{\textquoteright}s roles using keyword search interfaces at home}, booktitle = {Proceedings of the 28th international conference on Human factors in computing systems}, year = {2010}, month = {2010///}, pages = {413 - 422}, author = {Druin, Allison and Foss,E. and Hutchinson,H. and Golub,E. and Hatley,L.} } @article {18501, title = {Chipping away at censorship firewalls with user-generated content}, journal = {Proc. 19th USENIX Security Symposium, Washington, DC}, year = {2010}, month = {2010///}, abstract = {Oppressive regimes and even democratic governmentsrestrict Internet access. Existing anti-censorship systems often require users to connect through proxies, but these systems are relatively easy for a censor to discover and block. This paper offers a possible next step in the cen- sorship arms race: rather than relying on a single system or set of proxies to circumvent censorship firewalls, we explore whether the vast deployment of sites that host user-generated content can breach these firewalls. To ex- plore this possibility, we have developed Collage, which allows users to exchange messages through hidden chan- nels in sites that host user-generated content. Collage has two components: a message vector layer for embedding content in cover traffic; and a rendezvous mechanism to allow parties to publish and retrieve messages in the cover traffic. Collage uses user-generated content (e.g., photo-sharing sites) as {\textquotedblleft}drop sites{\textquotedblright} for hidden messages. To send a message, a user embeds it into cover traffic and posts the content on some site, where receivers retrieve this content using a sequence of tasks. Collage makes it difficult for a censor to monitor or block these messages by exploiting the sheer number of sites where users can exchange messages and the variety of ways that a mes- sage can be hidden. Our evaluation of Collage shows that the performance overhead is acceptable for sending small messages (e.g., Web articles, email). We show how Collage can be used to build two applications: a direct messaging application, and a Web content delivery system. }, author = {Burnett,S. and Feamster, Nick and Vempala,S.} } @conference {18556, title = {Circumventing censorship with collage}, booktitle = {Proceedings of the ACM SIGCOMM 2010 conference}, series = {SIGCOMM {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {471 - 472}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Oppressive regimes and even democratic governments restrict Internet access. Existing anti-censorship systems often require users to connect through proxies, but these systems are relatively easy for a censor to discover and block. We explore a possible next step in the censorship arms race: rather than relying on a single system or set of proxies to circumvent censorship firewalls, we use the vast deployment of sites that host user-generated content to breach these firewalls. We have developed Collage, which allows users to exchange messages through hidden channels in sites that host user-generated content. To send a message, a user embeds it into cover traffic and posts the content on some site, where receivers retrieve this content. Collage makes it difficult for a censor to monitor or block these messages by exploiting the sheer number of sites where users can exchange messages and the variety of ways that a message can be hidden. We have built a censorship-resistant news reader using Collage that can retrieve from behind a censorship firewall and show Collage{\textquoteright}s effectiveness with a live demonstration of its complete infrastructure.}, keywords = {Availability, censorship}, isbn = {978-1-4503-0201-2}, doi = {10.1145/1851182.1851269}, url = {http://doi.acm.org/10.1145/1851182.1851269}, author = {Burnett,Sam and Feamster, Nick and Vempala,Santosh} } @conference {13937, title = {Clear Panels: a technique to design mobile application interactivity}, booktitle = {Proceedings of the 8th ACM Conference on Designing Interactive Systems}, year = {2010}, month = {2010///}, pages = {360 - 363}, author = {Brown,Q. and Bonsignore,E. and Hatley,L. and Druin, Allison and Walsh,G. and Foss,E. and Brewer,R. and Hammer,J. and Golub,E.} } @article {13914, title = {Connecting generations: developing co-design methods for older adults and children}, journal = {Behaviour \& Information Technology}, volume = {99999}, year = {2010}, month = {2010///}, pages = {1 - 11}, author = {Xie,B. and Druin, Allison and Fails,J. and Massey,S. and Golub,E. and Franckel,S. and Schneider,K.} } @conference {18559, title = {Decoupling policy from configuration in campus and enterprise networks}, booktitle = {Local and Metropolitan Area Networks (LANMAN), 2010 17th IEEE Workshop on}, year = {2010}, month = {2010/05//}, pages = {1 - 6}, abstract = {This paper surveys our ongoing work on the use of software-defined networking to simplify two acute policy problems in campus and enterprise network operations: access control and information flow control. We describe how the current coupling of high-level policy with low-level configuration makes these problems challenging today. We describe the specific policy problems faced by campus and enterprise network operators; illustrate our approach, which leverages recent trends in separating the network{\textquoteright}s $\#$x201C;control plane $\#$x201D; from the data plane; and show how this approach can be applied to simplify these two enterprise network management tasks. We also describe our ongoing deployment efforts to build a campus network testbed where trial designs can be deployed and evaluated. We close with a summary of current and future research challenges for solving challenges within enterprise networks within the context of this new paradigm.}, keywords = {Access control, Business communication, campus network, decoupling policy, enterprise network management tasks, enterprise network operator, information flow control, software defined network, software radio, telecommunication network management, telecommunication security}, doi = {10.1109/LANMAN.2010.5507162}, author = {Feamster, Nick and Nayak,A. and Kim,Hyojoon and Clark,R. and Mundada,Y. and Ramachandran,A. and bin Tariq,M.} } @article {13286, title = {Design, Analysis and Comparison of Spatial Indexes for Tetrahedral Meshes}, volume = {DISI-TR-2010-05}, year = {2010}, month = {2010///}, institution = {Department of Computer Science and Information Science, University of Genoa}, abstract = {We address the problem of performing spatial queries on tetrahedral meshes. These latterarise in several application domains including 3D GIS, scientific visualization, finite element analysis. We have defined and implemented a family of spatial indexes, that we call tetrahedral trees. Tetrahedral trees are based on a subdivision of a cubic domain containing the mesh defined either by an octree or a 3D kd-tree. For each of them, we have four variants of the spatial index, depending on four different subdivision criteria. Here, we present such indexes, we discuss how to construct them and perform classical spatial queries such as point location and window queries. We compare the various tetrahedral trees based in memory usage, performances in spatial queries and computation times for constructing them. }, author = {De Floriani, Leila and Fellegara,R. and Magillo,P.} } @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} } @article {18525, title = {Distributed Implementation of Coordinated, Network-Wide Policies and Protocols with FlowFlex}, volume = {GT-CS-10-07}, year = {2010}, month = {2010///}, institution = {Georgia Institute of Technology}, abstract = {The increasing programmability of network devices gives protocol designers and network operators considerably more flexibility in defining custom protocols and traffic processing functions. Today, network operators and protocol designers have the option of either operating at flow-level granularity, which offers coordinated control; or packet-level granularity, which offers flexibility, but not coordinated control. Today{\textquoteright}s network programming paradigms force operators to choose between the fine-grained control and expressiveness of packet processing and the coordination of flow processing, which makes it difficult to quickly realize a distributed implementation of a global, network-wide policy. Designers must also choose between the flexibility of hardware-based solutions and the fast development cycles offered by software. This paper proposes a system called FlowFlex that offers network designers the best of both worlds: with FlowFlex, operators can quickly design, implement, and deploy network systems and protocols that offer fast, distributed, implementations that require coordinated control and fine-grained operations on packets. We present the design and implementation of the FlowFlex framework and show how it can improve both expressiveness and efficiency for three real-world networking applications.}, url = {http://hdl.handle.net/1853/35002}, author = {Mundada,Y. and Sherwood,R. and Feamster, Nick} } @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.} } @article {15171, title = {Efficient rational secret sharing in standard communication networks}, journal = {Theory of Cryptography}, year = {2010}, month = {2010///}, pages = {419 - 436}, abstract = {We propose a new methodology for rational secret sharing leading to various instantiations (in both the two-party and multi-party settings) that are simple and efficient in terms of computation, share size, and round complexity. Our protocols do not require physical assumptions or simultaneous channels, and can even be run over asynchronous, point-to-point networks.We also propose new equilibrium notions (namely, computational versions of strict Nash equilibrium and stability with respect to trembles) and prove that our protocols satisfy them. These notions guarantee, roughly speaking, that at each point in the protocol there is a unique legal message a party can send. This, in turn, ensures that protocol messages cannot be used as subliminal channels, something achieved in prior work only by making strong assumptions on the communication network. }, doi = {10.1007/978-3-642-11799-2_25}, author = {Fuchsbauer,G. and Katz, Jonathan and Naccache,D.} } @article {19585, title = {Evaluating Call-By-Need on the Control Stack}, journal = {arXiv:1009.3174 [cs]}, year = {2010}, note = {Comment: Symposium on Trends in Functional Programming (TFP 2010), Norman, Oklahoma, May 2010}, month = {2010/09/16/}, abstract = {Ariola and Felleisen{\textquoteright}s call-by-need {\lambda}-calculus replaces a variable occurrence with its value at the last possible moment. To support this gradual notion of substitution, function applications-once established-are never discharged. In this paper we show how to translate this notion of reduction into an abstract machine that resolves variable references via the control stack. In particular, the machine uses the static address of a variable occurrence to extract its current value from the dynamic control stack.}, keywords = {Computer Science - Programming Languages, D.3.1}, url = {http://arxiv.org/abs/1009.3174}, author = {Chang, Stephen and David Van Horn and Felleisen, Matthias} } @inbook {14196, title = {An Experimental Study of Color-Based Segmentation Algorithms Based on the Mean-Shift Concept}, booktitle = {Computer Vision {\textendash} ECCV 2010Computer Vision {\textendash} ECCV 2010}, series = {Lecture Notes in Computer Science}, volume = {6312}, year = {2010}, month = {2010///}, pages = {506 - 519}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We point out a difference between the original mean-shift formulation of Fukunaga and Hostetler and the common variant in the computer vision community, namely whether the pairwise comparison is performed with the original or with the filtered image of the previous iteration. This leads to a new hybrid algorithm, called Color Mean Shift, that roughly speaking, treats color as Fukunaga{\textquoteright}s algorithm and spatial coordinates as Comaniciu{\textquoteright}s algorithm. We perform experiments to evaluate how different kernel functions and color spaces affect the final filtering and segmentation results, and the computational speed, using the Berkeley and Weizmann segmentation databases. We conclude that the new method gives better results than existing mean shift ones on four standard comparison measures ( improvement on RAND and BDE measures respectively for color images), with slightly higher running times ( ). Overall, the new method produces segmentations comparable in quality to the ones obtained with current state of the art segmentation algorithms.}, isbn = {978-3-642-15551-2}, url = {http://dx.doi.org/10.1007/978-3-642-15552-9_37}, author = {Bitsakos,K. and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Daniilidis,Kostas and Maragos,Petros and Paragios,Nikos} } @article {17152, title = {Exploring distributions: design and evaluation}, journal = {University of Maryland, Human-Computer Interaction Lab Tech Report HCIL-2010-01}, year = {2010}, month = {2010///}, abstract = {Visual overviews of tables of numerical and categorical data have been proposed for tables with a single value per cell.In this paper we address the problem of exploring tables including columns consisting of distributions, e.g. the distributions of movie ratings or trust ratings in recommender systems, age distributions in demographic data, usage distributions in logs of telephone calls etc. We propose a novel way of displaying and interacting with distribution data, and present the results of a usability study that demonstrates the benefits of the interface in providing an overview of the data and facilitating the discovery of interesting clusters, patterns, outliers and relationships between columns. }, author = {Sopan,A. and Freire,M. and Taieb-Maimon,M. and Golbeck,J. and Shneiderman, Ben} } @article {18702, title = {Exploring the Linkage Dependence of Polyubiquitin Conformations Using Molecular Modeling}, journal = {Journal of Molecular Biology}, volume = {395}, year = {2010}, month = {2010/01/29/}, pages = {803 - 814}, abstract = {Posttranslational modification of proteins by covalent attachment of a small protein ubiquitin (Ub) or a polymeric chain of Ub molecules (called polyubiquitin) is involved in controlling a vast variety of processes in eukaryotic cells. The question of how different polyubiquitin signals are recognized is central to understanding the specificity of various types of polyubiquitination. In polyubiquitin, monomers are linked to each other via an isopeptide bond between the C-terminal glycine of one Ub and a lysine of the other. The functional outcome of polyubiquitination depends on the particular lysine involved in chain formation and appears to rely on linkage-dependent conformation of polyubiquitin. Thus, K48-linked chains, a universal signal for proteasomal degradation, under physiological conditions adopt a closed conformation where functionally important residues L8, I44, and V70 are sequestered at the interface between two adjacent Ub monomers. By contrast, K63-linked chains, which act as a nonproteolytic regulatory signal, adopt an extended conformation that lacks hydrophobic interubiquitin contact. Little is known about the functional roles of the so-called {\textquotedblleft}noncanonical{\textquotedblright} chains (linked via K6, K11, K27, K29, or K33, or linked head-to-tail), and no structural information on these chains is available, except for information on the crystal structure of the head-to-tail-linked diubiquitin (Ub2). In this study, we use molecular modeling to examine whether any of the noncanonical chains can adopt a closed conformation similar to that in K48-linked polyubiquitin. Our results show that the eight possible Ub2 chains can be divided into two groups: chains linked via K6, K11, K27, or K48 are predicted to form a closed conformation, whereas chains linked via K29, K33, or K63, or linked head-to-tail are unable to form such a contact due to steric occlusion. These predictions are validated by the known structures of K48-, K63-, and head-to-tail-linked chains. Our study also predicts structural models for Ub2 chains linked via K6, K11, or K27. The implications of these findings for linkage-selective recognition of noncanonical polyubiquitin signals by various receptors are discussed.}, keywords = {head-to-tail, isopeptide linkage, modeling, noncanonical linkage, polyubiquitin}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2009.10.039}, url = {http://www.sciencedirect.com/science/article/pii/S0022283609012790}, author = {Fushman, David and Walker,Olivier} } @conference {15874, title = {Exploring the Relationships among ICTs: A Scalable Computational Approach Using KL Divergence and Hierarchical Clustering}, booktitle = {Hawaii International Conference on System Sciences}, year = {2010}, month = {2010///}, pages = {1 - 10}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Different information and communication technologies (ICTs) are related in complex ways and, accordingly, their diffusion trajectories are related, too. How can the relationships among multiple ICTs be described and analyzed in a scalable way? In this study, we offer a scalable methodology, based on computational analysis of discourse, to examine the relationships among ICTs. Specifically, we employed Kullback-Leibler (KL) divergence to compare the semantic similarity of forty-seven ICTs discussed in the trade magazine InformationWeek over a decade. Using hierarchical clustering, we have found that the similarity of the technologies can be mapped in a hierarchy and similar technologies demonstrated similar discourses. The results establish the validity of our approach and demonstrate its scalability and richness. This analytical approach not only enables diffusion researchers to undertake multi-innovation, multi-source, and multi-period studies, but also helps practitioners effectively adopt and efficiently use new ICTs in their organizations.}, isbn = {978-0-7695-3869-3}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2010.203}, author = {Tsui,Chia-jung and Wang,Ping and Fleischmann,Kenneth R. and Oard, Douglas and Sayeed,Asad B.} } @conference {14280, title = {From program verification to program synthesis}, booktitle = {ACM SIGPLAN Notices}, volume = {45}, year = {2010}, month = {2010///}, pages = {313 - 326}, author = {Srivastava,S. and Gulwani,S. and Foster, Jeffrey S.} } @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} } @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 {14173, title = {Illusory motion due to causal time filtering}, journal = {Vision research}, volume = {50}, year = {2010}, month = {2010///}, pages = {315 - 329}, author = {Ferm{\"u}ller, Cornelia and Ji,H. and Kitaoka,A.} } @article {14487, title = {On the importance of sharing negative results}, journal = {SIGKDD explorations}, volume = {12}, year = {2010}, month = {2010///}, pages = {3 - 4}, author = {Giraud-Carrier,C. and Dunham,M.H. and Atreya,A. and Elkan,C. and Perlich,C. and Swirszcz,G. and Shi,X. and Philip,S.Y. and F{\"u}rnkranz,J. and Sima,J.F.} } @article {13798, title = {Interlingual Annotation of Parallel Text Corpora: A New Framework for Annotation and Evaluation}, journal = {Natural Language Engineering}, volume = {16}, year = {2010}, month = {2010///}, pages = {197 - 243}, abstract = {This paper focuses on an important step in the creation of a system of meaning representation and the development of semantically annotated parallel corpora, for use in applications such as machine translation, question answering, text summarization, and information retrieval. The work described below constitutes the first effort of any kind to annotate multiple translations of foreign-language texts with interlingual content. Three levels of representation are introduced: deep syntactic dependencies (IL0), intermediate semantic representations (IL1), and a normalized representation that unifies conversives, nonliteral language, and paraphrase (IL2). The resulting annotated, multilingually induced, parallel corpora will be useful as an empirical basis for a wide range of research, including the development and evaluation of interlingual NLP systems and paraphrase-extraction systems as well as a host of other research and development efforts in theoretical and applied linguistics, foreign language pedagogy, translation studies, and other related disciplines.}, doi = {10.1017/S1351324910000070}, author = {Dorr, Bonnie J and Passonneau,Rebecca J. and Farwell,David and Green,Rebecca and Habash,Nizar and Helmreich,Stephen and Hovy,Eduard and Levin,Lori and Miller,Keith J. and Mitamura,Teruko and Rambow,Owen and Siddharthan,Advaith} } @article {18522, title = {An Internet Wide View into DNS Lookup Patterns}, year = {2010}, month = {2010///}, institution = {VeriSign Labs, School of Computer Science, Georgia Tech}, abstract = {This paper analyzes the DNS lookup patterns from a largeauthoritative top-level domain server and characterizes how the lookup patterns for unscrupulous domains may differ from those for legitimate domains. We examine domains for phishing attacks and spam and malware related domains, and see how these lookup patterns vary in terms of both their temporal and spatial characteristics. We find that malicious domains tend to exhibit more variance in the networks that look up these domains, and we also find that these domains become popular considerably more quickly after their initial registration time. We also note that miscreant domains ex- hibit distinct clusters, in terms to the networks that look up these domains. The distinct spatial and temporal character- istics of these domains, and their tendency to exhibit simi- lar lookup behavior, suggests that it may be possible to ulti- mately develop more effective blacklisting techniques based on these differing lookup patterns. }, author = {Hao,S. and Feamster, Nick and Pandrangi,R.} } @article {15883, title = {Investigating multi-label classification for human values}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {47}, year = {2010}, month = {2010///}, pages = {1 - 4}, author = {Ishita,E. and Oard, Douglas and Fleischmann,K.R. and Cheng,A.S. and Templeton,T.C.} } @conference {13932, title = {Investigating the impact of design processes on children}, booktitle = {Proceedings of the 9th International Conference on Interaction Design and Children}, year = {2010}, month = {2010///}, pages = {198 - 201}, author = {Guha,M.L. and Druin, Allison and Fails,J. A} } @conference {18578, title = {Joint analysis of network incidents and intradomain routing changes}, booktitle = {Network and Service Management (CNSM), 2010 International Conference on}, year = {2010}, month = {2010/10//}, pages = {198 - 205}, abstract = {This paper studies how intradomain routing instability relates to events in network trouble tickets for two networks: a VPN provider and the Internet2 backbone network. Our goal in performing this joint analysis of routing and trouble tickets is to better understand the likely underlying causes of intradomain routing instability. We develop a method to correlate trouble tickets with instability events and find that, although unplanned events last longer than scheduled maintenance, there is no single underlying cause for most instability, and that these causes differ across networks. In comparison to a similar study from Labovitz et al. from ten years ago, we find that, while certain causes of instability such as maintenance and circuit problems remain significant, power issues have become much less prevalent, and software-related problems have become more common.}, keywords = {correlation method, Internet, Internet2 backbone network, intradomain routing instability, network maintenance, network routing joint analysis, telecommunication network routing, Virtual private networks, VPN provider}, doi = {10.1109/CNSM.2010.5691306}, author = {Medem,A. and Teixeira,R. and Feamster, Nick and Meulle,M.} } @conference {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 {16055, title = {ManyNets: an interface for multiple network analysis and visualization}, booktitle = {Proceedings of the 28th international conference on Human factors in computing systems}, series = {CHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {213 - 222}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Traditional network analysis tools support analysts in studying a single network. ManyNets offers these analysts a powerful new approach that enables them to work on multiple networks simultaneously. Several thousand networks can be presented as rows in a tabular visualization, and then inspected, sorted and filtered according to their attributes. The networks to be displayed can be obtained by subdivision of larger networks. Examples of meaningful subdivisions used by analysts include ego networks, community extraction, and time-based slices. Cell visualizations and interactive column overviews allow analysts to assess the distribution of attributes within particular sets of networks. Details, such as traditional node-link diagrams, are available on demand. We describe a case study analyzing a social network geared towards film recommendations by means of decomposition. A small usability study provides feedback on the use of the interface on a set of tasks issued from the case study.}, keywords = {exploratory analysis, graphical user interface, Information Visualization, interaction, network analysis, table interface}, isbn = {978-1-60558-929-9}, doi = {10.1145/1753326.1753358}, url = {http://doi.acm.org/10.1145/1753326.1753358}, author = {Freire,Manuel and Plaisant, Catherine and Shneiderman, Ben and Golbeck,Jen} } @conference {16025, title = {The Metacognitive Loop: An Architecture for Building Robust Intelligent Systems}, booktitle = {2010 AAAI Fall Symposium Series}, year = {2010}, month = {2010/03/11/}, abstract = {The Metacognitive Loop: An Architecture for Building Robust Intelligent Systems}, keywords = {commonsense, ontologies, robust intelligent systems}, url = {http://www.aaai.org/ocs/index.php/FSS/FSS10/paper/view/2161}, author = {Shahri,Hamid Haidarian and Dinalankara,Wikum and Fults,Scott and Wilson,Shomir and Perlis, Don and Schmill,Matt and Oates,Tim and Josyula,Darsana and Anderson,Michael} } @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.} } @conference {14279, title = {Mixing type checking and symbolic execution}, booktitle = {ACM SIGPLAN Notices}, volume = {45}, year = {2010}, month = {2010///}, pages = {436 - 447}, author = {Khoo,Y.P. and Chang,B.Y.E. and Foster, Jeffrey S.} } @conference {13896, title = {Mobile collaboration: collaboratively reading and creating children{\textquoteright}s stories on mobile devices}, booktitle = {Proceedings of the 9th International Conference on Interaction Design and Children}, year = {2010}, month = {2010///}, pages = {20 - 29}, author = {Fails,J. A and Druin, Allison and Guha,M.L.} } @article {13708, title = {A modality lexicon and its use in automatic tagging}, journal = {Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC{\textquoteright}10)}, year = {2010}, month = {2010///}, pages = {1402 - 1407}, abstract = {This paper describes our resource-building results for an eight-week JHU Human Language Technology Center of Excellence SummerCamp for Applied Language Exploration (SCALE-2009) on Semantically-Informed Machine Translation. Specifically, we describe the construction of a modality annotation scheme, a modality lexicon, and two automated modality taggers that were built using the lexicon and annotation scheme. Our annotation scheme is based on identifying three components of modality: a trigger, a target and a holder. We describe how our modality lexicon was produced semi-automatically, expanding from an initial hand-selected list of modality trigger words and phrases. The resulting expanded modality lexicon is being made publicly available. We demonstrate that one tagger{\textemdash}a structure-based tagger{\textemdash}results in precision around 86\% (depending on genre) for tagging of a standard LDC data set. In a machine translation application, using the structure-based tagger to annotate English modalities on an English-Urdu training corpus improved the translation quality score for Urdu by 0.3 Bleu points in the face of sparse training data. }, author = {Baker,K. and Bloodgood,M. and Dorr, Bonnie J and Filardo,N.W. and Levin,L. and Piatko,C.} } @conference {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} } @article {16049, title = {Non-visual exploration of geographic maps: Does sonification help?}, journal = {Disability \& Rehabilitation: Assistive Technology}, volume = {5}, year = {2010}, month = {2010/05//}, pages = {164 - 174}, abstract = {Purpose. This study aims at evaluating the effectiveness of sonification as a mean to provide access to geo-referenced information to users with visual impairments.Method. Thiry-five participants (10 congenitally blind, 10 with acquired blindness and 15 blindfolded sighted) completed four tasks of progressive difficulty. During each task, participants first explored a sonified map by using either a tablet or a keyboard to move across regions and listened to sounds giving information about the current location. Then the participants were asked to identify, among four tactile maps, the one that crossmodally corresponds to the sonifed map they just explored. Finally, participants answered a self-report questionnaire of understanding and satisfaction. Results. Participants achieved high accuracy in all of the four tactile map discrimination tasks. No significant performance difference was found neither between subjects that used keyboard or tablet, nor between the three groups of blind and sighted participants. Differences between groups and interfaces were found in the usage strategies. High levels of satisfaction and understanding of the tools and tasks emerged from users{\textquoteright} reports. }, isbn = {1748-3107, 1748-3115}, doi = {10.3109/17483100903100277}, url = {http://informahealthcare.com/doi/abs/10.3109/17483100903100277}, author = {Delogu,Franco and Palmiero,Massimiliano and Federici,Stefano and Plaisant, Catherine and Zhao,Haixia and Belardinelli,Olivetti} } @article {14513, title = {Object Classification Using Taxonomies}, volume = {12/414,065}, year = {2010}, month = {2010/07/22/}, abstract = {As provided herein objects from a source catalog, such as a provider{\textquoteright}s catalog, can be added to a target catalog, such as an enterprise master catalog, in a scalable manner utilizing catalog taxonomies. A baseline classifier determines probabilities for source objects to target catalog classes. Source objects can be assigned to those classes with probabilities that meet a desired threshold and meet a desired rate. A classification cost for target classes can be determined for respective unassigned source objects, which can comprise determining an assignment cost and separation cost for the source objects for respective desired target classes. The separation and assignment costs can be combined to determine the classification cost, and the unassigned source objects can be assigned to those classes having a desired classification cost.}, url = {http://www.google.com/patents?id=oXDSAAAAEBAJ}, author = {Tsaparas,Panayiotis and Papadimitriou,Panagiotis and Fuxman,Ariel D. and Getoor, Lise and Agrawal,Rakesh}, editor = {Microsoft Corporation} } @conference {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.} } @conference {18591, title = {Outsourcing home network security}, booktitle = {Proceedings of the 2010 ACM SIGCOMM workshop on Home networks}, series = {HomeNets {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {37 - 42}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The growth of home and small enterprise networks brings with it a large number of devices and networks that are either managed poorly or not at all. Hosts on these networks may become compromised and become sources of spam, denial-of-service traffic, or the site of a scam or phishing attack site. Although a typical user now knows how to apply software updates and run anti-virus software, these techniques still require user vigilance, and they offer no recourse when a machine ultimately becomes compromised. Rather than having individual networks managed independently, we propose to outsource the management and operation of these networks to a third party that has both operations expertise and a broader view of network activity. Our approach harnesses two trends: (1) the advent of programmable network switches, which offer flexibility and the possibility for remote management; and (2) the increasing application of distributed network monitoring and inference algorithms to network security problems (an appealing technique because of its ability to reveal coordinated behavior that may represent an attack).}, keywords = {home networking, NETWORK SECURITY, programmable networking}, isbn = {978-1-4503-0198-5}, doi = {10.1145/1851307.1851317}, url = {http://doi.acm.org/10.1145/1851307.1851317}, author = {Feamster, Nick} } @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} } @article {16391, title = {The problem with zoning: nonlinear effects of interactions between location preferences and externalities on land use and utility}, journal = {Environment and Planning B: Planning and Design}, volume = {37}, year = {2010}, month = {2010///}, pages = {408 - 428}, author = {Zellner,M.L. and Riolo,R.L. and Rand, William and Brown,D.G. and Page,S.E. and Fernandez,L.E.} } @article {15667, title = {Realistic Compression of Kinetic Sensor Data}, volume = {CS-TR-4959}, year = {2010}, month = {2010/06/06/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {We introduce a realistic analysis for a framework for storing andprocessing kinetic data observed by sensor networks. The massive data sets generated by these networks motivates a significant need for compression. We are interested in the kinetic data generated by a finite set of objects moving through space. Our previously introduced framework and accompanying compression algorithm assumed a given set of sensors, each of which continuously observes these moving objects in its surrounding region. The model relies purely on sensor observations; it allows points to move freely and requires no advance notification of motion plans. Here, we extend the initial theoretical analysis of this framework and compression scheme to a more realistic setting. We extend the current understanding of empirical entropy to introduce definitions for joint empirical entropy, conditional empirical entropy, and empirical independence. We also introduce a notion of limited independence between the outputs of the sensors in the system. We show that, even with this notion of limited independence and in both the statistical and empirical settings, the previously introduced compression algorithm achieves an encoding size on the order of the optimal. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/10114}, author = {Friedler,Sorelle A. and Mount, Dave} } @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} } @article {14733, title = {SCORE: agile research group management}, journal = {Commun. ACM}, volume = {53}, year = {2010}, month = {2010/10//}, pages = {30 - 31}, abstract = {Adapting agile software development methodology toward more efficient management of academic research groups.}, isbn = {0001-0782}, doi = {10.1145/1831407.1831421}, url = {http://doi.acm.org/10.1145/1831407.1831421}, author = {Hicks, Michael W. and Foster, Jeffrey S.} } @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.} } @inbook {16284, title = {Sequencing and Genome Assembly Using Next-Generation Technologies}, booktitle = {Computational BiologyComputational Biology}, series = {Methods in Molecular Biology}, volume = {673}, year = {2010}, month = {2010///}, pages = {1 - 17}, publisher = {Humana Press}, organization = {Humana Press}, abstract = {Several sequencing technologies have been introduced in recent years that dramatically outperform the traditional Sanger technology in terms of throughput and cost. The data generated by these technologies are characterized by generally shorter read lengths (as low as 35 bp) and different error characteristics than Sanger data. Existing software tools for assembly and analysis of sequencing data are, therefore, ill-suited to handle the new types of data generated. This paper surveys the recent software packages aimed specifically at analyzing new generation sequencing data.}, isbn = {978-1-60761-842-3}, url = {http://dx.doi.org/10.1007/978-1-60761-842-3_1}, author = {Nagarajan,Niranjan and Pop, Mihai}, editor = {Feny{\"o},David} } @article {14734, title = {Serializing C intermediate representations for efficient and portable parsing}, journal = {Software: Practice and Experience}, volume = {40}, year = {2010}, month = {2010/03/01/}, pages = {225 - 238}, abstract = {C static analysis tools often use intermediate representations (IRs) that organize program data in a simple, well-structured manner. However, the C parsers that create IRs are slow, and because they are difficult to write, only a few implementations exist, limiting the languages in which a C static analysis can be written. To solve these problems, we investigate two language-independent, on-disk representations of C IRs: one using XML and the other using an Internet standard binary encoding called eXternal Data Representation (XDR). We benchmark the parsing speeds of both options, finding the XML to be about a factor of 2 slower than parsing C and the XDR over 6 times faster. Furthermore, we show that the XML files are far too large at 19 times the size of C source code, whereas XDR is only 2.2 times the C size. We also demonstrate the portability of our XDR system by presenting a C source code querying tool in Ruby. Our solution and the insights we gained from building it will be useful to analysis authors and other clients of C IRs. We have made our software freely available for download at http://www.cs.umd.edu/projects/PL/scil/. Copyright {\textcopyright} 2010 John Wiley\&Sons, Ltd.}, keywords = {C, intermediate representations, parsing, static analysis, XDR, XML}, isbn = {1097-024X}, doi = {10.1002/spe.954}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.954/abstract}, author = {Meister,Jeffrey A and Foster, Jeffrey S. and Hicks, Michael W.} } @conference {13332, title = {Spatial indexing on tetrahedral meshes}, booktitle = {Proceedings of the 18th SIGSPATIAL International Conference on Advances in Geographic Information Systems}, series = {GIS {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {506 - 509}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We address the problem of performing spatial queries on tetrahedral meshes. These latter arise in several application domains including 3D GIS, scientific visualization, finite element analysis. We have defined and implemented a family of spatial indexes, that we call tetrahedral trees. Tetrahedral trees subdivide a cubic domain containing the mesh in an octree or 3D kd-tree fashion, with three different subdivision criteria. Here, we present and compare such indexes, their memory usage, and spatial queries on them.}, keywords = {kd-trees, octrees, spatial indexes, tetrahedral meshes}, isbn = {978-1-4503-0428-3}, doi = {10.1145/1869790.1869873}, url = {http://doi.acm.org/10.1145/1869790.1869873}, author = {De Floriani, Leila and Fellegara,Riccardo and Magillo,Paola} } @article {15559, title = {Spatio-temporal range searching over compressed kinetic sensor data}, journal = {Algorithms{\textendash}ESA 2010}, year = {2010}, month = {2010///}, pages = {386 - 397}, abstract = {As sensor networks increase in size and number, efficient techniques are required to process the very large data sets that they generate. Frequently, sensor networks monitor objects in motion within their vicinity; the data associated with the movement of these objects are known as kinetic data. In an earlier paper we introduced an algorithm which, given a set of sensor observations, losslessly compresses this data to a size that is within a constant factor of the asymptotically optimal joint entropy bound. In this paper we present an efficient algorithm for answering spatio-temporal range queries. Our algorithm operates on a compressed representation of the data, without the need to decompress it. We analyze the efficiency of our algorithm in terms of a natural measure of information content, the joint entropy of the sensor outputs. We show that with space roughly equal to entropy, queries can be answered in time that is roughly logarithmic in entropy. In addition, we show experimentally that on real-world data our range searching structures use less space and have faster query times than the naive versions. These results represent the first solutions to range searching problems over compressed kinetic sensor data.}, doi = {10.1007/978-3-642-15775-2_33}, author = {Friedler,S. and Mount, Dave} } @article {15811, title = {Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings}, journal = {J. Am. Chem. Soc.}, volume = {132}, year = {2010}, month = {2010///}, pages = {8961 - 8972}, abstract = {We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein?protein complex by utilizing the RDCs? sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein?protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein?protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes.We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein?protein complex by utilizing the RDCs? sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein?protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein?protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes. }, isbn = {0002-7863}, doi = {10.1021/ja100447p}, url = {http://dx.doi.org/10.1021/ja100447p}, author = {Berlin,Konstantin and O{\textquoteright}Leary,Dianne P. and Fushman, David} } @article {18601, title = {SwitchBlade: a platform for rapid deployment of network protocols on programmable hardware}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {40}, year = {2010}, month = {2010/08//}, pages = {183 - 194}, abstract = {We present SwitchBlade, a platform for rapidly deploying custom protocols on programmable hardware. SwitchBlade uses a pipeline-based design that allows individual hardware modules to be enabled or disabled on the fly, integrates software exception handling, and provides support for forwarding based on custom header fields. SwitchBlade{\textquoteright}s ease of programmability and wire-speed performance enables rapid prototyping of custom data-plane functions that can be directly deployed in a production network. SwitchBlade integrates common packet-processing functions as hardware modules, enabling different protocols to use these functions without having to resynthesize hardware. SwitchBlade{\textquoteright}s customizable forwarding engine supports both longest-prefix matching in the packet header and exact matching on a hash value. SwitchBlade{\textquoteright}s software exceptions can be invoked based on either packet or flow-based rules and updated quickly at runtime, thus making it easy to integrate more flexible forwarding function into the pipeline. SwitchBlade also allows multiple custom data planes to operate in parallel on the same physical hardware, while providing complete isolation for protocols running in parallel. We implemented SwitchBlade using NetFPGA board, but SwitchBlade can be implemented with any FPGA. To demonstrate SwitchBlade{\textquoteright}s flexibility, we use SwitchBlade to implement and evaluate a variety of custom network protocols: we present instances of IPv4, IPv6, Path Splicing, and an OpenFlow switch, all running in parallel while forwarding packets at line rate.}, keywords = {netfpga, network virtualization}, isbn = {0146-4833}, doi = {10.1145/1851275.1851206}, url = {http://doi.acm.org/10.1145/1851275.1851206}, author = {Anwer,Muhammad Bilal and Motiwala,Murtaza and Bin Tariq,Mukarram and Feamster, Nick} } @conference {14292, title = {Symbolic security analysis of ruby-on-rails web applications}, booktitle = {Proceedings of the 17th ACM conference on Computer and communications security}, year = {2010}, month = {2010///}, pages = {585 - 594}, author = {Chaudhuri,A. and Foster, Jeffrey S.} } @article {18607, title = {Transit portal: BGP connectivity as a service}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {40}, year = {2010}, month = {2010/08//}, pages = {463 - 464}, keywords = {bgp-mux, transit portal}, isbn = {0146-4833}, doi = {10.1145/1851275.1851265}, url = {http://doi.acm.org/10.1145/1851275.1851265}, author = {Valancius,Vytautas and Kim,Hyojoon and Feamster, Nick} } @article {15558, title = {A unified approach to approximate proximity searching}, journal = {Algorithms{\textendash}ESA 2010}, year = {2010}, month = {2010///}, pages = {374 - 385}, author = {Arya,S. and da Fonseca,G. and Mount, Dave} } @conference {14306, title = {Using symbolic evaluation to understand behavior in configurable software systems}, booktitle = {Software Engineering, 2010 ACM/IEEE 32nd International Conference on}, volume = {1}, year = {2010}, month = {2010///}, pages = {445 - 454}, author = {Reisner,E. and Song,C. and Ma,K.K. and Foster, Jeffrey S. and Porter, Adam} } @conference {15862, title = {Values of Stakeholders in the Net Neutrality Debate: Applying Content Analysis to Telecommunications Policy}, booktitle = {Hawaii International Conference on System Sciences}, year = {2010}, month = {2010///}, pages = {1 - 10}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Net neutrality is an important telecommunications policy debate. This debate is closely tied to technological innovation, economic development, and information access. Values help shape stakeholders{\textquoteright} positions on this debate. This paper examines the role of values in shaping the Net neutrality debate through a content analysis of public hearings on Net neutrality. The paper presents a quantitative analysis that reveals the top values implicated in the Net neutrality debate and statistically significant differences among individuals on opposite sides of the Net neutrality debate. A qualitative analysis reveals insights into the connection between specific values and positions on the Net neutrality debate. The paper concludes that values, technology, and policy are interconnected, and that it is useful to understand the values of the various stakeholders within policy debates.}, isbn = {978-0-7695-3869-3}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2010.434}, author = {Cheng,An-Shou and Fleischmann,Kenneth R. and Wang,Ping and Ishita,Emi and Oard, Douglas} } @article {14757, title = {Viewpoint Adapting agile software development methodology toward more efficient management of academic research groups.}, journal = {Communications of the ACM}, volume = {53}, year = {2010}, month = {2010///}, pages = {30 - 30}, author = {Hicks, Michael W. and Foster, Jeffrey S.} } @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.} } @article {18524, title = {Which Factors Affect Access Network Performance?}, volume = {GT-CS-10-04}, year = {2010}, month = {2010///}, institution = {Georgia Institute of Technology}, abstract = {This paper presents an analysis of the performance of residential access networks using over four months of round-trip, download, and upload measurements from more than 7,000 users across four ADSL and cable providers in France. Previous studies have characterized residential access network performance, but this paper presents the first study of how access network performance relates to other factors, such as choice of access provider, service-level agreement, and geographic location. We first explore the extent to which user performance matches the capacity advertised by an access provider, and whether the ability to achieve this capacity depends on the user{\textquoteright}s access network. We then analyze the extent to which various factors influence the performance that users experience. Finally, we explore how different groups of users experience simultaneous performance anomalies and analyze the common characteristics of users that share fate (e.g., whether users that experience simultaneous performance degradation share the same provider, city). Our analysis informs both users and designers of networked services who wish to improve the reliability and performance of access networks through multihoming and may also assist operators with troubleshooting network issues by narrowing down likely causes.}, url = {http://hdl.handle.net/1853/37336}, author = {Sundaresan,S. and Feamster, Nick and Dicioccio,L. and Teixeira,R.} } @conference {18613, title = {Wide-area route control for distributed services}, booktitle = {Proceedings of the 2010 USENIX conference on USENIX annual technical conference}, series = {USENIXATC{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {2 - 2}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Many distributed services would benefit from control over the flow of traffic to and from their users, to offer better performance and higher reliability at a reasonable cost. Unfortunately, although today{\textquoteright}s cloud-computing platforms offer elastic computing and bandwidth resources, they do not give services control over wide-area routing. We propose replacing the data center{\textquoteright}s border router with a Transit Portal (TP) that gives each service the illusion of direct connectivity to upstream ISPs, without requiring each service to deploy hardware, acquire IP address space, or negotiate contracts with ISPs. Our TP prototype supports many layer-two connectivity mechanisms, amortizes memory and message overhead over multiple services, and protects the rest of the Internet from misconfigured and malicious applications. Our implementation extends and synthesizes open-source software components such as the Linux kernel and the Quagga routing daemon. We also implement a management plane based on the GENI control framework and couple this with our four-site TP deployment and Amazon EC2 facilities. Experiments with an anycast DNS application demonstrate the benefits the TP offers to distributed services.}, url = {http://dl.acm.org/citation.cfm?id=1855840.1855842}, author = {Valancius,Vytautas and Feamster, Nick and Rexford,Jennifer and Nakao,Akihiro} } @conference {14193, title = {Active segmentation for robotics}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems, 2009. IROS 2009}, year = {2009}, month = {2009/10/10/15}, pages = {3133 - 3139}, publisher = {IEEE}, organization = {IEEE}, abstract = {The semantic robots of the immediate future are robots that will be able to find and recognize objects in any environment. They need the capability of segmenting objects in their visual field. In this paper, we propose a novel approach to segmentation based on the operation of fixation by an active observer. Our approach is different from current approaches: while existing works attempt to segment the whole scene at once into many areas, we segment only one image region, specifically the one containing the fixation point. Furthermore, our solution integrates monocular cues (color, texture) with binocular cues (stereo disparities and optical flow). Experiments with real imagery collected by our active robot and from the known databases demonstrate the promise of the approach.}, keywords = {binocular cues, image colour analysis, Image segmentation, Image texture, Intelligent robots, Layout, Machine vision, monocular cues, Navigation, optical flow, Orbital robotics, Robot sensing systems, robot vision, Robot vision systems, robotics active segmentation, Robotics and automation, semantic robot, Simultaneous localization and mapping, stereo disparity, stereo image processing}, isbn = {978-1-4244-3803-7}, doi = {10.1109/IROS.2009.5354325}, author = {Mishra,A. and Aloimonos, J. and Ferm{\"u}ller, Cornelia} } @article {15876, title = {Automatic classification of human values: Applying computational thinking to information ethics}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {46}, year = {2009}, month = {2009///}, pages = {1 - 4}, author = {Fleischmann,K.R. and Oard, Douglas and Cheng,A.S. and Wang,P. and Ishita,E.} } @article {18695, title = {Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains}, journal = {Nature Structural \& Molecular Biology}, volume = {16}, year = {2009}, month = {2009///}, pages = {883 - 889}, abstract = {Ubiquitin (denoted Ub) receptor proteins as a group must contain a diverse set of binding specificities to distinguish the many forms of polyubiquitin (polyUb) signals. Previous studies suggested that the large class of ubiquitin-associated (UBA) domains contains members with intrinsic specificity for Lys63-linked polyUb or Lys48-linked polyUb, thus explaining how UBA-containing proteins can mediate diverse signaling events. Here we show that previously observed Lys63-polyUb selectivity in UBA domains is the result of an artifact in which the dimeric fusion partner, glutathione S-transferase (GST), positions two UBAs for higher affinity, avid interactions with Lys63-polyUb, but not with Lys48-polyUb. Freed from GST, these UBAs are either nonselective or prefer Lys48-polyUb. Accordingly, NMR experiments reveal no Lys63-polyUb{\textendash}specific binding epitopes for these UBAs. We reexamine previous conclusions based on GST-UBAs and present an alternative model for how UBAs achieve a diverse range of linkage specificities.}, keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation}, isbn = {1545-9993}, doi = {10.1038/nsmb.1637}, url = {http://www.nature.com/nsmb/journal/v16/n8/abs/nsmb.1637.html}, author = {Sims,Joshua J. and Haririnia,Aydin and Dickinson,Bryan C. and Fushman, David and Cohen,Robert E.} } @conference {12399, title = {Better vocabularies for assistive communication aids: connecting terms using semantic networks and untrained annotators}, booktitle = {Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility}, series = {Assets {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {171 - 178}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The difficulties of navigating vocabulary in an assistive communication device are exacerbated for individuals with lexical access disorders like those due to aphasia. We present the design and implementation of a vocabulary network based on WordNet, a resource that attempts to model human semantic memory, that enables users to find words easily. To correct for the sparsity of links among words, we augment WordNet with additional connections derived from human judgments of semantic similarity collected in an online experiment. We evaluate the resulting system, the visual vocabulary for aphasia (ViVA), and describe its potential to adapt to a user{\textquoteright}s profile and enable faster search and improved navigation.}, keywords = {adaptive tools, aphasia, assistive communication, semantic networks, visual vocabularies}, isbn = {978-1-60558-558-1}, doi = {10.1145/1639642.1639673}, url = {http://doi.acm.org/10.1145/1639642.1639673}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Fellbaum,Christiane and Cook,Perry} } @conference {18555, title = {Characterizing VLAN-induced sharing in a campus network}, booktitle = {Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference}, series = {IMC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {116 - 121}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many enterprise, campus, and data-center networks have complex layer-2 virtual LANs ("VLANs") below the IP layer. The interaction between layer-2 and IP topologies in these VLANs introduces hidden dependencies between IP level network and the physical infrastructure that has implications for network management tasks such as planning for capacity or reliability, and for fault diagnosis. This paper characterizes the extent and effect of these dependencies in a large campus network. We first present the design and implementation of EtherTrace, a tool that we make publicly available, which infers the layer-2 topology using data passively collected from Ethernet switches. Using this tool, we infer the layer-2 topology for a large campus network and compare it with the IP topology. We find that almost 70\% of layer-2 edges are shared by 10 or more IP edges, and a single layer-2 edge may be shared by as many as 34 different IP edges. This sharing of layer-2 edges and switches among IP paths commonly results from trunking multiple VLANs to the same access router, or from colocation of academic departments that share layer-2 infrastructure, but have logically separate IP subnet and routers. We examine how this sharing affects the accuracy and specificity of fault diagnosis. For example, applying network tomography to the IP topology to diagnose failures caused by layer-2 devices results in only 54\% accuracy, compared to 100\% accuracy when our tomography algorithm takes input across layers.}, keywords = {network diagnosis, network virtualization, VLAN, vlan-induced dependency}, isbn = {978-1-60558-771-4}, doi = {10.1145/1644893.1644907}, url = {http://doi.acm.org/10.1145/1644893.1644907}, author = {Bin Tariq,Mukarram and Mansy,Ahmed and Feamster, Nick and Ammar,Mostafa} } @conference {14208, title = {Combining powerful local and global statistics for texture description}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition, 2009. CVPR 2009}, year = {2009}, month = {2009/06/20/25}, pages = {573 - 580}, publisher = {IEEE}, organization = {IEEE}, abstract = {A texture descriptor is proposed, which combines local highly discriminative features with the global statistics of fractal geometry to achieve high descriptive power, but also invariance to geometric and illumination transformations. As local measurements SIFT features are estimated densely at multiple window sizes and discretized. On each of the discretized measurements the fractal dimension is computed to obtain the so-called multifractal spectrum, which is invariant to geometric transformations and illumination changes. Finally to achieve robustness to scale changes, a multi-scale representation of the multifractal spectrum is developed using a framelet system, that is, a redundant tight wavelet frame system. Experiments on classification demonstrate that the descriptor outperforms existing methods on the UIUC as well as the UMD high-resolution dataset.}, keywords = {Computer science, discretized measurements, fractal geometry, Fractals, geometric transformations, global statistics, Histograms, illumination transformations, image classification, image resolution, Image texture, lighting, local measurements SIFT features, local statistics, MATHEMATICS, multifractal spectrum, multiscale representation, Power engineering and energy, Power engineering computing, Robustness, Solids, Statistics, texture description, UMD high-resolution dataset, wavelet frame system, Wavelet transforms}, isbn = {978-1-4244-3992-8}, doi = {10.1109/CVPR.2009.5206741}, author = {Yong Xu and Si-Bin Huang and Hui Ji and Ferm{\"u}ller, Cornelia} } @article {16253, title = {Complete Genome Sequence of Aggregatibacter (Haemophilus) Aphrophilus NJ8700}, journal = {Journal of BacteriologyJ. Bacteriol.}, volume = {191}, year = {2009}, month = {2009/07/15/}, pages = {4693 - 4694}, abstract = {We report the finished and annotated genome sequence of Aggregatibacter aphrophilus strain NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss characteristics that may affect its dual roles in human health and disease. This strain has a rough appearance, and its genome contains genes encoding a type VI secretion system and several factors that may participate in host colonization.}, isbn = {0021-9193, 1098-5530}, doi = {10.1128/JB.00447-09}, url = {http://jb.asm.org/content/191/14/4693}, author = {Di Bonaventura,Maria Pia and DeSalle,Rob and Pop, Mihai and Nagarajan,Niranjan and Figurski,David H and Fine,Daniel H and Kaplan,Jeffrey B and Planet,Paul J} } @article {15548, title = {Compressing kinetic data from sensor networks}, journal = {Algorithmic Aspects of Wireless Sensor Networks}, year = {2009}, month = {2009///}, pages = {191 - 202}, abstract = {We introduce a framework for storing and processing kinetic data observed by sensor networks. These sensor networks generate vast quantities of data, which motivates a significant need for data compression. We are given a set of sensors, each of which continuously monitors some region of space. We are interested in the kinetic data generated by a finite set of objects moving through space, as observed by these sensors. Our model relies purely on sensor observations; it allows points to move freely and requires no advance notification of motion plans. Sensor outputs are represented as random processes, where nearby sensors may be statistically dependent. We model the local nature of sensor networks by assuming that two sensor outputs are statistically dependent only if the two sensors are among the k nearest neighbors of each other. We present an algorithm for the lossless compression of the data produced by the network. We show that, under the statistical dependence and locality assumptions of our framework, asymptotically this compression algorithm encodes the data to within a constant factor of the information-theoretic lower bound optimum dictated by the joint entropy of the system.}, doi = {10.1007/978-3-642-05434-1_20}, author = {Friedler,S. and Mount, Dave} } @conference {17037, title = {Creativity challenges and opportunities in social computing}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {3283 - 3286}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {There is a convergence in recent theories of creativity that go beyond characteristics and cognitive processes of individuals to recognize the importance of the social construction of creativity. In parallel, there has been a rise in social computing supporting the collaborative construction of knowledge. The panel will discuss the challenges and opportunities from the confluence of these two developments by bringing together the contrasting and controversial perspective of the individual panel members. It will synthesize from different perspectives an analytic framework to understand these new developments, and how to promote rigorous research methods and how to identify the unique challenges in developing evaluation and assessment methods for creativity research.}, keywords = {creativity, social computing}, isbn = {978-1-60558-247-4}, doi = {10.1145/1520340.1520470}, url = {http://doi.acm.org/10.1145/1520340.1520470}, author = {Fischer,Gerhard and Jennings,Pamela and Maher,Mary Lou and Resnick,Mitchel and Shneiderman, Ben} } @conference {15891, title = {Cross-document coreference resolution: A key technology for learning by reading}, booktitle = {AAAI Spring Symposium on Learning by Reading and Learning to Read}, year = {2009}, month = {2009///}, author = {Mayfield,J. and Alexander,D. and Dorr, Bonnie J and Eisner,J. and Elsayed,T. and Finin,T. and Fink,C. and Freedman,M. and Garera,N. and McNamee,P. and others} } @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} } @conference {18562, title = {Detecting network neutrality violations with causal inference}, booktitle = {Proceedings of the 5th international conference on Emerging networking experiments and technologies}, series = {CoNEXT {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {289 - 300}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present NANO, a system that detects when ISPs apply policies that discriminate against specific classes of applications, users, or destinations. Existing systems for detecting discrimination are typically specific to an application or to a particular discrimination mechanism and rely on active measurement tests. Unfortunately, ISPs can change discrimination policies and mechanisms, and they can evade these tests by giving probe traffic higher priority. NANO detects ISP discrimination by passively collecting performance data from clients. To distinguish discrimination from other causes of degradation (e.g., overload, misconfiguration, failure), NANO establishes a causal relationship between an ISP and observed performance by adjusting for confounding factors. NANO agents deployed at participating clients across the Internet collect performance data for selected services and report this information to centralized servers, which analyze the measurements to establish causal relationship between an ISP and performance degradations. We have implemented NANO and deployed clients in a controlled environment on Emulab. We run a combination of controlled experiments on Emulab and wide-area experiments on PlanetLab that show that NANO can determine the extent and criteria for discrimination for a variety of discrimination policies and applications.}, keywords = {causal inference, network neutrality}, isbn = {978-1-60558-636-6}, doi = {10.1145/1658939.1658972}, url = {http://doi.acm.org/10.1145/1658939.1658972}, author = {Bin Tariq,Mukarram and Motiwala,Murtaza and Feamster, Nick and Ammar,Mostafa} } @conference {18563, title = {Detecting spammers with SNARE: spatio-temporal network-level automatic reputation engine}, booktitle = {Proceedings of the 18th conference on USENIX security symposium}, series = {SSYM{\textquoteright}09}, year = {2009}, month = {2009///}, pages = {101 - 118}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Users and network administrators need ways to filter email messages based primarily on the reputation of the sender. Unfortunately, conventional mechanisms for sender reputation--notably, IP blacklists--are cumbersome to maintain and evadable. This paper investigates ways to infer the reputation of an email sender based solely on network-level features, without looking at the contents of a message. First, we study first-order properties of network-level features that may help distinguish spammers from legitimate senders. We examine features that can be ascertained without ever looking at a packet{\textquoteright}s contents, such as the distance in IP space to other email senders or the geographic distance between sender and receiver. We derive features that are lightweight, since they do not require seeing a large amount of email from a single IP address and can be gleaned without looking at an email{\textquoteright}s contents--many such features are apparent from even a single packet. Second, we incorporate these features into a classification algorithm and evaluate the classifier{\textquoteright}s ability to automatically classify email senders as spammers or legitimate senders. We build an automated reputation engine, SNARE, based on these features using labeled data from a deployed commercial spam-filtering system. We demonstrate that SNARE can achieve comparable accuracy to existing static IP blacklists: about a 70\%detection rate for less than a 0.3\%false positive rate. Third, we show how SNARE can be integrated into existing blacklists, essentially as a first-pass filter.}, url = {http://dl.acm.org/citation.cfm?id=1855768.1855775}, author = {Hao,Shuang and Syed,Nadeem Ahmed and Feamster, Nick and Gray,Alexander G. and Krasser,Sven} } @article {18519, title = {Determining the causes of intradomain routing changes}, year = {2009}, month = {2009///}, institution = {University Pierre and Marie Curie}, abstract = {This paper studies how intradomain routinginstability relates to events in network trouble tickets for two networks: a VPN provider and the Internet2 backbone network. Our goal in performing this joint analysis of routing and trouble tickets is to better understand the likely underlying causes of intradomain routing instability. We develop a method to correlate trouble tickets with instability events and find that, although unplanned events last longer than scheduled maintenance, there is no single underlying cause for most instability, and that these causes differ across networks. In comparison to a similar study from Labovitz et al. from ten years ago, we find that, while certain causes of instability such as maintenance and circuit problems remain significant, power issues have become much less prevalent, and software-related problems have become more common. }, author = {Medem,A. and Teixeira,R. and Feamster, Nick and Meulle,M.} } @conference {14677, title = {Directing JavaScript with arrows}, booktitle = {Proceedings of the 5th symposium on Dynamic languages}, series = {DLS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {49 - 58}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {JavaScript programmers make extensive use of event-driven programming to help build responsive web applications. However, standard approaches to sequencing events are messy, and often lead to code that is difficult to understand and maintain. We have found that arrows, a generalization of monads, are an elegant solution to this problem. Arrows allow us to easily write asynchronous programs in small, modular units of code, and flexibly compose them in many different ways, while nicely abstracting the details of asynchronous program composition. In this paper, we present Arrowlets, a new JavaScript library that offers arrows to the everyday JavaScript programmer. We show how to use Arrowlets to construct a variety of state machines, including state machines that branch and loop. We also demonstrate how Arrowlets separate computation from composition with examples such as a drag-and-drop handler and a bubblesort animation.}, keywords = {arrowlets, arrows, events, javascript, web programming}, isbn = {978-1-60558-769-1}, doi = {10.1145/1640134.1640143}, url = {http://doi.acm.org/10.1145/1640134.1640143}, author = {Khoo,Yit Phang and Hicks, Michael W. and Foster, Jeffrey S. and Sazawal,Vibha} } @article {18494, title = {Dynamics of online scam hosting infrastructure}, journal = {Passive and Active Network Measurement}, year = {2009}, month = {2009///}, pages = {219 - 228}, abstract = {This paper studies the dynamics of scam hosting infrastructure, with an emphasis on the role of fast-flux service networks. By monitoring changes in DNS records of over 350 distinct spam-advertised domains collected from URLs in 115,000 spam emails received at a large spam sinkhole, we measure the rates and locations of remapping DNS records, and the rates at which {\textquotedblleft}fresh{\textquotedblright} IP addresses are used. We find that, unlike the short-lived nature of the scams themselves, the infrastructure that hosts these scams has relatively persistent features that may ultimately assist detection.}, doi = {10.1007/978-3-642-00975-4_22}, author = {Konte,M. and Feamster, Nick and Jung,J.} } @inbook {19635, title = {Efficient Robust Private Set Intersection}, booktitle = {Applied Cryptography and Network Security}, series = {Lecture Notes in Computer Science}, year = {2009}, month = {2009/01/01/}, pages = {125 - 142}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Computing Set Intersection privately and efficiently between two mutually mistrusting parties is an important basic procedure in the area of private data mining. Assuring robustness, namely, coping with potentially arbitrarily misbehaving (i.e., malicious) parties, while retaining protocol efficiency (rather than employing costly generic techniques) is an open problem. In this work the first solution to this problem is presented.}, keywords = {Coding and Information Theory, Computer Communication Networks, Cryptographic protocols, Data Encryption, Data Structures, Cryptology and Information Theory, Information Systems Applications (incl.Internet), Privacy Preserving Data Mining, Secure Two-party Computation, Set Intersection, Systems and Data Security}, isbn = {978-3-642-01956-2, 978-3-642-01957-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-01957-9_8}, author = {Dana Dachman-Soled and Malkin, Tal and Raykova, Mariana and Yung, Moti}, editor = {Abdalla, Michel and Pointcheval, David and Fouque, Pierre-Alain and Vergnaud, Damien} } @conference {14278, title = {Efficient systematic testing for dynamically updatable software}, booktitle = {Proceedings of the 2nd International Workshop on Hot Topics in Software Upgrades}, year = {2009}, month = {2009///}, pages = {9 - 9}, author = {Hayden,C.M. and Hardisty,E.A. and Hicks, Michael W. and Foster, Jeffrey S.} } @conference {14689, title = {Efficient systematic testing for dynamically updatable software}, booktitle = {Proceedings of the 2nd International Workshop on Hot Topics in Software Upgrades}, series = {HotSWUp {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {9:1{\textendash}9:5 - 9:1{\textendash}9:5}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Recent years have seen significant advances in dynamic software updating (DSU) systems, which allow programs to be patched on the fly. However, a significant challenge remains: How can we ensure the act of applying a patch does not itself introduce errors? In this paper, we address this problem by presenting a new systematic testing methodology for updatable programs. Our idea is to transform standard system tests into update tests that execute as before, but each transformed test applies a patch at a different update point during execution. To mitigate the increase in the number of tests, we developed an algorithm for test suite minimization that finds a subset of update points that, if fully tested, yields the equivalent to full update point coverage. We implemented our approach and evaluated it on OpenSSH and vsftpd, two widely used server applications. We found that minimization is highly effective, reducing the number of update tests required for full coverage by 93\%.}, isbn = {978-1-60558-723-3}, doi = {10.1145/1656437.1656449}, url = {http://doi.acm.org/10.1145/1656437.1656449}, author = {Hayden,Christopher M and Hardisty,Eric A. and Hicks, Michael W. and Foster, Jeffrey S.} } @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 {18523, title = {A Fast, Virtualized Data Plane for the NetFPGA}, journal = {NetFPGA Developers Workshop, Stanford, California}, year = {2009}, month = {2009///}, pages = {90 - 94}, abstract = {Network virtualization allows many networks to share thesame underlying physical topology; this technology has of- fered promise both for experimentation and for hosting mul- tiple networks on a single shared physical infrastructure. Much attention has focused on virtualizing the network con- trol plane, but, ultimately, a limiting factor in the deployment of these virtual networks is data-plane performance: Virtual networks must ultimately forward packets at rates that are comparable to native, hardware-based approaches. Aside from proprietary solutions from vendors, hardware support for virtualized data planes is limited. The advent of open, programmable network hardware promises flexibility, speed, and resource isolation, but, unfortunately, hardware does not naturally lend itself to virtualization. We leverage emerg- ing trends in programmable hardware to design a flexible, hardware-based data plane for virtual networks. We present the design, implementation, and preliminary evaluation of this hardware-based data plane and show how the proposed design can support many virtual networks without compro- mising performance or isolation. }, author = {Anwer,M.B. and Feamster, Nick} } @conference {18835, title = {Formal Representation of Product Design Specifications for Validating Product Design}, year = {2009}, month = {2009///}, pages = {1411 - 1422}, publisher = {ASME}, organization = {ASME}, abstract = {As collaborative efforts in electro-mechanical design have scaled to large, distributed groups working for years on a single product, an increasingly large gulf has developed between the original stated goals of the project and the final design solution. It has thus become necessary to validate the final design solution against a set of requirements to ensure that these goals have, in fact, been met. This process has become tedious for complex products with hundreds of design aspects and requirements. By formalizing the representation of requirements and the design solution, tools can be developed to a large extent automatically perform this validation. In this paper, we propose a formal approach for relating product requirements to the design solution. First, we present a formal model for representing product requirements. Then, we introduce the Core Product Model (CPM) and the Open Assembly Model (OAM) for representing the design solution. Finally, we link these models formally and provide an example with an actual consumer device.}, isbn = {978-0-7918-4899-9}, doi = {10.1115/DETC2009-87307}, url = {http://link.aip.org/link/ASMECP/v2009/i48999/p1411/s1\&Agg=doi}, author = {Weissman,Alexander and Gupta, Satyandra K. and Fiorentini,Xenia and Sudarsan,Rachuri and Sriram,Ram} } @article {17186, title = {HEALTH AND WELLBEING}, journal = {The fourth paradigm: data-intensive scientific discovery}, year = {2009}, month = {2009///}, pages = {57 - 57}, author = {Gillam,M. and Feied,C. and MOODY,E. and Shneiderman, Ben and Smith,M. and DICKASON,J.} } @conference {13892, title = {How children search the internet with keyword interfaces}, booktitle = {Proceedings of the 8th International Conference on Interaction Design and Children}, year = {2009}, month = {2009///}, pages = {89 - 96}, author = {Druin, Allison and Foss,E. and Hatley,L. and Golub,E. and Guha,M.L. and Fails,J. and Hutchinson,H.} } @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.} } @article {15763, title = {Improvement and analysis of computational methods for prediction of residual dipolar couplings}, journal = {Journal of Magnetic Resonance}, volume = {201}, year = {2009}, month = {2009/11//}, pages = {25 - 33}, abstract = {We describe a new, computationally efficient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a molecule. This method is applicable to bicelles, PEG/hexanol, and other alignment media that can be modeled by steric restrictions introduced by a planar barrier. This method is used to further explore and compare various representations of protein shape by an equivalent ellipsoid. We also examine the accuracy of the alignment tensor and residual dipolar couplings (RDC) prediction using various ab initio methods. We separately quantify the inaccuracy in RDC prediction caused by the inaccuracy in the orientation and in the magnitude of the alignment tensor, concluding that orientation accuracy is much more important in accurate prediction of RDCs.}, keywords = {Ab initio prediction, Alignment tensor, PALES, Residual dipolar coupling}, isbn = {1090-7807}, doi = {10.1016/j.jmr.2009.07.028}, url = {http://www.sciencedirect.com/science/article/pii/S1090780709002304}, author = {Berlin,Konstantin and O{\textquoteright}Leary,Dianne P. and Fushman, David} } @conference {16317, title = {Incremental covering array failure characterization in large configuration spaces}, booktitle = {Proceedings of the eighteenth international symposium on Software testing and analysis}, year = {2009}, month = {2009///}, pages = {177 - 188}, author = {Fouch{\'e},S. and Cohen,M. B and Porter, Adam} } @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 {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 {18581, title = {Measurement methods for fast and accurate blackhole identification with binary tomography}, booktitle = {Proceedings of the 9th ACM SIGCOMM conference on Internet measurement conference}, series = {IMC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {254 - 266}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Binary tomography - the process of identifying faulty network links through coordinated end-to-end probes - is a promising method for detecting failures that the network does not automatically mask (e.g., network "blackholes"). Because tomography is sensitive to the quality of the input, however, na{\"\i}ve end-to-end measurements can introduce inaccuracies. This paper develops two methods for generating inputs to binary tomography algorithms that improve their inference speed and accuracy. Failure confirmation is a per-path probing technique to distinguish packet losses caused by congestion from persistent link or node failures. Aggregation strategies combine path measurements from unsynchronized monitors into a set of consistent observations. When used in conjunction with existing binary tomography algorithms, our methods identify all failures that are longer than two measurement cycles, while inducing relatively few false alarms. In two wide-area networks, our techniques decrease the number of alarms by as much as two orders of magnitude. Compared to the state of the art in binary tomography, our techniques increase the identification rate and avoid hundreds of false alarms.}, keywords = {diagnosis, network tomography, troubleshooting}, isbn = {978-1-60558-771-4}, doi = {10.1145/1644893.1644924}, url = {http://doi.acm.org/10.1145/1644893.1644924}, author = {Cunha,{\'I}talo and Teixeira,Renata and Feamster, Nick and Diot,Christophe} } @article {14228, title = {MEASURING 1ST ORDER STRETCH WITH A SINGLE FILTER}, journal = {Relation}, volume = {10}, year = {2009}, month = {2009///}, pages = {691 - 691}, abstract = {We analytically develop a filter that is able to measurethe linear stretch of the transformation around a point, and present results of applying it to real signals. We show that this method is a real-time alternative solution for measuring local signal transformations. Experimentally, this method can accurately measure stretch, however, it is sensitive to shift. }, author = {Bitsakos,K. and Domke, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {18513, title = {Measuring vlan-induced dependencies on a campus network}, booktitle = {Proceedings of the ACM SIGCOMM Internet measurement conference}, year = {2009}, month = {2009///}, abstract = {Many enterprise, campus, and data-center networks have complexlayer-2 virtual LANs ({\textquotedblleft}VLANs{\textquotedblright}) underlying the layer-3 network. The interac- tion between layer-2 and layer-3 topologies can introduce dependencies that are not visible when analyzed solely from layer 3; this paper studies the extent and impact of these dependencies. We first present EtherTrace, a tool that infers the layer-2 topology using data passively collected from Ethernet switches. Using this tool, we infer the layer-2 topology for a large campus network and compare the two topologies. Our comparison yields some striking initial findings: almost 70\% of layer-2 edges are shared by 10 or more IP edges, and a single layer-2 edge may be shared by as many as 34 different IP edges. This sharing has significant implications for both robustness and for network tomography. Applying network tomography to the IP topology to diagnose failures caused by layer-2 devices results in only 54\% accuracy, compared to 100\% accuracy when tomography is performed at layer 2. }, author = {Mansy,A. and Tariq,M.B. and Feamster, Nick and Ammar,M.} } @conference {14337, title = {Mobile Living Labs 09: Methods and Tools for Evaluation in the Wild}, booktitle = {Proceedings of the 11th International Conference on Human-Computer Interaction with Mobile Devices and Services}, series = {MobileHCI {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {107:1{\textendash}107:2 - 107:1{\textendash}107:2}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In a Mobile Living Lab, mobile devices are used to evaluate concepts and prototypes in real-life settings. In other words, the lab is brought to the people. This workshop provides a forum for researchers and practitioners to share experiences and issues with methods and tools for Mobile Living Labs. In particular, we seek to bring together people who have applied methods for Mobile Living Labs and people who build tools for those methods.The aim of the workshop is twofold. First, to make an up-to-date overview of current methods and tools for conducting user studies in Mobile Living Labs -- highlighting their individual strengths and weaknesses. Second, to uncover challenges that are not adequately addressed by current methods and tools and to come up with ideas and requirements that could fill this gap thus serving as beacons for further research and development in this area. }, keywords = {field study, in-situ evaluation, living labs, methods, mobile, tools, user experience}, isbn = {978-1-60558-281-8}, doi = {10.1145/1613858.1613981}, url = {http://doi.acm.org/10.1145/1613858.1613981}, author = {ter Hofte,Henri and Jensen,Kasper L{\o}vborg and Nurmi,Petteri and Jon Froehlich} } @article {18534, title = {A Narrow Waist for Multipath Routing}, year = {2009}, month = {2009///}, institution = {School of Computer Science, Georgia Tech}, abstract = {Many applications can use multipath routing to improvereliability or throughput, and many multipath routing pro- tocols exist. Despite this diversity of mechanisms and applications, no common interface exists to allow an ap- plication to select these paths. This paper presents a de- sign for such a common interface, called path bits. Path bits are a small string of opaque, semantic-free bits in a packet header; these bits have a simple property: changing a packet{\textquoteright}s path bits should, with high probability, result in the packet taking a different path to the destination. This paper presents the design of path bits and demonstrates that they are simple enough to be easily implemented in both hardware and software and expressive enough to sup- port a variety of applications that can benefit from mul- tipath routing. We present both hardware and software implementations of multipath routing protocols that im- plement the path bits abstraction, as well as implementa- tions of applications that can use this abstraction with only small modifications. }, author = {Motiwala,M. and bin Tariq,M. and Anwer,B. and Andersen,D. and Feamster, Nick} } @article {18538, title = {An OpenFlow switch element for Click}, journal = {Symposium on Click Modular Router}, year = {2009}, month = {2009///}, author = {Mundada,Y. and Sherwood,R. and Feamster, Nick} } @article {14284, title = {Profile-guided static typing for dynamic scripting languages}, journal = {ACM SIGPLAN Notices}, volume = {44}, year = {2009}, month = {2009///}, pages = {283 - 300}, author = {Furr,M. and An,J.D. and Foster, Jeffrey S.} } @article {14339, title = {Promoting energy efficient behaviors in the home through feedback: The role of human-computer interaction}, journal = {Proc. HCIC Workshop}, volume = {9}, year = {2009}, month = {2009///}, author = {Jon Froehlich} } @article {19201, title = {Promoting energy efficient behaviors in the home through feedback: The role of human-computer interaction}, journal = {Proc. HCIC Workshop}, volume = {9}, year = {2009}, month = {2009}, author = {Jon Froehlich} } @conference {17329, title = {Promoting social creativity: a component of a national initiative for social participation}, booktitle = {Proceedings of the seventh ACM conference on Creativity and cognition}, series = {C\&$\#$38;C {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {7 - 8}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This panel will discuss group processes that promote social creativity in science, engineering, arts, and humanities. We will offer positive and negative examples of social creativity projects, while suggesting research directions for dramatically increased social participation. The goal is to develop strategies that would expand resources and opportunities for research and education in social creativity. This requires our community to develop a unified position, then reach out to national science funding agencies, while building the case for the importance of this topic beyond our own community. How can social creativity, collaborative discovery, distributed innovation, and collective intelligence be framed as an international priority to cope with the problems of the 21st century and how can we identify a clear set of research challenges? The theme of technology-mediated social participation is outlined in the white paper for a National Initiative for Social Participation (http://iparticipate.wikispaces.com). The white paper suggests that successful research challenges should have three key elements: (1) compelling national need (healthcare, national security, community safety, education, innovation, cultural heritage, energy sustainability, environmental protection, etc.), (2) scientific foundation based on established theories and well-defined research questions (privacy, reciprocity, trust, motivation, recognition, etc.), and (3) computer science research challenges (security, privacy protection, scalability, visualization, end-user development, distributed data handling for massive user-generated content, network analysis of community evolution, cross network comparison, etc.). We seek recommendations for ways to increase the resources and attention for this field. We hope to inspire: universities to change course content, add courses, and offer new degree programs industry to help researchers on social creativity government to support these ideas and try them out in government applications scientists and artists to open themselves to more social/collaborative approaches}, keywords = {research agenda, social creativity, social participation}, isbn = {978-1-60558-865-0}, doi = {10.1145/1640233.1640237}, url = {http://doi.acm.org/10.1145/1640233.1640237}, author = {Shneiderman, Ben and Churchill,Elizabeth and Fischer,Gerhard and Goldberg,Ken} } @article {18527, title = {Pushing Enterprise Security Down the Network Stack}, volume = {GT-CS-09-03}, year = {2009}, month = {2009///}, institution = {Georgia Institute of Technology}, abstract = {Network security is typically reactive: Networks provide connectivity and subsequently alter this connectivity according to various security policies, as implemented in middleboxes, or at higher layers. This approach gives rise to complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. In this paper, we propose a proactive approach to securing networks, whereby security-related actions (e.g., dropping or redirecting traffic) are embedded into the network fabric itself, leaving only a fixed set of actions to higher layers. We explore this approach in the context of network access control. Our design uses programmable switches to manipulate traffic at lower layers; these switches interact with policy and monitoring at higher layers. We apply our approach to Georgia Tech{\textquoteright}s network access control system, show how the new design can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.}, url = {http://hdl.handle.net/1853/30782}, author = {Clark,R. and Feamster, Nick and Nayak,A. and Reimers,A.} } @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 {18598, title = {Resonance: dynamic access control for enterprise networks}, booktitle = {Proceedings of the 1st ACM workshop on Research on enterprise networking}, series = {WREN {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {11 - 18}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Enterprise network security is typically reactive, and it relies heavily on host security and middleboxes. This approach creates complicated interactions between protocols and systems that can cause incorrect behavior and slow response to attacks. We argue that imbuing the network layer with mechanisms for dynamic access control can remedy these ills. We propose Resonance, a system for securing enterprise networks, where the network elements themselves enforce dynamic access control policies based on both flow-level information and real-time alerts. Resonance uses programmable switches to manipulate traffic at lower layers; these switches take actions (e.g., dropping or redirecting traffic) to enforce high-level security policies based on input from both higherlevel security policies and distributed monitoring and inference systems. We describe the design of Resonance, apply it to Georgia Tech{\textquoteright}s network access control system, show how it can both overcome the current shortcomings and provide new security functions, describe our proposed deployment, and discuss open research questions.}, keywords = {Access control, enterprise networks, programmable networks}, isbn = {978-1-60558-443-0}, doi = {10.1145/1592681.1592684}, url = {http://doi.acm.org/10.1145/1592681.1592684}, author = {Nayak,Ankur Kumar and Reimers,Alex and Feamster, Nick and Clark,Russ} } @article {14254, title = {Robust Wavelet-Based Super-Resolution Reconstruction: Theory and Algorithm}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {31}, year = {2009}, month = {2009/04//}, pages = {649 - 660}, abstract = {We present an analysis and algorithm for the problem of super-resolution imaging, that is the reconstruction of HR (high-resolution) images from a sequence of LR (low-resolution) images. Super-resolution reconstruction 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. Both are important for the performance of super-resolution imaging. Image alignment is addressed with a new batch algorithm, which simultaneously estimates the homographies between multiple image frames by enforcing the surface normal vectors to be the same. This approach can handle longer video sequences quite well. Reconstruction is addressed with a wavelet-based iterative reconstruction algorithm with an efficient de-noising scheme. The technique is based on a new analysis of video formation. At a high level our method could be described as a better-conditioned iterative back projection scheme with an efficient regularization criteria in each iteration step. Experiments with both simulated and real data demonstrate that our approach has better performance than existing super-resolution methods. It can remove even large amounts of mixed noise without creating artifacts.}, keywords = {batch algorithm, better-conditioned iterative back projection scheme, Enhancement, homography estimation, image denoising, image denoising scheme, image frame alignment, Image processing software, Image reconstruction, image resolution, image sequence, Image sequences, iterative methods, regularization criteria, robust wavelet-based iterative super-resolution reconstruction, surface normal vector, video formation analysis, video sequence, video signal processing, Wavelet transforms}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2008.103}, author = {Hui Ji and Ferm{\"u}ller, Cornelia} } @article {14743, title = {The ruby intermediate language}, journal = {SIGPLAN Not.}, volume = {44}, year = {2009}, month = {2009/10//}, pages = {89 - 98}, abstract = {Ruby is a popular, dynamic scripting language that aims to "feel natural to programmers" and give users the "freedom to choose" among many different ways of doing the same thing. While this arguably makes programming in Ruby easier, it makes it hard to build analysis and transformation tools that operate on Ruby source code. In this paper, we present the Ruby Intermediate Language (RIL), a Ruby front-end and intermediate representation that addresses these. RIL includes an extensible GLR parser for Ruby, and an automatic translation into an easy-to-analyze intermediate form. This translation eliminates redundant language constructs, unravels the often subtle ordering among side effecting operations, and makes implicit interpreter operations explicit. We also describe several additional useful features of RIL, such as a dynamic instrumentation library for profiling source code and a dataflow analysis engine. We demonstrate the usefulness of RIL by presenting a static and dynamic analysis to eliminate null pointer errors in Ruby programs. We hope that RIL{\textquoteright}s features will enable others to more easily build analysis tools for Ruby, and that our design will inspire the of similar frameworks for other dynamic languages.}, keywords = {intermediate language, profile guided anlaysis, ril, ruby}, isbn = {0362-1340}, doi = {10.1145/1837513.1640148}, url = {http://doi.acm.org/10.1145/1837513.1640148}, author = {Furr,Michael and An,Jong-hoon (David) and Foster, Jeffrey S. and Hicks, Michael W.} } @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 {13856, title = {Semantically informed machine translation (SIMT)}, journal = {SCALE summer workshop final report, Human Language Technology Center Of Excellence}, year = {2009}, month = {2009///}, author = {Baker,K. and Bethard,S. and Bloodgood,M. and Brown,R. and Callison-Burch,C. and Coppersmith,G. and Dorr, Bonnie J and Filardo,W. and Giles,K. and Irvine,A. and others} } @conference {14322, title = {Sensing and predicting the pulse of the city through shared bicycling}, booktitle = {International Joint Conference on Artificial Intelligence}, year = {2009}, month = {2009///}, pages = {1420 - 1426}, author = {Jon Froehlich and Neumann, J. and Oliver,N.} } @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 {15151, title = {Signing a linear subspace: Signature schemes for network coding}, journal = {Public Key Cryptography{\textendash}PKC 2009}, year = {2009}, month = {2009///}, pages = {68 - 87}, abstract = {Network coding offers increased throughput and improved robustness to random faults in completely decentralized networks. In contrast to traditional routing schemes, however, network coding requires intermediate nodes to modify data packets en route; for this reason, standard signature schemes are inapplicable and it is a challenge to provide resilience to tampering by malicious nodes.We propose two signature schemes that can be used in conjunction with network coding to prevent malicious modification of data. Our schemes can be viewed as signing linear subspaces in the sense that a signature σ on a subspace V authenticates exactly those vectors in V. Our first scheme is (suitably) homomorphic and has constant public-key size and per-packet overhead. Our second scheme does not rely on random oracles and is based on weaker assumptions. We also prove a lower bound on the length of signatures for linear subspaces showing that our schemes are essentially optimal in this regard. }, doi = {10.1007/978-3-642-00468-1_5}, author = {Boneh,D. and Freeman,D. and Katz, Jonathan and Waters,B.} } @conference {14738, title = {Static type inference for Ruby}, booktitle = {Proceedings of the 2009 ACM symposium on Applied Computing}, series = {SAC {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1859 - 1866}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many general-purpose, object-oriented scripting languages are dynamically typed, which provides flexibility but leaves the programmer without the benefits of static typing, including early error detection and the documentation provided by type annotations. This paper describes Diamondback Ruby (DRuby), a tool that blends Ruby{\textquoteright}s dynamic type system with a static typing discipline. DRuby provides a type language that is rich enough to precisely type Ruby code we have encountered, without unneeded complexity. When possible, DRuby infers static types to discover type errors in Ruby programs. When necessary, the programmer can provide DRuby with annotations that assign static types to dynamic code. These annotations are checked at run time, isolating type errors to unverified code. We applied DRuby to a suite of benchmarks and found several bugs that would cause run-time type errors. DRuby also reported a number of warnings that reveal questionable programming practices in the benchmarks. We believe that DRuby takes a major step toward bringing the benefits of combined static and dynamic typing to Ruby and other object-oriented languages.}, keywords = {Contracts, dynamic typing, ruby, Type inference}, isbn = {978-1-60558-166-8}, doi = {10.1145/1529282.1529700}, url = {http://doi.acm.org/10.1145/1529282.1529700}, author = {Furr,Michael and An,Jong-hoon (David) and Foster, Jeffrey S. and Hicks, Michael W.} } @article {18721, title = {Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13}, journal = {Molecular Cell}, volume = {35}, year = {2009}, month = {2009/08/14/}, pages = {280 - 290}, abstract = {SummaryDegradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of~one ubiquitin subunit (the {\textquotedblleft}proximal{\textquotedblright} one) is covalently bonded to G76 of the other (the {\textquotedblleft}distal{\textquotedblright} subunit). We demonstrate that S5a{\textquoteright}s UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains. }, keywords = {Proteins}, isbn = {1097-2765}, doi = {10.1016/j.molcel.2009.06.010}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509004018}, author = {Zhang,Naixia and Wang,Qinghua and Ehlinger,Aaron and Randles,Leah and Lary,Jeffrey W. and Kang,Yang and Haririnia,Aydin and Storaska,Andrew J. and Cole,James L. and Fushman, David and Walters,Kylie J.} } @article {14657, title = {A Testing Based Empirical Study of Dynamic Software Update Safety Restrictions}, journal = {Technical Reports of the Computer Science Department}, year = {2009}, month = {2009/10/16/}, abstract = {Recent years have seen significant advances in dynamic softwareupdating (DSU) systems, which allow programs to be patched on the fly. Most DSU systems employ automatic safety checks to avoid applying a patch if doing so may lead to incorrect behavior. This paper presents what we believe is the first comprehensive empirical evaluation of the two most significant DSU safety checks: activeness safety (AS), which disallows patches that modify functions on the stack, and con-freeness safety (CFS), which allows modifications to active functions, but only when doing so will be type safe. To measure the checks{\textquoteright} effectiveness, we tested them against three years of updates to Open-SSH and vsftpd. We performed this testing using a novel DSU testing methodology that systematically applies updates throughout the execution of a test suite. After testing updates to both applications in this way, we tracked how often the safety checks allow updates and which updates result in test failures. We found that updating without safety checks produced many failures, and that both AS and CFS dramatically reduced, but did not fully eliminate, these failures. CFS yielded more failures than AS, but AS was more restrictive than CFS, disallowing far more successful updates. Our results suggest that neither AS nor CFS is likely suitable for general-purpose DSU on its own. Indeed, we found that selecting update points manually could avoid all failures while still permitting sufficient updates. Our results present a challenge and important insights for future work: to discover safe and sufficient update points fully automatically. }, url = {http://drum.lib.umd.edu/handle/1903/9802}, author = {Hayden,Christopher M and Hardisty,Eric A. and Hicks, Michael W. and Foster, Jeffrey S.} } @conference {14740, title = {Tests to the left of me, types to the right: how not to get stuck in the middle of a ruby execution}, booktitle = {Proceedings for the 1st workshop on Script to Program Evolution}, series = {STOP {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {14 - 16}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Ruby is a popular dynamic scripting language that permits terse, expressive code, but provides no static checks to detect errors before running the program. To address this, we have developed Diamond-back Ruby (DRuby), a tool that blends the benefits of static and dynamic typing. This paper briefly describes the main features of DRuby, which we will present in a tool demonstration. The presentation will concentrate on the development of a small, statically typed Ruby program, illustrating how DRuby might be used in practice. The audience will learn about some of the practical design decisions that went into DRuby, and how to use it to develop a type-safe Ruby program.}, isbn = {978-1-60558-543-7}, doi = {10.1145/1570506.1570508}, url = {http://doi.acm.org/10.1145/1570506.1570508}, author = {Furr,Michael and An,Jong-hoon (David) and Foster, Jeffrey S. and Hicks, Michael W.} } @article {18724, title = {Together, Rpn10 and Dsk2 Can Serve as a Polyubiquitin Chain-Length Sensor}, journal = {Molecular Cell}, volume = {36}, year = {2009}, month = {2009/12/24/}, pages = {1018 - 1033}, abstract = {SummaryAs a signal for substrate targeting, polyubiquitin meets various layers of receptors upstream to the 26S proteasome. We obtained structural information on two receptors, Rpn10 and Dsk2, alone and in complex with (poly)ubiquitin or with each other. A~hierarchy of affinities emerges with Dsk2 binding monoubiquitin tighter than Rpn10 does, whereas Rpn10 prefers the ubiquitin-like domain of Dsk2 to monoubiquitin, with increasing affinities for longer polyubiquitin chains. We demonstrated the formation of ternary complexes of both receptors simultaneously with (poly)ubiquitin and found that, depending on the ubiquitin chain length, the orientation of the resulting complex is entirely different, providing for alternate signals. Dynamic rearrangement provides a chain-length sensor, possibly explaining how accessibility of Dsk2 to the proteasome is limited unless it carries a properly tagged cargo. We propose a mechanism for a malleable ubiquitin signal that depends both on chain length and combination of receptors to produce tetraubiquitin as an efficient signal threshold. }, keywords = {Proteins, signaling}, isbn = {1097-2765}, doi = {10.1016/j.molcel.2009.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S1097276509008260}, author = {Zhang,Daoning and Chen,Tony and Ziv,Inbal and Rosenzweig,Rina and Matiuhin,Yulia and Bronner,Vered and Glickman,Michael H. and Fushman, David} } @article {18529, title = {Towards an Internet Connectivity Market}, volume = {GT-CS-09-01}, year = {2009}, month = {2009///}, institution = {Georgia Institute of Technology}, abstract = {Today{\textquoteright}s Internet achieves end-to-end connectivity through bilateral contracts between neighboring networks; unfortunately, this {\textquotedblleft}one size fits all{\textquotedblright} connectivity results in less efficient paths, unsold capacity and unmet demand, and sometimes catastrophic market failures that result in global disconnectivity. This paper presents the design and evaluation of MINT, a Market for Internet Transit. MINT is a connectivity market and corresponding set of protocols that allows ISPs to offer path segments on an open market. Edge networks bid for end-to-end paths, and a mediator matches bids for paths to collections of path segments that form end-to-end paths. MINT can be deployed using protocols that are present in today{\textquoteright}s routers, and it operates in parallel with the existing routing infrastructure and connectivity market. We present MINT{\textquoteright}s market model and protocol design; evaluate how MINT improves efficiency, the utility of edge networks, and the profits of transit networks; and how MINT can operate at Internet scale.}, url = {http://hdl.handle.net/1853/30622}, author = {Feamster, Nick and Hassan,U. and Sundaresan,S. and Valancius,V. and Johari,R. and Vazirani,V.} } @article {14301, title = {Triaging Checklists: a Substitute for a PhD in Static Analysis}, journal = {Evaluation and Usability of Programming Languages and Tools (PLATEAU) PLATEAU 2009}, year = {2009}, month = {2009///}, abstract = {Static analysis tools have achieved great success in recentyears in automating the process of detecting defects in soft- ware. However, these sophisticated tools have yet to gain widespread adoption, since many of these tools remain too difficult to understand and use. In previous work, we dis- covered that even with an effective code visualization tool, users still found it hard to determine if warnings reported by these tools were true errors or false warnings. The fun- damental problem users face is to understand enough of the underlying algorithm to determine if a warning is caused by imprecision in the algorithm, a challenge that even experts with PhDs may take a while to achieve. In our current work, we propose to use triaging checklists to provide users with systematic guidance to identify false warnings by taking into account specific sources of imprecision in the particular tool. Additionally, we plan to provide checklist assistants, which is a library of simple analyses designed to aid users in an- swering checklist questions. }, author = {Phang,K.Y. and Foster, Jeffrey S. and Hicks, Michael W. and Sazawal,V.} } @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 {15843, title = {Understanding IT Innovations Through Computational Analysis of Discourse}, journal = {ICIS 2009 Proceedings}, year = {2009}, month = {2009/01/01/}, url = {http://aisel.aisnet.org/icis2009/102}, author = {Tsui,Chia-jung and Wang,Ping and Fleischmann,Kenneth and Oard, Douglas and Sayeed,Asad} } @article {12885, title = {Using Satellite Images of Environmental Changes to Predict Infectious Disease Outbreaks}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {15}, year = {2009}, month = {2009/09//}, pages = {1341 - 1346}, abstract = {A strong global satellite imaging system is essential for predicting outbreaks., Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today{\textquoteright}s ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response.}, isbn = {1080-6040}, doi = {10.3201/eid/1509.081334}, author = {Ford,Timothy E. and Rita R Colwell and Rose,Joan B. and Morse,Stephen S. and Rogers,David J. and Yates,Terry L.} } @article {14273, title = {Viewpoint Invariant Texture Description Using Fractal Analysis}, journal = {International Journal of Computer Vision}, volume = {83}, year = {2009}, month = {2009///}, pages = {85 - 100}, abstract = {Image texture provides a rich visual description of the surfaces in the scene. Many texture signatures based on various statistical descriptions and various local measurements have been developed. Existing signatures, in general, are not invariant to 3D geometric transformations, which is a serious limitation for many applications. In this paper we introduce a new texture signature, called the multifractal spectrum (MFS). The MFS is invariant under the bi-Lipschitz map, which includes view-point changes and non-rigid deformations of the texture surface, as well as local affine illumination changes. It provides an efficient framework combining global spatial invariance and local robust measurements. Intuitively, the MFS could be viewed as a {\textquotedblleft}better histogram{\textquotedblright} with greater robustness to various environmental changes and the advantage of capturing some geometrical distribution information encoded in the texture. Experiments demonstrate that the MFS codes the essential structure of textures with very low dimension, and thus represents an useful tool for texture classification.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1007/s11263-009-0220-6}, author = {Yong Xu and Hui Ji and Ferm{\"u}ller, Cornelia} } @conference {14849, title = {Visibility constraints on features of 3D objects}, booktitle = {Computer Vision and Pattern Recognition, 2009. CVPR 2009. IEEE Conference on}, year = {2009}, month = {2009/06//}, pages = {1231 - 1238}, abstract = {To recognize three-dimensional objects it is important to model how their appearances can change due to changes in viewpoint. A key aspect of this involves understanding which object features can be simultaneously visible under different viewpoints. We address this problem in an image-based framework, in which we use a limited number of images of an object taken from unknown viewpoints to determine which subsets of features might be simultaneously visible in other views. This leads to the problem of determining whether a set of images, each containing a set of features, is consistent with a single 3D object. We assume that each feature is visible from a disk of viewpoints on the viewing sphere. In this case we show the problem is NP-hard in general, but can be solved efficiently when all views come from a circle on the viewing sphere. We also give iterative algorithms that can handle noisy data and converge to locally optimal solutions in the general case. Our techniques can also be used to recover viewpoint information from the set of features that are visible in different images. We show that these algorithms perform well both on synthetic data and images from the COIL dataset.}, keywords = {3D, algorithms;synthetic, complexity;iterative, constraints;computational, data;synthetic, dataset;NP-hard;image-based, features;COIL, framework;iterative, images;three-dimensional, methods;object, object, recognition;, recognition;viewing, sphere;visibility}, doi = {10.1109/CVPR.2009.5206726}, author = {Basri,R. and Felzenszwalb,P. F and Girshick,R. B and Jacobs, David W. and Klivans,C. J} } @article {18544, title = {Accountable internet protocol (aip)}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {38}, year = {2008}, month = {2008/08//}, pages = {339 - 350}, abstract = {This paper presents AIP (Accountable Internet Protocol), a network architecture that provides accountability as a first-order property. AIP uses a hierarchy of self-certifying addresses, in which each component is derived from the public key of the corresponding entity. We discuss how AIP enables simple solutions to source spoofing, denial-of-service, route hijacking, and route forgery. We also discuss how AIP{\textquoteright}s design meets the challenges of scaling, key management, and traffic engineering.}, keywords = {accountability, address, internet architecture, scalability, Security}, isbn = {0146-4833}, doi = {10.1145/1402946.1402997}, url = {http://doi.acm.org/10.1145/1402946.1402997}, author = {Andersen,David G. and Balakrishnan,Hari and Feamster, Nick and Koponen,Teemu and Moon,Daekyeong and Shenker,Scott} } @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 {15857, title = {Advancing social science research by applying computational linguistics}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {45}, year = {2008}, month = {2008///}, pages = {1 - 12}, author = {Cheng,A.S. and Fleischmann,K.R. and Wang,P. and Oard, Douglas} } @article {18694, title = {Affinity Makes the Difference: Nonselective Interaction of the UBA Domain of Ubiquilin-1 with Monomeric Ubiquitin and Polyubiquitin Chains}, journal = {Journal of Molecular Biology}, volume = {377}, year = {2008}, month = {2008/03/14/}, pages = {162 - 180}, abstract = {Ubiquilin/PLIC proteins belong to the family of UBL{\textendash}UBA proteins implicated in the regulation of the ubiquitin-dependent proteasomal degradation of cellular proteins. A human presenilin-interacting protein, ubiquilin-1, has been suggested as potential therapeutic target for treating Huntington{\textquoteright}s disease. Ubiquilin{\textquoteright}s interactions with mono- and polyubiquitins are mediated by its UBA domain, which is one of the tightest ubiquitin binders among known ubiquitin-binding domains. Here we report the three-dimensional structure of the UBA domain of ubiquilin-1 (UQ1-UBA) free in solution and in complex with ubiquitin. UQ1-UBA forms a compact three-helix bundle structurally similar to other known UBAs, and binds to the hydrophobic patch on ubiquitin with a Kd of 20~μM. To gain structural insights into UQ1-UBA{\textquoteright}s interactions with polyubiquitin chains, we have mapped the binding interface between UQ1-UBA and Lys48- and Lys63-linked di-ubiquitins and characterized the strength of UQ1-UBA binding to these chains. Our NMR data show that UQ1-UBA interacts with the individual ubiquitin units in both chains in a mode similar to its interaction with mono-ubiquitin, although with an improved binding affinity for the chains. Our results indicate that, in contrast to UBA2 of hHR23A that has strong binding preference for Lys48-linked chains, UQ1-UBA shows little or no binding selectivity toward a particular chain linkage or between the two ubiquitin moieties in the same chain. The structural data obtained in this study provide insights into the possible structural reasons for the diversity of polyubiquitin chain recognition by UBA domains.}, keywords = {polyubiquitin, protein{\textendash}protein interaction, UBA domain, ubiquilin, ubiquitin}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2007.12.029}, url = {http://www.sciencedirect.com/science/article/pii/S0022283607016452}, author = {Zhang,Daoning and Raasi,Shahri and Fushman, David} } @inbook {19602, title = {Algorithms for Location Estimation Based on RSSI Sampling}, booktitle = {Algorithmic Aspects of Wireless Sensor Networks}, series = {Lecture Notes in Computer Science}, year = {2008}, month = {2008/01/01/}, pages = {72 - 86}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {In this paper, we re-examine the RSSI measurement model for location estimation and provide the first detailed formulation of the probability distribution of the position of a sensor node. We also show how to use this probabilistic model to efficiently compute a good estimation of the position of the sensor node by sampling multiple readings from the beacons (where we do not merely use the mean of the samples) and then minimizing a function with an acceptable computational effort. The results of the simulation of our method in TOSSIM indicate that the location of the sensor node can be computed in a small amount of time and that the quality of the solution is competitive with previous approaches.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Communication Networks, Data structures, Discrete Mathematics in Computer Science, Information Systems and Communication Service}, isbn = {978-3-540-92861-4, 978-3-540-92862-1}, url = {http://link.springer.com/chapter/10.1007/978-3-540-92862-1_7}, author = {Charalampos Papamanthou and Preparata, Franco P. and Tamassia, Roberto}, editor = {Fekete, S{\'a}ndor P.} } @conference {18546, title = {Answering what-if deployment and configuration questions with wise}, booktitle = {Proceedings of the ACM SIGCOMM 2008 conference on Data communication}, series = {SIGCOMM {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {99 - 110}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Designers of content distribution networks often need to determine how changes to infrastructure deployment and configuration affect service response times when they deploy a new data center, change ISP peering, or change the mapping of clients to servers. Today, the designers use coarse, back-of-the-envelope calculations, or costly field deployments; they need better ways to evaluate the effects of such hypothetical "what-if" questions before the actual deployments. This paper presents What-If Scenario Evaluator (WISE), a tool that predicts the effects of possible configuration and deployment changes in content distribution networks. WISE makes three contributions: (1) an algorithm that uses traces from existing deployments to learn causality among factors that affect service response-time distributions; (2) an algorithm that uses the learned causal structure to estimate a dataset that is representative of the hypothetical scenario that a designer may wish to evaluate, and uses these datasets to predict future response-time distributions; (3) a scenario specification language that allows a network designer to easily express hypothetical deployment scenarios without being cognizant of the dependencies between variables that affect service response times. Our evaluation, both in a controlled setting and in a real-world field deployment at a large, global CDN, shows that WISE can quickly and accurately predict service response-time distributions for many practical What-If scenarios.}, keywords = {content distribution networks, performance modeling, what-if scenario evaluation}, isbn = {978-1-60558-175-0}, doi = {10.1145/1402958.1402971}, url = {http://doi.acm.org/10.1145/1402958.1402971}, author = {Tariq,Mukarram and Zeitoun,Amgad and Valancius,Vytautas and Feamster, Nick and Ammar,Mostafa} } @conference {18548, title = {Authenticated out-of-band communication over social links}, booktitle = {Proceedings of the first workshop on Online social networks}, series = {WOSN {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {61 - 66}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many existing host-based applications rely on their own authentication mechanisms and peer discovery services. Although social networking sites already provide mechanisms for users both to discover other users (e.g., by logging on to the social network Web site) and to communicate securely with each other (e.g., using instant messages within the social networking site), today{\textquoteright}s applications have no way to exploit the relationships and trust that are inherent in these networks. This paper proposes Authenticatr, a framework that allows applications to use the authentication and peer discovery mechanisms inherent in social networking sites to bootstrap their own authenticated communication channels. We describe motivating applications, detail the interface that Authenticatr exposes to applications, and discuss practical considerations and security threats.}, keywords = {Authentication, Security, social networks}, isbn = {978-1-60558-182-8}, doi = {10.1145/1397735.1397749}, url = {http://doi.acm.org/10.1145/1397735.1397749}, author = {Ramachandran,Anirudh V. and Feamster, Nick} } @conference {14205, title = {Bilateral symmetry of object silhouettes under perspective projection}, booktitle = {19th International Conference on Pattern Recognition, 2008. ICPR 2008}, year = {2008}, month = {2008/12/08/11}, pages = {1 - 4}, publisher = {IEEE}, organization = {IEEE}, abstract = {Symmetry is an important property of objects and is exhibited in different forms e.g., bilateral, rotational, etc. This paper presents an algorithm for computing the bilateral symmetry of silhouettes of shallow objects under perspective distortion, exploiting the invariance of the cross ratio to projective transformations. The basic idea is to use the cross ratio to compute a number of midpoints of cross sections and then fit a straight line through them. The goodness-of-fit determines the likelihood of the line to be the axis of symmetry. We analytically estimate the midpointpsilas location as a function of the vanishing point for a given object silhouette. Hence finding the symmetry axis amounts to a 2D search in the space of vanishing points. We present experiments on two datasets as well as Internet images of symmetric objects that validate our approach.}, keywords = {Automation, bilateral symmetry, Computer vision, Frequency, Image analysis, Image coding, Image reconstruction, Internet, Internet images, Object detection, object silhouettes, perspective distortion, perspective projection, SHAPE, symmetric objects}, isbn = {978-1-4244-2174-9}, doi = {10.1109/ICPR.2008.4761501}, author = {Bitsakos,K. and Yi,H. and Yi,L. and Ferm{\"u}ller, Cornelia} } @conference {18554, title = {Can great research be taught?: independent research with cross-disciplinary thinking and broader impact}, booktitle = {Proceedings of the 39th SIGCSE technical symposium on Computer science education}, series = {SIGCSE {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {471 - 475}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a course we have developed for preparing new Ph.D. students in computer science for a career in research. The course is intended to teach the skills needed for research and independent work, prepare students psychologically and socially for years lying before them, and help them find a good Ph.D. topic by providing principles and examples. In this course, we emphasize and encourage impact through cross-disciplinary research and broader societal outreach. To our knowledge, the course represents a first-of-its-kind systematic introduction to a graduate research career. This paper describes our high-level goals for this curricular initiative, the structure of the course (including lecture components and assignments), and the challenges we faced in developing this course. As we continue to develop this course, which is now in its second year, we hope it will serve as a model "introduction of Ph.D. research" course for other computer science departments.}, keywords = {graduate education, ph.d., research}, isbn = {978-1-59593-799-5}, doi = {10.1145/1352135.1352294}, url = {http://doi.acm.org/10.1145/1352135.1352294}, author = {Feamster, Nick and Gray,Alexander} } @article {14304, title = {Checking type safety of foreign function calls}, journal = {ACM Transactions on Programming Languages and Systems (TOPLAS)}, volume = {30}, year = {2008}, month = {2008///}, pages = {18 - 18}, author = {Furr,M. and Foster, Jeffrey S.} } @book {14504, title = {On classification, ranking, and probability estimation}, year = {2008}, month = {2008///}, publisher = {Internationales Begegnungs- und Forschungszentrum fur Informatik (IBFI), Schloss Dagstuhl, Germany}, organization = {Internationales Begegnungs- und Forschungszentrum fur Informatik (IBFI), Schloss Dagstuhl, Germany}, abstract = {Given a binary classification task, a ranker is an algorithm that can sort a set of instances from highest to lowest expectation that the instance is positive. In contrast to a classifier, a ranker does not output class predictions {\~A}{\textcent}{\^a}{\quotesinglbase}{\textlnot}{\^a}{\texteuro}{\oe} although it can be turned into a classifier with help of an additional procedure to split the ranked list into two. A straightforward way to compute rankings is to train a scoring classifier to assign numerical scores to instances, for example the predicted odds that an instance is positive. However, rankings can be computed without scores, as we demonstrate in this paper. We propose a lexicographic ranker, LexRank , whose rankings are derived not from scores, but from a simple ranking of attribute values obtained from the training data. Although various metrics can be used, we show that by using the odds ratio to rank the attribute values we obtain a ranker that is conceptually close to the naive Bayes classifier, in the sense that for every instance of LexRank there exists an instance of naive Bayes that achieves the same ranking. However, the reverse is not true, which means that LexRank is more biased than naive Bayes. We systematically develop the relationships and differences between classification, ranking, and probability estimation, which leads to a novel connection between the Brier score and ROC curves. Combining LexRank with isotonic regression, which derives probability estimates from the ROC convex hull, results in the lexicographic probability estimator LexProb.}, author = {Flach,P. and Matsubara,E.T. and De Raedt,L. and Dietterich,T. and Getoor, Lise and Kersting,K. and Muggleton,S. H} } @article {17021, title = {Community response grid (CRG) for a university campus: Design requirements and implications}, journal = {Proceedings of the 5th International ISCRAM Conference}, year = {2008}, month = {2008///}, pages = {34 - 43}, abstract = {This paper describes the initial stages of the participatory design of a community-oriented emergency responsesystem for a university campus. After reviewing related work and the current University emergency response system, this paper describes our participatory design process, discusses initial findings from a design requirement survey and from our interactions with different stakeholders, and proposes a Web interface design for a community response grid system. The prototyping of the system demonstrates the possibility of fostering a social-network-based community participation in emergency response, and also identifies concerns raised by potential users and by the professional responder community. }, author = {Wu,P.F. and Qu,Y. and Preece,J. and Fleischmann,K. and Golbeck,J. and Jaeger,P. and Shneiderman, Ben} } @conference {14669, title = {Contextual effects for version-consistent dynamic software updating and safe concurrent programming}, booktitle = {Proceedings of the 35th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {37 - 49}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper presents a generalization of standard effect systems that we call contextual effects. A traditional effect system computes the effect of an expression e. Our system additionally computes the effects of the computational context in which e occurs. More specifically, we computethe effect of the computation that has already occurred(the prior effect) and the effect of the computation yet to take place (the future effect). Contextual effects are useful when the past or future computation of the program is relevant at various program points. We present two substantial examples. First, we show how prior and future effects can be used to enforce transactional version consistency(TVC), a novel correctness property for dynamic software updates. TV Censures that programmer-designated transactional code blocks appear to execute entirely at the same code version, even if a dynamic update occurs in the middle of the block. Second, we show how future effects can be used in the analysis of multi-threaded programs to find thread-shared locations. This is an essential step in applications such as data race detection.}, keywords = {computation effects, contextual effects, data race detection, dynamic software updating, type and effect systems, version consistency}, isbn = {978-1-59593-689-9}, doi = {10.1145/1328438.1328447}, url = {http://doi.acm.org/10.1145/1328438.1328447}, author = {Neamtiu,Iulian and Hicks, Michael W. and Foster, Jeffrey S. and Pratikakis,Polyvios} } @conference {13119, title = {Decentralized discovery of camera network topology}, booktitle = {Distributed Smart Cameras, 2008. ICDSC 2008. Second ACM/IEEE International Conference on}, year = {2008}, month = {2008/09//}, pages = {1 - 10}, abstract = {One of the primary uses of camera networks is the observation and tracking of objects within some domain. Substantial research has gone into tracking objects within single and multiple views. However, few such approaches scale to large numbers of sensors, and those that do require an understanding of the network topology. Camera network topology models camera adjacency in the context of tracking: when an object/entity leaves one camera, which cameras could it appear at next? This paper presents a decentralized approach for estimating a camera networkpsilas topology based on sequential Bayesian estimation using a modified multinomial distribution. Central to this method is an information-theoretic appearance model for observation weighting. The distributed nature of the approach utilizes all of the sensors as processing agents in collectively recovering the network topology. Experimental results are presented using camera networks varying in size from 10-100 nodes.}, keywords = {adjacency;camera, Bayesian, camera, discovery;modified, distribution;sequential, estimation;Bayes, methods;distributed, multinomial, network, sensors;, sensors;image, topology;decentralized}, doi = {10.1109/ICDSC.2008.4635696}, author = {Farrell,R. and Davis, Larry S.} } @article {17063, title = {Designing community-based emergency communication system: A preliminary study}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {45}, year = {2008}, month = {2008///}, pages = {1 - 3}, author = {Fei Wu,P. and Qu,Y. and Fleischmann,K. and Golbeck,J. and Jaeger,P. and Preece,J. and Shneiderman, Ben} } @article {18511, title = {Detecting botnet membership with dnsbl counterintelligence}, journal = {Botnet Detection}, year = {2008}, month = {2008///}, pages = {131 - 142}, doi = {DOI: 10.1007/978-0-387-68768-1_7}, author = {Ramachandran,A. and Feamster, Nick and Dagon,D.} } @article {14678, title = {Directing javascript with arrows (functional pearl)}, year = {2008}, month = {2008///}, abstract = {JavaScript, being a single-threaded language, makes extensive use of event-driven programming to enable responsive web applications. However, standard approaches to sequencing events are messy, and often lead to code that is difficult to understand and maintain. We have found that arrows, a generalization of monads, are an elegant solution to this problem. Arrows allow us to easily write asynchronous programs in small, modular units of code, and flexibly compose them in many different ways, while nicely abstracting the details of asynchronous program composition. In particular, we show how to use arrows to construct a variety of state machines, such as autoscrollers and drag-and-drop handlers.}, author = {Khoo,Y.P. and Hicks, Michael W. and Foster, Jeffrey S. and Sazawal,V.} } @conference {18565, title = {Distinguishing persistent failures from transient losses}, booktitle = {Proceedings of the 2008 ACM CoNEXT Conference}, series = {CoNEXT {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {50:1{\textendash}50:2 - 50:1{\textendash}50:2}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network tomography is a promising technique to identify the location of of IP faults. The goal of tomography is to infer the status of network internal characteristics based on end-to-end observations. In particular, binary tomography identifies the set of failed links from end-to-end path meausrments. Upon detecting the failure of one or more of the monitored paths, a monitor sends its measurements to a central coordinator. The coordinator then runs the binary tomography algorithm, which takes as input the topology of the network and the status (i.e., up or down) of all monitored paths and finds the minimum set of links that explain the observations.}, isbn = {978-1-60558-210-8}, doi = {10.1145/1544012.1544062}, url = {http://doi.acm.org/10.1145/1544012.1544062}, author = {Cunha,{\'I}talo and Teixeira,Renata and Feamster, Nick and Diot,Christophe} } @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 {18518, title = {A Dynamic Reputation Service for Spotting Spammers}, volume = {GT-CS-08-09}, year = {2008}, month = {2008///}, institution = {School of Computer Science, Georgia Tech}, abstract = {This paper presents the design, implementation, evalu-ation, and initial deployment of SpamSpotter, the first open, large-scale, real-time reputation system for filtering spam. Existing blacklists (e.g., SpamHaus) have trouble keeping pace with spammers{\textquoteright} increasing ability to send spam from {\textquotedblleft}fresh{\textquotedblright} IP addresses, and filters based purely on content are easily evadable. In contrast, SpamSpotter dynamically classifies email senders in real time based on their global sending behavior, rather than based on ephemeral features such as an IP address or the content of the message. In implementing SpamSpotter, we address significant challenges involving both dynamism (i.e., de- termining when to {\textquotedblleft}retrain{\textquotedblright} our dynamic classification algorithms) and scale (i.e., maintaining fast, accurate per- formance in the face of tremendous email message vol- ume). We have evaluated the performance and accuracy of SpamSpotter using traces from a large email-hosting provider and a spam appliance vendor that receives 300 million messages a day. Our evaluation shows that SpamSpotter is scalable, fast, and accurate. SpamSpotter is also operational today: it will currently answer queries from existing spam filtering software (e.g., SpamAssas- sin) with only minor configuration changes. }, author = {Ramachandran,A. and Hao,S. and Khandelwal,H. and Feamster, Nick and Vempala,S.} } @article {17132, title = {Enabling teachers to explore grade patterns to identify individual needs and promote fairer student assessment}, journal = {Computers \& Education}, volume = {51}, year = {2008}, month = {2008/12//}, pages = {1467 - 1485}, abstract = {Exploring student test, homework, and other assessment scores is a challenge for most teachers, especially when attempting to identify cross-assessment weaknesses and produce final course grades. During the course, teachers need to identify subject weaknesses in order to help students who are struggling with a particular topic. This identification often needs to happen across multiple assessment data points and should be considered in comparison to the class{\textquoteright}s progress as a whole. When determining grades, fairness to all is essential, but there are special needs for students who did poorly on one exam or had a steadily increasing grasp of the subject. We present eduViz, a visualization tool designed to help teachers explore and assign grades. Teachers can see the trajectory of student scores, the relationship of a particular student to the class, and use categories they have defined in order to filter their assessment information. Query response is immediate and all logical comparisons are possible. Teachers can easily compare their query to the class or per student average as well as view scores by raw point total or percentage. Additionally, eduViz provides a grade assignment interface which allows teachers to view sorted student scores in a scatterplot. This scatterplot is coupled with a unique partition slider which allows users to move color coordinated bands on the scatterplot to indicate grade ranges. As these grade ranges are set, a histogram is updated to show the number of students assigned to each grade range. These features give teachers new and powerful ways to explore and assign grades so that they can better understand student strengths and weaknesses and make the most of the time they have available. Interviews with 16 expert teachers indicate that eduViz is a success across fields, provides teachers with a useful tool to understand and help their classes, and encourages reflective practice.}, keywords = {Evaluation methodologies, Human{\textendash}computer interface, Improving classroom teaching, Pedagogical issues, Teaching/learning strategies}, isbn = {0360-1315}, doi = {10.1016/j.compedu.2008.01.005}, url = {http://www.sciencedirect.com/science/article/pii/S0360131508000353}, author = {Friedler,Sorelle A. and Tan,Yee Lin and Peer,Nir J. and Shneiderman, Ben} } @inbook {13365, title = {Energy Efficient Monitoring in Sensor Networks}, booktitle = {LATIN 2008: Theoretical InformaticsLATIN 2008: Theoretical Informatics}, series = {Lecture Notes in Computer Science}, volume = {4957}, year = {2008}, month = {2008///}, pages = {436 - 448}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper we study a set of problems related to efficient energy management for monitoring applications in wireless sensor networks. We study several generalizations of a basic problem called Set k -Cover, which can be described as follows: we are given a set of sensors, and a set of regions to be monitored. Each region can be monitored by a subset of the sensors. To increase the lifetime of the sensor network, we would like to partition the sensors into k sets (or time-slots) and activate each partition in a different time-slot. The goal is to find the partitioning that maximizes the coverage of the regions. This problem is known to be NP -hard. We first develop improved approximation algorithms for this problem based on its similarities to the max k -cut problem. We then consider a variation, called Set ( k , α )-cover, where each sensor is allowed to be active in α different time-slots. We develop a randomized routing algorithm for this problem. We then consider extensions where each sensor can monitor only a bounded number of regions in any time-slot. We develop the first approximation algorithms for this problem. An experimental evaluation of the algorithms we propose can be found in the full version of the paper.}, isbn = {978-3-540-78772-3}, url = {http://dx.doi.org/10.1007/978-3-540-78773-0_38}, author = {Deshpande, Amol and Khuller, Samir and Malekian,Azarakhsh and Toossi,Mohammed}, editor = {Laber,Eduardo and Bornstein,Claudson and Nogueira,Loana and Faria,Luerbio} } @article {14432, title = {Exploiting Prior Knowledge in Intelligent Assistants: Combining Relational Models with Hierarchies}, journal = {Probabilistic, Logical and Relational Learning - A Further Synthesis}, year = {2008}, month = {2008///}, abstract = {Statitsical relational models have been successfully used to model static probabilistic relationships between the entities of the domain. In this talk, we illustrate their use in a dynamic decison-theoretic setting where the task is to assist a user by inferring his intentional structure and taking appropriate assistive actions. We show that the statistical relational models can be used to succintly express the system{\textquoteright}s prior knowledge about the user{\textquoteright}s goal-subgoal structure and tune it with experience. As the system is better able to predict the user{\textquoteright}s goals, it improves the effectiveness of its assistance. We show through experiments that both the hierarchical structure of the goals and the parameter sharing facilitated by relational models significantly improve the learning speed.}, author = {Natarajan,S. and Tadepalli,P. and Fern,A. and De Raedt,L. and Dietterich,T. and Getoor, Lise and Kersting,K. and Muggleton,S. H} } @article {18508, title = {Fast flux service networks: Dynamics and roles in hosting online scams}, volume = {GT-CS-08-07}, year = {2008}, month = {2008///}, institution = {School of Computer Science, Georgia Tech}, abstract = {This paper studies the dynamics of fast flux service networks and their role in online scam hosting infrastructures. By monitoring changes in DNS records of over 350 distinct fast flux domains collected from URLs in 115,000 spam emails at a large spam sinkhole, we measure the rate of change of DNS records, accumulation of new distinct IPs in the hosting infrastructure, and location of change both for individual domains and across 21 different scam campaigns. We find that fast flux networks redirect clients at much different rates{\textemdash}and at different locations in the DNS hierarchy{\textemdash}than conventional load-balanced Web sites. We also find that the IP addresses in the fast flux infrastructure itself change rapidly, and that this infrastructure is shared extensively across scam campaigns, and some of these IP addresses are also used to send spam. Finally, we compared IP addresses in fast-flux infrastructure and flux domains with various blacklists (i.e., SBL, XBL/PBL, and URIBL) and found that nearly one-third of scam sites were not listed in the URL blacklist at the time they were hosting scams. We also observed many hosting sites and nameservers that were listed in both the SBL and XBL both before and after we observed fast-flux activity; these observations lend insight into both the responsiveness of existing blacklists and the life cycles of fast-flux nodes.}, url = {http://hdl.handle.net/1853/30451}, author = {Konte,M. and Feamster, Nick and Jung,J.} } @conference {18567, title = {Fast monitoring of traffic subpopulations}, booktitle = {Proceedings of the 8th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {257 - 270}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Network accounting, forensics, security, and performance monitoring applications often need to examine detailed traces from subsets of flows ("subpopulations"), where the application desires flexibility in specifying the subpopulation (e.g., to detect a portscan, the application must observe many packets between a source and a destination with one packet to each port). However, the dynamism and volume of network traffic on many high-speed links necessitates traffic sampling, which adversely affects subpopulation monitoring: because many subpopulations of interest to operators are low-volume flows, conventional sampling schemes (e.g., uniform random sampling) miss much of the subpopulation{\textquoteright}s traffic. Today{\textquoteright}s routers and network devices provide scant support for monitoring specific traffic subpopulations. This paper presents the design, implementation, and evaluation of FlexSample, a traffic monitoring engine that dynamically extracts traffic from subpopulations that operators define using conditions on packet header fields. FlexSample uses a fast, flexible counter array to provide rough estimates of packets{\textquoteright} membership in respective subpopulations. Based on these coarse estimates, FlexSample then makes per-packet sampling decisions to sample proportionately from each subpopulation (as specified by a network operator), subject to an overall sampling constraint. We apply FlexSample to extract subpopulations such as port scans and traffic to high-degree nodes and find that it is able to capture significantly more packets from these subpopulations than conventional approaches.}, keywords = {counters, flexsample, sampling, traffic statistics, traffic subpopulations}, isbn = {978-1-60558-334-1}, doi = {10.1145/1452520.1452551}, url = {http://doi.acm.org/10.1145/1452520.1452551}, author = {Ramachandran,Anirudh and Seetharaman,Srinivasan and Feamster, Nick and Vazirani,Vijay} } @conference {18569, title = {Fighting spam, phishing, and online scams at the network level}, booktitle = {Proceedings of the 4th Asian Conference on Internet Engineering}, series = {AINTEC {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {39 - 40}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Recent estimates indicate that upwards of 90\% of all email traffic is spam [4]. Spam is more than just a nuisance: it consumes resources on the network and at mail servers, and much of it is also used to mount attacks on users via malware and social engineering attacks (e.g., phishing). In recent years, spammers have increased their virulence, by sending spam from large collections of compromised machines ("botnets"), encapsulating their messages in content that is difficult to filter (e.g., images), and by targeting their messages towards specific groups of users. Indeed, spammers show no sign of slowing, and, worse, their techniques may carry over to other domains (e.g., VoIP, mobile devices) in the future.}, isbn = {978-1-60558-127-9}, doi = {10.1145/1503370.1503382}, url = {http://doi.acm.org/10.1145/1503370.1503382}, author = {Feamster, Nick} } @article {18517, title = {Fishing for Phishing from the Network Stream}, volume = {GT-CS-08-08}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {Phishing is an increasingly prevalent social-engineering attack that attempts identity theft using spoofed Web pages of legitimate organizations. Unfortunately, current phishing detection methods are neither complete nor responsive because they rely on user reports, and many also require clientside software. Anti-phishing techniques could be more effective if they (1) could detect phishing attacks automatically from the network traffic; (2) could operate without cooperation from end-users. This paper performs a preliminary study to determine the feasibility of detecting phishing attacks in real-time, from the network traffic stream itself. We develop a model to identify the stages where in-network phishing detection is feasible and the data sources that can be analyzed to provide relevant information at each stage. Based on this model, we develop and evaluate a detection method based on features that exist in the network traffic it- self and are correlated with confirmed phishing attacks.}, url = {http://hdl.handle.net/1853/25463}, author = {Ramachandran,A. and Feamster, Nick and Krishnamurthy,B. and Spatscheck,O. and Van der Merwe,J.} } @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.} } @inbook {14698, title = {Formalizing Soundness of Contextual Effects}, booktitle = {Theorem Proving in Higher Order LogicsTheorem Proving in Higher Order Logics}, series = {Lecture Notes in Computer Science}, volume = {5170}, year = {2008}, month = {2008///}, pages = {262 - 277}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A contextual effect system generalizes standard type and effect systems: where a standard effect system computes the effect of an expression e , a contextual effect system additionally computes the prior and future effect of e , which characterize the behavior of computation prior to and following, respectively, the evaluation of e . This paper describes the formalization and proof of soundness of contextual effects, which we mechanized using the Coq proof assistant. Contextual effect soundness is an unusual property because the prior and future effect of a term e depends not on e itself (or its evaluation), but rather on the evaluation of the context in which e appears. Therefore, to state and prove soundness we must {\textquotedblleft}match up{\textquotedblright} a subterm in the original typing derivation with the possibly-many evaluations of that subterm during the evaluation of the program, in a way that is robust under substitution. We do this using a novel typed operational semantics. We conjecture that our approach could prove useful for reasoning about other properties of derivations that rely on the context in which that derivation appears.}, isbn = {978-3-540-71065-3}, url = {http://dx.doi.org/10.1007/978-3-540-71067-7_22}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W. and Neamtiu,Iulian}, editor = {Mohamed,Otmane and Mu{\~n}oz,C{\'e}sar and Tahar,Sofi{\`e}ne} } @conference {12106, title = {A Framework for Software Engineering Experimental Replications}, booktitle = {Engineering of Complex Computer Systems, 2008. ICECCS 2008. 13th IEEE International Conference on}, year = {2008}, month = {2008/04/31/3}, pages = {203 - 212}, abstract = {Experimental replications are very important to the advancement of empirical software engineering. Replications are one of the key mechanisms to confirm previous experimental findings. They are also used to transfer experimental knowledge, to train people, and to expand a base of experimental evidence. Unfortunately, experimental replications are difficult endeavors. It is not easy to transfer experimental know-how and experimental findings. Based on our experience, this paper discusses this problem and proposes a Framework for Improving the Replication of Experiments (FIRE). The FIRE addresses knowledge sharing issues both at the intra-group (internal replications) and inter-group (external replications) levels. It encourages coordination of replications in order to facilitate knowledge transfer for lower cost, higher quality replications and more generalizable results.}, keywords = {engineering, engineering;, evidence;experimental, experimental, Experiments;experimental, for, Framework, Improving, knowledge, of, replication, replication;software, sharing;software, the, transfer;knowledge}, doi = {10.1109/ICECCS.2008.38}, author = {Mendonca,M.G. and Maldonado,J.C. and de Oliveira,M.C.F. and Carver, J. and Fabbri,C.P.F. and Shull, F. and Travassos,G.H. and Hohn,E.N. and Basili, Victor R.} } @article {14135, title = {H (div) preconditioning for a mixed finite element formulation of the stochastic diffusion problem}, year = {2008}, month = {2008///}, institution = {Citeseer}, author = {Elman, Howard and Furnival, D. G and Powell, C. E} } @conference {13263, title = {A hierarchical spatial index for triangulated surfaces}, booktitle = {Int. Conf. on Computer Graphics Theory and Applications (GRAPP)}, year = {2008}, month = {2008///}, pages = {86 - 91}, abstract = {We present the PM2-Triangle quadtree (PM2T-quadtree), a new hierarchical spatial index for triangle mesheswhich has been designed for performing spatial queries on triangle-based terrain models. The PM2T-quadtree is based on a recursive space decomposition into square blocks. Here, we propose a highly compact data structure encoding a PM2T-quadtree, which decouples the spatial indexing structure from the combinatorial description of the mesh. We compare the PM2T-quadtree against other spatial indexes by considering the structure of the underlying domain subdivision, the storage costs of their data structures and the performance in geometric queries. }, author = {De Floriani, Leila and Facinoli,M. and Magillo,P. and Dimitri,D.} } @article {14970, title = {High Performance Computing Algorithms for Land Cover}, year = {2008}, month = {2008///}, institution = {CiteSeerX}, abstract = {Global and regional land cover studies require the ability to apply complex models on selected subsets of large amounts of multi-sensor and multi-temporal data sets that have been derived from raw instrument measurements using widely accepted pre-processing algorithms. The computational and storage requirements of most such studies far exceed what is possible on a single workstation environment. We have been pursuing a new approach that couples scalable and open distributed heterogeneous hardware with the development of high performance software for processing, indexing, and organizing remotely sensed data. Hierarchical data management tools are used to ingest raw data, create metadata, and organize the archived data so as to automatically achieve computational load balancing among the available nodes and minimize I/O overheads. We illustrate our approach with four specific examples. The first is the development of the first fast operational scheme for the atmospheric correction of Landsat TM scenes, while the second example focuses on image segmentation using a novel hierarchical connected components algorithm. Retrieval of global BRDF (Bidirectional Reflectance Distribution Function) in the red and near infrared wavelengths using four years (1983 to 1986) of Pathfinder AVHRR Land (PAL) data set is the focus of our third example. The fourth example is the development of a hierarchical data organization scheme that allows on-demand processing and retrieval of regional and global AVHRR data sets. Our results show that substantial improvements in computational times can be achieved by using the high performance computing technology.}, url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.58.4213}, author = {Dynamics Using Remote and Satya Kalluri and Bader,David A. and John Townshend and JaJa, Joseph F. and Zengyan Zhang and Fallah-adl,Hassan} } @article {18492, title = {Hosting virtual networks on commodity hardware}, volume = {GT-CS-07-10}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {This paper describes Trellis, a software platform for hostingmultiple virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topol- ogy, control protocols, and forwarding tables, which low- ers the barrier for deploying custom services on an isolated, reconfigurable, and programmable network, while amor- tizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed vir- tual networks. We describe the design and implementation, of Trellis, including kernel-level performance optimizations, and evaluate its supported packet-forwarding rates against other virtualization technologies. We are in the process of upgrading the VINI facility to use Trellis. We also plan to release Trellis as part of MyVINI, a standalone software dis- tribution that allows researchers and application developers to deploy their own virtual network hosting platforms. }, author = {Bhatia,S. and Motiwala,M. and Muhlbauer,W. and Valancius,V. and Bavier,A. and Feamster, Nick and Peterson,L. and Rexford,J.} } @article {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.} } @article {18532, title = {Learning To Predict Bad Behavior}, journal = {NIPS 2007 Workshop on Machine Learning in Adversarial Environments for Computer Security}, year = {2008}, month = {2008///}, author = {Ahmed Syed,N. and Feamster, Nick and Gray,A.} } @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 {14229, title = {Measuring 1st order stretchwith a single filter}, booktitle = {IEEE International Conference on Acoustics, Speech and Signal Processing, 2008. ICASSP 2008}, year = {2008}, month = {2008/04/31/March}, pages = {909 - 912}, publisher = {IEEE}, organization = {IEEE}, abstract = {We analytically develop a filter that is able to measure the linear stretch of the transformation around a point, and present results of applying it to real signals. We show that this method is a real-time alternative solution for measuring local signal transformations. Experimentally, this method can accurately measure stretch, however, it is sensitive to shift.}, keywords = {Cepstral analysis, Educational institutions, filter, filtering theory, Fourier transforms, Frequency domain analysis, Frequency estimation, Gabor filters, Image analysis, IMAGE PROCESSING, linear stretch measurement, local signal transformation measurement, Nonlinear filters, Phase estimation, Signal analysis, Speech processing}, isbn = {978-1-4244-1483-3}, doi = {10.1109/ICASSP.2008.4517758}, author = {Bitsakos,K. and Domke, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {19197, title = {Measuring the pulse of the city through shared bicycle programs}, journal = {Proc. of UrbanSense08}, year = {2008}, month = {2008}, author = {Jon Froehlich and Neumann, J. and Oliver,N.} } @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 {18585, title = {MINT: a Market for INternet Transit}, booktitle = {Proceedings of the 2008 ACM CoNEXT Conference}, series = {CoNEXT {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {70:1{\textendash}70:6 - 70:1{\textendash}70:6}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Today{\textquoteright}s Internet{\textquoteright}s routing paths are inefficient with respect to both connectivity and the market for interconnection. The former manifests itself via needlessly long paths, de-peering, etc. The latter arises because of a primitive market structure that results in unfulfilled demand and unused capacity. Today{\textquoteright}s networks make pairwise, myopic interconnection decisions based on business considerations that may not mirror considerations of the edge networks (or end systems) that would benefit from the existence of a particular interconnection. These bilateral contracts are also complex and difficult to enforce. This paper proposes MINT, a market structure and routing protocol suite that facilitates the sale and purchase of end-to-end Internet paths. We present MINT{\textquoteright}s structure, explain how it improves connectivity and market efficiency, explore the types of connectivity that might be exchanged (vs. today{\textquoteright}s "best effort" connectivity), and argue that MINT{\textquoteright}s deployment is beneficial to both stub networks and transit providers. We discuss research challenges, including the design both of the protocol that maintains information about connectivity and of the market clearing algorithms. Our preliminary evaluation shows that such a market quickly reaches equilibrium and exhibits price stability.}, isbn = {978-1-60558-210-8}, doi = {10.1145/1544012.1544082}, url = {http://doi.acm.org/10.1145/1544012.1544082}, author = {Valancius,Vytautas and Feamster, Nick and Johari,Ramesh and Vazirani,Vijay} } @article {14708, title = {Modular Information Hiding and Type-Safe Linking for C}, journal = {IEEE Transactions on Software Engineering}, volume = {34}, year = {2008}, month = {2008/06//May}, pages = {357 - 376}, abstract = {This paper presents CMod, a novel tool that provides a sound module system for C. CMod works by enforcing four rules that are based on principles of modular reasoning and on current programming practice. CMod{\textquoteright}s rules flesh out the convention that .h header files are module interfaces and .c source files are module implementations. Although this convention is well-known, existing explanations of it are incomplete, omitting important subtleties needed for soundness. In contrast, we have proven formally that CMod{\textquoteright}s rules enforce both information hiding and type-safe linking. To use CMod, the programmer develops and builds their software as usual, redirecting the compiler and linker to CMod{\textquoteright}s wrappers. We evaluated CMod by applying it to 30 open source programs, totaling more than one million LoC. Violations to CMod{\textquoteright}s rules revealed more than a thousand information hiding errors, dozens of typing errors, and hundreds of cases that, although not currently bugs, make programming mistakes more likely as the code evolves. At the same time, programs generally adhere to the assumptions underlying CMod{\textquoteright}s rules, and so we could fix rule violations with a modest effort. We conclude that CMod can effectively support modular programming in C: it soundly enforces type-safe linking and information-hiding while being largely compatible with existing practice.}, keywords = {C language, CMOD, Code design, Coding Tools and Techniques, compiler, data encapsulation, Information hiding, modular information hiding, modular reasoning, modules, object-oriented programming, open source programs, packages, program compilers, public domain software, reliability, software reusability, type-safe linking}, isbn = {0098-5589}, doi = {10.1109/TSE.2008.25}, author = {Srivastava,S. and Hicks, Michael W. and Foster, Jeffrey S. and Jenkins,P.} } @article {18707, title = {Mutations in the Hydrophobic Core of Ubiquitin Differentially Affect Its Recognition by Receptor Proteins}, journal = {Journal of Molecular Biology}, volume = {375}, year = {2008}, month = {2008/01/25/}, pages = {979 - 996}, abstract = {Ubiquitin (Ub) is one of the most highly conserved signaling proteins in eukaryotes. In carrying out its myriad functions, Ub conjugated to substrate proteins interacts with dozens of receptor proteins that link the Ub signal to various biological outcomes. Here we report mutations in conserved residues of Ub{\textquoteright}s hydrophobic core that have surprisingly potent and specific effects on molecular recognition. Mutant Ubs bind tightly to the Ub-associated domain of the receptor proteins Rad23 and hHR23A but fail to bind the Ub-interacting motif present in the receptors Rpn10 and S5a. Moreover, chains assembled on target substrates with mutant Ubs are unable to support substrate degradation by the proteasome in vitro or sustain viability of yeast cells. The mutations have relatively little effect on Ub{\textquoteright}s overall structure but reduce its rigidity and cause a slight displacement of the C-terminal β-sheet, thereby compromising association with Ub-interacting motif but not with Ub-associated domains. These studies emphasize an unexpected role for Ub{\textquoteright}s core in molecular recognition and suggest that the diversity of protein{\textendash}protein interactions in which Ub engages placed enormous constraints on its evolvability.}, keywords = {hydrophobic core mutation, molecular recognition, proteasomal degradation, ubiquitin, ubiquitin receptors}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2007.11.016}, url = {http://www.sciencedirect.com/science/article/pii/S0022283607014763}, author = {Haririnia,Aydin and Verma,Rati and Purohit,Nisha and Twarog,Michael Z. and Deshaies,Raymond J. and Bolon,Dan and Fushman, David} } @article {18502, title = {NANO: Network Access Neutrality Observatory}, volume = {GT-CS-08-03}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {This paper tackles a technical problem that is of growing interest in light of the ongoing network neutrality debate: We aim to develop a system that can reliably determine whether particular ISP is discriminating against a service using only passive measurements from end-hosts. This problem presents significant challenges because many types of discrimination can often resemble commonplace performance degradations (e.g., resulting from failure or misconfiguration). To distinguish discrimination from degradation, we propose a statistical method to estimate causal effect and develop a system, NANO, based on this method. NANO aggregates passive measurements from end-hosts, stratifies the measurements to account for possible confounding factors, and distinguishes when an ISP is discriminating against a particular service or group of clients. Preliminary simulation results demonstrate the promise of NANO for both detecting various types of discrimination and absolving an ISP when it is not discriminating.}, url = {http://hdl.handle.net/1853/25461}, author = {Tariq,M.B. and Motiwala,M. and Feamster, Nick} } @article {18503, title = {Packets with provenance}, volume = {GT-CS-08-02}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {Traffic classification and distinction allows network operators to provision resources, enforce trust, control unwanted traffic, and traceback unwanted traffic to its source. Today{\textquoteright}s classification mechanisms rely primarily on IP addresses and port numbers; unfortunately, these fields are often too coarse and ephemeral, and moreover, they do not reflect traffic{\textquoteright}s provenance, associated trust, or relationship to other processes or hosts. This paper presents the design, analysis, user-space implementation, and evaluation of Pedigree, which consists of two components: a trusted tagger that resides on hosts and tags packets with information about their provenance (i.e., identity and history of potential input from hosts and resources for the process that generated them), and an arbiter, which decides what to do with the traffic that carries certain tags. Pedigree allows operators to write traffic classification policies with expressive semantics that reflect properties of the actual process that generated the traffic. Beyond offering new function and flexibility in traffic classification, Pedigree represents a new and interesting point in the design space between filtering and capabilities, and it allows network operators to leverage host-based trust models to decide treatment of network traffic.}, url = {http://hdl.handle.net/1853/25467}, author = {Ramachandran,A. and Bhandankar,K. and Tariq,M.B. and Feamster, Nick} } @conference {14714, title = {Path projection for user-centered static analysis tools}, booktitle = {Proceedings of the 8th ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, series = {PASTE {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {57 - 63}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The research and industrial communities have made great strides in developing sophisticated defect detection tools based on static analysis. To date most of the work in this area has focused on developing novel static analysis algorithms, but has neglected study of other aspects of static analysis tools, particularly user interfaces. In this work, we present a novel user interface toolkit called Path Projection that helps users visualize, navigate, and understand program paths, a common component of many tools{\textquoteright} error reports. We performed a controlled user study to measure the benefit of Path Projection in triaging error reports from Locksmith, a data race detection tool for C. We found that Path Projection improved participants{\textquoteright} time to complete this task without affecting accuracy, while participants felt Path Projection was useful and strongly preferred it to a more standard viewer.}, isbn = {978-1-60558-382-2}, doi = {10.1145/1512475.1512488}, url = {http://doi.acm.org/10.1145/1512475.1512488}, author = {Khoo,Yit Phang and Foster, Jeffrey S. and Hicks, Michael W. and Sazawal,Vibha} } @article {18592, title = {Path splicing}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {38}, year = {2008}, month = {2008/08//}, pages = {27 - 38}, abstract = {We present path splicing, a new routing primitive that allows network paths to be constructed by combining multiple routing trees ("slices") to each destination over a single network topology. Path splicing allows traffic to switch trees at any hop en route to the destination. End systems can change the path on which traffic is forwarded by changing a small number of additional bits in the packet header. We evaluate path splicing for intradomain routing using slices generated from perturbed link weights and find that splicing achieves reliability that approaches the best possible using a small number of slices, for only a small increase in latency and no adverse effects on traffic in the network. In the case of interdomain routing, where splicing derives multiple trees from edges in alternate backup routes, path splicing achieves near-optimal reliability and can provide significant benefits even when only a fraction of ASes deploy it. We also describe several other applications of path splicing, as well as various possible deployment paths.}, keywords = {multi-path routing, path diversity, path splicing}, isbn = {0146-4833}, doi = {10.1145/1402946.1402963}, url = {http://doi.acm.org/10.1145/1402946.1402963}, author = {Motiwala,Murtaza and Elmore,Megan and Feamster, Nick and Vempala,Santosh} } @conference {18593, title = {Photo-based authentication using social networks}, booktitle = {Proceedings of the first workshop on Online social networks}, series = {WOSN {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {55 - 60}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present Lineup, a system that uses the social network graph in Facebook and auxiliary information (e.g., "tagged" user photos) to build a photo-based Web site authentication framework. Lineup{\textquoteright}s underlying mechanism leverages the concept of CAPTCHAs, programs that are designed to distinguish bots from human users. Lineup extends this functionality to help a Web site ascertain a user{\textquoteright}s identity or membership in a certain group (e.g., an interest group, invitees to a certain event) in order to infer some level of trust. Lineup works by presenting a user with photographs and asking the user to identify subjects in the photo whom a user with the appropriate identity or group membership should know. We present the design and implementation for Lineup, describe a preliminary prototype implementation, and discuss Lineup{\textquoteright}s security properties, including possible guarantees and threats.}, keywords = {social networks, trust}, isbn = {978-1-60558-182-8}, doi = {10.1145/1397735.1397748}, url = {http://doi.acm.org/10.1145/1397735.1397748}, author = {Yardi,Sarita and Feamster, Nick and Bruckman,Amy} } @article {18594, title = {Practical issues with using network tomography for fault diagnosis}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {38}, year = {2008}, month = {2008/09//}, pages = {53 - 58}, abstract = {This paper investigates the practical issues in applying network tomography to monitor failures. We outline an approach for selecting paths to monitor, detecting and confirming the existence of a failure, correlating multiple independent observations into a single failure event, and applying existing binary networking tomography algorithms to identify failures. We evaluate the ability of network tomography algorithms to correctly detect and identify failures in a controlled environment on the VINI testbed.}, keywords = {Environment, Fault detection, network tomography}, isbn = {0146-4833}, doi = {10.1145/1452335.1452343}, url = {http://doi.acm.org/10.1145/1452335.1452343}, author = {Huang,Yiyi and Feamster, Nick and Teixeira,Renata} } @article {16067, title = {Promoting Insight-Based Evaluation of Visualizations: From Contest to Benchmark Repository}, journal = {Visualization and Computer Graphics, IEEE Transactions on}, volume = {14}, year = {2008}, month = {2008/02//jan}, pages = {120 - 134}, abstract = {Information visualization (InfoVis) is now an accepted and growing field, but questions remain about the best uses for and the maturity of novel visualizations. Usability studies and controlled experiments are helpful, but generalization is difficult. We believe that the systematic development of benchmarks will facilitate the comparison of techniques and help identify their strengths under different conditions. We were involved in the organization and management of three InfoVis contests for the 2003, 2004, and 2005 IEEE InfoVis Symposia, which requested teams to report on insights gained while exploring data. We give a summary of the state of the art of evaluation in InfoVis, describe the three contests, summarize their results, discuss outcomes and lessons learned, and conjecture the future of visualization contests. All materials produced by the contests are archived in the InfoVis benchmark repository.}, keywords = {Computer-Assisted;Software;Software Validation;User-Computer Interface;, Factual;Evaluation Studies as Topic;Image Interpretation, InfoVis contest;benchmark repository;information visualization;data visualisation;Algorithms;Benchmarking;Computer Graphics;Databases}, isbn = {1077-2626}, doi = {10.1109/TVCG.2007.70412}, author = {Plaisant, Catherine and Fekete,J.-D. and Grinstein,G.} } @conference {16010, title = {The role of metacognition in robust AI systems}, booktitle = {AAAI-08 Workshop on Metareasoning,(Chicago, IL)}, year = {2008}, month = {2008///}, author = {Schmill,M. D and Oates,T. and Anderson,M. and Fults,S. and Josyula,D. and Perlis, Don and Wilson,S.} } @article {19202, title = {Route prediction from trip observations}, journal = {SAE SP}, volume = {2193}, year = {2008}, month = {2008}, author = {Jon Froehlich and Krumm,J.} } @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.} } @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 {12907, title = {Seasonal Cholera from Multiple Small Outbreaks, Rural Bangladesh}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {14}, year = {2008}, month = {2008/05//}, pages = {831 - 833}, abstract = {Clinical and environmental Vibrio cholerae organisms collected from February 2004 through April 2005 were systematically isolated from 2 rural Bangladeshi locales. Their genetic relatedness was evaluated at 5 loci that contained a variable number of tandem repeats (VNTR). The observed minimal overlap in VNTR patterns between the 2 communities was consistent with sequential, small outbreaks from local sources.}, isbn = {1080-6040}, doi = {10.3201/eid1405.071116}, author = {Stine,O. Colin and Alam,Munirul and Tang,Li and Nair,G. Balakrish and Siddique,A. Kasem and Faruque,Shah M. and Huq,Anwar and Rita R Colwell and Sack,R. Bradley and Morris,J. Glenn} } @article {18509, title = {Securing enterprise networks using traffic tainting}, journal = {Special Interest Group on Data Communication}, year = {2008}, month = {2008///}, abstract = {Enterprise networks are vulnerable to attacks ranging from dataleaks to the spread of malware to insider threats. Previous defenses have largely focused on securing hosts; unfortunately, when hosts are compromised, these defenses become ineffective. Rather than attempting to harden the host against every possible attack (which is impractical) or constraining the software that can run on a host (which is inconvenient), we place a small amount of trusted code on the host to assist with tracking the provenance of network traf- fic, moving the rest of the trust and function to the network. We present Pedigree, a system that tracks information flow across pro- cesses and hosts within a network by annotating traffic with taints that reflect the process that generated the traffic and the inputs that process has taken (we call this function traffic tainting). A tagger on the host annotates network traffic with information about the {\textquotedblleft}taints{\textquotedblright} that the sending process has acquired. Network devices act as arbiters to take appropriate actions (e.g., blocking) based on the taints associated with the traffic and the enterprise network{\textquoteright}s secu- rity policy. We have implemented Pedigree{\textquoteright}s host-based tagger as a Linux kernel module and the arbiter using the OpenFlow platform. This demonstration presents a prototype deployment of Pedigree that identifies and prevents both sensitive data leaks and the spread of malware in a typical enterprise network setting. The demon- stration will show that Pedigree can defend against these attacks without significant overhead at the host or the filtering device. }, author = {Ramachandran,A. and Mundada,Y. and Tariq,M.B. and Feamster, Nick} } @article {15965, title = {A self-help guide for autonomous systems}, journal = {AI Magazine}, volume = {29}, year = {2008}, month = {2008///}, pages = {67 - 67}, author = {Anderson,M. L and Fults,S. and Josyula,D. P and Oates,T. and Perlis, Don and Wilson,S. and Wright,D.} } @article {14098, title = {Sequence diversity and evolution of multigene families in Trypanosoma cruzi}, journal = {Molecular and Biochemical Parasitology}, volume = {157}, year = {2008}, month = {2008/01//}, pages = {65 - 72}, abstract = {Several copies of genes belonging to three multigene families present in the genome of Trypanosoma cruzi were sequenced and comparatively analyzed across six different strains of the parasite belonging to the T. cruzi I lineage (Colombiana, Silvio X10 and Dm28c), the T. cruzi II lineage (Esmeraldo and JG) and a hybrid strain (CL Brener). For all three gene families analyzed, our results support the division in T. cruzi I and II lineages. Furthermore, in agreement with its hybrid nature, sequences derived from the CL Brener clone clustered together with T. cruzi II sequences as well as with a third group of sequences. Paralogous sequences encoding Amastin, an amastigote surface glycoprotein and TcAG48, an antigenic RNA binding protein, which are clustered in the parasite genome, present higher intragenomic variability in T. cruzi II and CL Brener strains, when compared to T. cruzi I strains. Paralogous sequences derived from the TcADC gene family, which encode various isoforms of adenylyl cyclases and are dispersed throughout the T. cruzi genome, exhibit similar degree of variability in all strains, except in the CL Brener strain, in which the sequences were more divergent. Several factors including mutation rates and gene conversion mechanisms, acting differently within the T. cruzi population, may contribute to create such distinct levels of sequence diversity in multigene families that are clustered in the T. cruzi genome.}, keywords = {Amastin, Gene conversion, Genetic diversity, Multigene families, Trypanosoma cruzi}, isbn = {0166-6851}, doi = {16/j.molbiopara.2007.10.002}, url = {http://www.sciencedirect.com/science/article/pii/S0166685107002769}, author = {Cerqueira,Gustavo C. and Bartholomeu,Daniella C. and DaRocha,Wanderson D. and Hou,Lihua and Freitas-Silva,Danielle M. and Machado,Carlos Renato and El-Sayed, Najib M. and Teixeira,Santuza M.R.} } @article {14574, title = {Sex and Age Dimorphism of Myocardial Gene Expression in Nonischemic Human Heart Failure}, journal = {Circulation: Cardiovascular Genetics}, volume = {1}, year = {2008}, month = {2008/12/01/}, pages = {117 - 125}, abstract = {Background{\textemdash} We report the first comprehensive analysis of gene expression differences by sex and age in left ventricular samples from 102 patients with dilated cardiomyopathy.Methods and Results{\textemdash} Gene expression data (HG-U133A gene chip, Affymetrix) were analyzed from 30 females and 72 males from 3 separate centers. More than 1800 genes displayed sexual dimorphism in the heart (adjusted P value <0.05). A significant number of these genes were highly represented in gene ontology pathways involved in ion transport and G-protein-coupled receptor signaling. Localization of these genes revealed enrichment on both the sex chromosomes as well as chromosomes 3, 4, and 14. The second goal of this study was to determine the effect of age on gene expression. Within the female cohort, >140 genes were differentially expressed in the <55 years age group compared with the >55 years age group. These genes were highly represented in gene ontology pathways involved in DNA damage. In contrast, zero genes in the male cohort <55 years met statistical significance when compared with the >55 years age group.Conclusions{\textemdash} Gene expression in dilated cardiomyopathy displayed evidence of sexual dimorphism similar to other somatic tissues and age dimorphism within the female cohort.}, doi = {10.1161/CIRCGENETICS.108.802652}, url = {http://circgenetics.ahajournals.org/content/1/2/117.abstract}, author = {Fermin,David R. and Barac,Ana and Lee,Sangjin and Polster,Sean P. and Hannenhalli, Sridhar and Bergemann,Tracy L. and Grindle,Suzanne and Dyke,David B. and Pagani,Francis and Miller,Leslie W. and Tan,Sarah and dos Remedios,Cris and Cappola,Thomas P. and Margulies,Kenneth B. and Hall,Jennifer L.} } @article {18533, title = {SNARE: Spatio-temporal Network-level Automatic Reputation Engine}, volume = {GT-CSE-08-02}, year = {2008}, month = {2008///}, institution = {Georgia Institute of Technology}, abstract = {Current spam filtering techniques classify email based oncontent and IP reputation blacklists or whitelists. Unfortu- nately, spammers can alter spam content to evade content- based filters, and spammers continually change the IP ad- dresses from which they send spam. Previous work has sug- gested that filters based on network-level behavior might be more efficient and robust, by making decisions based on how messages are sent, as opposed to what is being sent or who is sending them. This paper presents a technique to identify spammers based on features that exploit the network-level spatio- temporal behavior of email senders to differentiate the spam- ming IPs from legitimate senders. Our behavioral classifier has two benefits: (1) it is early (i.e., it can automatically detect spam without seeing a large amount of email from a sending IP address{\textemdash}sometimes even upon seeing only a single packet); (2) it is evasion-resistant (i.e., it is based on spatial and temporal features that are difficult for a sender to change). We build classifiers based on these features us- ing two different machine learning methods, support vec- tor machine and decision trees, and we study the efficacy of these classifiers using labeled data from a deployed com- mercial spam-filtering system. Surprisingly, using only fea- tures from a single IP packet header (i.e., without looking at packet contents), our classifier can identify spammers with about 93\% accuracy and a reasonably low false-positive rate (about 7\%). After looking at a single message spammer identification accuracy improves to more than 94\% with a false rate of just over 5\%. These suggest an effective sender reputation mechanism. }, url = {http://hdl.handle.net/1853/25135}, author = {Feamster, Nick and Gray,A.G. and Krasser,S. and Syed,N.A.} } @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.} } @conference {15573, title = {Tradeoffs in Approximate Range Searching Made Simpler}, booktitle = {Computer Graphics and Image Processing, 2008. SIBGRAPI {\textquoteright}08. XXI Brazilian Symposium on}, year = {2008}, month = {2008/10//}, pages = {237 - 244}, abstract = {Range searching is a fundamental problem in computational geometry. The problem involves preprocessing a set of n points in R^d into a data structure, so that it is possible to determine the subset of points lying within a given query range. In approximate range searching, a parameter eps epsiv gt; 0 is given, and for a given query range R the points lying within distance eps diam(R) of the range{\textquoteright}s boundary may be counted or not. In this paper we present three results related to the issue of tradeoffs in approximate range searching. First, we introduce the range sketching problem. Next, we present a space-time tradeoff for smooth convex ranges, which generalize spherical ranges. Finally, we show how to modify the previous data structure to obtain a space-time tradeoff for simplex ranges. In contrast to existing results, which are based on relatively complex data structures, all three of our results are based on simple, practical data structures.}, keywords = {approximate range searching, computational geometry, data structure, Data structures, query range}, doi = {10.1109/SIBGRAPI.2008.24}, author = {Arya,S. and Fonseca,G. and Mount, Dave} } @conference {18608, title = {Trellis: a platform for building flexible, fast virtual networks on commodity hardware}, booktitle = {Proceedings of the 2008 ACM CoNEXT Conference}, series = {CoNEXT {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {72:1{\textendash}72:6 - 72:1{\textendash}72:6}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We describe Trellis, a platform for hosting virtual networks on shared commodity hardware. Trellis allows each virtual network to define its own topology, control protocols, and forwarding tables, while amortizing costs by sharing the physical infrastructure. Trellis synthesizes two container-based virtualization technologies, VServer and NetNS, as well as a new tunneling mechanism, EGRE, into a coherent platform that enables high-speed virtual networks. We describe the design and implementation of Trellis and evaluate its packet-forwarding rates relative to other virtualization technologies and native kernel forwarding performance.}, isbn = {978-1-60558-210-8}, doi = {10.1145/1544012.1544084}, url = {http://doi.acm.org/10.1145/1544012.1544084}, author = {Bhatia,Sapan and Motiwala,Murtaza and Muhlbauer,Wolfgang and Mundada,Yogesh and Valancius,Vytautas and Bavier,Andy and Feamster, Nick and Peterson,Larry and Rexford,Jennifer} } @article {18609, title = {UFO: a resilient layered routing architecture}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {38}, year = {2008}, month = {2008/09//}, pages = {59 - 62}, abstract = {Conventional wisdom has held that routing protocols cannot achieve both scalability and high availability. Despite scaling relatively well, today{\textquoteright}s Internet routing system does not react quickly to changing network conditions (e.g., link failures or excessive congestion). Overlay networks, on the other hand, can respond quickly to changing network conditions, but their reliance on aggressive probing does not scale to large topologies. The paper presents a layered routing architecture called UFO (Underlay Fused with Overlays), which achieves the best of both worlds by having the "underlay" provide explicit notification about network conditions to help improve the efficiency and scalability of routing overlays.}, keywords = {network monitoring, overlay networks, routing architecture}, isbn = {0146-4833}, doi = {10.1145/1452335.1452344}, url = {http://doi.acm.org/10.1145/1452335.1452344}, author = {Zhu,Yaping and Bavier,Andy and Feamster, Nick and Rangarajan,Sampath and Rexford,Jennifer} } @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.} } @article {14190, title = {A View-Point Invariant Texture Descriptor}, journal = {Journal of VisionJ Vis}, volume = {8}, year = {2008}, month = {2008/05/10/}, pages = {354 - 354}, abstract = {A new texture descriptor based on fractal geometry, called the multi fractal spectrum (MFS) is introduced. The key quantity in the study of fractal geometry is the fractal dimension, which is a measure of how an object changes over scale. Consider the intensity of an image as a 3D surface and slice it at regular intervals at the dimension of height. For each interval we obtain a point set, for which we compute the fractal dimension. The vector composed of the fractal dimensions of all point sets is called the MFS of intensity. Replacing the intensity with other quantities, such as the density function, or the output of various filters (e.g. Laplacian, Gradient filters), different MFS descriptors are obtained. The MFS is shown mathematically to be invariant under any smooth mapping (bi-Lipschitz maps), which includes view-point changes and non-rigid deformations of the surface as well as local affine illumination changes. Computational experiments on unstructured textures, such as landscapes and shelves in a supermarket, demonstrate the robustness of the MFS to environmental changes. On standard data sets the MFS performs comparable to the top texture descriptors in the task of classification. However, in contrast to other descriptors, it has extremely low dimension and can be computed very efficiently and robustly. Psychophysical demonstrate that humans can differentiate black and white textures on the basis of the fractal dimension.}, isbn = {, 1534-7362}, doi = {10.1167/8.6.354}, url = {http://www.journalofvision.org/content/8/6/354}, author = {Ferm{\"u}ller, Cornelia and Yong Xu and Hui Ji} } @conference {16765, title = {Virtual access points for vehicular networks}, booktitle = {Proceedings of the 1st international conference on MOBILe Wireless MiddleWARE, Operating Systems, and Applications}, year = {2008}, month = {2008///}, pages = {14 - 14}, author = {Frangiadakis,N. and C{\^a}mara,D. and Filali,F. and Loureiro,A. A.F and Roussopoulos, Nick} } @article {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 {14663, title = {Appendix to CMod: Modular Information Hiding and Type-Safe Linking for C}, journal = {Technical Reports of the Computer Science Department}, year = {2007}, month = {2007/06/30/undef}, abstract = {This brief note is an appendix to the paper "CMod: Modular Information Hiding and Type-Safe Linking for C." It consists of the proof of soundness for the formal language presented in that paper.}, author = {Srivastava,S. and Hicks, Michael W. and Foster, Jeffrey S.} } @conference {16019, title = {Application of MCL in a dialog agent}, booktitle = {Third Language and Technology Conference}, year = {2007}, month = {2007///}, author = {Josyula,D. P and Fults,S. and Anderson,M. L and Wilson,S. and Perlis, Don} } @conference {14318, title = {Barrier pointing: using physical edges to assist target acquisition on mobile device touch screens}, booktitle = {Proceedings of the 9th international ACM SIGACCESS conference on Computers and accessibility, October}, year = {2007}, month = {2007///}, pages = {15 - 17}, author = {Jon Froehlich and Wobbrock,J.O. and Kane,S.K.} } @article {14200, title = {Better flow estimation from color images}, journal = {EURASIP Journal on Advances in Signal Processing}, volume = {2007}, year = {2007}, month = {2007/01//}, pages = {133 - 133}, abstract = {One of the difficulties in estimating optical flow is bias. Correcting the bias using the classical techniques is very difficult. The reason is that knowledge of the error statistics is required, which usually cannot be obtained because of lack of data. In this paper, we present an approach which utilizes color information. Color images do not provide more geometric information than monochromatic images to the estimation of optic flow. They do, however, contain additional statistical information. By utilizing the technique of instrumental variables, bias from multiple noise sources can be robustly corrected without computing the parameters of the noise distribution. Experiments on synthesized and real data demonstrate the efficiency of the algorithm.}, isbn = {1110-8657}, doi = {10.1155/2007/53912}, url = {http://dx.doi.org/10.1155/2007/53912}, author = {Hui Ji and Ferm{\"u}ller, Cornelia} } @article {18497, title = {Bitstore: An incentive-compatible solution for blocked downloads in bittorrent}, journal = {Proc. Joint Workshop on The Economics of Networked Systems and Incentive-Based Computing (NetEcon)}, year = {2007}, month = {2007///}, abstract = {As many as 30\% of all files shared on public BitTorrentnetworks suffer from the lack of {\textquotedblleft}seeders{\textquotedblright} (peers that have complete copies of the file being shared); peers attempting to download such a file ({\textquotedblleft}leechers{\textquotedblright}) may have to wait indef- initely to obtain certain file chunks that are not distributed in the file{\textquoteright}s network of peers (the {\textquotedblleft}swarm{\textquotedblright}). We call this the Blocked Leecher Problem (BLP). To alleviate BLP, we propose BitStore, a larger, secure network of BitTorrent users (not necessarily all sharing the same content) where nodes offer their resources (such as disk space and bandwidth) for public use. Peers sharing any file can use the storage network to maintain replicas for each chunk of the file. Any leecher seeking chunks that are absent from in its own swarm can query the public network, locate the node storing the said chunks, and retrieve them. BitStore also provides robust incentives for nodes contributing re- sources: In return for storing and serving chunks, such nodes can negotiate micropayments using a second-price auction. Peers who receive these credits may later use them to re- trieve blocks they need from the storage network. This paper quantifies the BLP, presents an overview of the BitStore design, and discusses various challenges related to storage management and incentives. }, author = {Ramachandran,A. and Sarma,A.D. and Feamster, Nick} } @article {18507, title = {Building a Better Mousetrap}, volume = {GIT-CSS-07-01}, year = {2007}, month = {2007///}, institution = {Georgia Institute of Technology. College of Computing}, abstract = {Routers in the network core are unable to maintain detailed statistics for every packet; thus, traffic statistics are often based on packet sampling, which reduces accuracy. Because tracking large ("heavy-hitter") traffic flows is important both for pricing and for traffic engineering, much attention has focused on maintaining accurate statistics for such flows, often at the expense of small-volume flows. Eradicating these smaller flows makes it difficult to observe communication structure, which is sometimes more important than maintaining statistics about flow sizes. This paper presents FlexSample, a sampling framework that allows network operators to get the best of both worlds: For a fixed sampling budget, FlexSample can capture significantly more small-volume flows for only a small increase in relative error of large traffic flows. FlexSample uses a fast, lightweight counter array that provides a coarse estimate of the size ("class") of each traffic flow; a router then can sample at different rates according to the class of the traffic using any existing sampling strategy. Given a fixed sampling rate and a target fraction of sampled packets to allocate across traffic classes, FlexSample computes packet sampling rates for each class that achieve these allocations online. Through analysis and trace-based experiments, we find that FlexSample captures at least 50\% more mouse flows than strategies that do not perform class-dependent packet sampling. We also show how FlexSample can be used to capture unique flows for specific applications.}, url = {http://hdl.handle.net/1853/14350}, author = {Ramachandran,A. and Seetharaman,S. and Feamster, Nick and Vazirani,V.} } @conference {16746, title = {Caching in Mobile Environments: A New Analysis and the Mobile-Cache System}, booktitle = {IEEE 18th International Symposium on Personal, Indoor and Mobile Radio Communications, 2007. PIMRC 2007}, year = {2007}, month = {2007/09/03/7}, pages = {1 - 5}, publisher = {IEEE}, organization = {IEEE}, abstract = {In the near future, we will be surrounded by ubiquitous wireless networks and so information dissemination for mobile users is a key issue. Hybrid push-pull constitutes a very effective and scalable solution. Our contribution is twofold. First we provide a new analysis that takes into account the user mobility. We argue that in a highly mobile setting, analysis and optimization goals discussed in past papers become irrelevant, since the most important aspect of the system is not delay, but rather the ability to answer as many queries as possible. As we show, the optimal pull-push bandwidth ratio depends on the mobility patterns of the users. Second, we use our findings to build Mobile-Cache, a system that can efficiently answer multiple queries over a wireless environment.}, keywords = {Bandwidth, Broadcasting, cache storage, Cities and towns, FCC, hybrid push-pull solution, information dissemination, Intelligent networks, Land mobile radio, mobile communication, Mobile computing, mobile environment, mobile radio, mobile-cache system, multiple query answering, pull-push bandwidth ratio, Query processing, Road safety, road vehicles, ubiquitous wireless network, Vehicle safety}, isbn = {978-1-4244-1144-3}, doi = {10.1109/PIMRC.2007.4394076}, author = {Frangiadakis,N. and Roussopoulos, Nick} } @article {14103, title = {Cofactor-independent phosphoglycerate mutase is an essential gene in procyclic form Trypanosoma brucei}, journal = {Parasitology research}, volume = {100}, year = {2007}, month = {2007///}, pages = {887 - 892}, author = {Djikeng,A. and Raverdy,S. and Foster, Jeffrey S. and Bartholomeu,D. and Zhang,Y. and El-Sayed, Najib M. and Carlow,C.} } @conference {14207, title = {Combining motion from texture and lines for visual navigation}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems, 2007. IROS 2007}, year = {2007}, month = {2007/11/29/Oct. }, pages = {232 - 239}, publisher = {IEEE}, organization = {IEEE}, abstract = {Two novel methods for computing 3D structure information from video for a piecewise planar scene are presented. The first method is based on a new line constraint, which clearly separates the estimation of distance from the estimation of slant. The second method exploits the concepts of phase correlation to compute from the change of image frequencies of a textured plane, distance and slant information. The two different estimates together with structure estimates from classical image motion are combined and integrated over time using an extended Kalman filter. The estimation of the scene structure is demonstrated experimentally in a motion control algorithm that allows the robot to move along a corridor. We demonstrate the efficacy of each individual method and their combination and show that the method allows for visual navigation in textured as well as un-textured environments.}, keywords = {3D structure information, CAMERAS, Computer vision, extended Kalman filter, Frequency, image frequencies, Image motion analysis, Image texture, Kalman filters, Layout, motion control, Motion estimation, Navigation, Optical computing, phase correlation, piecewise planar scene, Robustness, Simultaneous localization and mapping, Speech processing, textured plane, video signal processing, visual navigation}, isbn = {978-1-4244-0912-9}, doi = {10.1109/IROS.2007.4399568}, author = {Bitsakos,K. and Li Yi and Ferm{\"u}ller, Cornelia} } @article {17023, title = {Community response grids: E-government, social networks, and effective emergency management}, journal = {Telecommunications Policy}, volume = {31}, year = {2007}, month = {2007/11//}, pages = {592 - 604}, abstract = {This paper explores the concept of developing community response grids (CRGs) for community emergency response and the policy implications of such a system. CRGs make use of the Internet and mobile communication devices, allowing residents and responders to share information, communicate, and coordinate activities in response to a major disaster. This paper explores the viability of using mobile communication technologies and the Web, including e-government, to develop response systems that would aid communities before, during, and after a major disaster, providing channels for contacting residents and responders, uploading information, distributing information, coordinating the responses of social networks, and facilitating resident-to-resident assistance. Drawing upon research from computer science, information studies, public policy, emergency management, and several other disciplines, the paper elaborates on the concept of and need for CRGs, examines related current efforts that can inform the development of CRGs, discusses how research about community networks can be used to instill trust and social capital in CRGs, and examines the issues of public policy, telecommunications, and e-government related to such a system.}, keywords = {Community response grid, E-government, Emergency response, Mobile communications, Public policy, social networks}, isbn = {0308-5961}, doi = {10.1016/j.telpol.2007.07.008}, url = {http://www.sciencedirect.com/science/article/pii/S0308596107000699}, author = {Jaeger,Paul T. and Shneiderman, Ben and Fleischmann,Kenneth R. and Preece,Jennifer and Qu,Yan and Fei Wu,Philip} } @article {17024, title = {Community Response Grids: Using Information Technology to Help Communities Respond to Bioterror Emergencies}, journal = {Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science}, volume = {5}, year = {2007}, month = {2007/12//}, pages = {335 - 346}, abstract = {Access to accurate and trusted information is vital in preparing for, responding to, and recovering from an mergency. To facilitate response in large-scale emergency situations, Community Response Grids (CRGs) integrate Internet and mobile technologies to enable residents to report information, professional emergency responders to disseminate instructions, and residents to assist one another. CRGs use technology to help residents and professional emergency responders to work together in community response to emergencies, including bioterrorism events. In a time of increased danger from bioterrorist threats, the application of advanced information and communication technologies to community response is vital in confronting such threats. This article describes CRGs, their underlying concepts, development efforts, their relevance to biosecurity and bioterrorism, and future research issues in the use of technology to facilitate community response.}, isbn = {1538-7135, 1557-850X}, doi = {10.1089/bsp.2007.0034}, url = {http://www.liebertonline.com/doi/abs/10.1089/bsp.2007.0034}, author = {Jaeger,Paul T. and Fleischmann,Kenneth R. and Preece,Jennifer and Shneiderman, Ben and Fei Wu,Philip and Qu,Yan} } @article {15508, title = {COMPUTING PERFECT AND STABLE MODELS USING ORDERED MODEL TREES}, journal = {Computational Intelligence}, volume = {11}, year = {2007}, month = {2007/04/02/}, pages = {89 - 112}, abstract = {Ordered model trees were introduced as a normal form for disjunctive deductive databases. They were also used to facilitate the computation of minimal models for disjunctive theories by exploiting the order imposed on the Herbrand base of the theory. In this work we show how the order on the Herbrand base can be used to compute perfect models of a disjunctive stratified finite theory. We are able to compute the stable models of a general finite theory by combining the order on the elements of the Herbrand base with previous results that had shown that the stable models of a theory T can be computed as the perfect models of a corresponding disjunctive theory ɛT resulting from applying the so called evidential transformation to T. While other methods consider many models that are rejected at the end, the use of atom ordering allows us to guarantee that every model generated belongs to the class of models being computed. As for negation-free databases, the ordered tree serves as the canonical representation of the database.}, keywords = {disjunctive database, model tree, ordered model tree, perfect model, stable model}, isbn = {1467-8640}, doi = {10.1111/j.1467-8640.1995.tb00024.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8640.1995.tb00024.x/abstract}, author = {Fern{\'a}ndez1,Jos{\'e} Alberto and Minker, Jack and Yahya,Adnan} } @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 {18697, title = {Crystal Structure and Solution NMR Studies of Lys48-linked Tetraubiquitin at Neutral pH}, journal = {Journal of Molecular Biology}, volume = {367}, year = {2007}, month = {2007/03/16/}, pages = {204 - 211}, abstract = {Ubiquitin modification of proteins is used as a signal in many cellular processes. Lysine side-chains can be modified by a single ubiquitin or by a polyubiquitin chain, which is defined by an isopeptide bond between the C terminus of one ubiquitin and a specific lysine in a neighboring ubiquitin. Polyubiquitin conformations that result from different lysine linkages presumably differentiate their roles and ability to bind specific targets and enzymes. However, conflicting results have been obtained regarding the precise conformation of Lys48-linked tetraubiquitin. We report the crystal structure of Lys48-linked tetraubiquitin at near-neutral pH. The two tetraubiquitin complexes in the asymmetric unit show the complete connectivity of the chain and the molecular details of the interactions. This tetraubiquitin conformation is consistent with our NMR data as well as with previous studies of diubiquitin and tetraubiquitin in solution at neutral pH. The structure provides a basis for understanding Lys48-linked polyubiquitin recognition under physiological conditions.}, keywords = {crystal structure, Lys48-linked, polyubiquitin chains, tetraubiquitin, ubiquitin}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2006.12.065}, url = {http://www.sciencedirect.com/science/article/pii/S0022283606017554}, author = {Eddins,Michael J. and Varadan,Ranjani and Fushman, David and Pickart,Cecile M. and Wolberger,Cynthia} } @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 {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)} } @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 {18700, title = {Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin}, journal = {Protein Science}, volume = {16}, year = {2007}, month = {2007///}, pages = {369 - 378}, abstract = {In solution, Lys48-linked di-ubiquitin exists in dynamic equilibrium between closed and open conformations. To understand the effect of interdomain motion in polyubiquitin chains on their ability to bind ligands, we cyclized di-ubiquitin by cross-linking the free C terminus of the proximal ubiquitin with the side chain of residue 48 in the distal ubiquitin, using a chemical cross-linker, 1,6-Hexane-bis-vinylsulfone. Our NMR studies confirm that the cyclization affects conformational dynamics in di-ubiquitin by restricting opening of the interface and shifting the conformational equilibrium toward closed conformations. The cyclization, however, did not rigidly lock di-ubiquitin in a single closed conformation: The chain undergoes slow exchange between at least two closed conformations, characterized by interdomain contacts involving the same hydrophobic patch residues (Leu8-Ile44-Val70) as in the uncyclized di-ubiquitin. Lowering the pH changes the relative populations of these conformations, but in contrast with the uncyclized di-ubiquitin, does not lead to opening of the interface. This restriction of domain motions inhibits direct access of protein molecules to the hydrophobic patch residues located at the very center of the interdomain interface in di-ubiquitin, although the residual motions are sufficient to allow access of small molecules to the interface. This renders di-ubiquitin unable to bind protein molecules (e.g., UBA2 domain) in the normal manner, and thus could interfere with Ub2 recognition by various downstream effectors. These results emphasize the importance of the opening/closing domain motions for the recognition and function of di-ubiquitin and possibly longer polyubiquitin chains.}, keywords = {cyclization, di-ubiquitin, interdomain dynamics, Lys48-linked ubiquitin chain, UBA domain}, isbn = {1469-896X}, doi = {10.1110/ps.062508007}, url = {http://onlinelibrary.wiley.com/doi/10.1110/ps.062508007/abstract}, author = {Dickinson,Bryan C. and Varadan,Ranjani and Fushman, David} } @article {18006, title = {Electron beam and optical proximity effect reduction for nanolithography: New results}, journal = {Journal of Vacuum Science \& Technology B}, volume = {25}, year = {2007}, month = {2007///}, pages = {2288 - 2294}, abstract = {Proximity effect correction by dose modulation is widely practiced in electron-beam lithography. Optical proximity control is also possible using a combination of shape adjustment and phase control. Assigning {\textquotedblleft}the right{\textquotedblright} dose (or fill factor and phase for optics) is a well known mathematical inverse problem. Linear programming, by definition, is the appropriate method for determining dose. In the past, the technique was too slow for full-scale implementation in mask making. Here, the authors discuss how recent developments in computer speed and architecture have improved the prospects for full-scale implementation. In addition, the authors discuss some numerical techniques, analogous to gridding and relaxation, that make linear programming more attractive in mask making.}, keywords = {electron beam lithography, Linear programming, masks, nanolithography, proximity effect (lithography)}, doi = {10.1116/1.2806967}, url = {http://link.aip.org/link/?JVB/25/2288/1}, author = {Peckerar,Martin and Sander,David and Srivastava,Ankur and Foli,Adakou and Vishkin, Uzi} } @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 {17596, title = {Fast and scalable approximation methods for finding minimum cost flows with ...}, volume = {10/053,079}, year = {2007}, month = {2007/10/09/}, abstract = {Broadly, techniques for solving network routing within a predetermined error are disclosed. These techniques may be applied to networks supporting dedicated reserve capacity, where reserved capacity on links in the network is dedicated for a particular commodity (generally, a source and sink pair of computers), and shared recovery, where reserved capacity on links is shared amongst two or more commodities. These techniques use an iterative process to determine flows on each of the links in a network. Costs are set for each commodity, and primary and secondary (i.e., backup) flows are initialized. A commodity is selected and demand for the commodity is routed through the shortest path. Costs are updated for each potential failure mode. For each commodity, the flows and costs are updated. Once all flows and costs are updated, then it is determined if a function is less than a predetermined value. If the function is less than a predetermined value, then the commodity selection, and...}, url = {http://www.google.com/patents?id=rkWpAAAAEBAJ}, author = {Fleischer,Lisa Karen and Saniee,Iraj and Shepherd,Frederick Bruce and Srinivasan, Aravind}, editor = {Lucent Technologies Inc.} } @conference {18570, title = {Filtering spam with behavioral blacklisting}, booktitle = {Proceedings of the 14th ACM conference on Computer and communications security}, series = {CCS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {342 - 351}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Spam filters often use the reputation of an IP address (or IP address range) to classify email senders. This approach worked well when most spam originated from senders with fixed IP addresses, but spam today is also sent from IP addresses for which blacklist maintainers have outdated or inaccurate information (or no information at all). Spam campaigns also involve many senders, reducing the amount of spam any particular IP address sends to a single domain; this method allows spammers to stay "under the radar". The dynamism of any particular IP address begs for blacklisting techniques that automatically adapt as the senders of spam change. This paper presents SpamTracker, a spam filtering system that uses a new technique called behavioral blacklisting to classify email senders based on their sending behavior rather than their identity. Spammers cannot evade SpamTracker merely by using "fresh" IP addresses because blacklisting decisions are based on sending patterns, which tend to remain more invariant. SpamTracker uses fast clustering algorithms that react quickly to changes in sending patterns. We evaluate SpamTracker{\textquoteright}s ability to classify spammers using email logs for over 115 email domains; we find that SpamTracker can correctly classify many spammers missed by current filtering techniques. Although our current datasets prevent us from confirming SpamTracker{\textquoteright}s ability to completely distinguish spammers from legitimate senders, our evaluation shows that SpamTracker can identify a significant fraction of spammers that current IP-based blacklists miss. SpamTracker{\textquoteright}s ability to identify spammers before existing blacklists suggests that it can be used in conjunction with existing techniques (e.g., as an input to greylisting). SpamTracker is inherently distributed and can be easily replicated; incorporating it into existing email filtering infrastructures requires only small modifications to mail server configurations.}, keywords = {blacklists, botnets, clustering, Security, spam}, isbn = {978-1-59593-703-2}, doi = {10.1145/1315245.1315288}, url = {http://doi.acm.org/10.1145/1315245.1315288}, author = {Ramachandran,Anirudh and Feamster, Nick and Vempala,Santosh} } @conference {19636, title = {Geometrical Characteristics of Regular Polyhedra: Application to EXAFS Studies of Nanoclusters}, booktitle = {X-RAY ABSORPTION FINE STRUCTURE - XAFS13: 13th International Conference}, volume = {882}, year = {2007}, month = {2007/02/02/}, pages = {746 - 748}, publisher = {AIP Publishing}, organization = {AIP Publishing}, abstract = {EXAFS data modeling of nanoparticles can be done at a very high level of detail if regular polyhedral geometries are considered as possible structural models. Such geometries can be characterized by unique sequence of indices (coordination numbers) of the first few coordination shells that serve as a signature of a shape, size, morphology and packing model of atoms in the cluster. We wrote a suite of programs for cluster geometry generation and its pair radial distribution function analysis. The programs generate x,y,z coordinates and calculate the coordination numbers of the corresponding clusters for any order of a large number of regular polyhedra. We present the results for the first few nearest neighboring shells in the icosahedral, cuboctahedral, hcp structures for the small, 10{\textendash}1000 atom clusters.}, keywords = {Atomic and molecular clusters, Cluster Analysis, Cluster geometric structure, Extended X-ray absorption fine structure spectroscopy, nanoparticles, Numerical modeling, Particle distribution functions, Polyhedra, Signal generators}, url = {http://scitation.aip.org/content/aip/proceeding/aipcp/10.1063/1.2644651}, author = {Dana Dachman-Soled and Frenkel, Anatoly I.} } @conference {19637, title = {Geometry and Charge State of Mixed-Ligand Au13 Nanoclusters}, booktitle = {X-RAY ABSORPTION FINE STRUCTURE - XAFS13: 13th International Conference}, volume = {882}, year = {2007}, month = {2007/02/02/}, pages = {749 - 751}, publisher = {AIP Publishing}, organization = {AIP Publishing}, abstract = {The integration of synthetic, experimental and theoretical tools into a self-consistent data analysis methodology allowed us to develop unique new levels of detail in nanoparticle characterization. We describe our methods using an example of Au 13 monolayer-protected clusters (MPCs), synthesized by ligand exchange methods. The combination of atom counting methods of scanning transmission electron microscopy and Au L3-edge EXAFS allowed us to characterize these clusters as icosahedral, with surface strain reduced from 5\% (as in ideal, regular icosahedra) to 3\%, due to the interaction with ligands. Charge transfer from Au to the thiol and phosphine ligands was evidenced by S and P K-edge XANES. A comparison of total energies of bare clusters of different geometries was performed by equivalent crystal theory calculations.}, keywords = {Atom surface interactions, Charge transfer, Data analysis, Extended X-ray absorption fine structure spectroscopy, Gold, nanoparticles, Scanning transmission electron microscopy, Surface strains, Total energy calculations, X-ray absorption near edge structure}, url = {http://scitation.aip.org/content/aip/proceeding/aipcp/10.1063/1.2644652}, author = {Frenkel, A. I. and Menard, L. D. and Northrup, P. and Rodriguez, J. A. and Zypman, F. and Dana Dachman-Soled and Gao, S.-P. and Xu, H. and Yang, J. C. and Nuzzo, R. G.} } @conference {12136, title = {Get Your Experience Factory Ready for the Next Decade{\textendash}Ten Years after "How to Build and Run One"}, booktitle = {Companion to the proceedings of the 29th International Conference on Software Engineering}, series = {ICSE COMPANION {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {167 - 168}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {This one-day tutorial aims at industry practitioners, managers and developers alike, who want to learn more about how to successfully design, implement and run an Experience Factory, to systematically build up and manage the experience of an organization. State-of- the art methods and techniques on how to initially set-up or to further develop and improve an organization{\textquoteright}s Experience Factory are discussed. Participants should come from organizations (not only from the software domain) that are interested in implementing an Experience Factory to help effectively support improvement activities (such as TQM, ISO 9000, CMMI, SPICE, or TSP) to gain competitive advantages.}, isbn = {0-7695-2892-9}, doi = {10.1109/ICSECOMPANION.2007.41}, url = {http://dx.doi.org/10.1109/ICSECOMPANION.2007.41}, author = {Basili, Victor R. and Bomarius,Frank and Feldmann,Raimund L.} } @inbook {14411, title = {Graphical Models in a Nutshell}, booktitle = {Introduction to Statistical Relational LearningIntroduction to Statistical Relational Learning}, year = {2007}, month = {2007///}, pages = {13 - 13}, author = {Koller,D. and Friedman,N. and Getoor, Lise and Taskar,B.} } @article {13002, title = {Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services}, journal = {Future Generation Comp Syst}, volume = {23}, year = {2007}, month = {2007///}, pages = {517 - 522}, abstract = {The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering the barriers to writing Grid services. The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed.}, author = {Bazinet,A. L and Myers,D. S and Fuetsch,J. and Cummings, Michael P.} } @conference {18573, title = {Holding the Internet Accountable}, booktitle = {Proc. 6th ACM Workshop on Hot Topics in Networks (Hotnets-VI)}, year = {2007}, month = {2007/11/01/}, abstract = {Today{\textquoteright}s IP network layer provides little to no protection against misconfiguration or malice. Despite some progress in improving the robustness and security of the IP layer, misconfigurations and attacks still occur frequently. We show how a network layer that provides accountability, i.e., the ability to associate each action with the responsible entity, provides a firm foundation for defenses against misconfiguration and malice. We present the design of a network layer that incorporates accountability called AIP (Accountable Internet Protocol) and show how its features{\textemdash}notably, its use of self-certifying addresses{\textemdash} can improve both source accountability (the ability to trace actions to a particular end host and stop that host from misbehaving) and control-plane accountability (the ability to pinpoint and prevent attacks on routing).}, url = {http://repository.cmu.edu/compsci/66}, author = {Andersen,David and Balakrishnan,Hari and Feamster, Nick and Koponen,Teemu and Moon,Daekyong and Shenker,Scott} } @conference {15986, title = {Hood College, Master of Business Administration, 2005 Hood College, Master of Science (Computer Science), 2001 Hood College, Bachelor of Science (Computer Science), 1998 Frederick Community College, Associate in Arts (Business Administration), 1993}, booktitle = {Proceedings of the Workshop on Metareasoning in Agent-Based Systems}, year = {2007}, month = {2007///}, author = {Anderson,M. L and Schmill,M. and Oates,T. and Perlis, Don and Josyula,D. and Wright,D. and Human,S. W.T.D.N and Metacognition,L. and Fults,S. and Josyula,D. P} } @article {18574, title = {How to lease the internet in your spare time}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {37}, year = {2007}, month = {2007/01//}, pages = {61 - 64}, abstract = {Today{\textquoteright}s Internet Service Providers (ISPs) serve two roles: managing their network infrastructure and providing (arguably limited) services to end users. We argue that coupling these roles impedes the deployment of new protocols and architectures, and that the future Internet should support two separate entities: infrastructure providers (who manage the physical infrastructure) and service providers (who deploy network protocols and offer end-to-end services). We present a high-level design for Cabo, an architecture that enables this separation; we also describe challenges associated with realizing this architecture.}, isbn = {0146-4833}, doi = {10.1145/1198255.1198265}, url = {http://doi.acm.org/10.1145/1198255.1198265}, author = {Feamster, Nick and Gao,Lixin and Rexford,Jennifer} } @article {14223, title = {Illusory Motion Due to Causal Time Filtering}, journal = {Journal of Vision}, volume = {7}, year = {2007}, month = {2007/06/30/}, pages = {977 - 977}, abstract = {Static patterns by Kitaoka (2006), the most well known of which is the {\textquotedblleft}Rotating Snake{\textquotedblright}, elicit forceful illusory motion. The patterns are composed of repeating patches of asymmetric intensity profile, in most cases organized circularly. Motion perception depends on the size of the patches and is found to occur in the periphery for larger patches and closer to the center of the eye for small patches. We propose as main cause for these illusions erroneous estimation of image motion due to eye movements. The reason is that image motion is estimated from the spatial and temporal energy of the image signal with filters which are symmetric in space, but asymmetric (causal) in time. In other words, only the past, but not the future, is used to estimate the temporal energy. It is shown that such filters mis-estimate the motion of locally asymmetric intensity signals for a range of spatial frequencies. This mis-estimation predicts the perceived motion in the different patterns of Kitaoka as well as the peripheral drift illusion, and accounts for the effect at varying patch size. This study builds upon our prior work on the distortion of image features and movement (Ferm{\"u}ller and Malm 2004). Kiatoka (2006): http://www.ritsumei.ac.jp/~akitaoka/index-e.html. C. Ferm{\"u}ller and H. Malm (2004).{\textquotedblleft} Uncertainty in visual processes predicts geometrical optical illusions {\textquotedblright}, Vision Research, 4, 727{\textendash}749.}, isbn = {, 1534-7362}, doi = {10.1167/7.9.977}, url = {http://www.journalofvision.org/content/7/9/977}, author = {Ferm{\"u}ller, Cornelia and Hui Ji} } @article {18576, title = {Implications of Autonomy for the Expressiveness of Policy Routing}, journal = {Networking, IEEE/ACM Transactions on}, volume = {15}, year = {2007}, month = {2007/12//}, pages = {1266 - 1279}, abstract = {Thousands of competing autonomous systems must cooperate with each other to provide global Internet connectivity. Each autonomous system (AS) encodes various economic, business, and performance decisions in its routing policy. The current interdomain routing system enables each AS to express policy using rankings that determine how each router in the AS chooses among different routes to a destination, and filters that determine which routes are hidden from each neighboring AS. Because the Internet is composed of many independent, competing networks, the interdomain routing system should provide autonomy, allowing network operators to set their rankings independently, and to have no constraints on allowed filters. This paper studies routing protocol stability under these conditions. We first demonstrate that ldquonext-hop rankings,rdquo commonly used in practice, may not ensure routing stability. We then prove that, when providers can set rankings and filters autonomously, guaranteeing that the routing system will converge to a stable path assignment imposes strong restrictions on the rankings ASes are allowed to choose. We discuss the implications of these results for the future of interdomain routing.}, keywords = {autonomous systems, global Internet connectivity, interdomain routing system, Internet, next-hop rankings, routing protocol, routing protocols, routing stability, stable path assignment}, isbn = {1063-6692}, doi = {10.1109/TNET.2007.896531}, author = {Feamster, Nick and Johari,R. and Balakrishnan,H.} } @conference {14701, title = {Improving software quality with static analysis}, booktitle = {Proceedings of the 7th ACM SIGPLAN-SIGSOFT workshop on Program analysis for software tools and engineering}, series = {PASTE {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {83 - 84}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {At the University of Maryland, we have been working to improve the reliability and security of software by developing new, effective static analysis tools. These tools scan software for bug patterns or show that the software is free from a particular class of defects. There are two themes common to our different projects: 1. Our ultimate focus is on utility: can a programmer actually improve the quality of his or her software using an analysis tool? The important first step toward answering this question is to engineer tools so that they can analyze existing, nontrivial programs, and to carefully report the results of such analyses experimentally. The desire to better understand a more human-centered notion of utility underlies much of our future work. 2. We release all of our tools open source. This allows other researchers to verify our results, and to reuse some or all of our implementations, which often required significant effort to engineer. We believe that releasing source code is important for accelerating the pace of research results software quality, and just as importantly allows feedback from the wider community. In this research group presentation, we summarize some recent work and sketch future directions.}, keywords = {bug patterns, bugs, C, Data races, FFIs, java, modularity, network protocols, Software quality}, isbn = {978-1-59593-595-3}, doi = {10.1145/1251535.1251549}, url = {http://doi.acm.org/10.1145/1251535.1251549}, author = {Foster, Jeffrey S. and Hicks, Michael W. and Pugh, William} } @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.} } @article {14285, title = {Inferring aliasing and encapsulation properties for Java}, journal = {ACM SIGPLAN Notices}, volume = {42}, year = {2007}, month = {2007///}, pages = {423 - 440}, author = {Ma,K.K. and Foster, Jeffrey S.} } @conference {13443, title = {Interactive visual clustering}, booktitle = {Proceedings of the 12th international conference on Intelligent user interfaces}, series = {IUI {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {361 - 364}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Interactive Visual Clustering (IVC) is a novel method that allows a user to explore relational data sets interactively, in order to produce a clustering that satisfies their objectives. IVC combines spring-embedded graph layout with user interaction and constrained clustering. Experimental results on several synthetic and real-world data sets show that IVC yields better clustering performance than alternative methods.}, keywords = {clustering, constraints, interaction}, isbn = {1-59593-481-2}, doi = {10.1145/1216295.1216367}, url = {http://doi.acm.org/10.1145/1216295.1216367}, author = {desJardins, Marie and MacGlashan,James and Ferraioli,Julia} } @conference {13142, title = {Learning Higher-order Transition Models in Medium-scale Camera Networks}, booktitle = {Computer Vision, 2007. ICCV 2007. IEEE 11th International Conference on}, year = {2007}, month = {2007/10//}, pages = {1 - 8}, abstract = {We present a Bayesian framework for learning higher- order transition models in video surveillance networks. Such higher-order models describe object movement between cameras in the network and have a greater predictive power for multi-camera tracking than camera adjacency alone. These models also provide inherent resilience to camera failure, filling in gaps left by single or even multiple non-adjacent camera failures. Our approach to estimating higher-order transition models relies on the accurate assignment of camera observations to the underlying trajectories of objects moving through the network. We addresses this data association problem by gathering the observations and evaluating alternative partitions of the observation set into individual object trajectories. Searching the complete partition space is intractable, so an incremental approach is taken, iteratively adding observations and pruning unlikely partitions. Partition likelihood is determined by the evaluation of a probabilistic graphical model. When the algorithm has considered all observations, the most likely (MAP) partition is taken as the true object trajectories. From these recovered trajectories, the higher-order statistics we seek can be derived and employed for tracking. The partitioning algorithm we present is parallel in nature and can be readily extended to distributed computation in medium-scale smart camera networks.}, keywords = {(artificial, approach;medium-scale, association, Bayesian, camera, cameras;video, framework;data, fusion;iterative, graphical, intelligence);optical, learning;incremental, likelihood;multicamera, likely, methods;higher, methods;learning, model, model;video, movement;probabilistic, network;Bayes, network;most, order, partition, problem;higher-order, statistics;higher-order, statistics;image, Surveillance, surveillance;, tracking;object, tracking;probability;video, transition}, doi = {10.1109/ICCV.2007.4409203}, author = {Farrell,R. and David Doermann and Davis, Larry S.} } @article {18706, title = {Mapping the Interactions between Lys48 and Lys63-Linked Di-ubiquitins and a Ubiquitin-Interacting Motif of S5a}, journal = {Journal of Molecular Biology}, volume = {368}, year = {2007}, month = {2007/05/04/}, pages = {753 - 766}, abstract = {Numerous cellular processes are regulated by (poly)ubiquitin-mediated signaling events, which involve a covalent modification of the substrate protein by a single ubiquitin or a chain of ubiquitin molecules linked via a specific lysine. Remarkably, the outcome of polyubiquitination is linkage-dependent. For example, Lys48-linked chains are the principal signal for proteasomal degradation, while Lys63-linked chains act as nonproteolytic signals. Despite significant progress in characterization of various cellular pathways involving ubiquitin, understanding of the structural details of polyubiquitin chain recognition by downstream cellular effectors is missing. Here we use NMR to study the interaction of a ubiquitin-interacting motif (UIM) of the proteasomal subunit S5a with di-ubiquitin, the simplest model for polyubiquitin chain, to gain insights into the mechanism of polyubiquitin recognition by the proteasome. We have mapped the binding interface and characterized the stoichiometry and the process of UIM binding to Lys48- and Lys63-linked di-ubiquitin chains. Our data provide the first direct evidence that UIM binding involves a conformational transition in Lys48-linked di-ubiquitin, which opens the hydrophobic interdomain interface. This allows UIM to enter the interface and bind directly to the same ubiquitin hydrophobic-patch surface as utilized in UIM:monoubiquitin complexes. The results indicate that up to two UIM molecules can bind di-ubiquitin, and the binding interface between UIM and ubiquitin units in di-ubiquitin is essentially the same for both Lys48- and Lys63-linked chains. Our data suggest possible structural models for the binding of UIM and of full-length S5a to di-ubiquitin.}, keywords = {chemical shift perturbation mapping, polyubiquitin, S5a, ubiquitin, ubiquitin-interacting motif}, isbn = {0022-2836}, doi = {10.1016/j.jmb.2007.02.037}, url = {http://www.sciencedirect.com/science/article/pii/S0022283607002185}, author = {Haririnia,Aydin and D{\textquoteright}Onofrio,Mariapina and Fushman, David} } @conference {18582, title = {Measuring the Contributions of Routing Dynamics to Prolonged End-to-End Internet Path Failures}, booktitle = {Global Telecommunications Conference, 2007. GLOBECOM {\textquoteright}07. IEEE}, year = {2007}, month = {2007/11//}, pages = {1855 - 1859}, abstract = {This paper studies the contributions of routing dynamics to the duration of long-lived end-to-end Internet path failures. Studies have shown that end-to-end Internet failures (periods of prolonged packet loss) are widespread. These failures are typically attributed to either congestion or routing dynamics. Unfortunately, the extent to which congestion and routing dynamics contribute to long-lasting path failures, and the effect of routing dynamics on end-to-end performance, are not well understood. This paper uses a joint analysis of active measurements and routing data to characterize end-to-end failures observed over one month on a topologically diverse Internet testbed. We find that routing dynamics coincide with most prolonged end-to-end failures, suggesting that routing dynamics contribute significantly to the duration of these failures. We also find that most long-lived end-to-end path failures that coincide with routing dynamics are caused by BGP convergence or instability. Our results provide new insights into the effects of routing instability on end-to-end Internet path performance.}, keywords = {diverse Internet topological testbed, Internet, prolonged end-to-end Internet path failure, routing dynamics, telecommunication network reliability, telecommunication network routing, telecommunication network topology}, doi = {10.1109/GLOCOM.2007.357}, author = {Wang,Feng and Feamster, Nick and Gao,Lixin} } @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.} } @article {15771, title = {Modified Cholesky Algorithms: A Catalog with New Approaches}, journal = {Mathematical Programming}, year = {2007}, month = {2007///}, url = {doi:10.1007/s10107-007-0177-6doi:10.1007/s10107-007-0177-6}, author = {Fang,Hawren and O{\textquoteright}Leary, Dianne P.} } @conference {18588, title = {Multiplexing BGP sessions with BGP-Mux}, booktitle = {Proceedings of the 2007 ACM CoNEXT conference}, series = {CoNEXT {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {44:1{\textendash}44:2 - 44:1{\textendash}44:2}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a BGP-session multiplexer called BGP-Mux, which provides stable, on-demand access to global BGP route feeds. This gateway allows arbitrary and even transient client BGP connections to be provisioned and torn down on demand without affecting globally visible BGP sessions. BGP-Mux provides two capabilities: (1) the ability for a client network to receive multiple unfiltered routes per destination from a set of upstream ASes; and (2) the ability to provision BGP sessions without introducing global instability. Several applications could benefit from these features:}, isbn = {978-1-59593-770-4}, doi = {10.1145/1364654.1364707}, url = {http://doi.acm.org/10.1145/1364654.1364707}, author = {Valancius,Vytautas and Feamster, Nick} } @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.} } @book {18596, title = {NETB{\textquoteright}07: Proceedings of the 3rd USENIX international workshop on Networking meets databases}, year = {2007}, month = {2007///}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, editor = {Cooper,Brian and Feamster, Nick} } @article {18590, title = {Network-Wide Prediction of BGP Routes}, journal = {Networking, IEEE/ACM Transactions on}, volume = {15}, year = {2007}, month = {2007/04//}, pages = {253 - 266}, abstract = {This paper presents provably correct algorithms for computing the outcome of the BGP route-selection process for each router in a network, without simulating the complex details of BGP message passing. The algorithms require only static inputs that can be easily obtained from the routers: the BGP routes learned from neighboring domains, the import policies configured on the BGP sessions, and the internal topology. Solving the problem would be easy if the route-selection process were deterministic and every router received all candidate BGP routes. However, two important features of BGP-the Multiple Exit Discriminator (MED) attribute and route reflectors-violate these properties. After presenting a simple route-prediction algorithm for networks that do not use these features, we present algorithms that capture the effects of the MED attribute and route reflectors in isolation. Then, we explain why the interaction between these two features precludes efficient route prediction. These two features also create difficulties for the operation of BGP itself, leading us to suggest improvements to BGP that achieve the same goals as MED and route reflection without introducing the negative side effects}, keywords = {BGP message passing, BGP route-selection process, border gateway protocol, Message passing, multiple exit discriminator attribute, network-wide prediction, route reflectors, route-prediction algorithm, routing protocols, telecommunication network topology}, isbn = {1063-6692}, doi = {10.1109/TNET.2007.892876}, author = {Feamster, Nick and Rexford,J.} } @article {14238, title = {Object detection using a shape codebook}, journal = {British Machine Vision Conference}, volume = {4}, year = {2007}, month = {2007///}, abstract = {This paper presents a method for detecting categories of objects in real-worldimages. 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 code- book for object detection. A shape codebook entry consists of two compo- nents: 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 be- tween 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 im- age edges as the shape codewords. Object detection is performed in a prob- abilistic voting framework. Experimental results on public datasets show performance similiar 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 fig- ure/ground segmentation and do not need a validation dataset). }, author = {Yu,X. and Yi,L. and Ferm{\"u}ller, Cornelia and David Doermann} } @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} } @conference {15997, title = {Ontologies for reasoning about failures in AI systems}, booktitle = {Proceedings from the Workshop on Metareasoning in Agent Based Systems at the Sixth International Joint Conference on Autonomous Agents and Multiagent Sytems}, year = {2007}, month = {2007///}, author = {Schmill,M. and Josyula,D. and Anderson,M. L and Wilson,S. and Oates,T. and Perlis, Don and Fults,S.} } @article {18498, title = {Path splicing: Reliable connectivity with rapid recovery}, journal = {ACM SIGCOMM HotNets VI}, year = {2007}, month = {2007///}, abstract = {We present path splicing, a primitive that constructs net-work paths from multiple independent routing processes that run over a single network topology. The routing processes compute distinct routing trees using randomly perturbed link weights. A few additional bits in packet headers give end systems access to a large number of paths. By changing these bits, nodes can redirect traffic without detailed knowl- edge of network paths. Assembling paths by {\textquotedblleft}splicing{\textquotedblright} segments can yield up to an exponential improvement in path diversity for only a linear increase in storage and mes- sage complexity. We present randomized approaches for slice construction and failure recovery that achieve near- optimal performance and are extremely simple to config- ure. Our evaluation of path splicing on realistic ISP topolo- gies demonstrates a dramatic increase in reliability that ap- proaches the best possible using only a small number of slices and for only a small increase in latency. }, author = {Motiwala,M. and Feamster, Nick and Vempala,S.} } @conference {18516, title = {Path splicing with network slicing}, booktitle = {Proc. ACM SIGCOMM Hot-Nets}, year = {2007}, month = {2007///}, author = {Feamster, Nick and Motiwala,M. and Vempala,S.} } @inbook {14410, title = {Probabilistic Relational Models}, booktitle = {Introduction to Statistical Relational LearningIntroduction to Statistical Relational Learning}, year = {2007}, month = {2007///}, pages = {129 - 129}, author = {Getoor, Lise and Friedman,N. and Koller,D. and Pfeffer,A. and Taskar,B.} } @article {15471, title = {Semantics-Preserving Design of Embedded Control Software from Synchronous Models}, journal = {Software Engineering, IEEE Transactions on}, volume = {33}, year = {2007}, month = {2007/08//}, pages = {497 - 509}, abstract = {The design of embedded controllers is experiencing a growth in complexity as embedded systems increase their functionality while they become ubiquitous in electronic appliances, cars, airplanes, etc. As requirements become more challenging, mathematical models gain importance for mastering complexity. Among the different computational models proposed, synchronous models have proved to be the most widely used for control dominated applications. While synchronous models simplify the way of dealing with concurrency by decoupling functional and timing aspects, their software implementation on multitasking and multiprocessor platforms is far from straightforward, because of the asynchronous nature of most industrial software platforms. Known solutions in the literature either restrict the solution space or focus on special cases. We present a method for preserving the synchronous semantics through buffer-based intertask communication mechanisms, grounded on an abstraction of the target platform. This allows us to deal with any task set and, most importantly, being independent of the implementation, to explore the design space effectively.}, keywords = {embedded control software, embedded systems, multiprocessing programs, multiprocessor, multitasking, semantics-preserving design, software engineering, software implementation, systems analysis}, isbn = {0098-5589}, doi = {10.1109/TSE.2007.70718}, author = {Mangeruca,L. and Baleani,M. and Ferrari,A. and Sangiovanni-Vincentelli,A.} } @article {14151, title = {Solving the stochastic steady-state diffusion problem using multigrid}, journal = {IMA journal of numerical analysis}, volume = {27}, year = {2007}, month = {2007///}, pages = {675 - 675}, author = {Elman, Howard and Furnival, D.} } @article {15688, title = {Storage routing for dtn congestion control}, journal = {Wireless communications and mobile computing}, volume = {7}, year = {2007}, month = {2007///}, pages = {1183 - 1196}, author = {Seligman,M. and Fall,K. and Mundur, Padma} } @article {17779, title = {Story creation from heterogeneous data sources}, journal = {Multimedia Tools and Applications}, volume = {33}, year = {2007}, month = {2007///}, pages = {351 - 377}, abstract = {There are numerous applications where there is a need to rapidly infer a story about a given subject from a given set of potentially heterogeneous data sources. In this paper, we formally define a story to be a set of facts about a given subject that satisfies a {\textquotedblleft}story length{\textquotedblright} constraint. An optimal story is a story that maximizes the value of an objective function measuring the goodness of a story. We present algorithms to extract stories from text and other data sources. We also develop an algorithm to compute an optimal story, as well as three heuristic algorithms to rapidly compute a suboptimal story. We run experiments to show that constructing stories can be efficiently performed and that the stories constructed by these heuristic algorithms are high quality stories. We have built a prototype STORY system based on our model{\textemdash}we briefly describe the prototype as well as one application in this paper.}, doi = {10.1007/s11042-007-0100-4}, author = {Fayzullin,M. and V.S. Subrahmanian and Albanese, M. and Cesarano,C. and Picariello, A.} } @article {18717, title = {Structural Biology: Analysis of {\textquoteright}downhill{\textquoteright} protein folding; Analysis of protein-folding cooperativity (Reply)}, journal = {Nature}, volume = {445}, year = {2007}, month = {2007/02/15/}, pages = {E17-E18 - E17-E18}, abstract = {Ferguson et al. and Zhou and Bai criticize the quality of our nuclear magnetic resonance (NMR) data and atom-by-atom analysis of global {\textquoteright}downhill{\textquoteright} folding, also claiming that the data are compatible with two-state folding.}, keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling., climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics}, isbn = {0028-0836}, doi = {10.1038/nature05645}, url = {http://www.nature.com/nature/journal/v445/n7129/full/nature05645.html?lang=en}, author = {Sadqi,Mourad and Fushman, David and Mu{\~n}oz,Victor} } @article {16807, title = {System for 802.11 connectivity at high speed}, volume = {UMIACS-TR-2007-27}, year = {2007}, month = {2007/05/13/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Measurements and ongoing research have shown that WLANconnection for moving vehicles is feasible. However none of the previous work suggests a solution addressing a complete array of the challenges in vehicular WLAN communications. To amend this we designed a system that provides wireless connection roaming at high velocities transparent to user level applications, and does not impose additional requirements to existing infrastructures. It offers simple deployment, security, and scalability. It remains efficient under - intermittent connectivity conditions and supports heterogeneous network mediums for increased robustness. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/4374}, author = {Frangiadakis,Nikolaos and Kuklov,Danila and Roussopoulos, Nick} } @article {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 {13918, title = {A theoretical model of children{\textquoteright}s storytelling using physically-oriented technologies (SPOT)}, journal = {Journal of Educational Multimedia and Hypermedia}, volume = {16}, year = {2007}, month = {2007///}, pages = {389 - 389}, author = {Guha,M.L. and Druin, Allison and Montemayor,J. and Chipman,G. and Farber,A.} } @conference {14283, title = {Type qualifier inference for Java}, booktitle = {ACM SIGPLAN Notices}, volume = {42}, year = {2007}, month = {2007///}, pages = {321 - 336}, author = {Greenfieldboyce,D. and Foster, Jeffrey S.} } @conference {18611, title = {Usage-based dhcp lease time optimization}, booktitle = {Proceedings of the 7th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {71 - 76}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The Dynamic Host Configuration Protocol (DHCP) is used to dynamically allocate address space to hosts on a local area network. Despite its widespread usage, few studies exist on DHCP usage patterns, and even less is known about the importance of setting the lease time (the time that a client retains ownership over some IP address) to an appropriate value. Lease time can greatly affect the tradeoff between address space utilization and the number of both renewal messages and client session expirations. In this paper, using a DHCP trace for 5 weekdays from the Georgia Tech campus network, we present the largest known study of DHCP utilization. We also explore how various strategies for setting lease times can dramatically reduce the number of renewals and expirations without prohibitively increasing address space utilization.}, keywords = {dhcp, network management, OPTIMIZATION, usage}, isbn = {978-1-59593-908-1}, doi = {10.1145/1298306.1298315}, url = {http://doi.acm.org/10.1145/1298306.1298315}, author = {Khadilkar,Manas and Feamster, Nick and Sanders,Matt and Clark,Russ} } @article {14182, title = {A 3D shape constraint on video}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {28}, year = {2006}, month = {2006/06//}, pages = {1018 - 1023}, abstract = {We propose to combine the information from multiple motion fields by enforcing a constraint on the surface normals (3D shape) of the scene in view. The fact that the shape vectors in the different views are related only by rotation can be formulated as a rank = 3 constraint. This constraint is implemented in an algorithm which solves 3D motion and structure estimation as a practical constrained minimization. Experiments demonstrate its usefulness as a tool in structure from motion providing very accurate estimates of 3D motion.}, keywords = {3D motion estimation, algorithms, Artificial intelligence, CAMERAS, decoupling translation from rotation, Estimation error, Fluid flow measurement, Image Enhancement, Image Interpretation, Computer-Assisted, Image reconstruction, Imaging, Three-Dimensional, Information Storage and Retrieval, integration of motion fields, Layout, minimisation, Minimization methods, Motion estimation, multiple motion fields, parameter estimation, Pattern Recognition, Automated, Photography, practical constrained minimization, SHAPE, shape and rotation., shape vectors, stability, structure estimation, surface normals, Three-dimensional motion estimation, video 3D shape constraint, Video Recording, video signal processing}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2006.109}, author = {Hui Ji and Ferm{\"u}ller, Cornelia} } @conference {15244, title = {Achieving anonymity via clustering}, booktitle = {Proceedings of the twenty-fifth ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems}, series = {PODS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {153 - 162}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Publishing data for analysis from a table containing personal records, while maintaining individual privacy, is a problem of increasing importance today. The traditional approach of de-identifying records is to remove identifying fields such as social security number, name etc. However, recent research has shown that a large fraction of the US population can be identified using non-key attributes (called quasi-identifiers) such as date of birth, gender, and zip code [15]. Sweeney [16] proposed the k-anonymity model for privacy where non-key attributes that leak information are suppressed or generalized so that, for every record in the modified table, there are at least k-1 other records having exactly the same values for quasi-identifiers. We propose a new method for anonymizing data records, where quasi-identifiers of data records are first clustered and then cluster centers are published. To ensure privacy of the data records, we impose the constraint that each cluster must contain no fewer than a pre-specified number of data records. This technique is more general since we have a much larger choice for cluster centers than k-Anonymity. In many cases, it lets us release a lot more information without compromising privacy. We also provide constant-factor approximation algorithms to come up with such a clustering. This is the first set of algorithms for the anonymization problem where the performance is independent of the anonymity parameter k. We further observe that a few outlier points can significantly increase the cost of anonymization. Hence, we extend our algorithms to allow an ε fraction of points to remain unclustered, i.e., deleted from the anonymized publication. Thus, by not releasing a small fraction of the database records, we can ensure that the data published for analysis has less distortion and hence is more useful. Our approximation algorithms for new clustering objectives are of independent interest and could be applicable in other clustering scenarios as well.}, keywords = {anonymity, Approximation algorithms, clustering, privacy}, isbn = {1-59593-318-2}, doi = {10.1145/1142351.1142374}, url = {http://doi.acm.org/10.1145/1142351.1142374}, author = {Aggarwal,Gagan and Feder,Tom{\'a}s and Kenthapadi,Krishnaram and Khuller, Samir and Panigrahy,Rina and Thomas,Dilys and Zhu,An} } @inbook {12623, title = {Acquisition of Articulated Human Body Models Using Multiple Cameras}, booktitle = {Articulated Motion and Deformable ObjectsArticulated Motion and Deformable Objects}, series = {Lecture Notes in Computer Science}, volume = {4069}, year = {2006}, month = {2006///}, pages = {78 - 89}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Motion capture is an important application in different areas such as biomechanics, computer animation, and human-computer interaction. Current motion capture methods typically use human body models in order to guide pose estimation and tracking. We model the human body as a set of tapered super-quadrics connected in an articulated structure and propose an algorithm to automatically estimate the parameters of the model using video sequences obtained from multiple calibrated cameras. Our method is based on the fact that the human body is constructed of several articulated chains that can be visualised as essentially 1-D segments embedded in 3-D space and connected at specific joint locations. The proposed method first computes a voxel representation from the images and maps the voxels to a high dimensional space in order to extract the 1-D structure. A bottom-up approach is then suggested in order to build a parametric (spline-based) representation of a general articulated body in the high dimensional space followed by a top-down probabilistic approach that registers the segments to the known human body model. We then present an algorithm to estimate the parameters of our model using the segmented and registered voxels.}, isbn = {978-3-540-36031-5}, url = {http://dx.doi.org/10.1007/11789239_9}, author = {Sundaresan,Aravind and Chellapa, Rama}, editor = {Perales,Francisco and Fisher,Robert} } @article {12396, title = {Adding dense, weighted connections to wordnet}, journal = {Proceedings of the Third International WordNet Conference}, year = {2006}, month = {2006///}, pages = {29 - 36}, abstract = {WORDNET, a ubiquitous tool for natural language processing, suffers from sparsity of connectionsbetween its component concepts (synsets). Through the use of human annotators, a subset of the connections between 1000 hand-chosen synsets was assigned a value of {\textquotedblleft}evocation{\textquotedblright} representing how much the first concept brings to mind the second. These data, along with existing similarity measures, constitute the basis of a method for predicting evocation between previously unrated pairs. }, author = {Jordan Boyd-Graber and Fellbaum,C. and Osherson,D. and Schapire,R.} } @conference {15689, title = {Alternative custodians for congestion control in delay tolerant networks}, booktitle = {Proceedings of the 2006 SIGCOMM workshop on Challenged networks}, series = {CHANTS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {229 - 236}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {delay tolerant network, Routing}, isbn = {1-59593-572-X}, doi = {10.1145/1162654.1162660}, url = {http://doi.acm.org/10.1145/1162654.1162660}, author = {Seligman,Matthew and Fall,Kevin and Mundur, Padma} } @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.} } @conference {12093, title = {Applying flow-sensitive CQUAL to verify MINIX authorization check placement}, booktitle = {Proceedings of the 2006 workshop on Programming languages and analysis for security}, series = {PLAS {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {3 - 6}, publisher = {ACM}, organization = {ACM}, address = {Ottawa, Ontario, Canada}, abstract = {We present the first use of flow-sensitive CQUAL to verify the placement of operating system authorization checks. Our analysis of MINIX 3 system servers and discovery of a non-exploitable Time-Of-Check/Time-Of-Use bug demonstrate the effectiveness of flow sensitive CQUAL and its advantage over earlier flow-insensitive versions. We also identify and suggest alternatives to current CQUAL usability features that encourage analysts to make omissions that cause the otherwise sound tool to produce false-negative results.}, keywords = {access controls, cqual, minix}, isbn = {1-59593-374-3}, doi = {10.1145/1134744.1134747}, author = {Fraser,Timothy and Petroni,Jr. and Arbaugh, William A.} } @conference {12085, title = {An architecture for specification-based detection of semantic integrity violations in kernel dynamic data}, booktitle = {Proceedings of the 15th conference on USENIX Security Symposium}, year = {2006}, month = {2006///}, pages = {20 - 20}, author = {Petroni Jr,N. L and Fraser,T. and Walters,A. A and Arbaugh, William A.} } @article {18491, title = {Can DNS-based blacklists keep up with bots}, journal = {Conference on email and anti-spam}, year = {2006}, month = {2006///}, author = {Ramachandran,A. and Dagon,D. and Feamster, Nick} } @conference {18530, title = {Can Information from End Systems Improve Routing}, booktitle = {Proceedings of the Workshop on Internet Routing Evolution and Design}, year = {2006}, month = {2006///}, author = {Feamster, Nick} } @conference {13894, title = {A case study of tangible flags: a collaborative technology to enhance field trips}, booktitle = {Proceedings of the 2006 conference on Interaction design and children}, year = {2006}, month = {2006///}, pages = {1 - 8}, author = {Chipman,G. and Druin, Allison and Beer,D. and Fails,J. A and Guha,M.L. and Simms,S.} } @article {18531, title = {Challenges and Opportunities in Internet Data Mining}, volume = {CMU-PDL-06-102}, year = {2006}, month = {2006///}, pages = {44 - 44}, institution = {Parallel Data Laboratory, Carnegie Mellon University}, abstract = {Internet measurement data provides the foundation for the operation and planning of the networks that comprise the Internet, and is a necessary component in research for analysis, simulation, and emulation. Despite its critical role, however, the management of this data{\textemdash}from collection and transmission to storage and its use within applications{\textemdash}remains primarily ad hoc, using techniques created and re-created by each corporation or researcher that uses the data. This paper examines several of the challenges faced when attempting to collect and archive large volumes of network measurement data, and outlines an architecture for an Internet data repository{\textemdash}the datapository designed to create a framework for collaboratively addressing these challenges.}, author = {Andersen,D.G. and Feamster, Nick} } @conference {14549, title = {Combination can be hard: Approximability of the unique coverage problem}, booktitle = {Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm}, year = {2006}, month = {2006///}, pages = {162 - 171}, author = {Demaine,E. D and Hajiaghayi, Mohammad T. and Feige,U. and Salavatipour,M. R} } @article {17533, title = {Community-oriented network measurement infrastructure (CONMI) workshop report}, journal = {ACM SIGCOMM Computer Communication Review}, volume = {36}, year = {2006}, month = {2006/04/28/}, pages = {41 - 41}, isbn = {01464833}, doi = {10.1145/1129582.1129594}, url = {http://dl.acm.org/citation.cfm?id=1129594}, author = {claffy,kc and Crovella,Mark and Friedman,Timur and Shannon,Colleen and Spring, Neil} } @article {14668, title = {Context-sensitive correlation analysis for detecting races}, journal = {Proceedings of the ACM Conference on Programming Language Design and Implementation (PLDI)}, year = {2006}, month = {2006///}, pages = {320 - 331}, author = {Pratikakis,P. and Foster, Jeffrey S. and Hicks, Michael W.} } @article {17042, title = {Creativity Support Tools: Report From a U.S. National Science Foundation Sponsored Workshop}, journal = {International Journal of Human-Computer Interaction}, volume = {20}, year = {2006}, month = {2006///}, pages = {61 - 77}, abstract = {Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools.Creativity support tools is a research topic with high risk but potentially very high payoff. The goal is to develop improved software and user interfaces that empower users to be not only more productive but also more innovative. Potential users include software and other engineers, diverse scientists, product and graphic designers, architects, educators, students, and many others. Enhanced interfaces could enable more effective searching of intellectual resources, improved collaboration among teams, and more rapid discovery processes. These advanced interfaces should also provide potent support in hypothesis formation, speedier evaluation of alternatives, improved understanding through visualization, and better dissemination of results. For creative endeavors that require composition of novel artifacts (e.g., computer programs, scientific papers, engineering diagrams, symphonies, artwork), enhanced interfaces could facilitate exploration of alternatives, prevent unproductive choices, and enable easy backtracking. This U.S. National Science Foundation sponsored workshop brought together 25 research leaders and graduate students to share experiences, identify opportunities, and formulate research challenges. Two key outcomes emerged: (a) encouragement to evaluate creativity support tools through multidimensional in-depth longitudinal case studies and (b) formulation of 12 principles for design of creativity support tools. }, isbn = {1044-7318}, doi = {10.1207/s15327590ijhc2002_1}, url = {http://www.tandfonline.com/doi/abs/10.1207/s15327590ijhc2002_1}, author = {Shneiderman, Ben and Fischer,Gerhard and Czerwinski,Mary and Resnick,Mitch and Myers,Brad and Candy,Linda and Edmonds,Ernest and Eisenberg,Mike and Giaccardi,Elisa and Hewett,Tom and Jennings,Pamela and Kules,Bill and Nakakoji,Kumiyo and Nunamaker,Jay and Pausch,Randy and Selker,Ted and Sylvan,Elisabeth and Terry,Michael} } @article {14210, title = {Depth estimation using the compound eye of dipteran flies}, journal = {Biological Cybernetics}, volume = {95}, year = {2006}, month = {2006///}, pages = {487 - 501}, abstract = {In the neural superposition eye of a dipteran fly every ommatidium has eight photoreceptors, each associated with a rhabdomere, two central and six peripheral, which altogether result in seven functional light guides. Groups of eight rhabdomeres in neighboring ommatidia have largely overlapping fields of view. Based on the hypothesis that the light signals collected by these rhabdomeres can be used individually, we investigated the feasibility of estimating 3D scene information. According to Pick (Biol Cybern 26:215{\textendash}224, 1977) the visual axes of these rhabdomeres are not parallel, but converge to a point 3{\textendash}6 mm in front of the cornea. Such a structure theoretically could estimate depth in a very simple way by assuming that locally the image intensity is well approximated by a linear function of the spatial coordinates. Using the measurements of Pick (Biol Cybern 26:215{\textendash}224, 1977) we performed simulation experiments to find whether this is practically possible. Our results indicate that depth estimation at small distances (up to about 1.5{\textendash}2 cm) is reasonably accurate. This would allow the insect to obtain at least an ordinal spatial layout of its operational space when walking.}, isbn = {0340-1200}, url = {http://dx.doi.org/10.1007/s00422-006-0097-1}, author = {Bitsakos,Konstantinos and Ferm{\"u}ller, Cornelia} } @article {17931, title = {An Efficient Computational Method for Predicting Rotational Diffusion Tensors of Globular Proteins Using an Ellipsoid Representation}, journal = {Journal of the American Chemical Society}, volume = {128}, year = {2006}, month = {2006///}, pages = {15432 - 15444}, abstract = {We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138?146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins.We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138?146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins. }, isbn = {0002-7863}, doi = {10.1021/ja062715t}, url = {http://dx.doi.org/10.1021/ja062715t}, author = {Ryabov,Yaroslav E. and Geraghty,Charles and Varshney, Amitabh and Fushman, David} } @inbook {14693, title = {Existential Label Flow Inference Via CFL Reachability}, booktitle = {Static AnalysisStatic Analysis}, series = {Lecture Notes in Computer Science}, volume = {4134}, year = {2006}, month = {2006///}, pages = {88 - 106}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In programming languages, existential quantification is useful for describing relationships among members of a structured type. For example, we may have a list in which there exists some mutual exclusion lock l in each list element such that l protects the data stored in that element. With this information, a static analysis can reason about the relationship between locks and locations in the list even when the precise identity of the lock and/or location is unknown. To facilitate the construction of such static analyses, this paper presents a context-sensitive label flow analysis algorithm with support for existential quantification. Label flow analysis is a core part of many static analysis systems. Following Rehof et al, we use context-free language (CFL) reachability to develop an efficient O(n 3) label flow inference algorithm. We prove the algorithm sound by reducing its derivations to those in a system based on polymorphically-constrained types, in the style of Mossin. We have implemented a variant of our analysis as part of a data race detection tool for C programs.}, isbn = {978-3-540-37756-6}, url = {http://dx.doi.org/10.1007/11823230_7}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W.}, editor = {Yi,Kwangkeun} } @article {14909, title = {First Steps Toward an Electronic Field Guide for Plants}, journal = {Taxon}, volume = {55}, year = {2006}, month = {2006///}, pages = {597 - 610}, abstract = {this paper, we will describe our progress towards building a digital collection of the Smithsonian{\textquoteright}s type specimens, developing recognition algorithms that can match an image of a leaf to the species of plant from which it comes, and designing user interfaces for interacting with an electronic field guide. To start, we are developing a prototype electronic field guide for the flora of Plummers Island, a small, well-studied island in the Potomac River. This prototype system contains multiple images for each of about 130 species of plants on the island, and should soon grow to cover all 200+ species currently recorded (Shetler et al., 2005). Images of full specimens are available, as well as images of isolated leaves of each species. A zoomable user interface allows a user to browse these images, zooming in on ones of interest. Visual recognition algorithms assist a botanist in locating the specimens that are most relevant to identify the species of a plant. The system currently runs on a small hand-held computer. We will describe the components of this prototype, and also describe some of the future challenges we anticipate if we are to provide botanists in the field with all the resources that are now currently available in the world{\textquoteright}s museums and herbaria. Type Specimen Digital Collection The first challenge in producing our electronic field guide is to create a digital collection covering all of the Smithsonian{\textquoteright}s 85,000 vascular plant type specimens. For each type specimen, the database should eventually include systematically acquired high-resolution digital images of the specimen, textual descriptions, links to decision trees, images of live plants, and 3D models. Figure 1: On the left, our set-up at the Smithsonian for digitally photographing type specimens. On the...}, author = {Haibin,Gaurav Agarwal and Agarwal,Gaurav and Ling,Haibin and Jacobs, David W. and Shirdhonkar,Sameer and Kress,W. John and Russell,Rusty and Belhumeur,Peter and Dixit,An and Feiner,Steve and Mahajan,Dhruv and Sunkavalli,Kalyan and Ramamoorthi,Ravi and White,Sean} } @article {14282, title = {Flow-insensitive type qualifiers}, journal = {ACM Transactions on Programming Languages and Systems (TOPLAS)}, volume = {28}, year = {2006}, month = {2006///}, pages = {1035 - 1087}, author = {Foster, Jeffrey S. and Johnson,R. and Kodumal,J. and Aiken,A.} } @article {19661, title = {How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior}, journal = {Proceedings of the IEEE}, volume = {94}, year = {2006}, month = {2006/07//}, pages = {1445 - 1463}, abstract = {Our understanding of social insect behavior has significantly influenced artificial intelligence (AI) and multirobot systems{\textquoteright} research (e.g., ant algorithms and swarm robotics). In this work, however, we focus on the opposite question: "How can multirobot systems research contribute to the understanding of social animal behavior?" As we show, we are able to contribute at several levels. First, using algorithms that originated in the robotics community, we can track animals under observation to provide essential quantitative data for animal behavior research. Second, by developing and applying algorithms originating in speech recognition and computer vision, we can automatically label the behavior of animals under observation. In some cases the automatic labeling is more accurate and consistent than manual behavior identification. Our ultimate goal, however, is to automatically create, from observation, executable models of behavior. An executable model is a control program for an agent that can run in simulation (or on a robot). The representation for these executable models is drawn from research in multirobot systems programming. In this paper we present the algorithms we have developed for tracking, recognizing, and learning models of social animal behavior, details of their implementation, and quantitative experimental results using them to study social insects}, keywords = {Acceleration, Animal behavior, ant movement tracking, Artificial intelligence, biology computing, Computer vision, control engineering computing, Insects, Intelligent robots, Labeling, monkey movement tracking, multi-robot systems, multirobot systems, robotics algorithms, Robotics and automation, social animal behavior, social animals, social insect behavior, Speech recognition, tracking}, isbn = {0018-9219}, author = {Balch, T. and Dellaert, F. and Feldman, A. and Guillory, A. and Isbell, C.L. and Zia Khan and Pratt, S.C. and Stein, A.N. and Wilde, H.} } @article {18577, title = {In VINI veritas: realistic and controlled network experimentation}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {36}, year = {2006}, month = {2006/08//}, pages = {3 - 14}, abstract = {This paper describes VINI, a virtual network infrastructure that allows network researchers to evaluate their protocols and services in a realistic environment that also provides a high degree of control over network conditions. VINI allows researchers to deploy and evaluate their ideas with real routing software, traffic loads, and network events. To provide researchers flexibility in designing their experiments, VINI supports simultaneous experiments with arbitrary network topologies on a shared physical infrastructure. This paper tackles the following important design question: What set of concepts and techniques facilitate flexible, realistic, and controlled experimentation (e.g., multiple topologies and the ability to tweak routing algorithms) on a fixed physical infrastructure? We first present VINI{\textquoteright}s high-level design and the challenges of virtualizing a single network. We then present PL-VINI, an implementation of VINI on PlanetLab, running the "Internet In a Slice". Our evaluation of PL-VINI shows that it provides a realistic and controlled environment for evaluating new protocols and services.}, keywords = {architecture, experimentation, Internet, Routing, virtualization}, isbn = {0146-4833}, doi = {10.1145/1151659.1159916}, url = {http://doi.acm.org/10.1145/1151659.1159916}, author = {Bavier,Andy and Feamster, Nick and Huang,Mark and Peterson,Larry and Rexford,Jennifer} } @article {16091, title = {Interactive sonification for blind people exploration of geo-referenced data: comparison between a keyboard-exploration and a haptic-exploration interfaces}, journal = {Cognitive Processing}, volume = {7}, year = {2006}, month = {2006///}, pages = {178 - 179}, isbn = {1612-4782}, url = {http://dx.doi.org/10.1007/s10339-006-0137-8}, author = {Delogu,Franco and Belardinelli,Marta and Palmiero,Massimiliano and Pasqualotto,Emanuele and Zhao,Haixia and Plaisant, Catherine and Federici,Stefano} } @article {18705, title = {Interdomain mobility in di-ubiquitin revealed by NMR}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {63}, year = {2006}, month = {2006///}, pages = {787 - 796}, abstract = {Domain orientation and dynamics can play an essential role in the function of multidomain proteins. Lys48-linked polyubiquitin chains, the principal signal for proteasomal protein degradation, adopt a closed conformation at physiological conditions, in which the functionally important residues Leu8, Ile44, and Val70 are sequestered at the interdomain interface. This interface must open in order for these groups to become available for interactions with various chain-recognition factors. Knowledge of the mechanism of domain motion leading to the opening of the interdomain interface in polyubiqutin is, therefore, essential for the understanding of the processes controlling molecular recognition events in polyubiquitin signaling. Here we use NMR to characterize the interdomain dynamics that open the interface in a di-ubiquitin chain. This process occurs via domain reorientations on a 10-ns time scale and with the amplitudes that are sufficient for making functionally important hydrophobic residues in polyubiquitin available for direct interactions with various ubiquitin-binding factors. The analysis revealed the structures of the interconverting conformational states of di-ubiquitin and the rates and amplitudes of this process at near-physiological and acidic pH. The proposed mechanism of domain reorientation is quite general and could serve as a paradigm of interdomain mobility in other multidomain systems. Proteins 2006. {\textcopyright} 2006 Wiley-Liss, Inc.}, keywords = {anisotropic diffusion, domain motion, interdomain orientation, polyubiquitin, spin relaxation}, isbn = {1097-0134}, doi = {10.1002/prot.20917}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.20917/abstract}, author = {Ryabov,Yaroslav and Fushman, David} } @conference {14703, title = {Lock inference for atomic sections}, booktitle = {Proceedings of the First ACM SIGPLAN Workshop on Languages, Compilers, and Hardware Support for Transactional Computing}, year = {2006}, month = {2006///}, abstract = {To prevent unwanted interactions in multithreaded programs, pro-grammers have traditionally employed pessimistic, blocking con- currency primitives. Using such primitives correctly and efficiently is notoriously difficult. To simplify the problem, recent research proposes that programmers specify atomic sections of code whose executions should be atomic with respect to one another, without dictating exactly how atomicity enforced. Much work has explored using optimistic concurrency, or software transactions, as a means to implement atomic sections. This paper proposes to implement atomic sections using a static whole-program analysis to insert necessary uses of pessimistic con- currency primitives. Given a program that contains programmer- specified atomic sections and thread creations, our mutex infer- ence algorithm efficiently infers a set of locks for each atomic section that should be acquired (released) upon entering (exiting) the atomic section. The key part of this algorithm is determining which memory locations in the program could be shared between threads, and using this information to generate the necessary locks. To determine sharing, our analysis uses the notion of continuation effects to track the locations accessed after each program point. As continuation effects are flow sensitive, a memory location may be thread-local before a thread creation and thread-shared afterward. We prove that our algorithm is correct, and provides parallelism according to the precision of the points-to analysis. While our al- gorithm also attempts to reduce the number locks while preserving parallelism, we show that minimizing the number of locks is NP- hard. }, author = {Hicks, Michael W. and Foster, Jeffrey S. and Pratikakis,P.} } @article {14704, title = {LOCKSMITH: context-sensitive correlation analysis for race detection}, journal = {SIGPLAN Not.}, volume = {41}, year = {2006}, month = {2006/06//}, pages = {320 - 331}, abstract = {One common technique for preventing data races in multi-threaded programs is to ensure that all accesses to shared locations are consistently protected by a lock. We present a tool called LOCKSMITH for detecting data races in C programs by looking for violations of this pattern. We call the relationship between locks and the locations they protect consistent correlation, and the core of our technique is a novel constraint-based analysis that infers consistent correlation context-sensitively, using the results to check that locations are properly guarded by locks. We present the core of our algorithm for a simple formal language λ> which we have proven sound, and discuss how we scale it up to an algorithm that aims to be sound for all of C. We develop several techniques to improve the precision and performance of the analysis, including a sharing analysis for inferring thread locality; existential quantification for modeling locks in data structures; and heuristics for modeling unsafe features of C such as type casts. When applied to several benchmarks, including multi-threaded servers and Linux device drivers, LOCKSMITH found several races while producing a modest number of false alarm.}, keywords = {context-sensitivity, correlation, locksmith, multi-threaded programming, race detection, Type inference}, isbn = {0362-1340}, doi = {10.1145/1133255.1134019}, url = {http://doi.acm.org/10.1145/1133255.1134019}, author = {Pratikakis,Polyvios and Foster, Jeffrey S. and Hicks, Michael W.} } @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 {16276, title = {Metagenomic Analysis of the Human Distal Gut Microbiome}, journal = {Science}, volume = {312}, year = {2006}, month = {2006/06/02/}, pages = {1355 - 1359}, abstract = {The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ({\textquotedblleft}microbiome{\textquotedblright}) contains at least 100 times as many genes as our own genome. We analyzed \~{}78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction{\textendash}amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway{\textendash}mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1124234}, url = {http://www.sciencemag.org/content/312/5778/1355}, author = {Gill,Steven R. and Pop, Mihai and DeBoy,Robert T. and Eckburg,Paul B and Turnbaugh,Peter J and Samuel,Buck S and Gordon,Jeffrey I and Relman,David A and Fraser-Liggett,Claire M and Nelson,Karen E.} } @conference {12838, title = {Model based verification and validation of distributed control architectures}, booktitle = {Proceedings of Convergence Convergence International Congress and Exposition on Transportation Electronics, Detroit, USA}, year = {2006}, month = {2006///}, author = {Ray,A. and Cleaveland, Rance and Jiang,S. and Fuhrman,T.} } @article {14081, title = {Molecular Characterization of Serine-, Alanine-, and Proline-Rich Proteins of Trypanosoma cruzi and Their Possible Role in Host Cell Infection}, journal = {Infect. Immun.}, volume = {74}, year = {2006}, month = {2006/03/01/}, pages = {1537 - 1546}, abstract = {We previously reported the isolation of a novel protein gene family, termed SAP (serine-, alanine-, and proline-rich protein), from Trypanosoma cruzi. Aided by the availability of the completed genome sequence of T. cruzi, we have now identified 39 full-length sequences of SAP, six pseudogenes and four partial genes. SAPs share a central domain of about 55 amino acids and can be divided into four groups based on their amino (N)- and carboxy (C)-terminal sequences. Some SAPs have conserved N- and C-terminal domains encoding a signal peptide and a glycosylphosphatidylinositol anchor addition site, respectively. Analysis of the expression of SAPs in metacyclic trypomastigotes by two-dimensional electrophoresis and immunoblotting revealed that they are likely to be posttranslationally modified in vivo. We have also demonstrated that some SAPs are shed into the extracellular medium. The recombinant SAP exhibited an adhesive capacity toward mammalian cells, where binding was dose dependent and saturable, indicating a possible ligand-receptor interaction. SAP triggered the host cell Ca2+ response required for parasite internalization. A cell invasion assay performed in the presence of SAP showed inhibition of internalization of the metacyclic forms of the CL strain. Taken together, these results show that SAP is involved in the invasion of mammalian cells by metacyclic trypomastigotes, and they confirm the hypothesis that infective trypomastigotes exploit an arsenal of surface glycoproteins and shed proteins to induce signaling events required for their internalization.}, doi = {

10.1128/IAI.74.3.1537-1546.2006

}, url = {http://iai.asm.org/cgi/content/abstract/74/3/1537}, author = {Baida,Renata C. P. and Santos,Marcia R. M. and Carmo,Mirian S. and Yoshida,Nobuko and Ferreira,Danielle and Ferreira,Alice Teixeira and El Sayed,Najib M. and Andersson,Bjorn and da Silveira,Jose Franco} } @article {14237, title = {Noise causes slant underestimation in stereo and motion}, journal = {Vision Research}, volume = {46}, year = {2006}, month = {2006/10//}, pages = {3105 - 3120}, abstract = {This paper discusses a problem, which is inherent in the estimation of 3D shape (surface normals) from multiple views. Noise in the image signal causes bias, which may result in substantial errors in the parameter estimation. The bias predicts the underestimation of slant found in psychophysical and computational experiments. Specifically, we analyze the estimation of 3D shape from motion and stereo using orientation disparity. For the case of stereo, we show that bias predicts the anisotropy in the perception of horizontal and vertical slant. For the case of 3D motion we demonstrate the bias by means of a new illusory display. Finally, we discuss statistically optimal strategies for the problem and suggest possible avenues for visual systems to deal with the bias.}, keywords = {Bias, Partial bias correction, shape estimation, Shape from motion, Stereo orientation disparity}, isbn = {0042-6989}, doi = {10.1016/j.visres.2006.04.010}, url = {http://www.sciencedirect.com/science/article/pii/S0042698906002124}, author = {Hui Ji and Ferm{\"u}ller, Cornelia} } @article {17309, title = {Nuclear Envelope Dystrophies Show a Transcriptional Fingerprint Suggesting Disruption of Rb{\textendash}MyoD Pathways in Muscle Regeneration}, journal = {BrainBrain}, volume = {129}, year = {2006}, month = {2006/04/01/}, pages = {996 - 1013}, abstract = {Mutations of lamin A/C (LMNA) cause a wide range of human disorders, including progeria, lipodystrophy, neuropathies and autosomal dominant Emery{\textendash}Dreifuss muscular dystrophy (EDMD). EDMD is also caused by X-linked recessive loss-of-function mutations of emerin, another component of the inner nuclear lamina that directly interacts with LMNA. One model for disease pathogenesis of LMNA and emerin mutations is cell-specific perturbations of the mRNA transcriptome in terminally differentiated cells. To test this model, we studied 125 human muscle biopsies from 13 diagnostic groups (125 U133A, 125 U133B microarrays), including EDMD patients with LMNA and emerin mutations. A Visual and Statistical Data Analyzer (VISDA) algorithm was used to statistically model cluster hierarchy, resulting in a tree of phenotypic classifications. Validations of the diagnostic tree included permutations of U133A and U133B arrays, and use of two probe set algorithms (MAS5.0 and MBEI). This showed that the two nuclear envelope defects (EDMD LMNA, EDMD emerin) were highly related disorders and were also related to fascioscapulohumeral muscular dystrophy (FSHD). FSHD has recently been hypothesized to involve abnormal interactions of chromatin with the nuclear envelope. To identify disease-specific transcripts for EDMD, we applied a leave-one-out (LOO) cross-validation approach using LMNA patient muscle as a test data set, with reverse transcription{\textendash}polymerase chain reaction (RT{\textendash}PCR) validations in both LMNA and emerin patient muscle. A high proportion of top-ranked and validated transcripts were components of the same transcriptional regulatory pathway involving Rb1 and MyoD during muscle regeneration (CRI-1, CREBBP, Nap1L1, ECREBBP/p300), where each was specifically upregulated in EDMD. Using a muscle regeneration time series (27 time points) we develop a transcriptional model for downstream consequences of LMNA and emerin mutations. We propose that key interactions between the nuclear envelope and Rb and MyoD fail in EDMD at the point of myoblast exit from the cell cycle, leading to poorly coordinated phosphorylation and acetylation steps. Our data is consistent with mutations of nuclear lamina components leading to destabilization of the transcriptome in differentiated cells.}, keywords = {EDMD = Emery{\textendash}Dreifuss muscular dystrophy, emerin, Emery-Dreifuss muscular dystrophy, FSHD = fascioscapulohumeral muscular dystrophy, IDG = individual discriminatory genes, JDG = jointly discriminatory genes, lamin A/C, LGMD = limb-girdle muscular dystrophy, LOO = leave-one-out, RT{\textendash}PCR = reverse transcription{\textendash}polymerase chain reaction; VISDA = Visual and Statistical Data Analyzer, Skeletal muscle, wFC = weighted Fisher criterion}, isbn = {0006-8950, 1460-2156}, doi = {10.1093/brain/awl023}, url = {http://brain.oxfordjournals.org/content/129/4/996}, author = {Bakay,Marina and Wang,Zuyi and Melcon,Gisela and Schiltz,Louis and Xuan,Jianhua and Zhao,Po and Sartorelli,Vittorio and Seo,Jinwook and Pegoraro,Elena and Angelini,Corrado and Shneiderman, Ben and Escolar,Diana and Chen,Yi-Wen and Winokur,Sara T and Pachman,Lauren M and Fan,Chenguang and Mandler,Raul and Nevo,Yoram and Gordon,Erynn and Zhu,Yitan and Dong,Yibin and Wang,Yue and Hoffman,Eric P} } @article {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} } @article {17783, title = {The priority curve algorithm for video summarization}, journal = {Information Systems}, volume = {31}, year = {2006}, month = {2006/11//}, pages = {679 - 695}, abstract = {In this paper, we introduce the concept of a priority curve associated with a video. We then provide an algorithm that can use the priority curve to create a summary (of a desired length) of any video. The summary thus created exhibits nice continuity properties and also avoids repetition. We have implemented the priority curve algorithm (PriCA) and compared it with other summarization algorithms in the literature with respect to both performance and the output quality. The quality of summaries was evaluated by a group of 200 students in Naples, Italy, who watched soccer videos. We show that PriCA is faster than existing algorithms and also produces better quality summaries. We also briefly describe a soccer video summarization system we have built on using the PriCA architecture and various (classical) image processing algorithms.}, keywords = {Content based retrieval, Video databases, Video summarization}, isbn = {0306-4379}, doi = {10.1016/j.is.2005.12.003}, url = {http://www.sciencedirect.com/science/article/pii/S0306437905001250}, author = {Albanese, M. and Fayzullin,M. and Picariello, A. and V.S. Subrahmanian} } @conference {14187, title = {A Projective Invariant for Textures}, booktitle = {2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition}, volume = {2}, year = {2006}, month = {2006///}, pages = {1932 - 1939}, publisher = {IEEE}, organization = {IEEE}, abstract = {Image texture analysis has received a lot of attention in the past years. Researchers have developed many texture signatures based on texture measurements, for the purpose of uniquely characterizing the texture. Existing texture signatures, in general, are not invariant to 3D transforms such as view-point changes and non-rigid deformations of the texture surface, which is a serious limitation for many applications. In this paper, we introduce a new texture signature, called the multifractal spectrum (MFS). It provides an efficient framework combining global spatial invariance and local robust measurements. The MFS is invariant under the bi-Lipschitz map, which includes view-point changes and non-rigid deformations of the texture surface, as well as local affine illumination changes. Experiments demonstrate that the MFS captures the essential structure of textures with quite low dimension.}, keywords = {Computer science, Computer vision, Educational institutions, Fractals, Geometry, Image texture, Level set, lighting, Robustness, Surface texture}, isbn = {0-7695-2597-0}, doi = {10.1109/CVPR.2006.38}, author = {Yong Xu and Hui Ji and Ferm{\"u}ller, Cornelia} } @article {18504, title = {Quantifying the effects of routing dynamics on end-to-end Internet path failures}, volume = {TR-05-CSE-03}, year = {2006}, month = {2006///}, institution = {University of Massachusetts}, author = {Wang,F. and Feamster, Nick and Gao,L.} } @conference {18487, title = {Revealing botnet membership using DNSBL counter-intelligence}, booktitle = {Proc. 2nd USENIX Steps to Reducing Unwanted Traffic on the Internet}, year = {2006}, month = {2006///}, pages = {49 - 54}, abstract = {Botnets{\textemdash}networks of (typically compromised) machines{\textemdash}are often used for nefarious activities (e.g., spam, click fraud, denial-of-service attacks, etc.). Identifying members of botnets could help stem these attacks, but passively detecting botnet membership (i.e., without disrupting the operation of the botnet) proves to be difficult. This paper studies the effectiveness of monitoring lookups to a DNS-based blackhole list (DNSBL) to expose botnet membership. We perform counter-intelligence based on the insight that botmasters themselves perform DNSBL lookups to determine whether their spamming bots are blacklisted. Using heuristics to identify which DNSBL lookups are perpetrated by a botmaster performing such reconnaissance, we are able to compile a list of likely bots. This paper studies the prevalence of DNSBL reconnaissance observed at a mirror of a well-known blacklist for a 45-day period, identifies the means by which botmasters are performing reconnaissance, and suggests the possibility of using counter-intelligence to discover likely bots. We find that bots are performing reconnaissance on behalf of other bots. Based on this finding, we suggest counter-intelligence techniques that may be useful for early bot detection. }, author = {Ramachandran,A. and Feamster, Nick and Dagon,D.} } @article {18506, title = {Revisiting Internet addressing: Back to the future}, volume = {MIT-CSAIL-TR-2006-025}, year = {2006}, month = {2006///}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {IP prefixes undermine three goals of Internet routing:accurate reflection of network-layer reachability, secure routing messages, and effective traffic control. This pa- per presents Atomic IP (AIP), a simple change to Inter- net addressing (which in fact reverts to how addressing once worked), that allows Internet routing to achieve these goals. }, author = {Vutukuru,M. and Feamster, Nick and Walfish,M. and Balakrishnan,H. and Shenker,S.} } @article {15810, title = {Stable Factorizations of Symmetric Tridiagonal and Triadic Matrices}, journal = {SIAM J. on Matrix Analysis and Applications}, volume = {28}, year = {2006}, month = {2006///}, pages = {576 - 595}, abstract = {We call a matrix triadic if it has no more than two nonzero off-diagonal elements in any column. A symmetric tridiagonal matrix is a special case. In this paper we consider $LXL^T$ factorizations of symmetric triadic matrices, where $L$ is unit lower triangular and $X$ is diagonal, block diagonal with $1\!\times\!1$ and $2\!\times\!2$ blocks, or the identity with $L$ lower triangular. We prove that with diagonal pivoting, the $LXL^T$ factorization of a symmetric triadic matrix is sparse, study some pivoting algorithms, discuss their growth factor and performance, analyze their stability, and develop perturbation bounds. These factorizations are useful in computing inertia, in solving linear systems of equations, and in determining modified Newton search directions.}, author = {Fang,Haw-ren and O{\textquoteright}Leary, Dianne P.} } @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} } @conference {14442, title = {Is there a grand challenge or X-prize for data mining?}, booktitle = {Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining}, series = {KDD {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {954 - 956}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This panel will discuss possible exciting and motivating Grand Challenge problems for Data Mining, focusing on bioinformatics, multimedia mining, link mining, text mining, and web mining.}, keywords = {Bioinformatics, data mining, grand challenge, image mining, link mining, multimedia mining, text mining, video mining, web mining, X-prize}, isbn = {1-59593-339-5}, doi = {10.1145/1150402.1150535}, url = {http://doi.acm.org/10.1145/1150402.1150535}, author = {Piatetsky-Shapiro,Gregory and Grossman,Robert and Djeraba,Chabane and Feldman,Ronen and Getoor, Lise and Zaki,Mohammed} } @conference {18610, title = {Understanding the network-level behavior of spammers}, booktitle = {Proceedings of the 2006 conference on Applications, technologies, architectures, and protocols for computer communications}, series = {SIGCOMM {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {291 - 302}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper studies the network-level behavior of spammers, including: IP address ranges that send the most spam, common spamming modes (e.g., BGP route hijacking, bots), how persistent across time each spamming host is, and characteristics of spamming botnets. We try to answer these questions by analyzing a 17-month trace of over 10 million spam messages collected at an Internet "spam sinkhole", and by correlating this data with the results of IP-based blacklist lookups, passive TCP fingerprinting information, routing information, and botnet "command and control" traces.We find that most spam is being sent from a few regions of IP address space, and that spammers appear to be using transient "bots" that send only a few pieces of email over very short periods of time. Finally, a small, yet non-negligible, amount of spam is received from IP addresses that correspond to short-lived BGP routes, typically for hijacked prefixes. These trends suggest that developing algorithms to identify botnet membership, filtering email messages based on network-level properties (which are less variable than email content), and improving the security of the Internet routing infrastructure, may prove to be extremely effective for combating spam.}, keywords = {BGP, botnet, network management, Security, spam}, isbn = {1-59593-308-5}, doi = {10.1145/1159913.1159947}, url = {http://doi.acm.org/10.1145/1159913.1159947}, author = {Ramachandran,Anirudh and Feamster, Nick} } @conference {16951, title = {A Visual Interface for Multivariate Temporal Data: Finding Patterns of Events across Multiple Histories}, booktitle = {Visual Analytics Science And Technology, 2006 IEEE Symposium On}, year = {2006}, month = {2006/11/31/Oct. }, pages = {167 - 174}, publisher = {IEEE}, organization = {IEEE}, abstract = {Finding patterns of events over time is important in searching patient histories, Web logs, news stories, and criminal activities. This paper presents PatternFinder, an integrated interface for query and result-set visualization for search and discovery of temporal patterns within multivariate and categorical data sets. We define temporal patterns as sequences of events with inter-event time spans. PatternFinder allows users to specify the attributes of events and time spans to produce powerful pattern queries that are difficult to express with other formalisms. We characterize the range of queries PatternFinder supports as users vary the specificity at which events and time spans are defined. Pattern Finder{\textquoteright}s query capabilities together with coupled ball-and-chain and tabular visualizations enable users to effectively query, explore and analyze event patterns both within and across data entities (e.g. patient histories, terrorist groups, Web logs, etc.)}, keywords = {ball-and-chain visualization, Chromium, Computer science, Data analysis, data visualisation, Data visualization, Database languages, event pattern discovery, Graphical user interfaces, History, Information Visualization, Medical treatment, multivariate temporal data, Pattern analysis, pattern recognition, PatternFinder integrated interface, Query processing, query visualization, result-set visualization, Spatial databases, tabular visualization, temporal pattern discovery, temporal pattern searching, Temporal query, user interface, User interfaces, visual databases, visual interface}, isbn = {1-4244-0591-2}, doi = {10.1109/VAST.2006.261421}, author = {Fails,J. A and Karlson,A. and Shahamat,L. and Shneiderman, Ben} } @inbook {19210, title = {Voting with Your Feet: An Investigative Study of the Relationship Between Place Visit Behavior and Preference}, booktitle = {UbiComp 2006: Ubiquitous Computing}, series = {Lecture Notes in Computer Science}, volume = {4206}, year = {2006}, month = {2006}, pages = {333 - 350}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Real world recommendation systems, personalized mobile search, and online city guides could all benefit from data on personal place preferences. However, collecting explicit rating data of locations as users travel from place to place is impractical. This paper investigates the relationship between explicit place ratings and implicit aspects of travel behavior such as visit frequency and travel time. We conducted a four-week study with 16 participants using a novel sensor-based experience sampling tool, called My Experience (Me), which we developed for mobile phones. Over the course of the study Me was used to collect 3,458 in-situ questionnaires on 1,981 place visits. Our results show that, first, sensor-triggered experience sampling is a useful methodology for collecting targeted information in situ. Second, despite the complexities underlying travel routines and visit behavior, there exist positive correlations between place preference and automatically detectable features like visit frequency and travel time. And, third, we found that when combined, visit frequency and travel time result in stronger correlations with place rating than when measured individually. Finally, we found no significant difference in place ratings due to the presence of others.}, isbn = {978-3-540-39634-5}, url = {http://dx.doi.org/10.1007/11853565_20}, author = {Jon Froehlich and Chen,Mike and Smith,Ian and Potter,Fred}, editor = {Dourish,Paul and Friday,Adrian} } @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} } @article {14363, title = {What are the grand challenges for data mining? - KDD-2006 panel report}, journal = {ACM SIGKDD Explorations Newsletter}, volume = {8}, year = {2006}, month = {2006///}, pages = {70 - 77}, abstract = {We discuss what makes exciting and motivating Grand Challenge problems for Data Mining, and propose criteria for a good Grand Challenge. We then consider possible GC problems from multimedia mining, link mining, large- scale modeling, text mining, and proteomics. This report is the result of a panel held at KDD-2006 conference.}, author = {Piatetsky-Shapiro,G. and Djeraba,C. and Getoor, Lise and Grossman,R. and Feldman,R. and Zaki,M.} } @article {14240, title = {On the Anisotropy in the Perception of Stereoscopic Slant}, journal = {Journal of VisionJ Vis}, volume = {5}, year = {2005}, month = {2005/09/23/}, pages = {516 - 516}, abstract = {Many visual processes computationally amount to estimation problems. It has been shown that noise in the image data causes consistent errors in the estimation, that is statistical bias [1]. Here we analyze the effects of bias on 3D shape estimation, and we found that it predicts the perceived underestimation of slant for many settings found in experiments.In particular, we concentrate on the problem of shape estimation from stereo using orientation disparity. We found that bias predicts the anisotropy in the perception of stereoscopic slant, an effect that has not been explained before. It has been found that a surface slanted about the horizontal axis is estimated much easier and more accurately than a surface slanted about the vertical axis [2,3]. In both cases there is an underestimation of slant, but it is much larger for slant about the vertical. Cagnello and Rogers [2] argued that this effect is due to orientation disparity, which when the texture on the plane is made up of mostly horizontal and vertical lines, is smaller for surfaces slanting about the vertical. However as shown in [3], the effect also exists, even though in weaker form, when the texture is made up of lines oriented at 45 degrees. For such a configuration the orientation disparity in the two configurations is about the same. Thus orientation disparity by itself cannot be the cause. But errors in the estimated position and orientation of edgels cause bias, which predicts all the above findings and other parametric studies that we performed. [1]. C. Fermuller, H. Malm. Uncertainty in visual processes predicts geometrical optical illusions, Vision Research, 44, 727-749, 2004. [2]. R. Cagnello, B.J.Rogers. Anisotropies in the perception of stereoscopic surfaces: the role of orientation disparity. Vision Research, 33>(16): 2189-2201, 1993. [3]. G.J. Mitchison. S.P. McKee. Mechannisms underlying the anisotropy of stereoscopic tilt perception. Vision Research, 30:1781-1791, 1990. }, isbn = {, 1534-7362}, doi = {10.1167/5.8.516}, url = {http://www.journalofvision.org/content/5/8/516}, author = {Ferm{\"u}ller, Cornelia and Hui Ji} } @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} } @conference {14294, title = {Checking type safety of foreign function calls}, booktitle = {ACM SIGPLAN Notices}, volume = {40}, year = {2005}, month = {2005///}, pages = {62 - 72}, author = {Furr,M. and Foster, Jeffrey S.} } @conference {13910, title = {Child{\textquoteright}s play: a comparison of desktop and physical interactive environments}, booktitle = {Proceedings of the 2005 conference on Interaction design and children}, year = {2005}, month = {2005///}, pages = {48 - 55}, author = {Fails,J. A and Druin, Allison and Guha,M.L. and Chipman,G. and Simms,S. and Churaman,W.} } @article {14206, title = {Chromatic Induction and Perspective Distortion}, journal = {Journal of VisionJ Vis}, volume = {5}, year = {2005}, month = {2005/09/23/}, pages = {1026 - 1026}, abstract = {A pattern presented by Robertson (1996), consisting of yellow and blue square waves with red squares superimposed on either the blue or yellow bands give rise to assimilation effects similar as in the White illusion. The red squares on the yellow bands appear more blue, and the red squares on the blue bands appear more yellow. Varying the position and orientation of the pattern in space changes the effect. For example, slanting the pattern or increasing the distance to the pattern in space increases the effect. But rotating the pattern by 90 degrees and slanting it, nearly eliminates the effect. These changes in color appearance can be explained as the result of averaging in receptive field of extended size.Due to perspective distortion, the area of the pattern in space mapping to an image patch changes with the position and orientation of the pattern. A computational simulation, implementing the distortion from 3D space to image space, followed by a color segmentation (k-means clustering) gave the same color distortion and segmentation as perceived. Thus the effect seems to be simple an artifact of sampling which causes averaging or smoothing with some filters. We propose the hypothesis that chromatic induction, which takes the two forms of chromatic contrast and assimilation, results, because the system samples with large fields and following in the segmentation stage attempts to compensate for the averaging effects in neighboring regions }, isbn = {, 1534-7362}, doi = {10.1167/5.8.1026}, url = {http://www.journalofvision.org/content/5/8/1026}, author = {Aloimonos, J. and Ferm{\"u}ller, Cornelia} } @conference {18496, title = {Correctness properties for Internet routing}, booktitle = {Allerton Conference on Communication, Control, and Computing}, year = {2005}, month = {2005///}, abstract = {This paper motivates and presents a correctness specifi-cation for Internet routing. This specification is based on three properties{\textemdash}route validity, path visibility, and safety. This specification may be of use to people de- veloping tools to check routing configurations, to people designing solutions to specific problems in the current sys- tem, and to designers of new protocols and routing archi- tectures, all of whom can benefit from knowing what it means for Internet routing to be {\textquotedblleft}correct{\textquotedblright}. }, author = {Feamster, Nick and Balakrishnan,H.} } @article {17797, title = {The CPR model for summarizing video}, journal = {Multimedia Tools and Applications}, volume = {26}, year = {2005}, month = {2005///}, pages = {153 - 173}, abstract = {Most past work on video summarization has been based on selecting key frames from videos. We propose a model of video summarization based on three important parameters: Priority (of frames), Continuity (of the summary), and non-Repetition (of the summary). In short, a summary must include high priority frames and must be continuous and non-repetitive. An optimal summary is one that maximizes an objective function based on these three parameters. We show examples of how CPR parameters can be computed and provide algorithms to find optimal summaries based on the CPR approach. Finally, we briefly report on the performance of these algorithms.}, doi = {10.1007/s11042-005-0451-7}, author = {Fayzullin,M. and V.S. Subrahmanian and Picariello, A. and Sapino,M. L} } @conference {18560, title = {Design and implementation of a routing control platform}, booktitle = {Proceedings of the 2nd conference on Symposium on Networked Systems Design \& Implementation - Volume 2}, series = {NSDI{\textquoteright}05}, year = {2005}, month = {2005///}, pages = {15 - 28}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {The routers in an Autonomous System (AS) must distribute the information they learn about how to reach external destinations. Unfortunately, today{\textquoteright}s internal Border Gateway Protocol (iBGP) architectures have serious problems: a "full mesh" iBGP configuration does not scale to large networks and "route reflection" can introduce problems such as protocol oscillations and persistent loops. Instead, we argue that a Routing Control Platform (RCP) should collect information about external destinations and internal topology and select the BGP routes for each router in an AS. RCP is a logically-centralized platform, separate from the IP forwarding plane, that performs route selection on behalf of routers and communicates selected routes to the routers using the unmodified iBGP protocol. RCP provides scalability without sacrificing correctness. In this paper, we present the design and implementation of an RCP prototype on commodity hardware. Using traces of BGP and internal routing data from a Tier-1 backbone, we demonstrate that RCP is fast and reliable enough to drive the BGP routing decisions for a large network. We show that RCP assigns routes correctly, even when the functionality is replicated and distributed, and that networks using RCP can expect comparable convergence delays to those using today{\textquoteright}s iBGP architectures.}, url = {http://dl.acm.org/citation.cfm?id=1251203.1251205}, author = {Caesar,Matthew and Caldwell,Donald and Feamster, Nick and Rexford,Jennifer and Shaikh,Aman and van der Merwe,Jacobus} } @conference {18561, title = {Detecting BGP configuration faults with static analysis}, booktitle = {Proceedings of the 2nd conference on Symposium on Networked Systems Design \& Implementation - Volume 2}, series = {NSDI{\textquoteright}05}, year = {2005}, month = {2005///}, pages = {43 - 56}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {The Internet is composed of many independent autonomous systems (ASes) that exchange reachability information to destinations using the Border Gateway Protocol (BGP). Network operators in each AS configure BGP routers to control the routes that are learned, selected, and announced to other routers. Faults in BGP configuration can cause forwarding loops, packet loss, and unintended paths between hosts, each of which constitutes a failure of the Internet routing infrastructure. This paper describes the design and implementation of rcc, the router configuration checker, a tool that finds faults in BGP configurations using static analysis. rcc detects faults by checking constraints that are based on a high-level correctness specification. rcc detects two broad classes of faults: route validity faults, where routers may learn routes that do not correspond to usable paths, and path visibility faults, where routers may fail to learn routes for paths that exist in the network. rcc enables network operators to test and debug configurations before deploying them in an operational network, improving on the status quo where most faults are detected only during operation. rcc has been downloaded by more than sixty-five network operators to date, some of whom have shared their configurations with us. We analyze network-wide configurations from 17 different ASes to detect a wide variety of faults and use these findings to motivate improvements to the Internet routing infrastructure.}, url = {http://dl.acm.org/citation.cfm?id=1251203.1251207}, author = {Feamster, Nick and Balakrishnan,Hari} } @inbook {14211, title = {Detecting Independent 3D Movement}, booktitle = {Handbook of Geometric ComputingHandbook of Geometric Computing}, year = {2005}, month = {2005///}, pages = {383 - 401}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-540-28247-1}, url = {http://dx.doi.org/10.1007/3-540-28247-5_12}, author = {Corrochano,Eduardo Bayro and Ogale, Abhijit S. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {14175, title = {Discovering a language for human activity}, booktitle = {Proceedings of the AAAI 2005 Fall Symposium on Anticipatory Cognitive Embodied Systems, Washington, DC}, year = {2005}, month = {2005///}, author = {Guerra-Filho,G. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {18699, title = {Diverse polyubiquitin interaction properties of ubiquitin-associated domains}, journal = {Nature Structural \& Molecular Biology}, volume = {12}, year = {2005}, month = {2005///}, pages = {708 - 714}, abstract = {The ubiquitin-associated (UBA) domain occurs frequently in proteins involved in ubiquitin-dependent signaling pathways. Although polyubiquitin chain binding is considered to be a defining feature of the UBA domain family, the generality of this property has not been established. Here we have surveyed the polyubiquitin interaction properties of 30 UBA domains, including 16 of 17 occurrences in budding yeast. The UBA domains sort into four classes that include linkage-selective polyubiquitin binders and domains that bind different chains (and monoubiquitin) in a nondiscriminatory manner; one notable class (30\%) did not bind any ubiquitin ligand surveyed. The properties of a given UBA domain are conserved from yeast to mammals. Their functional relevance is further suggested by the ability of an ectopic UBA domain to alter the specificity of a deubiquitylating enzyme in a predictable manner. Conversely, non-UBA sequences can modulate the interaction properties of a UBA domain.}, keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation}, isbn = {1545-9993}, doi = {10.1038/nsmb962}, url = {http://www.nature.com/nsmb/journal/v12/n8/full/nsmb962.html}, author = {Raasi,Shahri and Varadan,Ranjani and Fushman, David and Pickart,Cecile M.} } @article {18545, title = {An empirical study of "bogon" route advertisements}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {35}, year = {2005}, month = {2005/01//}, pages = {63 - 70}, abstract = {An important factor in the robustness of the interdomain routing system is whether the routers in autonomous systems (ASes) filter routes for "bogon" address space---i.e., private address space and address space that has not been allocated by the Internet Assigned Numbers Authority (IANA). This paper presents an empirical study of bogon route announcements, as observed at eight vantage points on the Internet. On average, we observe several bogon routes leaked every few days; a small number of ASes also temporarily leak hundreds of bogon routes. About 40\% of these bogon routes are not withdrawn for at least a day. We observed 110 different ASes originating routes for bogon prefixes and a few ASes that were responsible for advertising a disproportionate number of these routes. We also find that some ASes that do filter unallocated prefixes continue to filter them for as long as five months after they have been allocated, mistakenly filtering valid routes. Both of these types of delinquencies have serious implications: the failure to filter valid prefixes can could make nefarious activities such as denial of service attacks difficult to trace; failure to update filters when new prefixes are allocated prevents legitimate routes from being globally visible.}, keywords = {anomalies, BGP, bogon prefixes}, isbn = {0146-4833}, doi = {10.1145/1052812.1052826}, url = {http://doi.acm.org/10.1145/1052812.1052826}, author = {Feamster, Nick and Jung,Jaeyeon and Balakrishnan,Hari} } @article {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 {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} } @conference {18571, title = {Geographic locality of IP prefixes}, booktitle = {Proceedings of the 5th ACM SIGCOMM conference on Internet Measurement}, series = {IMC {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {13 - 13}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Information about the geographic locality of IP prefixes can be useful for understanding the issues related to IP address allocation, aggregation, and BGP routing table growth. In this paper, we use traceroute data and geographic mappings of IP addresses to study the geographic properties of IP prefixes and their implications on Internet routing. We find that (1) IP prefixes may be too coarse-grained for expressing routing policies, (2) address allocation policies and the granularity of routing contribute significantly to routing table size, and (3) not considering the geographic diversity of contiguous prefixes may result in overestimating the opportunities for aggregation in the BGP routing table.}, url = {http://dl.acm.org/citation.cfm?id=1251086.1251099}, author = {Freedman,Michael J. and Vutukuru,Mythili and Feamster, Nick and Balakrishnan,Hari} } @article {18221, title = {Handling uneven embedding capacity in binary images: a revisit}, journal = {Proceedings of SPIE}, volume = {5681}, year = {2005}, month = {2005/03/21/}, pages = {194 - 205}, abstract = {Hiding data in binary images can facilitate the authentication and annotation of important document images in digital domain. A representative approach is to first identify pixels whose binary color can be flipped without introducing noticeable artifacts, and then embed one bit in each non-overlapping block by adjusting the flippable pixel values to obtain the desired block parity. The distribution of these flippable pixels is highly uneven across the image, which is handled by random shuffling in the literature. In this paper, we revisit the problem of data embedding for binary images and investigate the incorporation of a most recent steganography framework known as the wet paper coding to improve the embedding capacity. The wet paper codes naturally handle the uneven embedding capacity through randomized projections. In contrast to the previous approach, where only a small portion of the flippable pixels are actually utilized in the embedding, the wet paper codes allow for a high utilization of pixels that have high flippability score for embedding, thus giving a significantly improved embedding capacity than the previous approach. The performance of the proposed technique is demonstrated on several representative images. We also analyze the perceptual impact and capacity-robustness relation of the new approach.}, isbn = {0277786X}, doi = {doi:10.1117/12.587379}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/5681/1/194_1?isAuthorized=no}, author = {M. Wu and Fridrich,Jessica and Goljan,Miroslav and Gou,Hongmei} } @conference {18575, title = {Implications of autonomy for the expressiveness of policy routing}, booktitle = {Proceedings of the 2005 conference on Applications, technologies, architectures, and protocols for computer communications}, series = {SIGCOMM {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {25 - 36}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Thousands of competing autonomous systems must cooperate with each other to provide global Internet connectivity. Each autonomous system (AS) encodes various economic, business, and performance decisions in its routing policy. The current interdomain routing system enables each AS to express policy using rankings that determine how each router inthe AS chooses among different routes to a destination, and filters that determine which routes are hidden from each neighboring AS. Because the Internet is composed of many independent, competing networks, the interdomain routing system should provide autonomy, allowing network operators to set their rankings independently, and to have no constraints on allowed filters. This paper studies routing protocol stability under these conditions. We first demonstrate that certain rankings that are commonly used in practice may not ensure routing stability. We then prove that, when providers can set rankings and filters autonomously, guaranteeing that the routing system will converge to a stable path assignment essentially requires ASes to rank routes based on AS-path lengths. We discuss the implications of these results for the future of interdomain routing.}, keywords = {autonomy, BGP, Internet, policy, protocol, Routing, Safety, stability}, isbn = {1-59593-009-4}, doi = {10.1145/1080091.1080096}, url = {http://doi.acm.org/10.1145/1080091.1080096}, author = {Feamster, Nick and Johari,Ramesh and Balakrishnan,Hari} } @conference {14224, title = {Integration of motion fields through shape}, booktitle = {IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2005. CVPR 2005}, volume = {2}, year = {2005}, month = {2005/06/20/25}, pages = {663- 669 vol. 2 - 663- 669 vol. 2}, publisher = {IEEE}, organization = {IEEE}, abstract = {Structure from motion from single flow fields has been studied intensively, but the integration of information from multiple flow fields has not received much attention. Here we address this problem by enforcing constraints on the shape (surface normals) of the scene in view, as opposed to constraints on the structure (depth). The advantage of integrating shape is two-fold. First, we do not need to estimate feature correspondences over multiple frames, but we only need to match patches. Second, the shape vectors in the different views are related only by rotation. This constraint on shape can be combined easily with motion estimation, thus formulating motion and structure estimation from multiple views as a practical constrained minimization problem using a rank-3 constraint. Based on this constraint, we develop a 3D motion technique, which locates through color and motion segmentation, planar patches in the scene, matches patches over multiple frames, and estimates the motion between multiple frames and the shape of the selected scene patches using the image gradients. Experiments evaluate the accuracy of the 3D motion estimation and demonstrate the motion and shape estimation of the technique by super-resolving an image sequence.}, keywords = {3D motion estimation, Automation, CAMERAS, computational geometry, Computer vision, constrained minimization problem, decoupling translation from rotation, Educational institutions, image colour analysis, image gradients, image resolution, Image segmentation, image sequence, Image sequences, integration of motion fields, Layout, minimisation, Motion estimation, motion field integration, motion segmentation, parameter estimation, planar patches, rank-3 constraint, scene patches, SHAPE, shape and rotation, shape estimation, structure estimation}, isbn = {0-7695-2372-2}, doi = {10.1109/CVPR.2005.190}, author = {Ji,H. and Ferm{\"u}ller, Cornelia} } @article {14230, title = {Motion segmentation using occlusions}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {27}, year = {2005}, month = {2005/06//}, pages = {988 - 992}, abstract = {We examine the key role of occlusions in finding independently moving objects instantaneously in a video obtained by a moving camera with a restricted field of view. In this problem, the image motion is caused by the combined effect of camera motion (egomotion), structure (depth), and the independent motion of scene entities. For a camera with a restricted field of view undergoing a small motion between frames, there exists, in general, a set of 3D camera motions compatible with the observed flow field even if only a small amount of noise is present, leading to ambiguous 3D motion estimates. If separable sets of solutions exist, motion-based clustering can detect one category of moving objects. Even if a single inseparable set of solutions is found, we show that occlusion information can be used to find ordinal depth, which is critical in identifying a new class of moving objects. In order to find ordinal depth, occlusions must not only be known, but they must also be filled (grouped) with optical flow from neighboring regions. We present a novel algorithm for filling occlusions and deducing ordinal depth under general circumstances. Finally, we describe another category of moving objects which is detected using cardinal comparisons between structure from motion and structure estimates from another source (e.g., stereo).}, keywords = {3D motion estimation, algorithms, Artificial intelligence, CAMERAS, Computer vision, Filling, hidden feature removal, Image Enhancement, Image Interpretation, Computer-Assisted, image motion, Image motion analysis, Image segmentation, Layout, MOTION, Motion detection, Motion estimation, motion segmentation, Movement, Object detection, occlusion, occlusions, optical flow, ordinal depth, Pattern Recognition, Automated, Photography, Reproducibility of results, segmentation, Semiconductor device modeling, Sensitivity and Specificity, video analysis., Video Recording}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2005.123}, author = {Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @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.} } @conference {14341, title = {Seeking the source: software source code as a social and technical artifact}, booktitle = {Proceedings of the 2005 international ACM SIGGROUP conference on Supporting group work}, series = {GROUP {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {197 - 206}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {data mining, social networks, socio-technical systems, software repositories}, isbn = {1-59593-223-2}, doi = {10.1145/1099203.1099239}, url = {http://doi.acm.org/10.1145/1099203.1099239}, author = {de Souza,Cleidson and Jon Froehlich and Dourish,Paul} } @article {18600, title = {Stable Policy Routing with Provider Independence}, volume = {MIT-CSAIL-TR-2005-009}, year = {2005}, month = {2005/02/08/}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {Thousands of competing autonomous systems (ASes) mustcooperate with each other to provide global Internet connectivity.These ASes encode various economic, business,and performance decisions in their routing policies. The currentinterdomain routing system enables ASes to express policyusing rankings that determine how each router in an ASorders the different routes to a destination, and filters thatdetermine which routes are hidden from each neighboringAS. Since the Internet is composed of many independent,competing networks, the interdomain routing system shouldallow providers to set their rankings independently, and tohave no constraints on allowed filters. This paper studiesrouting protocol stability under these constraints. We firstdemonstrate that certain rankings that are commonly usedin practice may not ensure routing stability. We then provethat, with ranking independence and unrestricted filtering,guaranteeing that the routing system will converge to a stablepath assignment essentially requires ASes to rank routesbased on AS-path lengths. Finally, we discuss the implicationsof these results for the future of interdomain routing.}, url = {http://dspace.mit.edu/handle/1721.1/30522}, author = {Feamster, Nick and Johari,Ramesh and Balakrishnan,Hari} } @article {18718, title = {Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain}, journal = {Molecular Cell}, volume = {18}, year = {2005}, month = {2005/06/10/}, pages = {687 - 698}, abstract = {SummaryAlthough functional diversity in polyubiquitin chain signaling has been ascribed to the ability of differently linked chains to bind in a distinctive manner to effector proteins, structural models of such interactions have been lacking. Here, we use NMR to unveil the structural basis of selective recognition of Lys48-linked di- and tetraubiquitin chains by the UBA2 domain of hHR23A. Although the interaction of UBA2 with Lys48-linked diubiquitin involves the same hydrophobic surface on each ubiquitin unit as that utilized in monoubiquitin:UBA complexes, our results show how the {\textquotedblleft}closed{\textquotedblright} conformation of Lys48-linked diubiquitin is crucial for high-affinity binding. Moreover, recognition of Lys48-linked diubiquitin involves a unique epitope on UBA, which allows the formation of a sandwich-like diubiqutin:UBA complex. Studies of the UBA-tetraubiquitin interaction suggest that this mode of UBA binding to diubiquitin is relevant for longer chains. }, isbn = {1097-2765}, doi = {10.1016/j.molcel.2005.05.013}, url = {http://www.sciencedirect.com/science/article/pii/S1097276505013195}, author = {Varadan,Ranjani and Assfalg,Michael and Raasi,Shahri and Pickart,Cecile and Fushman, David} } @article {14072, title = {Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock}, journal = {Environmental Microbiology}, volume = {7}, year = {2005}, month = {2005/06/01/}, pages = {789 - 797}, abstract = {Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85{\textdegree}C to 65{\textdegree}C and 95{\textdegree}C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95{\textdegree}C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an α subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65{\textdegree}C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18~kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.}, isbn = {1462-2920}, doi = {10.1111/j.1462-2920.2005.00751.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2005.00751.x/abstract}, author = {Boonyaratanakornkit,Boonchai B and Simpson,Anjana J. and Whitehead,Timothy A and Fraser,Claire M. and El-Sayed, Najib M. and Clark,Douglas S} } @conference {14752, title = {Understanding source code evolution using abstract syntax tree matching}, booktitle = {Proceedings of the 2005 international workshop on Mining software repositories}, series = {MSR {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {1 - 5}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Mining software repositories at the source code level can provide a greater understanding of how software evolves. We present a tool for quickly comparing the source code of different versions of a C program. The approach is based on partial abstract syntax tree matching, and can track simple changes to global variables, types and functions. These changes can characterize aspects of software evolution useful for answering higher level questions. In particular, we consider how they could be used to inform the design of a dynamic software updating system. We report results based on measurements of various versions of popular open source programs. including BIND, OpenSSH, Apache, Vsftpd and the Linux kernel.}, keywords = {abstract syntax trees, software evolution, source code analysis}, isbn = {1-59593-123-6}, doi = {10.1145/1082983.1083143}, url = {http://doi.acm.org/10.1145/1082983.1083143}, author = {Neamtiu,Iulian and Foster, Jeffrey S. and Hicks, Michael W.} } @inbook {18726, title = {Using NMR Spectroscopy to Monitor Ubiquitin Chain Conformation and Interactions with Ubiquitin-Binding Domains}, booktitle = {Ubiquitin and Protein Degradation, Part B}, volume = {Volume 399}, year = {2005}, month = {2005///}, pages = {177 - 192}, publisher = {Academic Press}, organization = {Academic Press}, abstract = {Polyubiquitin (polyUb) chains function as signaling molecules that mediate a diverse set of cellular events. The outcome of polyubiquitination depends on the specific linkage between Ub moieties in the chain, and differently linked chains function as distinct intracellular signals. Although an increasing number of Ub-binding proteins that transmit the regulatory information conferred by (poly)ubiquitination have been identified, the molecular mechanisms of linkage-specific signaling and recognition still remain to be understood. Knowledge of the chain structure is expected to provide insights into the basis of diversity in polyUb signaling. Here we describe several NMR approaches aimed at determining the physiological conformation of polyUb and characterization of the chains{\textquoteright} interactions with ubiquitin-binding proteins.}, isbn = {0076-6879}, url = {http://www.sciencedirect.com/science/article/pii/S0076687905990125}, author = {Varadan,Ranjani and Assfalg,Michael and Fushman, David}, editor = {Deshaies,Raymond J.} } @article {17803, title = {An algebra for powerpoint sources}, journal = {Multimedia Tools and Applications}, volume = {24}, year = {2004}, month = {2004///}, pages = {273 - 301}, abstract = {There are now millions of PowerPoint documents available within corporate intranets and/or over the Internet. In this paper, we develop a formal model of PowerPoint databases. We propose a relational style algebra called pptA (PowerPoint Algebra) to query PowerPoint databases. The algebra contains some new operators (such as the APPLY operator that changes properties of objects, slides and presentations) as well as interesting twists on relational operators (e.g. join and cartesian product allow different entities being joined together to share attributes whose values may be merged). We prove a set of equivalence results within this algebra. We have implemented a version of pptA{\textemdash}the paper provides a cost model and experimental results on the conditions under which these equivalences are useful.}, doi = {10.1023/B:MTAP.0000039422.87260.52}, author = {Fayzullin,M. and V.S. Subrahmanian} } @article {14263, title = {The Argus eye: a new imaging system designed to facilitate robotic tasks of motion}, journal = {IEEE Robotics \& Automation Magazine}, volume = {11}, year = {2004}, month = {2004/12//}, pages = {31 - 38}, abstract = {This article describes an imaging system that has been designed to facilitate robotic tasks of motion. The system consists of a number of cameras in a network, arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and, consequently, the estimation of shape models from the individual cameras. The reason is, inherent ambiguities of confusion between translation and rotation disappear. Pairs of cameras may also be arranged in multiple stereo configurations, which provide additional advantages for segmentation. Algorithms for the calibration of the system and the three-dimensional (3-D) motion estimation are provided.}, keywords = {Argus eye, Calibration, CAMERAS, computational geometry, Design automation, Eyes, image formation, imaging system, Information geometry, Layout, Motion estimation, multiple stereo configurations, panoramic robots, robot vision, Robot vision systems, robotic motion tasks, Robotics and automation, SHAPE, shape model estimation, system calibration}, isbn = {1070-9932}, doi = {10.1109/MRA.2004.1371606}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia} } @article {14167, title = {The Argus eye, a new tool for robotics}, journal = {IEEE Robotics and Automation Magazine}, volume = {11}, year = {2004}, month = {2004///}, pages = {31 - 38}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {13508, title = {Automatic recognition of spontaneous speech for access to multilingual oral history archives}, journal = {IEEE Transactions on Speech and Audio Processing, Special Issue on Spontaneous Speech Processing}, volume = {12}, year = {2004}, month = {2004/07//}, pages = {420 - 435}, abstract = {The MALACH project has the goal of developing the technologies needed to facilitate access to large collections of spontaneous speech. Its aim is to dramatically improve the state of the art in key Automatic Speech Recognition (ASR), Natural Language Processing (NLP) technologies for use in large-scale retrieval systems. The project leverages a unique collection of oral history interviews with survivors of the Holocaust that has been assembled and extensively annotated by the Survivors of the Shoah Visual History Foundation. This paper describes the collection, 116,000 hours of interviews in 32 languages, and the way in which system requirements have been discerned through user studies. It discusses ASR methods for very difficult speech (heavily accented, emotional, and elderly spontaneous speech), including transcription to create training data and methods for language modeling and speaker adaptation. Results are presented for for English and Czech. NLP results are presented for named entity tagging, topic segmentation, and supervised topic classification, and the architecture of an integrated search system that uses these results is described.}, author = {Byrne,W. and David Doermann and Franz,M. and Gustman,S. and Hajic,J. and Oard, Douglas and Picheny,M. and Psutka,J. and Ramabhadran,B.} } @inbook {14203, title = {Bias in Shape Estimation}, booktitle = {Computer Vision - ECCV 2004Computer Vision - ECCV 2004}, series = {Lecture Notes in Computer Science}, volume = {3023}, year = {2004}, month = {2004///}, pages = {405 - 416}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper analyses the uncertainty in the estimation of shape from motion and stereo. It is shown that there are computational limitations of a statistical nature that previously have not been recognized. Because there is noise in all the input parameters, we cannot avoid bias. The analysis rests on a new constraint which relates image lines and rotation to shape. Because the human visual system has to cope with bias as well, it makes errors. This explains the underestimation of slant found in computational and psychophysical experiments, and demonstrated here for an illusory display. We discuss properties of the best known estimators with regard to the problem, as well as possible avenues for visual systems to deal with the bias.}, isbn = {978-3-540-21982-8}, url = {http://dx.doi.org/10.1007/978-3-540-24672-5_32}, author = {Hui Ji and Ferm{\"u}ller, Cornelia}, editor = {Pajdla,Tom{\'a}{\v s} and Matas,Jir{\'\i}} } @conference {14550, title = {Bidimensional Parameters and Local Treewidth}, booktitle = {Latin 2004: Theoretical Informatics: 6th Latin American Symposium, Buenos Aires, Argentina, April 5-8, 2004: Proceedings}, year = {2004}, month = {2004///}, pages = {109 - 109}, author = {Fomin,E. D.D.F.V and Hajiaghayi, Mohammad T. and Thilikos,D. M} } @conference {18552, title = {BorderGuard: detecting cold potatoes from peers}, booktitle = {Proceedings of the 4th ACM SIGCOMM conference on Internet measurement}, series = {IMC {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {213 - 218}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Internet Service Providers often establish contractual "peering" agreements, where they agree to forward traffic to each other{\textquoteright}s customers at no cost. Consistent route advertisement at all peering points is a common provision in these agreements, because it gives an AS the flexibility to select egress points for the traffic (e.g., performing "hot potato" routing). Verifying "consistent export" is challenging because route advertisements are exchanged at multiple peering points and may be modified by routing policies. In this paper, we propose two algorithms to detect inconsistent routes using routing and configuration data from an AS{\textquoteright}s border routers. The first algorithm requires access to all eBGP routes advertised by a peer. Because this data is often unavailable, we propose another algorithm that detects inconsistencies using readily available data. We have applied our algorithms to the routes advertised by the peers of AT\&T{\textquoteright}s commercial IP backbone. Although a peer may intentionally send inconsistent advertisements to prevent its neighbor from performing hot-potato routing, we also discuss several configuration scenarios where a peer may inadvertently advertise inconsistent routes, despite having consistent export policies. Finally, we explain how simple modifications to the routers could make detection of inconsistent advertisements much easier than it is today.}, keywords = {anomalies, BGP, inconsistent advertisement, peering}, isbn = {1-58113-821-0}, doi = {10.1145/1028788.1028815}, url = {http://doi.acm.org/10.1145/1028788.1028815}, author = {Feamster, Nick and Mao,Zhuoqing Morley and Rexford,Jennifer} } @conference {15901, title = {Building an information retrieval test collection for spontaneous conversational speech}, booktitle = {Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {41 - 48}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Test collections model use cases in ways that facilitate evaluation of information retrieval systems. This paper describes the use of search-guided relevance assessment to create a test collection for retrieval of spontaneous conversational speech. Approximately 10,000 thematically coherent segments were manually identified in 625 hours of oral history interviews with 246 individuals. Automatic speech recognition results, manually prepared summaries, controlled vocabulary indexing, and name authority control are available for every segment. Those features were leveraged by a team of four relevance assessors to identify topically relevant segments for 28 topics developed from actual user requests. Search-guided assessment yielded sufficient inter-annotator agreement to support formative evaluation during system development. Baseline results for ranked retrieval are presented to illustrate use of the collection.}, keywords = {assessment, Automatic speech recognition, oral history, search-guided relevance}, isbn = {1-58113-881-4}, doi = {10.1145/1008992.1009002}, url = {http://doi.acm.org/10.1145/1008992.1009002}, author = {Oard, Douglas and Soergel,Dagobert and David Doermann and Huang,Xiaoli and Murray,G. Craig and Wang,Jianqiang and Ramabhadran,Bhuvana and Franz,Martin and Gustman,Samuel and Mayfield,James and Kharevych,Liliya and Strassel,Stephanie} } @conference {18602, title = {The case for separating routing from routers}, booktitle = {Proceedings of the ACM SIGCOMM workshop on Future directions in network architecture}, series = {FDNA {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {5 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Over the past decade, the complexity of the Internet{\textquoteright}s routing infrastructure has increased dramatically. This complexity and the problems it causes stem not just from various new demands made of the routing infrastructure, but also from fundamental limitations in the ability of today{\textquoteright}s distributed infrastructure to scalably cope with new requirements.The limitations in today{\textquoteright}s routing system arise in large part from the fully distributed path-selection computation that the IP routers in an autonomous system (AS) must perform. To overcome this weakness, interdomain routing should be separated from today{\textquoteright}s IP routers, which should simply forward packets (for the most part). Instead, a separate Routing Control Platform (RCP) should select routes on behalf of the IP routers in each AS and exchange reachability information with other domains.Our position is that an approach like RCP is a good way of coping with complexity while being responsive to new demands and can lead to a routing system that is substantially easier to manage than today. We present a design overview of RCP based on three architectural principles path computation based on a consistent view of network state, controlled interactions between routing protocol layers, and expressive specification of routing policies and discuss the architectural strengths and weaknesses of our proposal.}, keywords = {BGP, interdomain routing, routing architecture}, isbn = {1-58113-942-X}, doi = {10.1145/1016707.1016709}, url = {http://doi.acm.org/10.1145/1016707.1016709}, author = {Feamster, Nick and Balakrishnan,Hari and Rexford,Jennifer and Shaikh,Aman and van der Merwe,Jacobus} } @inbook {18696, title = {Characterization of the Overall Rotational Diffusion of a Protein From 15N Relaxation Measurements and Hydrodynamic Calculations}, booktitle = {Protein NMR Techniques}, series = {Methods in Molecular Biology}, volume = {278}, year = {2004}, month = {2004///}, pages = {139 - 159}, publisher = {Humana Press}, organization = {Humana Press}, abstract = {In this chapter, we discuss experimental and theoretical methods for characterizing the overall rotational diffusion of molecules in solution. The methods are illustrated for the B3 domain of protein G, a small protein with rotational anisotropy of D par / D perp = 1.4. The rotational diffusion tensor of the protein is determined directly from 15 N relaxation measurements. The experimental data are treated assuming various possible models for the overall tumbling: isotropic, axially symmetric, and fully anisotropic, and the results of these analyses are compared to determine an adequate diffusion model for the protein. These experimentally derived characteristics of the protein are compared with the results of theoretical calculations of the diffusion tensor using various hydrodynamic models, to find optimal models and parameter sets for theoretical predictions. We also derive model-free characteristics of internal backbone motions in the protein, to show that different models for the overall motion can result in significantly different pictures of motion. This emphasizes the necessity of accurately characterizing the overall tumbling of a molecule to determine its local dynamics.}, keywords = {Biomedical and Life Sciences}, isbn = {978-1-59259-809-0}, url = {http://www.springerlink.com/content/h6w35487x3q1g6x7/abstract/}, author = {Blake-Hall,Jennifer and Walker,Olivier and Fushman, David}, editor = {Downing,A. Kristina and Walker,John M.} } @conference {14289, title = {A comparison of bug finding tools for Java}, booktitle = {Software Reliability Engineering, 2004. ISSRE 2004. 15th International Symposium on}, year = {2004}, month = {2004///}, pages = {245 - 256}, author = {Rutar,N. and Almazan,C.B. and Foster, Jeffrey S.} } @conference {14209, title = {Compound eye sensor for 3D ego motion estimation}, booktitle = {2004 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2004. (IROS 2004). Proceedings}, volume = {4}, year = {2004}, month = {2004/10/28/Sept.}, pages = {3712- 3717 vol.4 - 3712- 3717 vol.4}, publisher = {IEEE}, organization = {IEEE}, abstract = {We describe a compound eye vision sensor for 3D ego motion computation. Inspired by eyes of insects, we show that the compound eye sampling geometry is optimal for 3D camera motion estimation. This optimality allows us to estimate the 3D camera motion in a scene-independent and robust manner by utilizing linear equations. The mathematical model of the new sensor can be implemented in analog networks resulting in a compact computational sensor for instantaneous 3D ego motion measurements in full six degrees of freedom.}, keywords = {3D camera motion estimation, CAMERAS, compound eye vision sensor, Computer vision, Equations, Eyes, Geometry, Image sensors, Insects, linear equations, Motion estimation, robot vision, Robustness, sampling geometry, Sampling methods, Sensor phenomena and characterization}, isbn = {0-7803-8463-6}, doi = {10.1109/IROS.2004.1389992}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J. and Brajovic,V.} } @conference {12069, title = {Copilot - a coprocessor-based kernel runtime integrity monitor}, booktitle = {Proceedings of the 13th conference on USENIX Security Symposium - Volume 13}, series = {SSYM{\textquoteright}04}, year = {2004}, month = {2004///}, pages = {13 - 13}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {San Diego, CA}, abstract = {Copilot is a coprocessor-based kernel integrity monitor for commodity systems. Copilot is designed to detect malicious modifications to a host{\textquoteright}s kernel and has correctly detected the presence of 12 real-world rootkits, each within 30 seconds of their installation with less than a 1\% penalty to the host{\textquoteright}s performance. Copilot requires no modifications to the protected host{\textquoteright}s software and can be expected to operate correctly even when the host kernel is thoroughly compromised - an advantage over traditional monitors designed to run on the host itself.}, keywords = {design, management, MONITORS, Security, security and protection}, url = {http://portal.acm.org/citation.cfm?id=1251375.1251388}, author = {Petroni,Jr. and Fraser,Timothy and Molina,Jesus and Arbaugh, William A.} } @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.} } @inbook {12943, title = {Free-Living to Freewheeling: The Evolution of Vibrio cholerae from Innocence to Infamy}, booktitle = {Infectious Disease and Host-Pathogen EvolutionInfectious Disease and Host-Pathogen Evolution}, year = {2004}, month = {2004///}, pages = {198 - 198}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, isbn = {9780521820660}, author = {Rita R Colwell and Faruque,S. M. and Nair,G. B.}, editor = {Dronamraju,Krishna R.} } @article {15179, title = {A generic construction for intrusion-resilient public-key encryption}, journal = {Topics in Cryptology{\textendash}CT-RSA 2004}, year = {2004}, month = {2004///}, pages = {1997 - 1997}, abstract = {In an intrusion-resilient cryptosystem [10], two entities (a user and a base) jointly evolve a secret decryption key; this provides very strong protection against an active attacker who can break into the user and base repeatedly and even simultaneously. Recently, a construction of an intrusion-resilient public-key encryption scheme based on specific algebraic assumptions has been shown [6]. We generalize this previous work and present a more generic construction for intrusion-resilient public-key encryption from any forward-secure public-key encryption scheme satisfying a certain homomorphic property.}, doi = {10.1007/978-3-540-24660-2_7}, author = {Dodis,Y. and Franklin,M. and Katz, Jonathan and Miyaji,A. and Yung,M.} } @article {14184, title = {A hierarchy of cameras for 3D photography}, journal = {Computer Vision and Image Understanding}, volume = {96}, year = {2004}, month = {2004/12//}, pages = {274 - 293}, abstract = {The view-independent visualization of 3D scenes is most often based on rendering accurate 3D models or utilizes image-based rendering techniques. To compute the 3D structure of a scene from a moving vision sensor or to use image-based rendering approaches, we need to be able to estimate the motion of the sensor from the recorded image information with high accuracy, a problem that has been well-studied. In this work, we investigate the relationship between camera design and our ability to perform accurate 3D photography, by examining the influence of camera design on the estimation of the motion and structure of a scene from video data. By relating the differential structure of the time varying plenoptic function to different known and new camera designs, we can establish a hierarchy of cameras based upon the stability and complexity of the computations necessary to estimate structure and motion. At the low end of this hierarchy is the standard planar pinhole camera for which the structure from motion problem is non-linear and ill-posed. At the high end is a camera, which we call the full field of view polydioptric camera, for which the motion estimation problem can be solved independently of the depth of the scene which leads to fast and robust algorithms for 3D Photography. In between are multiple view cameras with a large field of view which we have built, as well as omni-directional sensors.}, keywords = {Camera design, Multi-view geometry, Polydioptric cameras, Spatio-temporal image analysis, structure from motion}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2004.03.013}, url = {http://www.sciencedirect.com/science/article/pii/S1077314204000505}, author = {Neumann, Jan and Ferm{\"u}ller, Cornelia and Aloimonos, 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 {16121, title = {Les le{\c c}ons tir{\'e}es des deux comp{\'e}titions de visualisation d{\textquoteright}information}, booktitle = {Proceedings of the 16th conference on Association Francophone d{\textquoteright}Interaction Homme-Machine}, series = {IHM 2004}, year = {2004}, month = {2004///}, pages = {7 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Information visualization needs benchmarks to carry on. A benchmark is aimed at comparing information visualization techniques or systems. A benchmark is made of a dataset, a list of tasks mostly based on finding facts about the dataset, and a list of interesting or important findings about the datasets (the nuggets to find). For the second year, we are organizing the InfoVis Contest aimed at collecting results for benchmarks. We describe here the main lessons we learned.}, keywords = {benchmark, contest, Evaluation, Information Visualization}, isbn = {1-58113-926-8}, doi = {10.1145/1148613.1148616}, url = {http://doi.acm.org/10.1145/1148613.1148616}, author = {Fekete,Jean-Daniel and Plaisant, Catherine} } @conference {18580, title = {Location diversity in anonymity networks}, booktitle = {Proceedings of the 2004 ACM workshop on Privacy in the electronic society}, series = {WPES {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {66 - 76}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Anonymity networks have long relied on diversity of node location for protection against attacks---typically an adversary who can observe a larger fraction of the network can launch a more effective attack. We investigate the diversity of two deployed anonymity networks, Mixmaster and Tor, with respect to an adversary who controls a single Internet administrative domain. Specifically, we implement a variant of a recently proposed technique that passively estimates the set of administrative domains (also known as autonomous systems, or ASes) between two arbitrary end-hosts without having access to either end of the path. Using this technique, we analyze the AS-level paths that are likely to be used in these anonymity networks. We find several cases in each network where multiple nodes are in the same administrative domain. Further, many paths between nodes, and between nodes and popular endpoints, traverse the same domain.}, keywords = {anonymity, interdomain routing, mix networks}, isbn = {1-58113-968-3}, doi = {10.1145/1029179.1029199}, url = {http://doi.acm.org/10.1145/1029179.1029199}, author = {Feamster, Nick and Dingledine,Roger} } @article {18512, title = {Managing the 802.11 energy/performance tradeoff with machine learning}, volume = {MIT-CSAIL-TR-2004-068}, year = {2004}, month = {2004///}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {This paper addresses the problem of managing the tradeoff betweenenergy consumption and performance in wireless devices implementingthe IEEE 802.11 standard. To save energy, the 802.11 specificationproposes a power-saving mode (PSM), where a device can sleep to saveenergy, periodically waking up to receive packets from a neighbor(e.g., an access point) that may have buffered packets for thesleeping device. Previous work has shown that a fixed polling time forwaking up degrades the performance of Web transfers, because networkactivity is bursty and time-varying. We apply a new online machinelearning algorithm to this problem and show, using ns simulation andtrace analysis, that it is able to adapt well to network activity. Thelearning process makes no assumptions about the underlying networkactivity being stationary or even Markov. Our learning power-savingalgorithm, LPSM, guides the learning using a "loss function" thatcombines the increased latency from potentially sleeping too long andthe wasted use of energy in waking up too soon. In our nssimulations, LPSM saved 7\%-20\% more energy than 802.11 in power-savingmode, with an associated increase in average latency by a factor of1.02, and not more than 1.2. LPSM is straightforward to implementwithin the 802.11 PSM framework.}, url = {http://hdl.handle.net/1721.1/30499}, author = {Monteleoni,C. and Balakrishnan,H. and Feamster, Nick and Jaakkola,T.} } @article {16334, title = {Measuring HPC productivity}, journal = {International Journal of High Performance Computing Applications}, volume = {18}, year = {2004}, month = {2004///}, pages = {459 - 473}, author = {Faulk,S. and Gustafson,J. and Johnson,P. and Porter, Adam and Tichy,W. and Votta,L.} } @conference {13902, title = {Mixing ideas: a new technique for working with young children as design partners}, booktitle = {Proceedings of the 2004 conference on Interaction design and children: building a community}, year = {2004}, month = {2004///}, pages = {35 - 42}, author = {Guha,M.L. and Druin, Allison and Chipman,G. and Fails,J. A and Simms,S. and Farber,A.} } @article {18542, title = {A model of BGP routing for network engineering}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {32}, year = {2004}, month = {2004/06//}, pages = {331 - 342}, abstract = {The performance of IP networks depends on a wide variety of dynamic conditions. Traffic shifts, equipment failures, planned maintenance, and topology changes in other parts of the Internet can all degrade performance. To maintain good performance, network operators must continually reconfigure the routing protocols. Operators configure BGP to control how traffic flows to neighboring Autonomous Systems (ASes), as well as how traffic traverses their networks. However, because BGP route selection is distributed, indirectly controlled by configurable policies, and influenced by complex interactions with intradomain routing protocols, operators cannot predict how a particular BGP configuration would behave in practice. To avoid inadvertently degrading network performance, operators need to evaluate the effects of configuration changes before deploying them on a live network. We propose an algorithm that computes the outcome of the BGP route selection process for each router in a single AS, given only a static snapshot of the network state, without simulating the complex details of BGP message passing. We describe a BGP emulator based on this algorithm; the emulator exploits the unique characteristics of routing data to reduce computational overhead. Using data from a large ISP, we show that the emulator correctly computes BGP routing decisions and has a running time that is acceptable for many tasks, such as traffic engineering and capacity planning.}, keywords = {BGP, modeling, Routing, traffic engineering}, isbn = {0163-5999}, doi = {10.1145/1012888.1005726}, url = {http://doi.acm.org/10.1145/1012888.1005726}, author = {Feamster, Nick and Winick,Jared and Rexford,Jennifer} } @article {18520, title = {Modeling BGP route selection within an AS}, journal = {IEEE/ACM Transactions on Networking}, year = {2004}, month = {2004///}, abstract = {This paper presents a provably correct model that computes the out-come of the BGP decision process for each router in a single AS, without simulating the complex details of BGP message passing. The model requires only static inputs that can be easily obtained from the routers: the set of candidate routes to a destination (and the routers in the AS at which they were learned), import policies and other session-level parameters, and internal topology. We pro- pose algorithms for computing route selection under four different network configurations: with the MED attribute compared across all routes, and compared only across routes from the same neigh- boring AS; and with a {\textquotedblleft}full mesh{\textquotedblright} internal BGP (iBGP) topology versus an iBGP topology that uses a scalability technique called {\textquotedblleft}route reflection{\textquotedblright}. For each scenario, we derive general properties of the routes that routers ultimately select, present an efficient al- gorithm for computing the outcome of BGP route selection, and prove the algorithm{\textquoteright}s correctness. Studying the general properties and computational overhead of modeling the route selection pro- cess in each of these cases provides insights into the unnecessary complexity introduced by the MED attribute and route reflection; we use these insights to propose improvements to BGP that achieve the same goals as MED and route reflection without introducing the negative side effects of these features. We have implemented some of the algorithms from this paper in a prototype and have shown them to be efficient and accurate enough for many traffic engineer- ing tasks. }, author = {Feamster, Nick and Rexford,J.} } @inbook {13830, title = {Multi-align: Combining Linguistic and Statistical Techniques to Improve Alignments for Adaptable MT}, booktitle = {Machine Translation: From Real Users to ResearchMachine Translation: From Real Users to Research}, series = {Lecture Notes in Computer Science}, volume = {3265}, year = {2004}, month = {2004///}, pages = {17 - 26}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {An adaptable statistical or hybrid MT system relies heavily on the quality of word-level alignments of real-world data. Statistical alignment approaches provide a reasonable initial estimate for word alignment. However, they cannot handle certain types of linguistic phenomena such as long-distance dependencies and structural differences between languages. We address this issue in Multi-Align, a new framework for incremental testing of different alignment algorithms and their combinations. Our design allows users to tune their systems to the properties of a particular genre/domain while still benefiting from general linguistic knowledge associated with a language pair. We demonstrate that a combination of statistical and linguistically-informed alignments can resolve translation divergences during the alignment process.}, isbn = {978-3-540-23300-8}, url = {http://dx.doi.org/10.1007/978-3-540-30194-3_3}, author = {Ayan,Necip and Dorr, Bonnie J and Habash,Nizar}, editor = {Frederking,Robert and Taylor,Kathryn} } @article {18709, title = {Polyubiquitin chains: polymeric protein signals}, journal = {Current Opinion in Chemical Biology}, volume = {8}, year = {2004}, month = {2004/12//}, pages = {610 - 616}, abstract = {The 76-residue protein ubiquitin exists within eukaryotic cells both as a monomer and in the form of isopeptide-linked polymers called polyubiquitin chains. In two well-described cases, structurally distinct polyubiquitin chains represent functionally distinct intracellular signals. Recently, additional polymeric structures have been detected in vivo and in vitro, and several large families of proteins with polyubiquitin chain-binding activity have been discovered. Although the molecular mechanisms governing specificity in chain synthesis and recognition are still incompletely understood, the scope of signaling by polyubiquitin chains is likely to be broader than originally envisioned.}, isbn = {1367-5931}, doi = {10.1016/j.cbpa.2004.09.009}, url = {http://www.sciencedirect.com/science/article/pii/S1367593104001413}, author = {Pickart,Cecile M. and Fushman, David} } @article {18595, title = {Practical verification techniques for wide-area routing}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {34}, year = {2004}, month = {2004/01//}, pages = {87 - 92}, abstract = {Protocol and system designers use verification techniques to analyze a system{\textquoteright}s correctness properties. Network operators need verification techniques to ensure the "correct" operation of BGP. BGP{\textquoteright}s distributed dependencies cause small configuration mistakes or oversights to spur complex errors, which sometimes have devastating effects on global connectivity. These errors are often difficult to debug because they are sometimes only exposed by a specific message arrival pattern or failure scenario.This paper presents an approach to BGP verification that is primarily based on static analysis of router configuration. We argue that: (1) because BGP{\textquoteright}s a configuration affects its fundamental behavior, verification is a program analysis problem, (2) BGP{\textquoteright}s complex, dynamic interactions are difficult to abstract and impossible to enumerate, which precludes existing verification techniques, (3) because of BGP{\textquoteright}s flexible, policy-based configuration, some aspects of BGP configuration must be checked against a higher-level specification of intended policy, and (4) although static analysis can catch many configuration errors, simulation and emulation are also necessary to determine the precise scenarios that could expose errors at runtime. Based on these observations, we propose the design of a BGP verification tool, discuss how it could be applied in practice, and describe future research challenges.}, isbn = {0146-4833}, doi = {10.1145/972374.972390}, url = {http://doi.acm.org/10.1145/972374.972390}, author = {Feamster, Nick} } @inbook {18019, title = {PRAM-On-Chip: A Quest for Not-So-Obvious Non-obviousness}, booktitle = {Mathematical Foundations of Computer Science 2004Mathematical Foundations of Computer Science 2004}, series = {Lecture Notes in Computer Science}, volume = {3153}, year = {2004}, month = {2004///}, pages = {104 - 105}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Consider situations where once you were told about a new technical idea you reacted by saying: {\textquotedblleft}but this is so obvious, I wonder how I missed it{\textquotedblright}. I found out recently that the US patent law has a nice formal way of characterizing such a situation. The US patent law protects inventions that meet three requirements: utility, novelty and non-obviousness. Non-obviousness is considered the most challenging of the three to establish. The talk will try to argue that a possible virtue for a technical contribution is when, in restrospect, its non-obviousness is not too obvious; and since hindsight is always 20/20, one may often need to resort to various types of circumstantial evidence in order to establish non-obviousness. There are two reasons for bringing this issue up in my talk: (i) seeking such a virtue has been an objective of my work over the years, and (ii) issues of taste in research are more legitimate for invited talks; there might be merit in reminding younger researchers that not every {\textquotedblleft}result{\textquotedblright} is necessarily also a {\textquotedblleft}contribution{\textquotedblright}; perhaps the criterion of not-so-obvious non-obviousness could be helpful in some cases to help recognize a contribution. The focus of the second focal point for my talk, the PRAM-On-Chip approach, meets at least one of the standard legal ways to support non-obviousness: {\textquotedblleft}Expressions of disbelief by experts constitute strong evidence of non-obviousness{\textquotedblright}. It is well documented that the whole PRAM algorithmic theory was considered {\textquotedblleft}unrealistic{\textquotedblright} by numerous experts in the field, prior to the PRAM-On-Chip project. In fact, I needed recently to use this documentation in a reply to the U.S. patent office. An introduction of the PRAM-On-Chip approach follows. Many parallel computer systems architectures have been proposed and built over the last several decades. The outreach of the few that survived has been severely limited due to their programmability problems. The question of how to think algorithmically in parallel has been the fundamental problem for which these architectures did not have an adequate answer. A computational model, the Parallel Random Access Model (PRAM), has been developed by numerous (theoretical computer science) algorithm researchers to address this question during the 1980s and 1990s and is considered by many as the easiest known approach to parallel programming. Despite the broad interest the PRAM generated, it had not been possible to build parallel machines that adequately support it using multi-chip multiprocessors, the only multiprocessors that were buildable in the 1990s since low-overhead coordination was not possible. Our main insight is that this is becoming possible with the increasing amounts of hardware that can be placed on a single chip. From the PRAM, as a starting point, a highly parallel explicit multi-threaded (XMT) on-chip processor architecture that relies on new low-overhead coordination mechanisms and whose performance objective is reducing single task completion time has been conceived and developed. Simulated program executions have shown dramatic performance gains over conventional processor architectures. Namely, in addition to the unique parallel programmability features, which set XMT apart from any other current approach, XMT also provides very competitive performance. If XMT will meet expectations, its introduction would greatly enhance the normal rate of improvement of conventional processor architectures leading to new applications.}, keywords = {Computer, Science}, isbn = {978-3-540-22823-3}, url = {http://dx.doi.org/10.1007/978-3-540-28629-5_5}, author = {Vishkin, Uzi}, editor = {Fiala,Jir{\'\i} and Koubek,V{\'a}clav and Kratochv{\'\i}l,Jan} } @conference {17802, title = {The priority curve algorithm for video summarization}, booktitle = {Proceedings of the 2nd ACM international workshop on Multimedia databases}, series = {MMDB {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {28 - 35}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we introduce the concept of a priority curve associated with a video. We then provide an algorithm that can use the priority curve to create a summary (of a desired length) of any video. The summary thus created exhibits nice continuity properties and also avoids repetition. We have implemented the priority curve algorithm (PCA) and compared it with other summarization algorithms in the literature. We show that PCA is faster than existing algorithms and also produces better quality summaries. The quality of summaries was evaluated by a group of 200 students in Naples, Italy, who watched soccer videos. We also briefly describe a soccer video summarization system we have built on using the PCA architecture and various (classical) image processing algorithms.}, keywords = {probabilistic, Summarization, system, video}, isbn = {1-58113-975-6}, doi = {10.1145/1032604.1032611}, url = {http://doi.acm.org/10.1145/1032604.1032611}, author = {Fayzullin,M. and V.S. Subrahmanian and Albanese, M. and Picariello, A.} } @article {12075, title = {Security issues in IEEE 802.11 wireless local area networks: a survey}, journal = {Wireless Communications and Mobile Computing}, volume = {4}, year = {2004}, month = {2004///}, pages = {821 - 833}, author = {Mishra,A. and Petroni Jr,N. L and Arbaugh, William A. and Fraser,T.} } @article {14256, title = {Self-Calibration from Image Derivatives}, journal = {International Journal of Computer Vision}, volume = {48}, year = {2004}, month = {2004///}, pages = {91 - 114}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia} } @article {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 {18713, title = {Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling}, journal = {Journal of Biological ChemistryJ. Biol. Chem.}, volume = {279}, year = {2004}, month = {2004/02/20/}, pages = {7055 - 7063}, abstract = {Diverse cellular events are regulated by post-translational modification of substrate proteins via covalent attachment of one or a chain of ubiquitin molecules. The outcome of (poly)ubiquitination depends upon the specific lysine residues involved in the formation of polyubiquitin chains. Lys48-linked chains act as a universal signal for proteasomal degradation, whereas Lys63-linked chains act as a specific signal in several non-degradative processes. Although it has been anticipated that functional diversity between alternatively linked polyubiquitin chains relies on linkage-dependent differences in chain conformation/topology, direct structural evidence in support of this model has been lacking. Here we use NMR methods to determine the structure of a Lys63-linked di-ubiquitin chain. The structure is characterized by an extended conformation, with no direct contact between the hydrophobic residues Leu8, Ile44, and Val70 on the ubiquitin units. This structure contrasts with the closed conformation observed for Lys48-linked di-ubiquitin wherein these residues form the interdomain interface (Cook, W. J., Jeffrey, L. C., Carson, M., Zhijian, C., and Pickart, C. M. (1992) J. Biol. Chem. 267, 16467-16471; Varadan, R., Walker, O., Pickart, C., and Fushman, D. (2002) J. Mol. Biol. 324, 637-647). Consistent with the open conformation of the Lys63-linked di-ubiquitin, our binding studies show that both ubiquitin domains in this chain can bind a ubiquitin-associated domain from HHR23A independently and in a mode similar to that for mono-ubiquitin. In contrast, Lys48-linked di-ubiquitin binds in a different, higher affinity mode that has yet to be determined. This is the first experimental evidence that alternatively linked polyubiquitin chains adopt distinct conformations.}, isbn = {0021-9258, 1083-351X}, doi = {10.1074/jbc.M309184200}, url = {http://www.jbc.org/content/279/8/7055}, author = {Varadan,Ranjani and Assfalg,Michael and Haririnia,Aydin and Raasi,Shahri and Pickart,Cecile and Fushman, David} } @article {18490, title = {Some foundational problems in interdomain routing}, journal = {Proceedings of Third Workshop on Hot Topics in Networks (HotNets-III)}, year = {2004}, month = {2004///}, abstract = {The substantial complexity of interdomain routing in theInternet comes from the need to support flexible poli- cies while scaling to a large number of Autonomous Systems. Despite impressive progress in characterizing the various ills of the Border Gateway Protocol (BGP), many problems remain unsolved, and the behavior of the routing system is still poorly understood. This paper argues that we must understand interdomain routing in terms of: (1) intrinsic properties and design tradeoffs of policy-based routing, independent of the specific routing protocol and (2) properties that relate to artifacts in to- day{\textquoteright}s protocol. We pose open questions for the research community that, if answered, should help us understand why BGP{\textquoteright}s many problems are so difficult to fix. Un- derstanding the fundamental properties of interdomain routing will help us decide how to make progress, be it making backward-compatible modifications to BGP or designing a radically different protocol. }, author = {Feamster, Nick and Balakrishnan,H. and Rexford,J.} } @article {18763, title = {A STEP TOWARDS INTEGRATED PRODUCT/PROCESS DEVELOPMENT OF MOLDED MULTI-MATERIAL STRUCTURES}, journal = {Tools And Methods Of Competitive Engineering}, year = {2004}, month = {2004///}, abstract = {Multi-material molding is emerging as a popularmethod for making multi-material structures. In multi-material molding processes, fabrication and assembly steps are performed concurrently inside the mold. Therefore using existing knowledge on how to design molded products often results in the selection of wrong design alternatives and correcting these mistakes unnecessarily delays the product development process. To overcome this difficulty we need to develop an integrated product/process development methodology for designing molded multi-material structures. This paper presents an overview of different multi-material molding technologies and the role of manufacturing considerations in shape synthesis of molded multi- material structures. }, url = {http://terpconnect.umd.edu/~skgupta/Publication/TMCE04_Gupta.pdf}, author = {Gupta,S.K. and Fowler,G.} } @article {13909, title = {Tools for children to create physical interactive storyrooms}, journal = {Computers in Entertainment (CIE)}, volume = {2}, year = {2004}, month = {2004///}, pages = {12 - 12}, author = {Montemayor,J. and Druin, Allison and Chipman,G. and Farber,A. and Guha,M.L.} } @article {18725, title = {Ubistatins Inhibit Proteasome-Dependent Degradation by Binding the Ubiquitin Chain}, journal = {Science}, volume = {306}, year = {2004}, month = {2004/10/01/}, pages = {117 - 120}, abstract = {To identify previously unknown small molecules that inhibit cell cycle machinery, we performed a chemical genetic screen in Xenopus extracts. One class of inhibitors, termed ubistatins, blocked cell cycle progression by inhibiting cyclin B proteolysis and inhibited degradation of ubiquitinated Sic1 by purified proteasomes. Ubistatins blocked the binding of ubiquitinated substrates to the proteasome by targeting the ubiquitin-ubiquitin interface of Lys48-linked chains. The same interface is recognized by ubiquitin-chain receptors of the proteasome, indicating that ubistatins act by disrupting a critical protein-protein interaction in the ubiquitin-proteasome system.}, doi = {10.1126/science.1100946}, url = {http://www.sciencemag.org/cgi/content/abstract/sci;306/5693/117}, author = {Verma,Rati and Peters,Noel R. and D{\textquoteright}Onofrio,Mariapina and Tochtrop,Gregory P. and Sakamoto,Kathleen M. and Varadan,Ranjani and Zhang,Mingsheng and Coffino,Philip and Fushman, David and Deshaies,Raymond J. and King,Randall W.} } @article {14271, title = {Uncertainty in visual processes predicts geometrical optical illusions}, journal = {Vision Research}, volume = {44}, year = {2004}, month = {2004/03//}, pages = {727 - 749}, abstract = {It is proposed in this paper that many geometrical optical illusions, as well as illusory patterns due to motion signals in line drawings, are due to the statistics of visual computations. The interpretation of image patterns is preceded by a step where image features such as lines, intersections of lines, or local image movement must be derived. However, there are many sources of noise or uncertainty in the formation and processing of images, and they cause problems in the estimation of these features; in particular, they cause bias. As a result, the locations of features are perceived erroneously and the appearance of the patterns is altered. The bias occurs with any visual processing of line features; under average conditions it is not large enough to be noticeable, but illusory patterns are such that the bias is highly pronounced. Thus, the broader message of this paper is that there is a general uncertainty principle which governs the workings of vision systems, and optical illusions are an artifact of this principle.}, keywords = {Bias, Estimation processes, Motion perception, NOISE, optical illusions}, isbn = {0042-6989}, doi = {10.1016/j.visres.2003.09.038}, url = {http://www.sciencedirect.com/science/article/pii/S0042698903006904}, author = {Ferm{\"u}ller, Cornelia and Malm,Henrik} } @mastersthesis {14347, title = {Unifying Artifacts and Activities in a Visual Tool for Distributed Software Teams THESIS}, year = {2004}, month = {2004///}, school = {UNIVERSITY OF CALIFORNIA}, author = {Jon Froehlich} } @conference {19182, title = {Unifying artifacts and activities in a visual tool for distributed software development teams}, booktitle = {26th International Conference on Software Engineering, 2004. ICSE 2004. Proceedings}, year = {2004}, month = {2004}, pages = {387 - 396}, publisher = {IEEE}, organization = {IEEE}, abstract = {In large projects, software developers struggle with two sources of complexity - the complexity of the code itself, and the complexity of the process of producing it. Both of these concerns have been subjected to considerable research investigation, and tools and techniques have been developed to help manage them. However, these solutions have generally been developed independently, making it difficult to deal with problems that inherently span both dimensions. We describe Augur, a visualization tool that supports distributed software development processes. Augur creates visual representations of both software artifacts and software development activities, and, crucially, allows developers to explore the relationship between them. Augur is designed not for managers, but for the developers participating in the software development process. We discuss some of the early results of informal evaluation with open source software developers. Our experiences to date suggest that combining views of artifacts and activities is both meaningful and valuable to software developers.}, keywords = {Augur, complexity management, distributed programming, distributed software development teams, open source software developers, program visualisation, Programming, public domain software, software artifacts, software engineering, software tools, visual representations, visual tool, visualization tool}, isbn = {0-7695-2163-0}, author = {Jon Froehlich and Dourish,P.} } @article {18612, title = {Verifying the Correctness of Wide-Area Internet Routing}, volume = {MIT-CSAIL-TR-2004-031}, year = {2004}, month = {2004/05/17/}, institution = {Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory}, abstract = {Several studies have shown that wide-area Internet routing is fragile, with failures occurring for a variety of reasons. Routing fragility is largely due to the flexible and powerful ways in which BGP can be configured to perform various tasks, which range from implementing the policies of commercial relationships to configuring backup paths. Configuring routers in an AS is like writing a distributed program, and BGP{\textquoteright}s flexible configuration and today{\textquoteright}s relatively low-level configuration languages make the process error-prone. The primary method used by operators to determine whether their complex configurations are correct is to try them out in operation.We believe that there is a need for a systematic approach to verifying router configurations before they are deployed. This paper develops a static analysis framework for configuration checking, and uses it in the design of rcc, a {\textquoteleft}{\textquoteleft}router configuration checker{\textquoteright}{\textquoteright}. rcc takes as input a set of router configurations and flags anomalies and errors, based on a set of well-defined correctness conditions. We have used rcc to check BGP configurations from 9 operational networks, testing nearly 700 real-world router configurations in the process. Every network we analyzed had configuration errors, some of which were potentially serious and had previously gone unnoticed. Our analysis framework and results also suggest ways in which BGP and configuration languages should be improved. rcc has also been downloaded by 30 network operators to date.}, url = {http://dspace.mit.edu/handle/1721.1/30471}, author = {Feamster, Nick and Balakrishnan,Hari} } @conference {14307, title = {Visualizing type qualifier inference with Eclipse}, booktitle = {Proceedings of the 2004 OOPSLA workshop on eclipse technology eXchange}, year = {2004}, month = {2004///}, pages = {57 - 61}, author = {Greenfieldboyce,D. and Foster, Jeffrey S.} } @article {19211, title = {WalkSAT as an Informed Heuristic to DPLL in SAT Solving}, journal = {Department of Computer Science, University of Washington, Seattle}, year = {2004}, month = {2004}, author = {Ferris,B. and Jon Froehlich} } @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 {14066, title = {2003 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics October 19-22, 2003, New Paltz. NY}, journal = {2003 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics: October 19-22, 2003, Mohonk Mountain House, New Paltz, NY, USA}, year = {2003}, month = {2003///}, pages = {238 - 238}, author = {Adams,N. and EssI,G. and Makino,S. and Martens,A.A.C.F.W.L. and Algazi,R. and Fellers,M. and Martin,R. and Avendano,C. and Fielder,L. and Mellody,M. and others} } @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 {17556, title = {Approximating the domatic number}, journal = {SIAM Journal on Computing}, volume = {32}, year = {2003}, month = {2003///}, pages = {172 - 195}, abstract = {A set of vertices in a graph is a dominating set if every vertex outside the set hasa neighbor in the set. The domatic number problem is that of partitioning the vertices of a graph into the maximum number of disjoint dominating sets. Let n denote the number of vertices, δ the minimum degree, and ∆ the maximum degree. We show that every graph has a domatic partition with (1 - o(1))(δ + 1)/ ln n dominating sets and, moreover, that such a domatic partition can be found in polynomial-time. This implies a (1 + o(1)) ln n-approximation algorithm for domatic number, since the domatic number is always at most δ+1. We also show this to be essentially best possible. Namely, extending the approximation hardness of set cover by combining multiprover protocols with zero-knowledge techniques, we show that for every ϵ > 0, a (1 - ϵ) ln n-approximation implies that NP ⊆ DTIME(nO(log log n)). This makes domatic number the first natural maximization problem (known to the authors) that is provably approximable to within polylogarithmic factors but no better. We also show that every graph has a domatic partition with (1 - o(1))(δ + 1)/ ln ∆ dominating sets, where the {\textquotedblleft}o(1){\textquotedblright} term goes to zero as ∆ increases. This can be turned into an efficient algorithm that produces a domatic partition of {\textohm}(δ/ ln ∆) sets. }, author = {Feige,U. and Halld{\'o}rsson,M.M. and Kortsarz,G. and Srinivasan, Aravind} } @inbook {18896, title = {Automating DAML-S Web Services Composition Using SHOP2}, booktitle = {The Semantic Web - ISWC 2003}, series = {Lecture Notes in Computer Science}, volume = {2870}, year = {2003}, month = {2003///}, pages = {195 - 210}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The DAML-S Process Model is designed to support the application of AI planning techniques to the automated composition of Web services. SHOP2 is an Hierarchical Task Network (HTN) planner well-suited for working with the Process Model. We have proven the correspondence between the semantics of SHOP2 and the situation calculus semantics of the Process Model. We have also implemented a system which soundly and completely plans over sets of DAML-S descriptions using a SHOP2 planner, and then executes the resulting plans over the Web. We discuss the challenges and difficulties of using SHOP2 in the information-rich and human-oriented context of Web services.}, keywords = {Computer science}, isbn = {978-3-540-20362-9}, url = {http://www.springerlink.com/content/rm5ejwlmbw0mdv97/abstract/}, author = {Wu,Dan and Parsia,Bijan and Sirin,Evren and Hendler,James and Nau, Dana S.}, editor = {Fensel,Dieter and Sycara,Katia and Mylopoulos,John} } @conference {14290, title = {Checking and inferring local non-aliasing}, booktitle = {ACM SIGPLAN Notices}, volume = {38}, year = {2003}, month = {2003///}, pages = {129 - 140}, author = {Aiken,A. and Foster, Jeffrey S. and Kodumal,J. and Terauchi,T.} } @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 {17812, title = {The CPR model for summarizing video}, booktitle = {Proceedings of the 1st ACM international workshop on Multimedia databases}, series = {MMDB {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {2 - 9}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Most past work on video summarization has been based on selecting key frames from videos. We propose a model of video summarization based on three important parameters: Priority (of frames), Continuity (of the summary), and non-Repetition (of the summary). In short, a summary must include high priority frames, must be continuous and non-repetitive. An optimal summary is one that maximizes an objective function based on these three parameters. We develop formal definitions of all these concepts and provide algorithms to find optimal summaries. We briefly report on the performance of these algorithms.}, keywords = {multimedia, Summarization, video}, isbn = {1-58113-726-5}, doi = {10.1145/951676.951679}, url = {http://doi.acm.org/10.1145/951676.951679}, author = {Fayzullin,M. and V.S. Subrahmanian and Picariello, A. and Sapino,M. L} } @inbook {16142, title = {Database Discovery with Dynamic Queries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {1 - 1}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Fredrikson,A. and North,C. and Plaisant, Catherine and Shneiderman, Ben and Tanin,E. and Pkisant,C.} } @article {18537, title = {Defeating Web censorship with untrusted messenger discovery}, journal = {Workshop on Privacy Enhancing Technologies}, year = {2003}, month = {2003///}, author = {Feamster, Nick and Balazinska,M. and Wang,W. and Balakrishnan,H. and Karger,D.} } @article {12301, title = {Deno: a decentralized, peer-to-peer object-replication system for weakly connected environments}, journal = {Computers, IEEE Transactions on}, volume = {52}, year = {2003}, month = {2003/07//}, pages = {943 - 959}, abstract = {This paper presents the design, implementation, and evaluation of the replication framework of Deno, a decentralized, peer-to-peer object-replication system targeted for weakly connected environments. Deno uses weighted voting for availability and pair-wise, epidemic information flow for flexibility. This combination allows the protocols to operate with less than full connectivity, to easily adapt to changes in group membership, and to make few assumptions about the underlying network topology. We present two versions of Deno{\textquoteright}s protocol that differ in the consistency levels they support. We also propose security extensions to handle a class of malicious actions that involve misrepresentation of protocol information. Deno has been implemented and runs on top of Linux and Win32 platforms. We use the Deno prototype to characterize the performance of the Deno protocols and extensions. Our study reveals several interesting results that provide fundamental insight into the benefits of decentralization and the mechanics of epidemic protocols.}, keywords = {actions;, connected, consistency, data, data;, databases;, decentralized, Deno;, distributed, environments;, epidemic, group, levels;, Linux;, malicious, management;, membership;, network, object, object-replication, of, operating, peer-to-peer, protocols;, replicated, replication;, Security, security;, synchronisation;, system;, systems;, topology;, Unix;, voting;, weakly, weighted, Win32;}, isbn = {0018-9340}, doi = {10.1109/TC.2003.1214342}, author = {Cetintemel,U. and Keleher,P. J and Bhattacharjee, Bobby and Franklin,M.J.} } @article {16289, title = {The Dog Genome: Survey Sequencing and Comparative Analysis}, journal = {ScienceScience}, volume = {301}, year = {2003}, month = {2003/09/26/}, pages = {1898 - 1903}, abstract = {A survey of the dog genome sequence (6.22 million sequence reads; 1.5{\texttimes} coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25\%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1086432}, url = {http://www.sciencemag.org/content/301/5641/1898}, author = {Kirkness,Ewen F. and Bafna,Vineet and Halpern,Aaron L. and Levy,Samuel and Remington,Karin and Rusch,Douglas B and Delcher,Arthur L. and Pop, Mihai and Wang,Wei and Fraser,Claire M. and Venter,J. Craig} } @article {19078, title = {The dog genome: survey sequencing and comparative analysis}, journal = {Science}, volume = {301}, year = {2003}, month = {2003}, author = {Kirkness,E. F and Bafna,V. and Halpern,A. L and Levy,S. and Remington,K. and Rusch,D. B and Delcher,A. L and Pop, Mihai and Wang,W. and Fraser,C. M and others} } @article {12952, title = {Emergence and Evolution of Vibrio Cholerae O139}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {100}, year = {2003}, month = {2003/02/04/}, pages = {1304 - 1309}, abstract = {The emergence of Vibrio cholerae O139 Bengal during 1992{\textendash}1993 was associated with large epidemics of cholera in India and Bangladesh and, initially, with a total displacement of the existing V. cholerae O1 strains. However, the O1 strains reemerged in 1994 and initiated a series of disappearance and reemergence of either of the two serogroups that was associated with temporal genetic and phenotypic changes sustained by the strains. Since the initial emergence of the O139 vibrios, new variants of the pathogen derived from multiple progenitors have been isolated and characterized. The clinical and epidemiological characteristics of these strains have been studied. Rapid genetic reassortment in O139 strains appears to be a response to the changing epidemiology of V. cholerae O1 and also a strategy for persistence in competition with strains of the O1 serogroup. The emergence of V. cholerae O139 has provided a unique opportunity to witness genetic changes in V. cholerae that may be associated with displacement of an existing serogroup by a newly emerging one and, thus, provide new insights into the epidemiology of cholera. The genetic changes and natural selection involving both environmental and host factors are likely to influence profoundly the genetics, epidemiology, and evolution of toxigenic V. cholerae, not only in the Ganges Delta region of India and Bangladesh, but also in other areas of endemic and epidemic cholera.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0337468100}, url = {http://www.pnas.org/content/100/3/1304}, author = {Faruque,Shah M. and Sack,David A. and Sack,R. Bradley and Rita R Colwell and Takeda,Yoshifumi and Nair,G. Balakrish} } @conference {12000, title = {Eye design in the plenoptic space of light rays}, booktitle = {Ninth IEEE International Conference on Computer Vision, 2003. Proceedings}, year = {2003}, month = {2003/10/13/16}, pages = {1160-1167 vol.2 - 1160-1167 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {Natural eye designs are optimized with regard to the tasks the eye-carrying organism has to perform for survival. This optimization has been performed by the process of natural evolution over many millions of years. Every eye captures a subset of the space of light rays. The information contained in this subset and the accuracy to which the eye can extract the necessary information determines an upper limit on how well an organism can perform a given task. In this work we propose a new methodology for camera design. By interpreting eyes as sample patterns in light ray space we can phrase the problem of eye design in a signal processing framework. This allows us to develop mathematical criteria for optimal eye design, which in turn enables us to build the best eye for a given task without the trial and error phase of natural evolution. The principle is evaluated on the task of 3D ego-motion estimation.}, keywords = {3D ego-motion estimation, Assembly, B-splines, Camera design, CAMERAS, captured image, compound eyes, Computer vision, data mining, eye, eye-carrying organism, Eyes, filter optimization, image representation, image resolution, Information geometry, Laboratories, light field reconstruction, light gathering power, light rays, mixed spherical-Cartesian coordinate system, Motion estimation, natural evolution process, natural eye designs, natural image statistics, optical nanotechnology, Optical signal processing, optimal eye design mathematical criteria, Organisms, plenoptic image formation, plenoptic space, plenoptic video geometry, sampling operators, sensory ecology, Signal design, Signal processing, signal processing framework, signal processing tool, square-summable sequences, visual acuity}, isbn = {0-7695-1950-4}, doi = {10.1109/ICCV.2003.1238623}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {16290, title = {The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria}, journal = {Nature}, volume = {423}, year = {2003}, month = {2003/05/01/}, pages = {81 - 86}, abstract = {Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax1. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity{\textemdash}including haemolysins, phospholipases and iron acquisition functions{\textemdash}and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax4. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.}, isbn = {0028-0836}, doi = {10.1038/nature01586}, url = {http://www.nature.com/nature/journal/v423/n6935/full/nature01586.html}, author = {Read,Timothy D. and Peterson,Scott N. and Tourasse,Nicolas and Baillie,Les W. and Paulsen,Ian T. and Nelson,Karen E. and Tettelin,Herv|[eacute]| and Fouts,Derrick E. and Eisen,Jonathan A. and Gill,Steven R. and Holtzapple,Erik K. and |[Oslash]|kstad,Ole Andreas and Helgason,Erlendur and Rilstone,Jennifer and Wu,Martin and Kolonay,James F. and Beanan,Maureen J. and Dodson,Robert J. and Brinkac,Lauren M. and Gwinn,Michelle and DeBoy,Robert T. and Madpu,Ramana and Daugherty,Sean C. and Durkin,A. Scott and Haft,Daniel H. and Nelson,William C. and Peterson,Jeremy D. and Pop, Mihai and Khouri,Hoda M. and Radune,Diana and Benton,Jonathan L. and Mahamoud,Yasmin and Jiang,Lingxia and Hance,Ioana R. and Weidman,Janice F. and Berry,Kristi J. and Plaut,Roger D. and Wolf,Alex M. and Watkins,Kisha L. and Nierman,William C. and Hazen,Alyson and Cline,Robin and Redmond,Caroline and Thwaite,Joanne E. and White,Owen and Salzberg,Steven L. and Thomason,Brendan and Friedlander,Arthur M. and Koehler,Theresa M. and Hanna,Philip C. and Kolst|[oslash]|,Anne-Brit and Fraser,Claire M.} } @article {13234, title = {Guest editors{\textquoteright} Introduction to the special section on energy minimization methods in computer vision and pattern recognition}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {25}, year = {2003}, month = {2003/11//}, pages = {1361 - 1363}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2003.1240110}, author = {Figueiredo,M.A.T. and Hancock,E.R. and Pelillo,M. and Zerubia, J.} } @article {18572, title = {Guidelines for interdomain traffic engineering}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {33}, year = {2003}, month = {2003/10//}, pages = {19 - 30}, abstract = {Network operators must have control over the flow of traffic into, out of, and across their networks. However, the Border Gateway Protocol (BGP) does not facilitate common traffic engineering tasks, such as balancing load across multiple links to a neighboring AS or directing traffic to a different neighbor. Solving these problems is difficult because the number of possible changes to routing policies is too large to exhaustively test all possibilities, some changes in routing policy can have an unpredictable effect on the flow of traffic, and the BGP decision process implemented by router vendors limits an operator{\textquoteright}s control over path selection.We propose fundamental objectives for interdomain traffic engineering and specific guidelines for achieving these objectives within the context of BGP. Using routing and traffic data from the AT\&T backbone we show how certain BGP policy changes can move traffic in a predictable fashion, despite limited knowledge about the routing policies in neighboring AS{\textquoteright}s. Then, we show how operators can gain greater flexibility by relaxing some steps in the BGP decision process and ensuring that neighboring AS{\textquoteright}s send consistent advertisements at each peering location. Finally, we show that an operator can manipulate traffic efficiently by changing the routes for a small number of prefixes (or groups of related prefixes) that consistently receive a large amount of traffic.}, isbn = {0146-4833}, doi = {10.1145/963985.963988}, url = {http://doi.acm.org/10.1145/963985.963988}, author = {Feamster, Nick and Borkenhagen,Jay and Rexford,Jennifer} } @inbook {17237, title = {Innovating the Interaction}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {295 - 295}, publisher = {Morgan Kaufmann}, organization = {Morgan Kaufmann}, address = {San Francisco}, isbn = {978-1-55860-915-0}, author = {Bederson, Benjamin B. and Plaisant, Catherine and Mushlin,R. and Snyder,A. and Li,J. and Heller,D. and Shneiderman, Ben and Hochheiser,H. and Fekete,J. D and Czenvinski,M.} } @article {16418, title = {The interaction between zoning regulations and residential preferences as a driver of urban form}, journal = {Proceedings of the 2003 UTEP Distinguished Faculty and Student Symposium}, year = {2003}, month = {2003///}, author = {Zellner,M.L. and Riolo,R and Rand, William and Page,S.E. and Brown,D.G. and Fernandez,L.E.} } @article {12190, title = {The International Children{\textquoteright}s Digital Library}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13928, title = {The International Children{\textquoteright}s Digital Library: Description and analysis of first use}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, pages = {315 - 315}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13904, title = {The International Children{\textquoteright}s Digital Library: viewing digital books online}, journal = {Interacting with Computers}, volume = {15}, year = {2003}, month = {2003///}, pages = {151 - 167}, author = {Hourcade,J. P and Bederson, Benjamin B. and Druin, Allison and Rose,A. and Farber,A. and Takayama,Y.} } @article {15183, title = {Intrusion-resilient public-key encryption}, journal = {Topics in Cryptology{\textemdash}CT-RSA 2003}, year = {2003}, month = {2003///}, pages = {19 - 32}, abstract = {Exposure of secret keys seems to be inevitable, and may in practice represent the most likely point of failure in a cryptographic system. Recently, the notion of intrusion-resilience [17] (which extends both the notions of forward security [3], [5] and key insulation [11]) was proposed as a means of mitigating the harmful effects that key exposure can have. In this model, time is divided into distinct periods; the public key remains fixed throughout the lifetime of the protocol but the secret key is periodically updated. Secret information is stored by both a user and a base; the user performs all cryptographic operations during a given time period, while the base helps the user periodically update his key. Intrusion-resilient schemes remain secure in the face of multiple compromises of both the user and the base, as long as they are not both compromised simultaneously. Furthermore, in case the user and base are compromised simultaneously, prior time periods remain secure (as in forward-secure schemes). Intrusion-resilient signature schemes have been previously constructed [17], [15]. Here, we give the first construction of an intrusion-resilient publickey encryption scheme, based on the recently-constructed forwardsecure encryption scheme of [8]. We also consider generic transformations for securing intrusion-resilient encryption schemes against chosenciphertext attacks.}, doi = {10.1007/3-540-36563-X_2}, author = {Dodis,Y. and Franklin,M. and Katz, Jonathan and Miyaji,A. and Yung,M.} } @article {18583, title = {Measuring the effects of internet path faults on reactive routing}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {31}, year = {2003}, month = {2003/06//}, pages = {126 - 137}, abstract = {Empirical evidence suggests that reactive routing systems improve resilience to Internet path failures. They detect and route around faulty paths based on measurements of path performance. This paper seeks to understand why and under what circumstances these techniques are effective.To do so, this paper correlates end-to-end active probing experiments, loss-triggered traceroutes of Internet paths, and BGP routing messages. These correlations shed light on three questions about Internet path failures: (1) Where do failures appear? (2) How long do they last? (3) How do they correlate with BGP routing instability?Data collected over 13 months from an Internet testbed of 31 topologically diverse hosts suggests that most path failures last less than fifteen minutes. Failures that appear in the network core correlate better with BGP instability than failures that appear close to end hosts. On average, most failures precede BGP messages by about four minutes, but there is often increased BGP traffic both before and after failures. Our findings suggest that reactive routing is most effective between hosts that have multiple connections to the Internet. The data set also suggests that passive observations of BGP routing messages could be used to predict about 20\% of impending failures, allowing re-routing systems to react more quickly to failures.}, isbn = {0163-5999}, doi = {10.1145/885651.781043}, url = {http://doi.acm.org/10.1145/885651.781043}, author = {Feamster, Nick and Andersen,David G. and Balakrishnan,Hari and Kaashoek,M. Frans} } @conference {14235, title = {New eyes for robotics}, booktitle = {2003 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2003. (IROS 2003). Proceedings}, volume = {1}, year = {2003}, month = {2003/10/27/31}, pages = {1018- 1023 vol.1 - 1018- 1023 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper describes an imaging system that has been designed to facilitate robotic tasks of motion. The system consists of a number of cameras in a network arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and consequently the estimation of shape models from the individual cameras. The reason is that inherent ambiguities of confusion between translation and rotation disappear. Pairs of cameras may also be arranged in multiple stereo configurations which provide additional advantages for segmentation. Algorithms for the calibration of the system and the 3D motion estimation are provided.}, keywords = {3D motion estimation, Argus eye, array signal processing, Birds, Calibration, CAMERAS, Control systems, Eyes, geometric configuration, imaging, imaging system, Layout, Motion estimation, multiple stereo configurations, Robot kinematics, robot vision, Robot vision systems, ROBOTICS, Robotics and automation, SHAPE, shape models}, isbn = {0-7803-7860-1}, doi = {10.1109/IROS.2003.1250761}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {16143, title = {Overlaying graph links on treemaps}, journal = {IEEE Symposium on Information Visualization Conference Compendium (demonstration)}, year = {2003}, month = {2003///}, abstract = {Every graph can be decomposed into a tree structure plus a set ofremaining edges. We describe a visualization technique that displays the tree structure as a Treemap and the remaining edges as curved links overlaid on the Treemap. Link curves are designed to show where the link starts and where it ends without requiring an explicit arrow that would clutter the already dense visualization. This technique is effective for visualizing structures where the underlying tree has some meaning, such as Web sites or XML documents with cross-references. Graphic attributes of the links {\textendash} such as color or thickness {\textendash} can be used to represent attributes of the edges. Users can choose to see all links at once or only the links to and from the node or branch under the cursor. }, author = {Fekete,J. D and Wang,D. and Dang,N. and Aris,A. and Plaisant, Catherine} } @article {12954, title = {Pathogenic Potential of Environmental Vibrio Cholerae Strains Carrying Genetic Variants of the Toxin-Coregulated Pilus Pathogenicity Island}, journal = {Infection and ImmunityInfect. Immun.}, volume = {71}, year = {2003}, month = {2003/02/01/}, pages = {1020 - 1025}, abstract = {The major virulence factors of toxigenic Vibrio cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXΦ), and toxin-coregulated pilus (TCP), an essential colonization factor which is also the receptor for CTXΦ. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island. To assess their pathogenic potential, we analyzed environmental strains of V. cholerae carrying genetic variants of the TCP pathogenicity island for colonization of infant mice, susceptibility to CTXΦ, and diarrheagenicity in adult rabbits. Analysis of 14 environmental strains, including 3 strains carrying a new allele of the tcpA gene, 9 strains carrying a new allele of the toxT gene, and 2 strains carrying conventional tcpA and toxT genes, showed that all strains colonized infant mice with various efficiencies in competition with a control El Tor biotype strain of V. cholerae O1. Five of the 14 strains were susceptible to CTXΦ, and these transductants produced CT and caused diarrhea in adult rabbits. These results suggested that the new alleles of the tcpA and toxT genes found in environmental strains of V. cholerae encode biologically active gene products. Detection of functional homologs of the TCP island genes in environmental strains may have implications for understanding the origin and evolution of virulence genes of V. cholerae.}, isbn = {0019-9567, 1098-5522}, doi = {10.1128/IAI.71.2.1020-1025.2003}, url = {http://iai.asm.org/content/71/2/1020}, author = {Faruque,Shah M. and Kamruzzaman,M. and Meraj,Ismail M. and Chowdhury,Nityananda and Nair,G. Balakrish and Sack,R. Bradley and Rita R Colwell and Sack,David A.} } @article {13410, title = {A planner for composing services described in DAML-S}, journal = {International Conference on Automated Planning and Scheduling (ICAPS) 2003 Workshop on planning for web services}, year = {2003}, month = {2003///}, author = {Sheshagiri,M. and desJardins, Marie and Finin,T.} } @article {14247, title = {Plenoptic video geometry}, journal = {The Visual Computer}, volume = {19}, year = {2003}, month = {2003///}, pages = {395 - 404}, abstract = {More and more processing of visual information is nowadays done by computers, but the images captured by conventional cameras are still based on the pinhole principle inspired by our own eyes. This principle though is not necessarily the optimal image-formation principle for automated processing of visual information. Each camera samples the space of light rays according to some pattern. If we understand the structure of the space formed by the light rays passing through a volume of space, we can determine the camera, or in other words the sampling pattern of light rays, that is optimal with regard to a given task. In this work we analyze the differential structure of the space of time-varying light rays described by the plenoptic function and use this analysis to relate the rigid motion of an imaging device to the derivatives of the plenoptic function. The results can be used to define a hierarchy of camera models with respect to the structure from motion problem and formulate a linear, scene-independent estimation problem for the rigid motion of the sensor purely in terms of the captured images.}, isbn = {0178-2789}, url = {http://dx.doi.org/10.1007/s00371-003-0203-5}, author = {Neumann, Jan and Ferm{\"u}ller, Cornelia} } @conference {12055, title = {Polydioptric camera design and 3D motion estimation}, booktitle = {2003 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2003. Proceedings}, volume = {2}, year = {2003}, month = {2003/06/18/20}, pages = {II- 294-301 vol.2 - II- 294-301 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {Most cameras used in computer vision applications are still based on the pinhole principle inspired by our own eyes. It has been found though that this is not necessarily the optimal image formation principle for processing visual information using a machine. We describe how to find the optimal camera for 3D motion estimation by analyzing the structure of the space formed by the light rays passing through a volume of space. Every camera corresponds to a sampling pattern in light ray space, thus the question of camera design can be rephrased as finding the optimal sampling pattern with regard to a given task. This framework suggests that large field-of-view multi-perspective (polydioptric) cameras are the optimal image sensors for 3D motion estimation. We conclude by proposing design principles for polydioptric cameras and describe an algorithm for such a camera that estimates its 3D motion in a scene independent and robust manner.}, keywords = {3D motion estimation, Algorithm design and analysis, Application software, CAMERAS, Computer vision, Eyes, field-of-view camera, Image motion analysis, image sampling, image sensor, Image sensors, Layout, light ray, Motion estimation, multiperspective camera, optimal camera, optimal image formation, optimal sampling pattern, pinhole principle, polydioptric camera design, ray space, scene independent estimation, space structure analysis, stereo image processing, visual information processing}, isbn = {0-7695-1900-8}, doi = {10.1109/CVPR.2003.1211483}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14819, title = {A search engine for 3D models}, journal = {ACM Trans. Graph.}, volume = {22}, year = {2003}, month = {2003/01//}, pages = {83 - 105}, abstract = {As the number of 3D models available on the Web grows, there is an increasing need for a search engine to help people find them. Unfortunately, traditional text-based search techniques are not always effective for 3D data. In this article, we investigate new shape-based search methods. The key challenges are to develop query methods simple enough for novice users and matching algorithms robust enough to work for arbitrary polygonal models. We present a Web-based search engine system that supports queries based on 3D sketches, 2D sketches, 3D models, and/or text keywords. For the shape-based queries, we have developed a new matching algorithm that uses spherical harmonics to compute discriminating similarity measures without requiring repair of model degeneracies or alignment of orientations. It provides 46 to 245\% better performance than related shape-matching methods during precision--recall experiments, and it is fast enough to return query results from a repository of 20,000 models in under a second. The net result is a growing interactive index of 3D models available on the Web (i.e., a Google for 3D models).}, keywords = {Search engine, shape matching, shape representation, shape retrieval}, isbn = {0730-0301}, doi = {10.1145/588272.588279}, url = {http://doi.acm.org/10.1145/588272.588279}, author = {Funkhouser,Thomas and Min,Patrick and Kazhdan,Michael and Chen,Joyce and Halderman,Alex and Dobkin,David and Jacobs, David W.} } @article {14260, title = {Statistical Bias Predicts Many Illusions}, journal = {Journal of VisionJ Vis}, volume = {3}, year = {2003}, month = {2003/10/22/}, pages = {636 - 636}, abstract = {There is a principle underlying visual computations that previously has not been recognized. This principle is about the effects of uncertainty. Many visual computations are estimation processes. Because of noise, and there are many sources of noise in the formation and processing of images, systematic errors occur in the estimation. In statistical terms we say the estimation is biased. To avoid the bias would require accurate estimation of the noise parameters, but this because of the large number of unknown parameters (the geometry and photometry of the changing scene) in general is not possible. Visual computations, which are estimation processes include the low level processes of feature extraction and the middle level processes of visual recovery. We hypothesize that the bias in the estimation of image features, that is points, lines, and image movement, is the main cause for most geometrical illusions as well as illusory motion patterns. Because of bias the location of image features is estimated erroneously and the appearance of patterns is altered. It is shown that many geometrical optical illusion patterns are such that the bias is highly pronounced. We analyzed the bias in visual shape recovery processes and found that it is consistent with what is empirically known about the estimation of shape. It has been observed from computational as well as psychophysical experiments, that for many configurations there is a tendency to underestimate the slant. The bias predicts this underestimation of slant. To demonstrate the power of the model we created illusory displays giving rise to erroneous shape estimation.}, isbn = {, 1534-7362}, doi = {10.1167/3.9.636}, url = {http://www.journalofvision.org/content/3/9/636}, author = {Ferm{\"u}ller, Cornelia} } @article {16410, title = {Statistical validation of spatial patterns in agent-based models}, journal = {Proceedings of Agent Based Simulation}, volume = {4}, year = {2003}, month = {2003///}, abstract = {We present and evaluate an agent-based model(ABM) of land use change at the rural-urban fringe. This paper is part of a project that links the ABM to surveys of residential preferences and historical patterns of development. Validation is an important issue for such models and we discuss the use of distributional phenomena as a method of validation. We then highlight the ability of our ABM to gen- erate two phenomena evident in empirical analysis of urban development patterns: a power law rela- tionship between frequency and cluster size and a negative exponential relationship between density and distance from city center. We discuss these results in the light of validation of ABMs. }, author = {Rand, William and Brown,D.G. and Page,S.E. and Riolo,R and Fernandez,L.E. and Zellner,M} } @article {18749, title = {A system for generating process and material selection advice during embodiment design of mechanical components}, journal = {Journal of manufacturing systems}, volume = {22}, year = {2003}, month = {2003///}, pages = {28 - 45}, abstract = {This paper describes a systematic approach to material and process selection during theembodiment design of mechanical components and a system for generating process and material selection advice. Quite often during the embodiment design stage, design requirements are not precisely defined. Therefore, the system described in this paper accounts for imprecision in design requirements during generation and evaluation of alternative process sequences and material options. To reduce the computational effort, the system uses a depth-first branch-and- bound search algorithm. This aids in exploring promising process sequences and material options that can be used to meet the given set of design requirements. Various process sequences and material options are evaluated by using a commercial cost estimation tool. }, url = {ftp://ftp.eng.umd.edu/:/home/glue/s/k/skgupta/backup/pub/Publication/JMS03_Gupta.pdf}, author = {Gupta,S.K. and Chen,Y. and Feng,S. and Sriram,R.} } @article {18505, title = {Techniques for interdomain traffic engineering}, journal = {Computer Communications Review}, volume = {33}, year = {2003}, month = {2003///}, abstract = {Network operators must have control over the flow of traffic into,out of, and across their networks. However, the Border Gateway Protocol (BGP) does not facilitate common traffic engineering tasks, such as balancing load across multiple links to a neighboring AS or directing traffic to a different neighbor. Solving these problems is difficult because the number of possible changes to routing policies is too large to exhaustively test all possibilities, some changes in routing policy can have an unpredictable effect on the flow of traf- fic, and the BGP decision process implemented by router vendors limits an operator{\textquoteright}s control over path selection. We analyze routing and traffic data from the AT\&T backbone to identify ways to use BGP policy for traffic engineering tasks. First, we show how cer- tain BGP policy changes can move traffic in a predictable fashion, despite limited knowledge about the routing policies in neighboring AS{\textquoteright}s. Then, we show how operators can gain greater flexibility by relaxing some steps in the BGP decision process and ensuring that neighboring AS{\textquoteright}s send consistent advertisements at each peering location. Finally, we show that an operator can manipulate traffic efficiently by changing the routes for a small number of prefixes (or groups of related prefixes) that consistently receive a large amount of traffic. These results can help operators accomplish common traffic engineering tasks using existing BGP features. }, author = {Feamster, Nick and Borkenhagen,J. and Rexford,J.} } @article {13344, title = {TelegraphCQ: An architectural status report}, journal = {IEEE Data Engineering Bulletin}, volume = {26}, year = {2003}, month = {2003///}, pages = {11 - 18}, author = {Krishnamurthy, S. and Chandrasekaran,S. and Cooper,O. and Deshpande, Amol and Franklin,M.J. and Hellerstein,J. M and Hong,W. and Madden,S. and Reiss,F. and Shah,M. A} } @conference {13405, title = {TelegraphCQ: continuous dataflow processing}, booktitle = {Proceedings of the 2003 ACM SIGMOD international conference on Management of data}, series = {SIGMOD {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {668 - 668}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-634-X}, doi = {10.1145/872757.872857}, url = {http://doi.acm.org/10.1145/872757.872857}, author = {Chandrasekaran,Sirish and Cooper,Owen and Deshpande, Amol and Franklin,Michael J. and Hellerstein,Joseph M. and Wei Hong and Krishnamurthy,Sailesh and Madden,Samuel R. and Reiss,Fred and Shah,Mehul A.} } @inbook {18603, title = {Thwarting Web Censorship with Untrusted Messenger Discovery}, booktitle = {Privacy Enhancing TechnologiesPrivacy Enhancing Technologies}, series = {Lecture Notes in Computer Science}, volume = {2760}, year = {2003}, month = {2003///}, pages = {125 - 140}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {All existing anti-censorship systems for the Web rely on proxies to grant clients access to censored information. Therefore, they face the proxy discovery problem : how can clients discover the proxies without having the censor discover and block these proxies? To avoid widespread discovery and blocking, proxies must not be widely published and should be discovered in-band. In this paper, we present a proxy discovery mechanism called keyspace hopping that meets this goal. Similar in spirit to frequency hopping in wireless networks, keyspace hopping ensures that each client discovers only a small fraction of the total number of proxies. However, requiring clients to independently discover proxies from a large set makes it practically impossible to verify the trustworthiness of every proxy and creates the possibility of having untrusted proxies. To address this, we propose separating the proxy into two distinct components{\textemdash}the messenger , which the client discovers using keyspace hopping and which simply acts as a gateway to the Internet; and the portal , whose identity is widely-published and whose responsibility it is to interpret and serve the client{\textquoteright}s requests for censored content. We show how this separation, as well as in-band proxy discovery, can be applied to a variety of anti-censorship systems.}, keywords = {Computer science}, isbn = {978-3-540-20610-1}, url = {http://www.springerlink.com/content/1gg8p94deqek968t/abstract/}, author = {Feamster, Nick and Balazinska,Magdalena and Wang,Winston and Balakrishnan,Hari and Karger,David}, editor = {Dingledine,Roger} } @article {18606, title = {Towards a logic for wide-area Internet routing}, journal = {SIGCOMM Comput. Commun. Rev.}, volume = {33}, year = {2003}, month = {2003/08//}, pages = {289 - 300}, abstract = {Interdomain routing is a massive distributed computing task that propagates topological information for global reachability. Today{\textquoteright}s interdomain routing protocol, BGP4, is exceedingly complex because the wide variety of goals that it must meet---including fast convergence, failure resilience, scalability, policy expression, and global reachability---are accomplished by mechanisms that have complicated interactions and unintended side effects. The complexity of wide-area routing configuration and protocol dynamics requires mechanisms for expressing wide-area routing that adhere to a set of logical rules. We propose a set of rules, called the routing logic, which can be used to determine whether a routing protocol satisfies various properties. We demonstrate how this logic can aid in analyzing the behavior of BGP4 under various configurations. We also speculate on how the logic can be used to analyze existing configuration in real-world networks, synthesize network-wide router configuration from a high-level policy language, and assist protocol designers in reasoning about new routing protocols.}, isbn = {0146-4833}, doi = {10.1145/972426.944767}, url = {http://doi.acm.org/10.1145/972426.944767}, author = {Feamster, Nick and Balakrishnan,Hari} } @conference {14179, title = {Uncertainty in 3D shape estimation}, booktitle = {ICCV Workshop on Statistical and Computational Theories of Vision}, year = {2003}, month = {2003///}, author = {Ji,H. and Ferm{\"u}ller, Cornelia} } @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 {14204, title = {Bias in visual motion processes: A theory predicting illusions}, journal = {Statistical Methods in Video Processing.(in conjunction with European Conference on Computer Vision)}, year = {2002}, month = {2002///}, abstract = {The first step in the interpretation of video sequences is theestimation of spatio-temporal image representations, that is the image motion or the correspondence of points or lines. Noise in the data, however, causes a serious problem for their estimation; in particular, it causes bias. As a result the location of image points, the orientation of image lines and the length and orientation of image motion vectors are esti- mated erroneously. It is suggested that machine vision sys- tems processing video should include statistical procedures to alleviate the bias. However, complete correction in gen- eral does not appear to be feasible, and this provides an ex- planation for most well-known geometrical optical illusions, such as the caf{\'e} wall, the Z{\"o}llner, the Poggendorff illusion and other recently discovered illusions of movement. }, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J. and Malm,H.} } @article {13907, title = {The child as learner, critic, inventor, and technology design partner: An analysis of three years of Swedish student journals}, journal = {International Journal of Technology and Design Education}, volume = {12}, year = {2002}, month = {2002///}, pages = {189 - 213}, author = {Druin, Allison and Fast,C.} } @inbook {14598, title = {Combinatorial Algorithms for Design of DNA Arrays}, booktitle = {Chip TechnologyChip Technology}, series = {Advances in Biochemical Engineering/Biotechnology}, volume = {77}, year = {2002}, month = {2002///}, pages = {1 - 19}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination ( border length minimization problem ) and reducing the complexity of masks ( mask decomposition problem ). We describe algorithms that reduce the number of rectangles in mask decomposition by 20{\textendash}30\% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.}, isbn = {978-3-540-43215-9}, url = {http://dx.doi.org/10.1007/3-540-45713-5_1}, author = {Hannenhalli, Sridhar and Hubbell,Earl and Lipshutz,Robert and Pevzner,Pavel}, editor = {Hoheisel,J{\"o}rg and Brazma,A. and B{\"u}ssow,K. and Cantor,C. and Christians,F. and Chui,G. and Diaz,R. and Drmanac,R. and Drmanac,S. and Eickhoff,H. and Fellenberg,K. and Hannenhalli, Sridhar and Hoheisel,J. and Hou,A. and Hubbell,E. and Jin,H. and Jin,P. and Jurinke,C. and Konthur,Z. and K{\"o}ster,H. and Kwon,S. and Lacy,S. and Lehrach,H. and Lipshutz,R. and Little,D. and Lueking,A. and McGall,G. and Moeur,B. and Nordhoff,E. and Nyarsik,L. and Pevzner,P. and Robinson,A. and Sarkans,U. and Shafto,J. and Sohail,M. and Southern,E. and Swanson,D. and Ukrainczyk,T. and van den Boom,D. and Vilo,J. and Vingron,M. and Walter,G. and Xu,C.} } @article {16250, title = {Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus Anthracis}, journal = {Science}, volume = {296}, year = {2002}, month = {2002/06/14/}, pages = {2028 - 2033}, abstract = {Comparison of the whole-genome sequence ofBacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced B. anthracischromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1071837}, url = {http://www.sciencemag.org/content/296/5575/2028}, author = {Read,Timothy D. and Salzberg,Steven L. and Pop, Mihai and Shumway,Martin and Umayam,Lowell and Jiang,Lingxia and Holtzapple,Erik and Busch,Joseph D and Smith,Kimothy L and Schupp,James M and Solomon,Daniel and Keim,Paul and Fraser,Claire M.} } @article {19075, title = {Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440}, journal = {Environmental microbiology}, volume = {4}, year = {2002}, month = {2002}, pages = {799 - 808}, abstract = {Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85\% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.}, author = {Nelson,K. E and Weinel,C. and Paulsen,IT and Dodson,RJ and Hilbert,H. and Martins dos Santos,VAP and Fouts,DE and Gill,S. R and Pop, Mihai and Holmes,M. and others} } @article {16411, title = {The complex interaction of agents and environments: An example in urban sprawl}, journal = {Proceedings of Agent Based Simulation}, year = {2002}, month = {2002///}, pages = {149 - 161}, abstract = {We present and evaluate a foundational agent-based model of land use change at therural-urban fringe within the context of a larger project that will link to surveys of the environmental and community preferences of residents with historical data on patterns of development. In this paper, we focus on the dynamics arising from a model of residential location resulting from preferences for services, density, and aesthetics focusing on the relationship between micro level preferences and policy relevant macro phenomena such as scattered development, largest city size, and the number of residential clusters. We consider two representations of agents{\textquoteright} utility functions {\textendash} one additively separable and one multiplicative {\textendash} to see if functional form has any impact on the dynamics of the system, and find that they produce similar results. Our analysis includes both representative agent runs, in which all agents have identical preferences, as well as runs in which the agents have diverse preferences. We find that diversity can increase sprawl through feedbacks associated with the spatial locations of services and agents. In addition, we examine cases in which the agents{\textquoteright} location decisions affect the aesthetic quality of neighboring sites and find that these feedbacks further exacerbate the sprawl effect. }, author = {Rand, William and Zellner,M and Page,S.E. and Riolo,R and Brown,D.G. and Fernandez,L.E.} } @conference {16914, title = {Content-based image retrieval using Fourier descriptors on a logo database}, booktitle = {Pattern Recognition, 2002. Proceedings. 16th International Conference on}, volume = {3}, year = {2002}, month = {2002///}, pages = {521 - 524 vol.3 - 521 - 524 vol.3}, abstract = {A system that enables the pictorial specification of queries in an image database is described. The queries are comprised of rectangle, polygon, ellipse, and B-spline shapes. The queries specify which shapes should appear in the target image as well as spatial constraints on the distance between them and their relative position. The retrieval process makes use of an abstraction of the contour of the shape which is invariant against translation, scale, rotation, and starting point, that is based on the use of Fourier descriptors. These abstractions are used in a system to locate logos in an image database. The utility of this approach is illustrated using some sample queries.}, keywords = {abstraction;, analysis;, constraints;, content-based, contour, database, database;, databases;, descriptors;, detection;, edge, Fourier, image, logos;, pictorial, processing;, query, retrieval;, SHAPE, spatial, specification;, theory;, visual}, doi = {10.1109/ICPR.2002.1047991}, author = {Folkers,A. and Samet, Hanan} } @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} } @conference {17889, title = {Executing Multiple Pipelined Data Analysis Operations in the Grid}, booktitle = {SC Conference}, year = {2002}, month = {2002///}, pages = {54 - 54}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Processing of data in many data analysis applications can be represented as an acyclic, coarse grain data flow, from data sources to the client. This paper is concerned with scheduling of multiple data analysis operations, each of which is represented as a pipelined chain of processing on data. We define the scheduling problem for effectively placing components onto Grid resources, and propose two scheduling algorithms. Experimental results are presented using a visualization application.}, doi = {http://doi.ieeecomputersociety.org/10.1109/SC.2002.10015}, author = {Spencer,Matthew and Ferreira,Renato and Beynon,Michael and Kurc,Tahsin and Catalyurek,Umit and Sussman, Alan and Saltz,Joel} } @conference {12037, title = {Eyes form eyes: New cameras for structure from motion}, booktitle = {Proceedings Workshop on Omnidirectional Vision (OMNIVIS)}, year = {2002}, month = {2002///}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {14219, title = {Eyes from eyes: new cameras for structure from motion}, booktitle = {Third Workshop on Omnidirectional Vision, 2002. Proceedings}, year = {2002}, month = {2002///}, pages = {19 - 26}, publisher = {IEEE}, organization = {IEEE}, abstract = {We investigate the relationship between camera design and the problem of recovering the motion and structure of a scene from video data. The visual information that could possibly be obtained is described by the plenoptic function. A camera can be viewed as a device that captures a subset of this function, that is, it measures some of the light rays in some part of the space. The information contained in the subset determines how difficult it is to solve subsequent interpretation processes. By examining the differential structure of the time varying plenoptic function we relate different known and new camera models to the spatiotemporal structure of the observed scene. This allows us to define a hierarchy of camera designs, where the order is determined by the stability and complexity of the computations necessary to estimate structure and motion. At the low end of this hierarchy is the standard planar pinhole camera for which the structure from motion problem is non-linear and ill-posed. At the high end is a new camera, which we call the full field of view polydioptric camera, for which the problem is linear and stable. In between are multiple-view cameras with large fields of view which we have built, as well as catadioptric panoramic sensors and other omni-directional cameras. We develop design suggestions for the polydioptric camera, and based upon this new design we propose a linear algorithm for ego-motion estimation, which in essence combines differential motion estimation with differential stereo.}, keywords = {Algorithm design and analysis, Camera design, CAMERAS, Design automation, differential stereo, Educational institutions, ego-motion estimation, Eyes, Geometrical optics, IMAGE PROCESSING, Layout, Motion estimation, observed scene, Optical films, polydioptric camera, RETINA}, isbn = {0-7695-1629-7}, doi = {10.1109/OMNVIS.2002.1044486}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14312, title = {Flow-sensitive type qualifiers}, journal = {ACM SIGPLAN Notices}, volume = {37}, year = {2002}, month = {2002///}, pages = {1 - 12}, author = {Foster, Jeffrey S. and Terauchi,T. and Aiken,A.} } @article {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 {13931, title = {How young can our design partners be}, booktitle = {Proceedings of the Participatory Design Conference}, year = {2002}, month = {2002///}, pages = {272 - 277}, author = {Farber,A. and Druin, Allison and Chipman,G. and Julian,D. and Somashekhar,S.} } @article {18489, title = {Infranet: Circumventing web censorship and surveillance}, journal = {Proceedings of the 11th USENIX Security Symposium}, year = {2002}, month = {2002///}, pages = {247 - 262}, abstract = {An increasing number of countries and companies routinely block or monitor access to parts of the Internet. To counteract these measures, we propose Infranet, a system that enables clients to surreptitiously retrieve sensitive content via cooperating Web servers distributed across the global Internet. These Infranet servers provide clients access to censored sites while continuing to host normal uncensored content. Infranet uses a tunnel protocol that provides a covert communication channel between its clients and servers, modulated over standard HTTP transactions that resemble innocuous Web browsing. In the upstream direction, Infranet clients send covert messages to Infranet servers by associating meaning to the sequence of HTTP requests being made. In the downstream direction, Infranet servers return content by hiding censored data in uncensored images using steganographic techniques. We describe the design, a prototype implementation, security properties, and performance of Infranet. Our security analysis shows that Infranet can successfully circumvent several sophisticated censoring techniques.}, author = {Feamster, Nick and Balazinska,M. and Harfst,G. and Balakrishnan,H. and Karger,D.} } @conference {16153, title = {Interactive information visualization of a million items}, booktitle = {Information Visualization, 2002. INFOVIS 2002. IEEE Symposium on}, year = {2002}, month = {2002///}, pages = {117 - 124}, abstract = {Existing information visualization techniques are usually limited to the display of a few thousand items. This article describes new interactive techniques capable of handling a million items (effectively visible and manageable on screen). We evaluate the use of hardware-based techniques available with newer graphics cards, as well as new animation techniques and non-standard graphical features such as stereovision and overlap count. These techniques have been applied to two popular information visualizations: treemaps and scatter plot diagrams; but are generic enough to be applied to other 2D representations as well.}, keywords = {animation, animation;, cards;, Computer, count;, data, diagrams;, Graphics, hardware-based, information, interactive, interpolation;, overlap, plot, scatter, stereovision;, systems;, techniques;, treemaps;, visualisation;, visualization;}, doi = {10.1109/INFVIS.2002.1173156}, author = {Fekete,J.-D. and Plaisant, Catherine} } @article {14418, title = {Learning structured statistical models from relational data}, journal = {Link{\"o}ping Electronic Articles in Computer and Information Science}, volume = {7}, year = {2002}, month = {2002///}, pages = {13 - 13}, abstract = {Here we describe tools for constructing statistical models from relational data. Our goal is to learn structured probabilistic models that represent statistical correlations both between the properties of an entity and between the properties of related entities. These statistical models can then be used for a variety of tasks including knowledge discovery, exploratory data analysis, data summarization and anomaly detection. Unfortunately, most statistical learning methods work only with "flat" data representations. Thus, to apply these methods, we are forced to convert the data into a flat form, thereby not only losing its compact representation and structure but also potentially introducing statistical skew. These drawbacks severely limit the ability of current statistical methods to model relational databases. Here we describe two complementary approaches: one approach suited to making probabilistic statements about individuals and the second approach suited to making statements about frequencies in relational data. We describe algorithms for both learning and making inferences in these models, and give experimental results.}, author = {Getoor, Lise and Friedman,N. and Koller,D.} } @article {16911, title = {A Linear Iterative Approach for Hierarchical Shortest Path Finding}, journal = {Technical Reports from UMIACS, UMIACS-TR-2002-97}, year = {2002}, month = {2002///}, abstract = {We present a hierarchical approach that subdivides a network with $n$ vertices into $r$ regions with the same number $m$ of vertices ($n = r m$) and creates higher levels merging a constant number $c$ of adjacent regions. We propose linear iterative algorithms to find a shortest path and to expand this path into the lowest level. Since our approach is non-recursive, the complexity constants are small and the algorithms are more efficient in practice than other recursive optimal approaches. A hybrid shortest path algorithm to perform intra-regional queries in the lowest level is introduced. This strategy uses a subsequence of vertices that belong to the shortest path while actually computing the whole shortest path. The hybrid algorithm requires $O(m)$ time and space assuming an uniform distribution of vertices. This represents a further improvement concerning space, since a path view approach requires $O(m^{1.5})$ space in the lowest level. For higher $k$-levels, a path view approach spends $O(1)$ time and requires $O(c^k m)$ space.}, author = {Samet, Hanan and Filho,Gutemberg Guerra} } @article {14507, title = {Method and apparatus for learning probabilistic relational models having attribute and link uncertainty and for performing selectivity estimation using probabilistic relational models}, volume = {09/922,324}, year = {2002}, month = {2002/08/01/}, abstract = {The invention comprises a method and apparatus for learning probabilistic models (PRM{\textquoteright}s) with attribute uncertainty. A PRM with attribute uncertainty defines a probability distribution over instantiations of a database. A learned PRM is useful for discovering interesting patterns and dependencies in the data. Unlike many existing techniques, the process is data-driven rather than hypothesis driven. This makes the technique particularly well-suited for exploratory data analysis. In addition, the invention comprises a method and apparatus for handling link uncertainty in PRM{\textquoteright}s. Link uncertainty is uncertainty over which entities are related in our domain. The invention comprises of two mechanisms for modeling link uncertainty: reference uncertainty and existence uncertainty. The invention includes learning algorithms for each form of link uncertainty. The third component of the invention is a technique for performing database selectivity estimation using probabilistic relational...}, url = {http://www.google.com/patents?id=FVqDAAAAEBAJ}, author = {Koller,Daphne and Getoor, Lise and Pfeffer,Avi and Friedman,Nir and Taskar,Ben} } @article {18495, title = {Network-wide BGP route prediction for traffic engineering}, journal = {Proceedings of ITCOM}, year = {2002}, month = {2002///}, abstract = {The Internet consists of about 13,000 Autonomous Systems (AS{\textquoteright}s) that exchange routing information using the BorderGateway Protocol (BGP). The operators of each AS must have control over the flow of traffic through their network and between neighboring AS{\textquoteright}s. However, BGP is a complicated, policy-based protocol that does not include any direct support for traffic engineering. In previous work, we have demonstrated that network operators can adapt the flow of traffic in an efficient and predictable fashion through careful adjustments to the BGP policies running on their edge routers. Nevertheless, many details of the BGP protocol and decision process make predicting the effects of these policy changes difficult. In this paper, we describe a tool that predicts traffic flow at network exit points based on the network topology, the import policy associated with each BGP session, and the routing advertisements received from neighboring AS{\textquoteright}s. We present a linear-time algorithm that computes a network-wide view of the best BGP routes for each destination prefix given a static snapshot of the network state, without simulating the complex details of BGP message passing. We describe how to construct this snapshot using the BGP routing tables and router configuration files available from operational routers. We verify the accuracy of our algorithm by applying our tool to routing and configuration data from AT\&T{\textquoteright}s commercial IP network. Our route prediction techniques help support the operation of large IP backbone networks, where interdomain routing is an important aspect of traffic engineering. }, author = {Feamster, Nick and Rexford,J.} } @conference {11901, title = {A non-intrusive Kalman filter-based tracker for pursuit eye movement}, booktitle = {American Control Conference, 2002. Proceedings of the 2002}, volume = {2}, year = {2002}, month = {2002///}, pages = {1443- 1447 vol.2 - 1443- 1447 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {In this paper, we introduce a new non-intrusive approach to estimating the eye position during pursuit motion of the eye. We introduce a new characterization for the pursuit eye movement. Our characterization is based on the decomposition of the pursuit eye motion into a deterministic component and random component. We use a discrete Kalman filter to estimate the random component and calculate the deterministic component. We add the two components to obtain an estimate of the eye position. Simulation results are provided to illustrate the eye position estimation.}, keywords = {Application software, characterization, Computer vision, Current measurement, deterministic component, Electric variables measurement, eye position estimation, eye tracking, gaze tracking, Human computer interaction, Kalman filter, Kalman filters, Lenses, Motion estimation, Optical reflection, pursuit eye movement, pursuit motion, random component, Skin, tracking}, isbn = {0-7803-7298-0}, doi = {10.1109/ACC.2002.1023224}, url = {http://ieeexplore.ieee.org/ielx5/7965/22015/01023224.pdf?tp=\&arnumber=1023224\&isnumber=22015}, author = {Abd-Almageed, Wael and Fadali,M. S and Bebis,G.} } @article {15299, title = {Omnibase: Uniform access to heterogeneous data for question answering}, journal = {Natural Language Processing and Information Systems}, year = {2002}, month = {2002///}, pages = {230 - 234}, abstract = {Although the World Wide Web contains a tremendous amount of information, the lack of uniform structure makes finding the right knowledge difficult. A solution is to turn the Web into a {\textquotedblleft}virtual database{\textquotedblright} and to access it through natural language.We built Omnibase, a system that integrates heterogeneous data sources using an object- property-value model. With the help of Omnibase, our Start natural language system can now access numerous heterogeneous data sources on the Web in a uniform manner, and answers millions of user questions with high precision.}, doi = {10.1007/3-540-36271-1_23}, author = {Katz,B. and Felshin,S. and Yuret,D. and Ibrahim,A. and Jimmy Lin and Marton,G. and Jerome McFarland,A. and Temelkuran,B.} } @article {18486, title = {Packet loss recovery for streaming video}, journal = {12th International Packet Video Workshop}, year = {2002}, month = {2002///}, abstract = {While there is an increasing demand for streaming video applica-tions on the Internet, various network characteristics make the de- ployment of these applications more challenging than traditional TCP-based applications like email and the Web. Packet loss can be detrimental to compressed video with interdependent frames be- cause errors potentially propagate across many frames. While la- tency requirements do not permit retransmission of all lost data, we leverage the characteristics of MPEG-4 to selectively retrans- mit only the most important data in the bitstream. When latency constraints do not permit retransmission, we propose a mechanism for recovering this data using postprocessing techniques at the re- ceiver. We quantify the effects of packet loss on the quality of MPEG-4 video, develop an analytical model to explain these ef- fects, present a system to adaptively deliver MPEG-4 video in the face of packet loss and variable Internet conditions, and evaluate the effectiveness of the system under various network conditions. }, author = {Feamster, Nick and Balakrishnan,H.} } @conference {13906, title = {Physical Programming: Designing Tools for Children to Create Physical Interactive}, booktitle = {Proceedings: SIGCHI}, year = {2002}, month = {2002///}, author = {Montemayor,J. and Druin, Allison and Farber,A. and Simms,S. and Churaman,W.} } @inbook {14248, title = {Polydioptric Cameras: New Eyes for Structure from Motion}, booktitle = {Pattern RecognitionPattern Recognition}, series = {Lecture Notes in Computer Science}, volume = {2449}, year = {2002}, month = {2002///}, pages = {618 - 625}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We examine the influence of camera design on the estimation of the motion and structure of a scene from video data. Every camera captures a subset of the light rays passing though some volume in space. By relating the differential structure of the time varying space of light rays to different known and new camera designs, we can establish a hierarchy of cameras. This hierarchy is based upon the stability and complexity of the computations necessary to estimate structure and motion. At the low end of this hierarchy is the standard planar pinhole camera for which the structure from motion problem is non-linear and ill-posed. At the high end is a camera, which we call the full field of view polydioptric camera, for which the problem is linear and stable. We develop design suggestions for the polydioptric camera, and based upon this new design we propose a linear algorithm for structure-from-motion estimation, which combines differential motion estimation with differential stereo.}, isbn = {978-3-540-44209-7}, url = {http://dx.doi.org/10.1007/3-540-45783-6_74}, author = {Neumann, Jan and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Van Gool,Luc} } @article {12045, title = {Polydioptric cameras: New eyes for structure from motion}, journal = {Pattern Recognition}, year = {2002}, month = {2002///}, pages = {618 - 625}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {17865, title = {Processing large-scale multi-dimensional data in parallel and distributed environments}, journal = {Parallel Computing}, volume = {28}, year = {2002}, month = {2002/05//}, pages = {827 - 859}, abstract = {Analysis of data is an important step in understanding and solving a scientific problem. Analysis involves extracting the data of interest from all the available raw data in a dataset and processing it into a data product. However, in many areas of science and engineering, a scientist{\textquoteright}s ability to analyze information is increasingly becoming hindered by dataset sizes. The vast amount of data in scientific datasets makes it a difficult task to efficiently access the data of interest, and manage potentially heterogeneous system resources to process the data. Subsetting and aggregation are common operations executed in a wide range of data-intensive applications. We argue that common runtime and programming support can be developed for applications that query and manipulate large datasets. This paper presents a compendium of frameworks and methods we have developed to support efficient execution of subsetting and aggregation operations in applications that query and manipulate large, multi-dimensional datasets in parallel and distributed computing environments.}, keywords = {Data-intensive applications, Distributed computing, Multi-dimensional datasets, PARALLEL PROCESSING, Runtime systems}, isbn = {0167-8191}, doi = {10.1016/S0167-8191(02)00097-2}, url = {http://www.sciencedirect.com/science/article/pii/S0167819102000972}, author = {Beynon,Michael and Chang,Chialin and Catalyurek,Umit and Kurc,Tahsin and Sussman, Alan and Andrade,Henrique and Ferreira,Renato and Saltz,Joel} } @conference {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.} } @article {18719, title = {Structural Properties of Polyubiquitin Chains in Solution}, journal = {Journal of Molecular Biology}, volume = {324}, year = {2002}, month = {2002/12/06/}, pages = {637 - 647}, abstract = {Because polyubiquitin chain structure modulates Ub-mediated signaling, knowledge of the physiological conformations of chain signals should provide insights into specific recognition. Here, we characterized the solution conformations of K48-linked Ub2 and Ub4 using a combination of NMR techniques, including chemical shift mapping of the interdomain interface, domain orientation measurements on the basis of 15N relaxation and residual dipolar couplings, and the solvent accessibility studies. Our data indicate a switch in the conformation of Ub2, from open to closed, with increasing pH. The closed conformation features a well-defined interface that is related to, but distinguishable from, that observed in the Ub2 crystal structure. This interface is dynamic in solution, such that important hydrophobic residues (L8, I44, V70) that are sequestered at the interface in the closed conformation may be accessible for direct interactions with recognition factors. Our results suggest that the distal two units of Ub4, which is the minimum signal for efficient proteasomal degradation, may adopt the closed Ub2 conformation.}, keywords = {chemical shift mapping, domain orientation measurements, polyubiquitin chains, spin relaxation, ubiquitin}, isbn = {0022-2836}, doi = {10.1016/S0022-2836(02)01198-1}, url = {http://www.sciencedirect.com/science/article/pii/S0022283602011981}, author = {Varadan,Ranjani and Walker,Olivier and Pickart,Cecile and Fushman, David} } @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 {18604, title = {Topology inference from BGP routing dynamics}, booktitle = {Proceedings of the 2nd ACM SIGCOMM Workshop on Internet measurment}, series = {IMW {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {243 - 248}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a method of inferring logical relationships between network prefixes within an Autonomous System (AS) using only passive monitoring of BGP messages. By clustering these prefixes based upon similarities between their update times, we create a hierarchy linking the prefixes within the larger AS. We can frequently identify groups of prefixes routed to the same ISP Point of Presence (POP), despite the lack of identifying information in the BGP messages. Similarly, we observe disparate prefixes under common organizational control, or with long shared network paths. In addition to discovering interesting network characteristics, our passive method facilitates topology discovery by potentially reducing the number of active probes required in traditional traceroute-based Internet mapping mechanisms.}, isbn = {1-58113-603-X}, doi = {10.1145/637201.637239}, url = {http://doi.acm.org/10.1145/637201.637239}, author = {Andersen,David G. and Feamster, Nick and Bauer,Steve and Balakrishnan,Hari} } @article {13479, title = {Virtual Telescopes in Education}, journal = {Journal of Digital Information}, volume = {2}, year = {2002}, month = {2002///}, abstract = {Virtual Telescopes in Education is providing the services required to operate a virtual observatory comprising distributed telescopes, including an interactive, constraint-based scheduling service, data and resource archive, proposal preparation and review environment, and a VTIE Journal. A major goal of VTIE is to elicit from learners questions about the nature of celestial objects and the physical processes that give rise to the spectacular imagery that catches their imaginations. Generation of constrained science questions will assist learners in the science process. To achieve interoperability with other NSDL resources, our approach follows the Open Archives Initiative and the W3C Semantic Web activity.}, author = {Hoban,S. and desJardins, Marie and Farrell,N. and Rathod,P. and Sachs,J. and Sansare,S. and Yesha,Y. and Keating,J. and Busschots,B. and Means,J. and others} } @article {12060, title = {Visual space-time geometry - A tool for perception and the imagination}, journal = {Proceedings of the IEEE}, volume = {90}, year = {2002}, month = {2002/07//}, pages = {1113 - 1135}, abstract = {Although the fundamental ideas underlying research efforts in the field of computer vision have not radically changed in the past two decades, there has been a transformation in the way work in this field is conducted. This is primarily due to the emergence of a number of tools, of both a practical and a theoretical nature. One such tool, celebrated throughout the nineties, is the geometry of visual space-time. It is known under a variety of headings, such as multiple view geometry, structure from motion, and model building. It is a mathematical theory relating multiple views (images) of a scene taken at different viewpoints to three-dimensional models of the (possibly dynamic) scene. This mathematical theory gave rise to algorithms that take as input images (or video) and provide as output a model of the scene. Such algorithms are one of the biggest successes of the field and they have many applications in other disciplines, such as graphics (image-based rendering, motion capture) and robotics (navigation). One of the difficulties, however is that the current tools cannot yet be fully automated, and they do not provide very accurate results. More research is required for automation and high precision. During the past few years we have investigated a number of basic questions underlying the structure from motion problem. Our investigations resulted in a small number of principles that characterize the problem. These principles, which give rise to automatic procedures and point to new avenues for studying the next level of the structure from motion problem, are the subject of this paper.}, keywords = {3-D motion estimation, Buildings, Computer vision, Geometry, Graphics, Image sequences, Layout, Mathematical model, mathematical theory, model building, Motion estimation, multiple view geometry, multiple views, Navigation, optical flow, optical illusions, patch correspondence, Rendering (computer graphics), Robotics and automation, Solid modeling, structure from motion, three-dimensional models, visual space-time}, isbn = {0018-9219}, doi = {10.1109/JPROC.2002.801440}, author = {Ferm{\"u}ller, Cornelia and Baker, P. and Aloimonos, J.} } @conference {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.} } @article {14198, title = {Animated heads: From 3d motion fields to action descriptions}, journal = {Proceedings of the IFIP TC5/WG5}, volume = {10}, year = {2001}, month = {2001///}, pages = {1 - 11}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {18318, title = {Attentive toys}, booktitle = {International Conference on Multimedia and Expo}, volume = {22}, year = {2001}, month = {2001///}, pages = {25 - 25}, author = {Haritaoglu,I. and Cozzi,A. and Koons,D. and Flickner,M. and Zotkin,Dmitry N and Yacoob,Yaser} } @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} } @conference {14293, title = {Detecting format string vulnerabilities with type qualifiers}, booktitle = {Proceedings of the 10th conference on USENIX Security Symposium-Volume 10}, year = {2001}, month = {2001///}, pages = {16 - 16}, author = {Shankar,U. and Talwar,K. and Foster, Jeffrey S. and Wagner,D.} } @conference {18566, title = {Dos and don{\textquoteright}ts of client authentication on the web}, booktitle = {Proceedings of the 10th conference on USENIX Security Symposium - Volume 10}, series = {SSYM{\textquoteright}01}, year = {2001}, month = {2001///}, pages = {19 - 19}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Client authentication has been a continuous source of problems on the Web. Although many well-studied techniques exist for authentication, Web sites continue to use extremely weak authentication schemes, especially in non-enterprise environments such as store fronts. These weaknesses often result from careless use of authenticators within Web cookies. Of the twenty-seven sites we investigated, we weakened the client authentication on two systems, gained unauthorized access on eight, and extracted the secret key used to mint authenticators from one. We provide a description of the limitations, requirements, and security models specific to Web client authentication. This includes the introduction of the interrogative adversary, a surprisingly powerful adversary that can adaptively query a Web site. We propose a set of hints for designing a secure client authentication scheme. Using these hints, we present the design and analysis of a simple authentication scheme secure against forgeries by the interrogative adversary. In conjunction with SSL, our scheme is secure against forgeries by the active adversary.}, url = {http://dl.acm.org/citation.cfm?id=1267612.1267631}, author = {Fu,Kevin and Sit,Emil and Smith,Kendra and Feamster, Nick} } @inbook {17594, title = {Experimental Analysis of Algorithms for Bilateral-Contract Clearing Mechanisms Arising in Deregulated Power Industry}, booktitle = {Algorithm EngineeringAlgorithm Engineering}, series = {Lecture Notes in Computer Science}, volume = {2141}, year = {2001}, month = {2001///}, pages = {172 - 184}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We consider the bilateral contract satisfaction problem arising from electrical power networks due to the proposed deregulation of the electric utility industry in the USA. Given a network and a (multi)set of pairs of vertices (contracts) with associated demands, the goal is to find the maximum number of simultaneously satisfiable contracts. We study how four different algorithms perform in fairly realistic settings; we use an approximate electrical power network from Colorado. Our experiments show that three heuristics outperform a theoretically better algorithm. We also test the algorithms on four types of scenarios that are likely to occur in a deregulated marketplace. Our results show that the networks that are adequate in a regulated marketplace might be inadequate for satisfying all the bilateral contracts in a deregulated industry.}, isbn = {978-3-540-42500-7}, url = {http://dx.doi.org/10.1007/3-540-44688-5_14}, author = {Barrett,Chris and Cook,Doug and Hicks,Gregory and Faber,Vance and Marathe,Achla and Marathe,Madhav and Srinivasan, Aravind and Sussmann,Yoram and Thornquist,Heidi}, editor = {Brodal,Gerth and Frigioni,Daniele and Marchetti-Spaccamela,Alberto} } @inbook {14217, title = {Eyes from Eyes}, booktitle = {3D Structure from Images {\textemdash} SMILE 20003D Structure from Images {\textemdash} SMILE 2000}, series = {Lecture Notes in Computer Science}, volume = {2018}, year = {2001}, month = {2001///}, pages = {204 - 217}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We describe a family of new imaging systems, called Argus eyes, that consist of common video cameras arranged in some network. The system we built consists of six cameras arranged so that they sample different parts of the visual sphere. This system has the capability of very accurately estimating its own 3D motion and consequently estimating shape models from the individual videos. The reason is that inherent ambiguities of confusion between translation and rotation disappear in this case. We provide an algorithm and several experiments using real outdoor or indoor images demonstrating the superiority of the new sensor with regard to 3D motion estimation.}, isbn = {978-3-540-41845-0}, url = {http://dx.doi.org/10.1007/3-540-45296-6_14}, author = {Baker,Patrick and Pless,Robert and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Pollefeys,Marc and Van Gool,Luc and Zisserman,Andrew and Fitzgibbon,Andrew} } @book {14218, title = {Eyes from Eyes: Analysis of Camera Design Using Plenoptic Video Geometry}, year = {2001}, month = {2001///}, publisher = {Computer Vision Laboratory, Center for Automation Research, University of Maryland}, organization = {Computer Vision Laboratory, Center for Automation Research, University of Maryland}, abstract = {We investigate the relationship between camera design and the problem of recovering the motion andstructure of a scene from video data. The visual information that could possibly be obtained is described by the plenoptic function. A camera can be viewed as a device that captures a subset of this function, that is, it measures some of the light rays in some part of the space. The information contained in the subset determines how difficult it is to solve subsequent interpretation processes. By examining the differential structure of the time varying plenoptic function we relate different known and new camera models to the spatio-temporal structure of the observed scene. This allows us to define a hierarchy of camera designs, where the order is determined by the stability and complexity of the computations necessary to estimate structure and motion. At the low end of this hierarchy is the standard planar pinhole camera for which the structure from motion problem is non-linear and ill-posed. At the high end is a camera, which we call the full field of view polydioptric camera, for which the problem is linear and stable. In between are multiple-view cameras with large fields of view which we have built, as well as catadioptric panoramic sensors and other omni-directional cameras. We develop design suggestions for the polydioptric camera, and based upon this new design we propose a linear algorithm for ego- motion estimation, which in essence combines differential motion estimation with differential stereo. }, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J. and University of Maryland (College Park, Md.). Center for Automation Research} } @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} } @inbook {14221, title = {Geometry of Eye Design: Biology and Technology}, booktitle = {Multi-Image Analysis}, series = {Lecture Notes in Computer Science}, volume = {2032}, year = {2001}, month = {2001///}, pages = {22 - 38}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Natural or artificial vision systems process the images that they collect with their eyes or cameras in order to derive information for performing tasks related to navigation and recognition. Since the way images are acquired determines how dificult it is to perform a visual task, and since systems have to cope with limited resources, the eyes used by a specific system should be designed to optimize subsequent image processing as it relates to particular tasks. Different ways of sampling light, i.e., different eyes, may be less or more powerful with respect to particular competences. This seems intuitively evident in view of the variety of eye designs in the biological world. It is shown here that a spherical eye (an eye or system of eyes providing panoramic vision) is superior to a camera-type eye (an eye with restricted field of view) as regards the competence of three-dimensional motion estimation. This result is derived from a statistical analysis of all the possible computational models that can be used for estimating 3D motion from an image sequence. The findings explain biological design in a mathematical manner, by showing that systems that fly and thus need good estimates of 3D motion gain advantages from panoramic vision. Also, insights obtained from this study point to new ways of constructing powerful imaging devices that suit particular tasks in robotics, visualization and virtual reality better than conventional cameras, thus leading to a new camera technology.}, isbn = {978-3-540-42122-1}, url = {http://dx.doi.org/10.1007/3-540-45134-X_2}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Klette,Reinhard and Gimel{\textquoteright}farb,Georgy and Huang,Thomas} } @article {18852, title = {Integrated Microelectromechanical System (MEMS) Inertial Measurement Unit (IMIMU)}, year = {2001}, month = {2001/12//}, institution = {CARNEGIE-MELLON UNIVERSITY}, abstract = {Processes, designs and design tools are developed to enable the monolithic integration of arrays of inertial microsensors with electronics. Accelerometers and gyroscopes, fabricated in a single CMOS process, are functional and demonstrate a single chip IMU. Two integrated post CMOS micro-machining processes are demonstrated. Thin-film microstructures are defined from the metal-dielectric stack of a conventional process. In the second process, a back-side silicon etch, followed by front-side DRIE produces bulk silicon microstructures. Accelerometer and gyroscope designs are developed with accompanying low noise electronic circuitry. Noise performance was limited to 1/f circuit noise. The chip output sensibility is set by the interface circuit design. A thermally stabilized accelerometer and circuit design is demonstrated using embedded polysilicon resistors as temperature sensors and heaters in a closed loop. Nested gyroscope topologies are demonstrated with a lateral MEMS accelerometer used as a coriolis acceleration sensor. Modeling and simulation tools that simultaneously consider the electromechanical transducer and the electronic circuit to predict system performance are developed. Electrical, electromechanical and mechanical parasitics required to enable predictive lumped parameter simulation are identified and can be extracted, enabling a designer to confidently estimate design performance prior to fabrication. Generic physics-based fault models for surface-micromachined actuators and sensors are developed that enable effective testing, diagnosis and design for manufacturability.}, keywords = {*ELECTROMECHANICAL DEVICES, *GYROSCOPES, *INERTIAL MEASUREMENT UNITS, *INERTIAL NAVIGATION, *MICROELECTROMECHANICAL SYSTEMS, ACCELEROMETERS, BULK MATERIALS, CHIPS(ELECTRONICS), CIRCUITS, CLOSED LOOP SYSTEMS, CORIOLIS EFFECT, Detectors, DIELECTRICS, ELECTRICAL AND ELECTRONIC EQUIPMENT, EMBEDDING, METALS, MICROSENSORS., MICROSTRUCTURE, MONOLITHIC STRUCTURES(ELECTRONICS), NAVIGATION AND GUIDANCE, PARASITES, PE63739E, PERFORMANCE(ENGINEERING), POLYSILICONS, RESISTORS, SILICON, TEMPERATURE SENSITIVE ELEMENTS, THERMAL STABILITY, THIN FILMS, tools, Topology, WUAFRLE1170030}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA399565}, author = {Fedder,Gary K. and Blanton,Shawn and Carley,L. R. and Gupta, Satyandra K. and Koester,David} } @article {18488, title = {On the interactions between layered quality adaptation and congestion control for streaming video}, journal = {11th International Packet Video Workshop}, year = {2001}, month = {2001///}, abstract = {This paper uses analysis and experiments to study the impact of var-ious congestion control algorithms and receiver buffering strategies on the performance of streaming media delivery. While traditional congestion avoidance schemes such as TCP{\textquoteright}s additive-increase/- multiplicativedecrease (AIMD) achieve high utilization, they also cause large oscillations in transmission rates that degrade the smooth- ness and perceptual quality of the video stream. We focus on un- derstanding the interactions of a family of congestion control al- gorithms that generalize AIMD, with buffer-based quality adapta- tion algorithms for hierarchically-encoded and simulcast video. Our work builds on and extends the results of Rejaie et al. [19]; we find that the combination of a non-AIMD algorithm that has smaller os- cillations than AIMD and a suitable receiver buffer allocation and management strategy provides a good combination of low playout delay and TCP-friendly congestion control. The paper describes these mechanisms and the results of experiments conducted using a prototype video server for MPEG-4 video, showing that our ap- proach can improve the interactivity and adaptivity of Internet video. }, author = {Feamster, Nick and Bansal,D. and Balakrishnan,H.} } @article {13897, title = {KidStory: A technology design partnership with children}, journal = {Behaviour \& Information Technology}, volume = {20}, year = {2001}, month = {2001///}, pages = {119 - 125}, author = {Tax{\'e}n,G. and Druin, Allison and Fast,C. and Kjellin,M.} } @article {14422, title = {Learning probabilistic models of relational structure}, journal = {MACHINE LEARNING-INTERNATIONAL WORKSHOP}, year = {2001}, month = {2001///}, pages = {170 - 177}, abstract = {Most real-world data is stored in relational form. Incontrast, most statistical learning methods work with {\textquotedblleft}flat{\textquotedblright} data representations, forcing us to convert our data into a form that loses much of the relational struc- ture. The recently introduced framework of proba- bilistic relational models (PRMs) allows us to repre- sent probabilistic models over multiple entities that utilize the relations between them. In this paper, we propose the use of probabilistic models not only for the attributes in a relational model, but for the rela- tional structure itself. We propose two mechanisms for modeling structural uncertainty: reference uncertainty and existence uncertainty. We describe the appropriate conditions for using each model and present learning algorithms for each. We present experimental results showing that the learned models can be used to pre- dict relational structure and, moreover, the observed relational structure can be used to provide better pre- dictions for the attributes in the model. }, author = {Getoor, Lise and Friedman,N. and Koller,D. and Taskar,B.} } @article {17628, title = {Near-optimal design of MP S tunnels with shared recovery}, journal = {DIMACS Mini-Workshop on Quality of Service Issues in the Internet}, year = {2001}, month = {2001///}, abstract = {We describe the optimization problem associ-ated with the concurrent routing of demands with guar- anteed shared recovery in case of network failures. This problem arises in routing with protection in meshes and is known to be hard. We describe the problem in the context of the efficient design of restorable MP S tunnels in optical networks. The underlying design gives rise to a stochastic optimization problem that is equivalent to a (very) large- scale linear programming (LP) problem that explicitly in- corporates the network failure scenarios. The feasible re- gion for this LP is given by combined packing and cover- ing constraints for concurrent and optimal multicommodity flows. We develop a novel -approximation procedure for this problem and demonstrate its performance for a variety of real network sizes. An attraction of our approach is that its main computation consists of routing flow along a pair of short paths and these paths are easily found. Commer- cial general-purpose LP solvers are typically unable to solve these problems once they become large enough, while our approach scales for large networks. We conclude that the proposed scheme provides guaranteed approximation to the design of restorable MP S tunnels with shared protection within realistic network settings. }, author = {Fleischer,L. and Meyerson,A. and Saniee,I. and Shepherd,FB and Srinivasan, Aravind} } @conference {14400, title = {Probabilistic models of relational structure}, booktitle = {In Proc. ICML}, year = {2001}, month = {2001///}, abstract = {Most real-world data is stored in relational form. In contrast, most statistical learning methods work with {\textquotedblleft}flat {\textquotedblright} data representations, forcing us to convert our data into a form that loses much of the relational structure. The recently introduced framework of probabilistic relational models (PRMs) allows us to represent probabilistic models over multiple entities that utilize the relations between them. In this paper, we propose the use of probabilistic models not only for the attributes in a relational model, but for the relational structure itself. We propose two mechanisms for modeling structural uncertainty: reference uncertainty and existence uncertainty. We describe the appropriate conditions for using each model and present learning algorithms for each. We present experimental results showing that the learned models can be used to predict relational structure and, moreover, the observed relational structure can be used to provide better predictions for the attributes in the model.}, author = {Getoor, Lise and Friedman,N. and Taskar,B.} } @article {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.} } @article {18710, title = {Rescuing a destabilized protein fold through backbone cyclization}, journal = {Journal of Molecular Biology}, volume = {308}, year = {2001}, month = {2001/05/18/}, pages = {1045 - 1062}, abstract = {We describe the physicochemical characterization of various circular and linear forms of the \~{}60 residue N-terminal Src homology 3 (SH3) domain from the murine c-Crk adapter protein. Structural, dynamic, thermodynamic, kinetic and biochemical studies reveal that backbone circularization does not prevent the adoption of the natural folded structure in any of the circular proteins. Both the folding and unfolding rate of the protein increased slightly upon circularization. Circularization did not lead to a significant thermodynamic stabilization of the full-length protein, suggesting that destabilizing enthalpic effects (e.g. strain) negate the expected favorable entropic contribution to overall stability. In contrast, we find circularization results in a dramatic stabilization of a truncated version of the SH3 domain lacking a key glutamate residue. The ability to rescue the destabilized mutant indicates that circularization may be a useful tool in protein engineering programs geared towards generating minimized proteins.}, keywords = {circular protein, ligation, SH3 domain}, isbn = {0022-2836}, doi = {10.1006/jmbi.2001.4631}, url = {http://www.sciencedirect.com/science/article/pii/S0022283601946315}, author = {Camarero,Julio A and Fushman, David and Sato,Satoshi and Giriat,Izabela and Cowburn,David and Raleigh,Daniel P and Muir,Tom W} } @conference {14188, title = {A spherical eye from multiple cameras (makes better models of the world)}, booktitle = {Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2001. CVPR 2001}, volume = {1}, year = {2001}, month = {2001///}, pages = {I-576- I-583 vol.1 - I-576- I-583 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {The paper describes an imaging system that has been designed specifically for the purpose of recovering egomotion and structure from video. The system consists of six cameras in a network arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and consequently the estimation of shape models from the individual cameras. The reason is that inherent ambiguities of confusion between translation and rotation disappear. We provide algorithms for the calibration of the system and 3D motion estimation. The calibration is based on a new geometric constraint that relates the images of lines parallel in space to the rotation between the cameras. The 3D motion estimation uses a constraint relating structure directly to image gradients.}, keywords = {3D motion estimation, Calibration, camera network, CAMERAS, Computer vision, egomotion recovery, geometric configuration, geometric constraint, image gradients, image sampling, imaging system, Laboratories, Layout, Motion estimation, multiple cameras, Pixel, Robot vision systems, SHAPE, shape models, Space technology, spherical eye, system calibration, video, video cameras, video signal processing, visual sphere sampling}, isbn = {0-7695-1272-0}, doi = {10.1109/CVPR.2001.990525}, author = {Baker, P. and Ferm{\"u}ller, Cornelia and Aloimonos, J. and Pless, R.} } @inbook {14261, title = {Statistics Explains Geometrical Optical Illusions}, booktitle = {Foundations of Image UnderstandingFoundations of Image Understanding}, series = {The Kluwer International Series in Engineering and Computer Science}, volume = {628}, year = {2001}, month = {2001///}, pages = {409 - 445}, publisher = {Springer US}, organization = {Springer US}, abstract = {Azriel Rosenfeld has been our mentor for the last decade. In everyday conversation he stressed the importance of intuition, the unreasonable effectiveness of mathematics in understanding the world, and the power of simplicity inherent in deep ideas. Because we mostly worked on 3D vision, he often argued that 2D vision has been, is, and will continue to be a large source of problems. Strangely enough, we arrived at this study, which is our first on 2D vision, through problems we encountered in our work in 3D motion and shape. Azriel Rosenfeld was also one of the first to apply statistics [ 27 , 28 ] to image analysis and understanding, and he always reminded us of the uncertainties involved in visual computations. This paper shows that statistics cannot be ignored, not even in the interpretation of two simple straight intersecting lines. It demonstrates that uncertainty in the visual data causes problems for the early visual processes. Because of noise, the estimation of features, such as lines, intersections of lines, and local image motion, is biased. The inevitability of this bias provides an explanation for many well-known geometrical optical illusions.}, isbn = {978-1-4615-1529-6}, url = {http://dx.doi.org/10.1007/978-1-4615-1529-6_14}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Davis, Larry S.} } @article {14170, title = {The Statistics of Optical Flow}, journal = {Computer Vision and Image Understanding}, volume = {82}, year = {2001}, month = {2001/04//}, pages = {1 - 32}, abstract = {When processing image sequences some representation of image motion must be derived as a first stage. The most often used representation is the optical flow field, which is a set of velocity measurements of image patterns. It is well known that it is very difficult to estimate accurate optical flow at locations in an image which correspond to scene discontinuities. What is less well known, however, is that even at the locations corresponding to smooth scene surfaces, the optical flow field often cannot be estimated accurately.Noise in the data causes many optical flow estimation techniques to give biased flow estimates. Very often there is consistent bias: the estimate tends to be an underestimate in length and to be in a direction closer to the majority of the gradients in the patch. This paper studies all three major categories of flow estimation methods{\textemdash}gradient-based, energy-based, and correlation methods, and it analyzes different ways of compounding one-dimensional motion estimates (image gradients, spatiotemporal frequency triplets, local correlation estimates) into two-dimensional velocity estimates, including linear and nonlinear methods. Correcting for the bias would require knowledge of the noise parameters. In many situations, however, these are difficult to estimate accurately, as they change with the dynamic imagery in unpredictable and complex ways. Thus, the bias really is a problem inherent to optical flow estimation. We argue that the bias is also integral to the human visual system. It is the cause of the illusory perception of motion in the Ouchi pattern and also explains various psychophysical studies of the perception of moving plaids. }, isbn = {1077-3142}, doi = {10.1006/cviu.2000.0900}, url = {http://www.sciencedirect.com/science/article/pii/S1077314200909007}, author = {Ferm{\"u}ller, Cornelia and Shulman,David and Aloimonos, J.} } @conference {12098, title = {A trend analysis of exploitations}, booktitle = {2001 IEEE Symposium on Security and Privacy, 2001. S\&P 2001. Proceedings}, year = {2001}, month = {2001///}, pages = {214 - 229}, publisher = {IEEE}, organization = {IEEE}, abstract = {We have conducted an empirical study of a number of computer security exploits and determined that the rates at which incidents involving the exploit are reported to CERT can be modeled using a common mathematical framework. Data associated with three significant exploits involving vulnerabilities in phf, imap, and bind can all be modeled using the formula C=I+S{\texttimes}√M where C is the cumulative count of reported incidents, M is the time since the start of the exploit cycle, and I and S are the regression coefficients determined by analysis of the incident report data. Further analysis of two additional exploits involving vulnerabilities in mountd and statd confirm the model. We believe that the models will aid in predicting the severity of subsequent vulnerability exploitations, based on the rate of early incident reports}, keywords = {Computer science, computer security exploits, Data analysis, data mining, Educational institutions, exploitations, Performance analysis, Predictive models, Regression analysis, Risk management, security of data, software engineering, system intrusions, System software, trend analysis, vulnerabilities, vulnerability exploitation}, isbn = {0-7695-1046-9}, doi = {10.1109/SECPRI.2001.924300}, author = {Browne,H. K and Arbaugh, William A. and McHugh,J. and Fithen,W. L} } @article {13353, title = {Adaptive query processing: Technology in evolution}, journal = {IEEE Data Engineering Bulletin}, volume = {23}, year = {2000}, month = {2000///}, pages = {7 - 18}, abstract = {As query engines are scaled and federated, they must cope with highly unpredictable and changeableenvironments. In the Telegraph project, we are attempting to architect and implement a continuously adaptive query engine suitable for global-area systems, massive parallelism, and sensor networks. To set the stage for our research, we present a survey of prior work on adaptive query processing, focusing on three characterizations of adaptivity: the frequency of adaptivity, the effects of adaptivity, and the extent of adaptivity. Given this survey, we sketch directions for research in the Telegraph project. }, author = {Hellerstein,J. M and Franklin,M.J. and Chandrasekaran,S. and Deshpande, Amol and Hildrum,K. and Madden,S. and Raman,V. and Shah,M. A} } @inbook {14197, title = {Analyzing Action Representations}, booktitle = {Algebraic Frames for the Perception-Action CycleAlgebraic Frames for the Perception-Action Cycle}, series = {Lecture Notes in Computer Science}, volume = {1888}, year = {2000}, month = {2000///}, pages = {1 - 21}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We argue that actions represent the basic seed of intelligence underlying perception of the environment, and the representations encoding actions should be the starting point upon which further studies of cognition are built. In this paper we make a first effort in characterizing these action representations. In particular, from the study of simple actions related to 3D rigid motion interpretation, we deduce a number of principles for the possible computations responsible for the interpretation of space-time geometry. Using these principles, we then discuss possible avenues on how to proceed in analyzing the representations of more complex human actions.}, isbn = {978-3-540-41013-3}, url = {http://dx.doi.org/10.1007/10722492_1}, author = {Aloimonos, J. and Ferm{\"u}ller, Cornelia}, editor = {Sommer,Gerald and Zeevi,Yehoshua} } @article {17576, title = {Combinatorial Problems Arising in Deregulated Electrical Power Industry: Survey and Future Directions}, journal = {NONCONVEX OPTIMIZATION AND ITS APPLICATIONS}, volume = {42}, year = {2000}, month = {2000///}, pages = {138 - 162}, author = {Cook,D. and Hicks,G. and Faber,V. and Marathe,M. V and Srinivasan, Aravind and Sussmann,Y. J and Thornquist,H.} } @conference {17847, title = {DataCutter: Middleware for filtering very large scientific datasets on archival storage systems}, booktitle = {NASA conference publication}, year = {2000}, month = {2000///}, pages = {119 - 134}, author = {Beynon, M. and Ferreira,R. and Kurc, T. and Sussman, Alan and Saltz, J.} } @article {18296, title = {Design and use of linear models for image motion analysis}, journal = {International Journal of Computer Vision}, volume = {36}, year = {2000}, month = {2000///}, pages = {171 - 193}, author = {Fleet,D. J and Black,M. J and Yacoob,Yaser and Jepson,A. D} } @conference {14287, title = {A first step towards automated detection of buffer overrun vulnerabilities}, booktitle = {The 2000 Network and Distributed Systems Security Conference. San Diego, CA}, volume = {14}, year = {2000}, month = {2000///}, author = {Wagner,D. and Foster, Jeffrey S. and Brewer,E.A. and Aiken,A.} } @article {14438, title = {From instances to classes in probabilistic relational models}, journal = {Proc. ICML 2000 Workshop on Attribute-Value and Relational Learning}, year = {2000}, month = {2000///}, abstract = {Probabilistic graphical models, in particular Bayesian net-works, are useful models for representing statistical pat- terns in propositional domains. Recent work develops ef- fective techniques for learning these models directly from data. However these techniques apply only to attribute-value (i.e., flat) representations of the data. Probabilistic relational models (PRMs) allow us to represent much richer depen- dency structures, involving multiple entities and the rela- tions between them; they allow the properties of an entity to depend probabilistically on properties of related entities. PRMs represent a generic dependence, which is then instan- tiated for specific circumstances, i.e., for a particular set of entities and relations between them. Friedman et al. showed how to learn PRMs from relational data, and presented tech- niques for learning both parameters and probabilistic depen- dency structure for the attributes in a relational model. Here we examine the benefit that class hierarchies can provide PRMs. We show how the introduction of subclasses allows us to use inheritance and specialization to refine our models. We show how to learn PRMs with class hierarchies (PRM- CH) in two settings. In the first, the class hierarchy is pro- vided, as part of the input, in the relational schema for the domain. In the second setting, in addition to learning the PRM, we must learn the class hierarchy. Finally we dis- cuss how PRM-CHs allow us to build models that can repre- sent models for both particular instances in our domain, and classes of objects in our domain, bridging the gap between a class-based model and an attribute-value-based model. }, author = {Getoor, Lise and Koller,D. and Friedman,N.} } @article {14971, title = {High performance computing algorithms for land cover dynamics using remote sensing data}, journal = {International Journal of Remote Sensing}, volume = {21}, year = {2000}, month = {2000///}, pages = {1513 - 1536}, abstract = {Global and regional land cover studies need to apply complex models on selected subsets of large volumes of multi-sensor and multi-temporal data sets that have been derived from raw instrument measurements using widely accepted pre-processing algorithms. The computational and storage requirements of most of these studies far exceed what is possible on a single workstation environment. We have been pursuing a new approach that couples scalable and open distributed heterogeneous hardware with the development of high performance software for processing, indexing and organizing remotely sensed data. Hierarchical data management tools are used to ingest raw data, create metadata and organize the archived data so as to automatically achieve computational load balancing among the available nodes and minimize input/output overheads. We illustrate our approach with four specific examples. The first is the development of the first fast operational scheme for the atmospheric correction of Landsat Thematic Mapper scenes, while the second example focuses on image segmentation using a novel hierarchical connected components algorithm. Retrieval of the global Bidirectional Reflectance Distribution Function in the red and near-infrared wavelengths using four years (1983 to 1986) of Pathfinder Advanced Very High Resolution Radiometer (AVHRR) Land data is the focus of our third example. The fourth example is the development of a hierarchical data organization scheme that allows on-demand processing and retrieval of regional and global AVHRR data sets. Our results show that substantial reductions in computational times can be achieved by the high performance computing technology.}, isbn = {0143-1161}, doi = {10.1080/014311600210290}, url = {http://www.tandfonline.com/doi/abs/10.1080/014311600210290}, author = {Kalluri, SNV and JaJa, Joseph F. and Bader, D.A. and Zhang,Z. and Townshend,J.R.G. and Fallah-Adl,H.} } @conference {14232, title = {Multi-camera networks: eyes from eyes}, booktitle = {IEEE Workshop on Omnidirectional Vision, 2000. Proceedings}, year = {2000}, month = {2000///}, pages = {11 - 18}, publisher = {IEEE}, organization = {IEEE}, abstract = {Autonomous or semi-autonomous intelligent systems, in order to function appropriately, need to create models of their environment, i.e., models of space time. These are descriptions of objects and scenes and descriptions of changes of space over time, that is, events and actions. Despite the large amount of research on this problem, as a community we are still far from developing robust descriptions of a system{\textquoteright}s spatiotemporal environment using video input (image sequences). Undoubtedly, some progress has been made regarding the understanding of estimating the structure of visual space, but it has not led to solutions to specific applications. There is, however, an alternative approach which is in line with today{\textquoteright}s {\textquotedblleft}zeitgeist.{\textquotedblright} The vision of artificial systems can be enhanced by providing them with new eyes. If conventional video cameras are put together in various configurations, new sensors can be constructed that have much more power and the way they {\textquotedblleft}see{\textquotedblright} the world makes it much easier to solve problems of vision. This research is motivated by examining the wide variety of eye design in the biological world and obtaining inspiration for an ensemble of computational studies that relate how a system sees to what that system does (i.e. relating perception to action). This, coupled with the geometry of multiple views that has flourished in terms of theoretical results in the past few years, points to new ways of constructing powerful imaging devices which suit particular tasks in robotics, visualization, video processing, virtual reality and various computer vision applications, better than conventional cameras. This paper presents a number of new sensors that we built using common video cameras and shows their superiority with regard to developing models of space and motion}, keywords = {Biosensors, CAMERAS, Computer vision, Eyes, Image sequences, intelligent systems, Layout, Machine vision, Robot vision systems, Robustness, Spatiotemporal phenomena, video cameras, Virtual reality}, isbn = {0-7695-0704-2}, doi = {10.1109/OMNVIS.2000.853797}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J. and Baker, P. and Pless, R. and Neumann, J. and Stuart, B.} } @article {14234, title = {New eyes for building models from video}, journal = {Computational Geometry}, volume = {15}, year = {2000}, month = {2000/02//}, pages = {3 - 23}, abstract = {Models of real-world objects and actions for use in graphics, virtual and augmented reality and related fields can only be obtained through the use of visual data and particularly video. This paper examines the question of recovering shape models from video information. Given video of an object or a scene captured by a moving camera, a prerequisite for model building is to recover the three-dimensional (3D) motion of the camera which consists of a rotation and a translation at each instant. It is shown here that a spherical eye (an eye or system of eyes providing panoramic vision) is superior to a camera-type eye (an eye with restricted field of view such as a common video camera) as regards the competence of 3D motion estimation. This result is derived from a geometric/statistical analysis of all the possible computational models that can be used for estimating 3D motion from an image sequence. Regardless of the estimation procedure for a camera-type eye, the parameters of the 3D rigid motion (translation and rotation) contain errors satisfying specific geometric constraints. Thus, translation is always confused with rotation, resulting in inaccurate results. This confusion does not happen for the case of panoramic vision. Insights obtained from this study point to new ways of constructing powerful imaging devices that suit particular tasks in visualization and virtual reality better than conventional cameras, thus leading to a new camera technology. Such new eyes are constructed by putting together multiple existing video cameras in specific ways, thus obtaining eyes from eyes. For a new eye of this kind we describe an implementation for deriving models of scenes from video data, while avoiding the correspondence problem in the video sequence.}, keywords = {model building, shape reconstruction, structure from motion, video analysis}, isbn = {0925-7721}, doi = {10.1016/S0925-7721(99)00044-9}, url = {http://www.sciencedirect.com/science/article/pii/S0925772199000449}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J. and Brodsk{\'y},Tom{\'a}{\v s}} } @inbook {14236, title = {New Eyes for Shape and Motion Estimation}, booktitle = {Biologically Motivated Computer VisionBiologically Motivated Computer Vision}, series = {Lecture Notes in Computer Science}, volume = {1811}, year = {2000}, month = {2000///}, pages = {23 - 47}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Motivated by the full field of view of insect eyes and their fast and accurate estimation of egomotion, we constructed a system of cameras to take advantage of the full field of view (FOV) constraints that insects use. In this paper, we develop a new ego-motion algorithm for a rigidly mounted set of cameras undergoing arbitrary rigid motion. This egomotion algorithm combines the unambiguous components of the motion computed by each separate camera. We prove that the cyclotorsion is resistant to errors and show this empirically. We show how to calibrate the system with two novel algorithms, one using secondary cameras and one using self calibration. Given this system calibration, the new 3D motion algorithm first computes the rotation and then the 3D translation. We apply this algorithm to a camera system constructed with four rigidly mounted synchronized cameras pointing in various directions and present motion estimation results at www.cfar.umd.edu/ pbaker/argus.html.}, isbn = {978-3-540-67560-0}, url = {http://dx.doi.org/10.1007/3-540-45482-9_12}, author = {Baker,Patrick and Pless,Robert and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Lee,Seong-Whan and B{\"u}lthoff,Heinrich and Poggio,Tomaso} } @conference {14186, title = {A New Framework for Multi-camera Structure from Motion}, booktitle = {Mustererkennung 2000, 22. DAGM-Symposium}, year = {2000}, month = {2000///}, pages = {75 - 82}, author = {Neumann, J. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14239, title = {Observability of 3D Motion}, journal = {International Journal of Computer Vision}, volume = {37}, year = {2000}, month = {2000///}, pages = {43 - 63}, abstract = {This paper examines the inherent difficulties in observing 3D rigid motion from image sequences. It does so without considering a particular estimator. Instead, it presents a statistical analysis of all the possible computational models which can be used for estimating 3D motion from an image sequence. These computational models are classified according to the mathematical constraints that they employ and the characteristics of the imaging sensor (restricted field of view and full field of view). Regarding the mathematical constraints, there exist two principles relating a sequence of images taken by a moving camera. One is the {\textquotedblleft}epipolar constraint,{\textquotedblright} applied to motion fields, and the other the {\textquotedblleft}positive depth{\textquotedblright} constraint, applied to normal flow fields. 3D motion estimation amounts to optimizing these constraints over the image. A statistical modeling of these constraints leads to functions which are studied with regard to their topographic structure, specifically as regards the errors in the 3D motion parameters at the places representing the minima of the functions. For conventional video cameras possessing a restricted field of view, the analysis shows that for algorithms in both classes which estimate all motion parameters simultaneously, the obtained solution has an error such that the projections of the translational and rotational errors on the image plane are perpendicular to each other. Furthermore, the estimated projection of the translation on the image lies on a line through the origin and the projection of the real translation. The situation is different for a camera with a full (360 degree) field of view (achieved by a panoramic sensor or by a system of conventional cameras). In this case, at the locations of the minima of the above two functions, either the translational or the rotational error becomes zero, while in the case of a restricted field of view both errors are non-zero. Although some ambiguities still remain in the full field of view case, the implication is that visual navigation tasks, such as visual servoing, involving 3D motion estimation are easier to solve by employing panoramic vision. Also, the analysis makes it possible to compare properties of algorithms that first estimate the translation and on the basis of the translational result estimate the rotation, algorithms that do the opposite, and algorithms that estimate all motion parameters simultaneously, thus providing a sound framework for the observability of 3D motion. Finally, the introduced framework points to new avenues for studying the stability of image-based servoing schemes.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/A:1008177429387}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14166, title = {The Ouchi illusion as an artifact of biased flow estimation}, journal = {Vision Research}, volume = {40}, year = {2000}, month = {2000/01//}, pages = {77 - 95}, abstract = {A pattern by Ouchi has the surprising property that small motions can cause illusory relative motion between the inset and background regions. The effect can be attained with small retinal motions or a slight jiggling of the paper and is robust over large changes in the patterns, frequencies and boundary shapes. In this paper, we explain that the cause of the illusion lies in the statistical difficulty of integrating local one-dimensional motion signals into two-dimensional image velocity measurements. The estimation of image velocity generally is biased, and for the particular spatial gradient distributions of the Ouchi pattern the bias is highly pronounced, giving rise to a large difference in the velocity estimates in the two regions. The computational model introduced to describe the statistical estimation of image velocity also accounts for the findings of psychophysical studies with variations of the Ouchi pattern and for various findings on the perception of moving plaids. The insight gained from this computational study challenges the current models used to explain biological vision systems and to construct robotic vision systems. Considering the statistical difficulties in image velocity estimation in conjunction with the problem of discontinuity detection in motion fields suggests that theoretically the process of optical flow computations should not be carried out in isolation but in conjunction with the higher level processes of 3D motion estimation, segmentation and shape computation.}, keywords = {Bias, MOTION, optical flow, Plaid, Statistics}, isbn = {0042-6989}, doi = {10.1016/S0042-6989(99)00162-5}, url = {http://www.sciencedirect.com/science/article/pii/S0042698999001625}, author = {Ferm{\"u}ller, Cornelia and Pless,Robert and Aloimonos, J.} } @article {13012, title = {Phylogenetic relationships of {\i}t Phytophthora species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI}, journal = {Mycol Res}, volume = {104}, year = {2000}, month = {2000/09//}, pages = {1055 - 1061}, abstract = {Phylogenetic relationships among Phytophthora species were investigated by sequence analysis of the internal transcribed spacer region I of the ribosomal DNA repeat unit. The extensive collection of isolates included taxa from all six morphological groups recognized by Waterhouse (1963) including molecular groups previously identified using isozymes and mtDNA restriction fragment length polymorphisms. Similar to previous studies, the inferred relationships indicated that molecular groups of P. cryptooea/drechsleri-like and P. megasperma-like taxa are polyphyletic. Morphological groups V and VI, which are differentiated by the presence of amphigynous or paragynous antheridia, are not monophyletic: species of the two groups are interspersed in the tree. Species with papillate and semi-papillate sporangia (groups I-IV) clustered together and this cluster was distinct from those of species with non-papillate sporangia. There was no congruence between the mode of antheridial attachment, sporangial caducity, or homo- or heterothallic habit and the molecular grouping of the species. Our study provides evidence that the antheridial position together with homo- or heterothallic habit does not reflect phylogenetic relationships within Phytophthora. Consequently, confirming studies done previously (Cooke \& Duncan 1997), this study provides evidence that the morphological characters used in Phytophthora taxonomy are of limited value for deducing phylogenetic relationships, because they exhibit convergent evolution.}, author = {F{\"o}rster,H and Cummings, Michael P. and Coffey,M. D} } @conference {14297, title = {Polymorphic versus monomorphic points-to analysis}, booktitle = {Proceedings of the 7th International Static Analysis Symposium, Lecture Notes in Computer Science. Springer Verlag}, year = {2000}, month = {2000///}, author = {Foster, Jeffrey S. and Fahndrich,M. and Aiken,A.} } @article {18314, title = {Robustly estimating changes in image appearance}, journal = {Computer Vision and Image Understanding}, volume = {78}, year = {2000}, month = {2000///}, pages = {8 - 31}, author = {Black,M. J and Fleet,D. J and Yacoob,Yaser} } @conference {14267, title = {The statistics of optical flow: implications for the process of correspondence in vision}, booktitle = {15th International Conference on Pattern Recognition, 2000. Proceedings}, volume = {1}, year = {2000}, month = {2000///}, pages = {119-126 vol.1 - 119-126 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper studies the three major categories of flow estimation methods: gradient-based, energy-based, and correlation methods; it analyzes different ways of compounding 1D motion estimates (image gradients, spatio-temporal frequency triplets, local correlation estimates) into 2D velocity estimates, including linear and nonlinear methods. Correcting for the bias would require knowledge of the noise parameters. In many situations, however, these are difficult to estimate accurately, as they change with the dynamic imagery in unpredictable and complex ways. Thus, the bias really is a problem inherent to optical flow estimation. We argue that the bias is also integral to the human visual system. It is the cause of the illusory perception of motion in the Ouchi pattern and also explains various psychophysical studies of the perception of moving plaids. Finally, the implication of the analysis is that flow or correspondence can be estimated very accurately only when feedback is utilized}, keywords = {Bias, Computer vision, correlation, correlation methods, energy-based method, flow estimation, Frequency estimation, gradient method, gradient methods, Image analysis, Image motion analysis, Image sequences, least squares, least squares approximations, Motion estimation, Nonlinear optics, Optical feedback, optical flow, Optical harmonic generation, Optical noise, Statistics, Visual perception}, isbn = {0-7695-0750-6}, doi = {10.1109/ICPR.2000.905288}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {11968, title = {Structure from motion: Beyond the epipolar constraint}, journal = {International Journal of Computer Vision}, volume = {37}, year = {2000}, month = {2000///}, pages = {231 - 258}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {17501, title = {Visualizing digital library search results with categorical and hierarchical axes}, booktitle = {Proceedings of the fifth ACM conference on Digital libraries}, series = {DL {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {57 - 66}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Digital library search results are usually shown as a textual list, with 10-20 items per page. Viewing several thousand search results at once on a two-dimensional display with continuous variables is a promising alternative. Since these displays can overwhelm some users, we created a simplified two-dimensional display that uses categorical and hierarchical axes, called hieraxes. Users appreciate the meaningful and limited number of terms on each hieraxis. At each grid point of the display we show a cluster of color-coded dots or a bar chart. Users see the entire result set and can then click on labels to move down a level in the hierarchy. Handling broad hierarchies and arranging for imposed hierarchies led to additional design innovations. We applied hieraxes to a digital video library of science topics used by middle school teachers, a legal information system, and a technical library using the ACM Computing Classification System. Feedback from usability testing with 32 subjects revealed strengths and weaknesses.}, keywords = {categorical axes, digital libraries, Graphical user interfaces, hierarchy, hieraxes, Information Visualization}, isbn = {1-58113-231-X}, doi = {10.1145/336597.336637}, url = {http://doi.acm.org/10.1145/336597.336637}, author = {Shneiderman, Ben and Feldman,David and Rose,Anne and Grau,Xavier Ferr{\'e}} } @conference {18761, title = {A web-based process/material advisory system}, year = {2000}, month = {2000///}, abstract = {This paper describes a web-based process/material advisorysystem that can be used during conceptual design. Given a set of design requirements for a part during conceptual design stage, our system produces process sequences that can meet the design requirements. Quite often during conceptual design stage, design requirements are not precisely defined. Therefore, we allow users to describe design requirements in terms of parameter ranges. Parameter ranges are used to capture uncertainties in design requirements. Our system accounts for uncertainties in design requirements in generating and evaluating process/material combinations. Our system uses a two step algorithm. During the first step, we generate a material/process option tree. This tree represents various process/material options that can be used to meet the given set of design requirements. During the second step, we evaluate various alternative process/material options using a depth first branch and bound algorithm to identify and recommend the least expensive process/material combination to the designer. Our system can be accessed on the World Wide Web using a standard browser. Our system allows designs to consider a wide variety of process/material options during the conceptual design stage and allows them to find the most cost-effective combination. By selecting the process/material combination during the early design stages, designers can ensure that the detailed design is compatible with all of the process constraints for the selected process. }, url = {http://www.mel.nist.gov/msidlibrary/doc/imece_feng.pdf}, author = {Chen,Y. S. and Gupta,S.K. and Feng,S.} } @article {12081, title = {Windows of Vulnerability: A Case Study Analysis}, volume = {33}, year = {2000}, month = {2000///}, pages = {52 - 59}, abstract = {The authors propose a life-cycle model for system vulnerabilities, applying to three case studies to show how systems remain vulnerable long after security fixes are available. Complex information and communication systems give rise to design, implementation, and management errors, leading to a vulnerability in an information technology product that can allow security policy violations. Using their vulnerability life-cycle model, the authors present a case study analysis of specific computer vulnerabilities. For each case, the authors provide background information about the vulnerability, such as how attackers exploited it and which systems were affected. They tie the case to the life-cycle model by identifying the dates for each state within the model. Finally, they use a histogram of reported intrusions to show the life of the vulnerability and conclude with an analysis specific to the particular vulnerability.}, isbn = {0018-9162}, author = {Arbaugh, William A. and Fithen,William L. and McHugh,John} } @inbook {14191, title = {Active Perception}, booktitle = {Wiley Encyclopedia of Electrical and Electronics EngineeringWiley Encyclopedia of Electrical and Electronics Engineering}, year = {1999}, month = {1999/12/27/}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, isbn = {9780471346081}, url = {http://onlinelibrary.wiley.com/doi/10.1002/047134608X.W5515/abstract?systemMessage=Wiley+Online+Library+will+be+disrupted+17+March+from+10-14+GMT+\%2806-10+EDT\%29+for+essential+maintenance\&userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14596, title = {Bacterial Start Site Prediction}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {27}, year = {1999}, month = {1999/09/01/}, pages = {3577 - 3582}, abstract = {With the growing number of completely sequenced bacterial genes, accurate gene prediction in bacterial genomes remains an important problem. Although the existing tools predict genes in bacterial genomes with high overall accuracy, their ability to pinpoint the translation start site remains unsatisfactory. In this paper, we present a novel approach to bacterial start site prediction that takes into account multiple features of a potential start site, viz., ribosome binding site (RBS) binding energy, distance of the RBS from the start codon, distance from the beginning of the maximal ORF to the start codon, the start codon itself and the coding/non-coding potential around the start site. Mixed integer programing was used to optimize the discriminatory system. The accuracy of this approach is up to 90\%, compared to 70\%, using the most common tools in fully automated mode (that is, without expert human post-processing of results). The approach is evaluated using Bacillus subtilis, Escherichia coli and Pyrococcus furiosus. These three genomes cover a broad spectrum of bacterial genomes, since B.subtilis is a Gram-positive bacterium, E.coli is a Gram-negative bacterium and P.furiosus is an archaebacterium. A significant problem is generating a set of {\textquoteleft}true{\textquoteright} start sites for algorithm training, in the absence of experimental work. We found that sequence conservation between P.furiosus and the related Pyrococcus horikoshii clearly delimited the gene start in many cases, providing a sufficient training set.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/27.17.3577}, url = {http://nar.oxfordjournals.org/content/27/17/3577}, author = {Hannenhalli, Sridhar and Hayes,William S and Hatzigeorgiou,Artemis G and Fickett,James W} } @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 {13938, title = {Designing PETS: a personal electronic teller of stories}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: the CHI is the limit}, series = {CHI {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {326 - 329}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We have begun the development of a new robotic pet that cansupport children in the storytelling process. Children can build their own pet by snapping together the modular animal parts of the PETS robot. After their pet is built, children can tell stories using the My Pets software. These stories can then be acted out by their robotic pet. This video paper describes the motivation for this research and the design process of our intergenerational design team in building the first PETS prototypes. We will discuss our progress to date and our focus for the future. }, keywords = {children, cooperative inquiry, design techniques, educational applications, intergenerational design team, PETS, ROBOTICS}, isbn = {0-201-48559-1}, doi = {10.1145/302979.303103}, url = {http://doi.acm.org/10.1145/302979.303103}, author = {Druin, Allison and Montemayor,Jamie and Hendler,Jim and McAlister,Britt and Boltman,Angela and Fiterman,Eric and Plaisant,Aurelie and Kruskal,Alex and Olsen,Hanne and Revett,Isabella and Schwenn,Thomas Plaisant and Sumida,Lauren and Wagner,Rebecca} } @article {14463, title = {Efficient learning using constrained sufficient statistics}, journal = {Proceedings of the 7th International Workshop on Artificial Intelligence and Statistics (AISTATS-99)}, year = {1999}, month = {1999///}, abstract = {Learning Bayesian networks is a central prob-lem for pattern recognition, density estima- tion and classification. In this paper, we propose a new method for speeding up the computational process of learning Bayesian network structure. This approach uses con- straints imposed by the statistics already col- lected from the data to guide the learning al- gorithm. This allows us to reduce the num- ber of statistics collected during learning and thus speed up the learning time. We show that our method is capable of learning struc- ture from data more efficiently than tradi- tional approaches. Our technique is of partic- ular importance when the size of the datasets is large or when learning from incomplete data. The basic technique that we introduce is general and can be used to improve learn- ing performance in many settings where suf- ficient statistics must be computed. In ad- dition, our technique may be useful for al- ternate search strategies such as branch and bound algorithms. }, author = {Friedman,N. and Getoor, Lise} } @conference {16174, title = {Excentric labeling: dynamic neighborhood labeling for data visualization}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: the CHI is the limit}, series = {CHI {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {512 - 519}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The widespread use of information visualization is hampered bythe lack of effective labeling techniques. An informal taxonomy of labeling methods is proposed. We then describe excentric labeling, a new dynamic technique to label a neighborhood of objects located around the cursor. This technique does not intrude into the existing interaction, it is not computationally intensive, and was easily applied to several visualization applications. A pilot study with eight subjects indicates a strong speed benefit over a zoom interface for tasks that involve the exploration of large numbers of objects. Observations and comments from users are presented. }, keywords = {dynamic labeling, Evaluation, label, Visualization}, isbn = {0-201-48559-1}, doi = {10.1145/302979.303148}, url = {http://doi.acm.org/10.1145/302979.303148}, author = {Fekete,Jean-Daniel and Plaisant, Catherine} } @conference {18568, title = {Field-to-frame transcoding with spatial and temporal downsampling}, booktitle = {Image Processing, 1999. ICIP 99. Proceedings. 1999 International Conference on}, volume = {4}, year = {1999}, month = {1999///}, pages = {271 -275 vol.4 - 271 -275 vol.4}, abstract = {We present an algorithm for transcoding high-rate compressed bitstreams containing field-coded interlaced video to lower-rate compressed bitstreams containing frame-coded progressive video. We focus on MPEG-2 to H.263 transcoding, however these results can be extended to other lower-rate video compression standards including MPEG-4 simple profile and MPEG-1. A conventional approach to the transcoding problem involves decoding the input bitstream, spatially and temporally downsampling the decoded frames, and re-encoding the result. The proposed transcoder achieves improved performance by exploiting the details of the MPEG-2 and H.263 compression standards when performing interlaced to progressive (or field to frame) conversion with spatial downsampling and frame-rate reduction. The transcoder reduces the MPEG-2 decoding requirements by temporally downsampling the data at the bitstream level and reduces the H.263 encoding requirements by largely bypassing H.263 motion estimation by reusing the motion vectors and coding modes given in the input bitstream. In software implementations, the proposed approach achieved a 5 times; speedup over the conventional approach with only a 0.3 and 0.5 dB loss in PSNR for the Carousel and Bus sequences}, keywords = {data compression, decoding, Encoding, field-coded interlaced video, field-to-frame transcoding, frame-coded progressive video, H.263 motion estimation, H.263 transcoding, high-rate compressed bitstreams, lower-rate compressed bitstreams, Motion estimation, MPEG-1, MPEG-2, MPEG-4, spatial downsampling, standards, temporal downsampling, transcoder, video coding, video compression standards}, doi = {10.1109/ICIP.1999.819593}, author = {Wee,S.J. and Apostolopoulos,J.G. and Feamster, Nick} } @article {18704, title = {Impact of Cl- and Na+ ions on simulated structure and dynamics of βARK1 PH domain}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {35}, year = {1999}, month = {1999///}, pages = {206 - 217}, abstract = {A nonzero net charge of proteins at pH 7 is usually compensated by the addition of charge-balancing counter ions during molecular dynamics simulation, which reduces electrostatic interactions. For highly charged proteins, like the βARK1 PH domain used here, it seems reasonable to also add explicit salt ions. To assess the impact of explicit salt ions, two molecular dynamics simulations of solvated βARK1 PH domain have been carried out with different numbers of Cl- and Na+ ions, based on the Cornell et al. force field and the Ewald summation, which was used in the treatment of long-range electrostatic interactions. Initial positions of ions were obtained from the AMBER CION program. Increasing the number of ions alters the average structure in loop regions, as well as the fluctuation amplitudes of dihedral angles. We found unnaturally strong interactions between side chains in the absence of salt ions. The presence of salt ions reduces these electrostatic interactions. The time needed for the equilibration of the ionic environment around the protein, after initial placement of ions close to oppositely charged side chains, is in the nanosecond time range, which can be shortened by using a higher ionic strength. Our results also suggest selecting those methods that do not place the ions initially close to the protein surface. Proteins 1999;35:206{\textendash}217. {\textcopyright} 1999 Wiley-Liss, Inc.}, keywords = {counter ions, electrostatic interaction, equilibration, GRK2 PH domain, hydrogen bonds, ionic solvent, ionic strength, molecular dynamics simulation, Proteins}, isbn = {1097-0134}, doi = {10.1002/(SICI)1097-0134(19990501)35:2<206::AID-PROT7>3.0.CO;2-A}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0134(19990501)35:2<206::AID-PROT7>3.0.CO;2-A/abstract}, author = {Pfeiffer,Stefania and Fushman, David and Cowburn,David} } @conference {17874, title = {Infrastructure for building parallel database systems for multi-dimensional data}, booktitle = {IPPS}, year = {1999}, month = {1999///}, pages = {582 - 582}, author = {Chang,C. and Ferreira,R. and Sussman, Alan and Saltz, J.} } @article {14408, title = {Learning probabilistic relational models}, journal = {International Joint Conference on Artificial Intelligence}, volume = {16}, year = {1999}, month = {1999///}, pages = {1300 - 1309}, abstract = {A large portion of real-world data is stored in com-mercial relational database systems. In contrast, most statistical learning methods work only with {\textquotedblleft}flat{\textquotedblright} data representations. Thus, to apply these methods, we are forced to convert our data into a flat form, thereby losing much of the relational structure present in our database. This paper builds on the recent work on probabilistic relational mod- els (PRMs), and describes how to learn them from databases. PRMs allow the properties of an object to depend probabilistically both on other proper- ties of that object and on properties of related ob- jects. Although PRMs are significantly more ex- pressive than standard models, such as Bayesian networks, we show how to extend well-known sta- tistical methods for learning Bayesian networks to learn these models. We describe both parameter estimation and structure learning {\textemdash} the automatic induction of the dependency structure in a model. Moreover, we show how the learning procedure can exploit standard database retrieval techniques for efficient learning from large datasets. We present experimental results on both real and synthetic re- lational databases. }, author = {Friedman,N. and Getoor, Lise and Koller,D. and Pfeffer,A.} } @conference {12041, title = {Motion Segmentation: A Synergistic Approach}, booktitle = {Computer Vision and Pattern Recognition, IEEE Computer Society Conference on}, volume = {2}, year = {1999}, month = {1999///}, pages = {2226 - 2226}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Since estimation of camera motion requires knowledge of independent motion, and moving object detection and localization requires knowledge about the camera motion, the two problems of motion estimation and segmentation need to be solved together in a synergistic manner. This paper provides an approach to treating both these problems simultaneously. The technique introduced here is based on a novel concept, {\textquoteleft}{\textquoteleft}scene ruggedness,{\textquoteright}{\textquoteright} which parameterizes the variation in estimated scene depth with the error in the underlying three-dimensional (3D) motion. The idea is that incorrect 3D motion estimates cause distortions in the estimated depth map, and as a result smooth scene patches are computed as rugged surfaces. The correct 3D motion can be distinguished, as it does not cause any distortion and thus gives rise to the background patches with the least depth variation between depth discontinuities, with the locations corresponding to independent motion being rugged. The algorithm presented employs a binocular observer whose nature is exploited in the extraction of depth discontinuities, a step that facilitates the overall procedure, but the technique can be extended to a monocular observer in a variety of ways.}, keywords = {epipolar minimization, independent motion detection, Motion analysis}, doi = {http://doi.ieeecomputersociety.org/10.1109/CVPR.1999.784633}, author = {Ferm{\"u}ller, Cornelia and Brodsky, Tomas and Aloimonos, J.} } @conference {18493, title = {An MPEG-2 to H. 263 transcoder}, booktitle = {SPIE Voice, Video, and Data Communications Conference}, year = {1999}, month = {1999///}, abstract = {We present an MPEG-2 to H.263 transcoder that accepts an interlaced MPEG-2 bitstream as the input and producesa lower-bitrate progressive H.263 bitstream as the output. As both DVD and digital television may use MPEG-2 interlaced sequences, a potential application of such a transcoder is the transmission of a digital television signal over a wireless medium. Another application is transcoding interlaced DVD content for use on lower-resolution thin clients with progressive displays. The proposed algorithm exploits the properties of the MPEG-2 and H.263 compression standards to perform interlaced to progressive ( eld to frame) conversion with spatial downsampling and frame-rate reduction in a CPU and memory e cient manner, while additionally minimizing picture quality degradation as measured by PSNR. This is the rst algorithm to our knowledge that e ectively uses both spatial and temporal downsampling in an MPEG-2 to H.263 eld to frame transcoder in order to achieve substantial bitrate reduction. This paper discusses recoding experiments used to determine appropriate source and target coding parameters for the transcoder, provides a detailed description of the transcoding algorithm, and describes the performance of a software implementation of the transcoder. }, author = {Feamster, Nick and Wee,S.} } @article {15853, title = {Multilingual Information Discovery and AccesS (MIDAS): A Joint ACM DL{\textquoteright}99/ ACM SIGIR{\textquoteright}99 Workshop.}, journal = {D-Lib MagazineD-Lib Magazine}, volume = {5}, year = {1999}, month = {1999///}, pages = {1 - 12}, abstract = {Discusses a multidisciplinary workshop that addressed issues concerning internationally distributed information networks. Highlights include multilingual information access in media other than character-coded text; cross-language information retrieval and multilingual metadata; and evaluation of multilingual systems. (LRW)}, keywords = {Distributed computing, Electronic Media}, isbn = {ISSN-1082-9873}, url = {http://www.eric.ed.gov/ERICWebPortal/detail?accno=EJ601937}, author = {Oard, Douglas and Peters,Carol and Ruiz,Miguel and Frederking,Robert and Klavans,Judith and Sheridan,Paraic} } @article {17855, title = {Object-relational queries into multidimensional databases with the active data repository}, journal = {Parallel Processing Letters}, volume = {9}, year = {1999}, month = {1999///}, pages = {173 - 195}, author = {Ferreira,R. and Kurc, T. and Beynon, M. and Chang,C. and Sussman, Alan and Saltz,J. H} } @book {14913, title = {Perceptual Organization in Computer Vision}, year = {1999}, month = {1999///}, publisher = {Academic Press}, organization = {Academic Press}, author = {Boyer,K.L. and Sarkar,S. and Feldman,J. and Granlund,G. and Horaud,R. and Hutchinson,S. and Jacobs, David W. and Kak,A. and Lowe,D. and Malik,J.} } @conference {17871, title = {Querying Very Large Multi-dimensional Datasets in ADR}, booktitle = {In Proceedings of SC99: High Performance Networking and Computing}, year = {1999}, month = {1999///}, author = {Chialin,T. K and Kurc, T. and Chang,C. and Ferreira,R. and Sussman, Alan and Saltz, J.} } @conference {16167, title = {Refining query previews techniques for data with multivalued attributes: the case of NASA EOSDIS}, booktitle = {Research and Technology Advances in Digital Libraries, 1999. ADL {\textquoteright}99. Proceedings. IEEE Forum on}, year = {1999}, month = {1999///}, pages = {50 - 59}, abstract = {Query Previews allow users to rapidly gain an understanding of the content and scope of a digital data collection. These previews present overviews of abstracted metadata, enabling users to rapidly and dynamically avoid undesired data. We present our recent work on developing query previews for a variety of NASA EOSDIS situations. We focus on approaches that successfully address the challenge of multi-valued attribute data. Memory requirements and processing time associated with running these new solutions remain independent of the number of records in the dataset. We describe two techniques and their respective prototypes used to preview NASA Earth science data}, keywords = {attribute, attributes;processing, collection;memory, computing;meta, data, data;abstracted, data;digital, data;multivalued, data;query, Earth, EOSDIS;NASA, libraries;geophysics, metadata;dataset;digital, NASA, previews, processing;, requirements;multi-valued, Science, techniques;undesired, time;query}, doi = {10.1109/ADL.1999.777690}, author = {Plaisant, Catherine and Venkatraman,M. and Ngamkajorwiwat,K. and Barth,R. and Harberts,B. and Feng,Wenlan} } @conference {12054, title = {Shape from Video}, booktitle = {Computer Vision and Pattern Recognition, IEEE Computer Society Conference on}, volume = {2}, year = {1999}, month = {1999///}, pages = {2146 - 2146}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper presents a novel technique for recovering the shape of a static scene from a video sequence due to a rigidly moving camera. The solution procedure consists of two stages. In the first stage, the rigid motion of the camera at each instant in time is recovered. This provides the transformation between successive viewing positions. The solution is achieved through new constraints which relate 3D motion and shape directly to the image derivatives. These constraints allow the combination of the processes of 3D motion estimation and segmentation by exploiting the geometry and statistics inherent in the data. In the second stage the scene surfaces are reconstructed through an optimization procedure which utilizes data from all the frames of a short video sequence. A number of experimental results demonstrate the potential of the approach.}, keywords = {epipolar minimization, model extraction, Motion analysis, vision and graphics}, doi = {http://doi.ieeecomputersociety.org/10.1109/CVPR.1999.784622}, author = {Brodsky, Tomas and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {18715, title = {Solution Structure of the Proapoptotic Molecule BID: A Structural Basis for Apoptotic Agonists and Antagonists}, journal = {Cell}, volume = {96}, year = {1999}, month = {1999/03/05/}, pages = {625 - 634}, abstract = {Members of the BCL2 family of proteins are key regulators of programmed cell death, acting either as apoptotic agonists or antagonists. Here we describe the solution structure of BID, presenting the structure of a proapoptotic BCL2 family member. An analysis of sequence/structure of BCL2 family members allows us to define a structural superfamily, which has implications for general mechanisms for regulating proapoptotic activity. It appears two criteria must be met for proapoptotic function within the BCL2 family: targeting of molecules to intracellular membranes, and exposure of the BH3 death domain. BID{\textquoteright}s activity is regulated by a Caspase 8{\textendash}mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, resulting in a change of cellular localization.}, isbn = {0092-8674}, doi = {10.1016/S0092-8674(00)80573-5}, url = {http://www.sciencedirect.com/science/article/pii/S0092867400805735}, author = {McDonnell,James M and Fushman, David and Milliman,Curt L. and Korsmeyer,Stanley J. and Cowburn,David} } @conference {11965, title = {Statistical biases in optic flow}, booktitle = {Computer Vision and Pattern Recognition, 1999. IEEE Computer Society Conference on.}, volume = {1}, year = {1999}, month = {1999///}, pages = {566 Vol. 1 - 566 Vol. 1}, publisher = {IEEE}, organization = {IEEE}, abstract = {The computation of optical flow from image derivatives is biased in regions of non uniform gradient distributions. A least-squares or total least squares approach to computing optic flow from image derivatives even in regions of consistent flow can lead to a systematic bias dependent upon the direction of the optic flow, the distribution of the gradient directions, and the distribution of the image noise. The bias a consistent underestimation of length and a directional error. Similar results hold for various methods of computing optical flow in the spatiotemporal frequency domain. The predicted bias in the optical flow is consistent with psychophysical evidence of human judgment of the velocity of moving plaids, and provides an explanation of the Ouchi illusion. Correction of the bias requires accurate estimates of the noise distribution; the failure of the human visual system to make these corrections illustrates both the difficulty of the task and the feasibility of using this distorted optic flow or undistorted normal flow in tasks requiring higher lever processing}, keywords = {Distributed computing, Frequency domain analysis, HUMANS, image derivatives, Image motion analysis, Image sequences, Least squares methods, Motion estimation, Optical computing, Optical distortion, optical flow, Optical noise, Ouchi illusion, perception of motion, Psychology, Spatiotemporal phenomena, statistical analysis, systematic bias, total least squares}, isbn = {0-7695-0149-4}, doi = {10.1109/CVPR.1999.786994}, author = {Ferm{\"u}ller, Cornelia and Pless, R. and Aloimonos, J.} } @conference {16173, title = {Temporal, geographical and categorical aggregations viewed through coordinated displays: a case study with highway incident data}, booktitle = {Proceedings of the 1999 workshop on new paradigms in information visualization and manipulation in conjunction with the eighth ACM internation conference on Information and knowledge management}, series = {NPIVM {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {26 - 34}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Information visualization displays can hold a limited number of data points, typically a few thousand, before they get crowded. One way to solve this problem with larger data sets is to create aggregates. Aggregations were used together with the Snap-Together Visualization system to coordinate the visual displays of aggregates and their content. If two displays each hold one thousand items then rapid access and visibility can be maintained for a million points. This paper presents examples based on a database of highway incident data.}, isbn = {1-58113-254-9}, doi = {10.1145/331770.331780}, url = {http://doi.acm.org/10.1145/331770.331780}, author = {Fredrikson,Anna and North,Chris and Plaisant, Catherine and Shneiderman, Ben} } @conference {14303, title = {A theory of type qualifiers}, booktitle = {ACM SIGPLAN Notices}, volume = {34}, year = {1999}, month = {1999///}, pages = {192 - 203}, author = {Foster, Jeffrey S. and F{\"a}hndrich,M. and Aiken,A.} } @conference {17443, title = {Trust me, I{\textquoteright}m accountable: trust and accountability online}, booktitle = {CHI {\textquoteright}99 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {79 - 80}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We live in an increasingly wired world. According to Robert Putnam, people are spending less time in persistent personal face to face interactions and more time in pursuits such as watching TV and using the Internet. At the same time, independently measured "social capital" -- the extent to which we trust and work for a common good -- is declining. In this panel, we explore: the impacts of electronic media on trust and accountability; whether and how electronic media can be designed and used to increase deserved trust and accountability; the relationship between protecting privacy and increasing the efficacy of communication; and how people{\textquoteright}s tendency to treat computers as social actors impacts these issues. In brief, how can modern technology enhance humanity{\textquoteright}s humanity?}, keywords = {accountability, anonymity, Communication, computers and society, ethics, Internet, media effects, privacy, Reciprocity, repute, social actors, social capital, social impacts, trust, value-sensitive design, wired world, WWW}, isbn = {1-58113-158-5}, doi = {10.1145/632716.632766}, url = {http://doi.acm.org/10.1145/632716.632766}, author = {Friedman,Batya and Thomas,John C. and Grudin,Jonathan and Nass,Clifford and Nissenbaum,Helen and Schlager,Mark and Shneiderman, Ben} } @article {18149, title = {XMT-M: A Scalable Decentralized Processor}, volume = {UMIACS-TR-99-55}, year = {1999}, month = {1999/10/09/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {A defining challenge for research in computer science and engineering hasbeen the ongoing quest for reducing the completion time of a single computation task. Even outside the parallel processing communities, there is little doubt that the key to further progress in this quest is to do parallel processing of some kind. A recently proposed parallel processing framework that spans the entire spectrum from (parallel) algorithms to architecture to implementation is the explicit multi-threading (XMT) framework. This framework provides: (i) simple and natural parallel algorithms for essentially every general-purpose application, including notoriously difficult irregular integer applications, and (ii) a multi-threaded programming model for these algorithms which allows an {\textquoteleft}{\textquoteleft}independence-of-order{\textquoteright}{\textquoteright} semantics: every thread can proceed at its own speed, independent of other concurrent threads. To the extent possible, the XMT framework uses established ideas in parallel processing. This paper presents XMT-M, a microarchitecture implementation of the XMT model that is possible with current technology. XMT-M offers an engineering design point that addresses four concerns: buildability, programmability, performance, and scalability. The XMT-M hardware is geared to execute multiple threads in parallel on a single chip: relying on very few new gadgets, it can execute parallel threads without busy-waits! Existing code can be run on XMT-M as a single thread without any modifications, thereby providing backward compatibility for commercial acceptance. Simulation-based studies of XMT-M demonstrate considerable improvements in performance relative to the best serial processor even for small, and therefore practical, input sizes. (Also cross-referenced as UMIACS-TR-99-55) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1030}, author = {Berkovich,Efraim and Nuzman,Joseph and Franklin,Manoj and Jacob,Bruce and Vishkin, Uzi} } @article {14181, title = {3D motion and shape representations in visual servo control}, journal = {The International Journal of Robotics Research}, volume = {17}, year = {1998}, month = {1998///}, pages = {4 - 4}, author = {Ferm{\"u}ller, Cornelia and Cheong, L. F and Aloimonos, J.} } @article {14195, title = {Ambiguity in Structure from Motion: Sphere versus Plane}, journal = {International Journal of Computer Vision}, volume = {28}, year = {1998}, month = {1998///}, pages = {137 - 154}, abstract = {If 3D rigid motion can be correctly estimated from image sequences, the structure of the scene can be correctly derived using the equations for image formation. However, an error in the estimation of 3D motion will result in the computation of a distorted version of the scene structure. Of computational interest are these regions in space where the distortions are such that the depths become negative, because in order for the scene to be visible it has to lie in front of the image, and thus the corresponding depth estimates have to be positive. The stability analysis for the structure from motion problem presented in this paper investigates the optimal relationship between the errors in the estimated translational and rotational parameters of a rigid motion that results in the estimation of a minimum number of negative depth values. The input used is the value of the flow along some direction, which is more general than optic flow or correspondence. For a planar retina it is shown that the optimal configuration is achieved when the projections of the translational and rotational errors on the image plane are perpendicular. Furthermore, the projection of the actual and the estimated translation lie on a line through the center. For a spherical retina, given a rotational error, the optimal translation is the correct one; given a translational error, the optimal rotational negative deptherror depends both in direction and value on the actual and estimated translation as well as the scene in view. The proofs, besides illuminating the confounding of translation and rotation in structure from motion, have an important application to ecological optics. The same analysis provides a computational explanation of why it is easier to estimate self-motion in the case of a spherical retina and why shape can be estimated easily in the case of a planar retina, thus suggesting that nature{\textquoteright}s design of compound eyes (or panoramic vision) for flying systems and camera-type eyes for primates (and other systems that perform manipulation) is optimal.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/A:1008063000586}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {12102, title = {Automated recovery in a secure bootstrap process}, booktitle = {Proceedings of the Symposium on Network and Distributed Systems Security (NDSS{\textquoteright}98)}, year = {1998}, month = {1998///}, pages = {155 - 167}, author = {Arbaugh, William A. and Keromytis,A. D and Farber,D. J and Smith,J. M} } @inbook {14202, title = {Beyond the Epipolar Constraint: Integrating 3D Motion and Structure Estimation}, booktitle = {3D Structure from Multiple Images of Large-Scale Environments3D Structure from Multiple Images of Large-Scale Environments}, series = {Lecture Notes in Computer Science}, volume = {1506}, year = {1998}, month = {1998///}, pages = {109 - 123}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper develops a novel solution to the problem of recovering the structure of a scene given an uncalibrated video sequence depicting the scene. The essence of the technique lies in a method for recovering the rigid transformation between the different views in the image sequence. Knowledge of this 3D motion allows for self-calibration and for subsequent recovery of 3D structure. The introduced method breaks away from applying only the traditionally used epipolar constraint and introduces a new constraint based on the interaction between 3D motion and shape. Up to now, structure from motion algorithms proceeded in two well defined steps, where the first and most important step is recovering the rigid transformation between two views, and the subsequent step is using this transformation to compute the structure of the scene in view. Here both aforementioned steps are accomplished in a synergistic manner. Existing approaches to 3D motion estimation are mostly based on the use of optic flow which however poses a problem at the locations of depth discontinuities. If we knew where depth discontinuities were, we could (using a multitude of approaches based on smoothness constraints) estimate accurately flow values for image patches corresponding to smooth scene patches; but to know the discontinuities requires solving the structure from motion problem first. In the past this dilemma has been addressed by improving the estimation of flow through sophisticated optimization techniques, whose performance often depends on the scene in view. In this paper the main idea is based on the interaction between 3D motion and shape which allows us to estimate the 3D motion while at the same time segmenting the scene. If we use a wrong 3D motion estimate to compute depth, then we obtain a distorted version of the depth function. The distortion, however, is such that the worse the motion estimate, the more likely we are to obtain depth estimates that are locally unsmooth, i.e., they vary more than the correct ones. Since local variability of depth is due either to the existence of a discontinuity or to a wrong 3D motion estimate, being able to differentiate between these two cases provides the correct motion, which yields the {\textquotedblleft}smoothest{\textquotedblright} estimated depth as well as the image locations of scene discontinuities. Although no optic flow values are computed, we show that our algorithm is very much related to minimizing the epipolar constraint when the scene in view is smooth. When however the imaged scene is not smooth, the introduced constraint has in general different properties from the epipolar constraint and we present experimental results with real sequences where it performs better.}, isbn = {978-3-540-65310-3}, url = {http://dx.doi.org/10.1007/3-540-49437-5_8}, author = {Brodsk{\'y},Tom{\'a}{\v s} and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Koch,Reinhard and Van Gool,Luc} } @conference {13538, title = {Developing High-Level Representations of Video Clips using VideoTrails}, booktitle = {Proceedings of the SPIEConference on Storage and Retrieval for Image and Video Databases VI}, volume = {3312}, year = {1998}, month = {1998///}, pages = {81 - 92}, abstract = {A high-level representation of a video clip comprising information about its physical and semantic structure isnecessary for providing appropriate processing, indexing and retrieval capabilities for video databases. We describe a novel technique which reduces a sequence of MPEG encoded video frames to a trail of points in a low dimensional space. In our earlier work, we presented techniques applicable in 3-D, but in this paper, we describe techniques that can be extended to higher dimensions where improved performance is expected. In the low-dimensional space, we can cluster frames, analyze transitions between clusters and compute properties of the resulting trail. Portions of the trail can be classi ed as either stationary or transitional, leading to high-level descriptions of the video. Tracking the interaction of clusters over time, we lay the groundwork for the complete analysis and representation of the video{\textquoteright}s physical and semantic structure. }, author = {Kobla,V. and David Doermann and Faloutsos,C.} } @conference {17832, title = {Digital dynamic telepathology{\textendash}the Virtual Microscope.}, booktitle = {Proceedings of the AMIA Symposium}, year = {1998}, month = {1998///}, pages = {912 - 912}, author = {Afework,A. and Beynon,M. D and Bustamante,F. and Cho,S. and Demarzo,A. and Ferreira,R. and Miller,R. and Silberman,M. and Saltz, J. and Sussman, Alan and others} } @article {14214, title = {Directions of Motion Fields are Hardly Ever Ambiguous}, journal = {International Journal of Computer Vision}, volume = {26}, year = {1998}, month = {1998///}, pages = {5 - 24}, abstract = {If instead of the full motion field, we consider only the direction of the motion field due to a rigid motion, what can we say about the three-dimensional motion information contained in it? This paper provides a geometric analysis of this question based solely on the constraint that the depth of the surfaces in view is positive. The motivation behind this analysis is to provide a theoretical foundation for image constraints employing only the sign of flow in various directions and justify their utilization for addressing 3D dynamic vision problems.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/A:1007928406666}, author = {Brodsky, Tomas and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14215, title = {Effects of Errors in the Viewing Geometry on Shape Estimation}, journal = {Computer Vision and Image Understanding}, volume = {71}, year = {1998}, month = {1998/09//}, pages = {356 - 372}, abstract = {A sequence of images acquired by a moving sensor contains information about the three-dimensional motion of the sensor and the shape of the imaged scene. Interesting research during the past few years has attempted to characterize the errors that arise in computing 3D motion (egomotion estimation) as well as the errors that result in the estimation of the scene{\textquoteright}s structure (structure from motion). Previous research is characterized by the use of optic flow or correspondence of features in the analysis as well as by the employment of particular algorithms and models of the scene in recovering expressions for the resulting errors. This paper presents a geometric framework that characterizes the relationship between 3D motion and shape in the presence of errors. We examine how the three-dimensional space recovered by a moving monocular observer, whose 3D motion is estimated with some error, is distorted. We characterize the space of distortions by its level sets, that is, we characterize the systematic distortion via a family of iso-distortion surfaces, which describes the locus over which the depths of points in the scene in view are distorted by the same multiplicative factor. The framework introduced in this way has a number of applications: Since the visible surfaces have positive depth (visibility constraint), by analyzing the geometry of the regions where the distortion factor is negative, that is, where the visibility constraint is violated, we make explicit situations which are likely to give rise to ambiguities in motion estimation, independent of the algorithm used. We provide a uniqueness analysis for 3D motion analysis from normal flow. We study the constraints on egomotion, object motion, and depth for an independently moving object to be detectable by a moving observer, and we offer a quantitative account of the precision needed in an inertial sensor for accurate estimation of 3D motion.}, isbn = {1077-3142}, doi = {10.1006/cviu.1997.0649}, url = {http://www.sciencedirect.com/science/article/pii/S1077314297906494}, author = {LoongFah Cheong and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {11952, title = {Effects of Errors in the Viewing Geometry on Shape Estimation* 1,* 2}, journal = {Computer Vision and Image Understanding}, volume = {71}, year = {1998}, month = {1998///}, pages = {356 - 372}, author = {Cheong, L. F and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @inbook {13763, title = {Enhancing Automatic Acquisition of Thematic Structure in a Large-Scale Lexicon for Mandarin Chinese}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {41 - 50}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes a refinement to our procedure for porting lexical conceptual structure (LCS) into new languages. Specifically we describe a two-step process for creating candidate thematic grids for Mandarin Chinese verbs, using the English verb heading the VP in the subde_nitions to separate senses, and roughly parsing the verb complement structure to match thematic structure templates. We accomplished a substantial reduction in manual effort, without substantive loss. The procedure is part of a larger process of creating a usable lexicon for interlingual machine translation from a large on-line resource with both too much and too little information.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_4}, author = {Olsen,Mari and Dorr, Bonnie J and Thomas,Scott}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @conference {18324, title = {A framework for modeling appearance change in image sequences}, booktitle = {Computer Vision, 1998. Sixth International Conference on}, year = {1998}, month = {1998/01//}, pages = {660 - 667}, abstract = {Image ldquo;appearance rdquo; may change over time due to a variety of causes such as: 1) object or camera motion; 2) generic photometric events including variations in illumination (e.g. shadows) and specular reflections; and 3) ldquo;iconic changes rdquo; which are specific to the objects being viewed and include complex occlusion events and changes in the material properties of the objects. We propose a general framework for representing and recovering these ldquo;appearance changes rdquo; in an image sequence as a ldquo;mixture rdquo; of different causes. The approach generalizes previous work on optical flow to provide a richer description of image events and more reliable estimates of image motion}, keywords = {appearance change, camera motion, complex occlusion events, generic photometric events, iconic changes, illumination, image motion, Image sequences, Motion estimation, optical flow}, doi = {10.1109/ICCV.1998.710788}, author = {Black,M. J and Fleet,D. J and Yacoob,Yaser} } @article {20053, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Mol Biochem Parasitol}, volume = {97}, year = {1998}, month = {1998 Nov 30}, pages = {221-4}, keywords = {Animals, Leishmania, Terminology as Topic, Trypanosoma}, issn = {0166-6851}, author = {Clayton, C and Adams, M and Almeida, R and Baltz, T and Barrett, M and Bastien, P and Belli, S and Beverley, S and Biteau, N and Blackwell, J and Blaineau, C and Boshart, M and Bringaud, F and Cross, G and Cruz, A and Degrave, W and Donelson, J and El-Sayed, N and Fu, G and Ersfeld, K and Gibson, W and Gull, K and Ivens, A and Kelly, J and Vanhamme, L} } @article {14241, title = {On the geometry of visual correspondence}, year = {1998}, month = {1998/10/15/undef}, abstract = {Image displacement fieldsoptical flow fields, stereo disparity fields, normal flow fieldsdue to rigid motion possess a global geometric structure which is independent of the scene in view. Motion vectors of certain lengths and directions are constraine d to lie on the imaging surface at particular loci whose location and form depends solely on the 3D motion parameters. If optical flow fields or stereo disparity fields are considered, then equal vectors are shown to lie on conic sections. Similarly, for normal motion fields, equal vectors lie within regions whose boundaries also constitute conics. By studying various properties of these curves and regions and their relationships, a characterization of the structure of rigid motion fields is given. The go al of this paper is to introduce a concept underlying the global structure of image displacement fields. This concept gives rise to various constraints that could form the basis of algorithms for the recovery of visual information from multiple views.}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {13442, title = {Hybrid planning: An approach to integrating generative and case-based planning}, journal = {Working Notes of the AAAI-98 Workshop on Case-Based Reasoning Integrations}, year = {1998}, month = {1998///}, author = {desJardins, Marie and Francis,A. and Wolverton,M.} } @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} } @inbook {13817, title = {Lexical Selection for Cross-Language Applications: Combining LCS with WordNet}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {438 - 447}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes experiments for testing the power of large-scale resources for lexical selection in machine translation (MT) and cross-language information retrieval (CLIR). We adopt the view that verbs with similar argument structure share certain meaning components, but that those meaning components are more relevant to argument realization than to idiosyncratic verb meaning. We verify this by demonstrating that verbs with similar argument structure as encoded in Lexical Conceptual Structure (LCS) are rarely synonymous in WordNet. We then use the results of this work to guide our implementation of an algorithm for cross-language selection of lexical items, exploiting the strengths of each resource: LCS for semantic structure and WordNet for semantic content. We use the Parka Knowledge-Based System to encode LCS representations and WordNet synonym sets and we implement our lexical-selection algorithm as Parka-based queries into a knowledge base containing both information types.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_39}, author = {Dorr, Bonnie J and Katsova,Maria}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @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} } @conference {14302, title = {Partial online cycle elimination in inclusion constraint graphs}, booktitle = {ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI)}, year = {1998}, month = {1998///}, author = {Aiken,A. and Fhndrich,M. and Foster, Jeffrey S. and Su,Z.} } @article {12103, title = {Security for virtual private intranets}, journal = {Computer}, volume = {31}, year = {1998}, month = {1998/09//}, pages = {48 - 55}, abstract = {As telecommuting grows, businesses must consider security when extending their network environment to employees{\textquoteright} homes. Researchers at the University of Pennsylvania have addressed the problem with smart cards, operating system modifications, and network authentication. We note the distinction between trust and integrity: trust is determined through the verification of components and the dependencies among them, while integrity demonstrates that components haven{\textquoteright}t been modified. Thus integrity checking in a trustworthy system is about preserving an established trust or trust relationship. Our solution to the challenge of isolating functional roles that may share a single hardware platform is called secure identity based lending (SIBL). SIBL provides multiple personalities by partitioning the hard drive into n+1 partitions, where n is the number of supported personalities. All personalities use the system partition for core operating system components and shared applications. Each of the personalities is also associated with one of the remaining partitions, which are encrypted using a symmetric algorithm}, keywords = {businesses, Clouds, Companies, core operating system components, cryptography, Data security, employee homes, encryption, functional roles, hard drive, Home computing, home working, integrity checking, Internet, Local area networks, multiple personalities, network authentication, network environment, operating system modifications, Operating systems, Roads, secure identity based lending, security management, security of data, shared applications, SIBL, single hardware platform, smart cards, symmetric algorithm, system partition, telecommuting, Teleworking, trust relationship, trustworthy system, virtual private intranets}, isbn = {0018-9162}, doi = {10.1109/2.708450}, author = {Arbaugh, William A. and Davin,J. R and Farber,D. J and Smith,J. M} } @conference {11993, title = {Self-calibration from image derivatives}, booktitle = {Sixth International Conference on Computer Vision, 1998}, year = {1998}, month = {1998/01/04/7}, pages = {83 - 89}, publisher = {IEEE}, organization = {IEEE}, abstract = {This study investigates the problem of estimating the calibration parameters from image motion fields induced by a rigidly moving camera with unknown calibration parameters, where the image formation is modeled with a linear pinhole-camera model. The equations obtained show the flow to be clearly separated into a component due to the translation and the calibration parameters and a component due to the rotation and the calibration parameters. A set of parameters encoding the latter component are linearly related to the flow, and from these parameters the calibration can be determined. However, as for discrete motion, in the general case it is not possible, to decouple image measurements from two frames only into their translational and rotational component. Geometrically, the ambiguity takes the form of a part of the rotational component being parallel to the translational component, and thus the scene can be reconstructed only up to a projective transformation. In general, for a full calibration at least four successive image frames are necessary with the 3D-rotation changing between the measurements. The geometric analysis gives rise to a direct self-calibration method that avoids computation of optical flow or point correspondences and uses only normal flow measurements. In this technique the direction of translation is estimated employing in a novel way smoothness constraints. Then the calibration parameters are estimated from the rotational components of several flow fields using Levenberg-Marquardt parameter estimation, iterative in the calibration parameters only. The technique proposed does not require calibration objects in the scene or special camera motions and it also avoids the computation of exact correspondence. This makes it suitable for the calibration of active vision systems which have to acquire knowledge about their intrinsic parameters while they perform other tasks, or as a tool for analyzing image sequences in large video databases}, keywords = {3D-rotation, active vision, Calibration, CAMERAS, discrete motion, Encoding, Equations, image derivatives, image formation, image measurements, Image motion analysis, image motion fields, Image reconstruction, Image sequences, large video databases, Layout, Levenberg-Marquardt parameter estimation, linear pinhole-camera model, Motion estimation, Motion measurement, Optical computing, parameter estimation, projective transformation, rigidly moving camera, self-calibration, smoothness constraints, unknown calibration parameters}, isbn = {81-7319-221-9}, doi = {10.1109/ICCV.1998.710704}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14257, title = {Shape from video: Beyond the epipolar constraint}, journal = {Proceedings of the DARPA Image Understanding Workshop}, year = {1998}, month = {1998///}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @inbook {14258, title = {Simultaneous estimation of viewing geometry and structure}, booktitle = {Computer Vision {\textemdash} ECCV{\textquoteright}98Computer Vision {\textemdash} ECCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1406}, year = {1998}, month = {1998///}, pages = {342 - 358}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Up to now, structure from motion algorithms proceeded in two well defined steps, where the first and most important step is recovering the rigid transformation between two views, and the subsequent step is using this transformation to compute the structure of the scene in view. This paper introduces a novel approach to structure from motion in which both aforementioned steps are accomplished in a synergistic manner. Existing approaches to 3D motion estimation are mostly based on the use of optic flow which however poses a problem at the locations of depth discontinuities. If we knew where depth discontinuities were, we could (using a multitude of approaches based on smoothness constraints) estimate accurately flow values for image patches corresponding to smooth scene patches; but to know the discontinuities requires solving the structure from motion problem first. In the past this dilemma has been addressed by improving the estimation of flow through sophisticated optimization techniques, whose performance often depends on the scene in view. In this paper we follow a different approach. The main idea is based on the interaction between 3D motion and shape which allows us to estimate the 3D motion while at the same time segmenting the scene. If we use a wrong 3D motion estimate to compute depth, then we obtain a distorted version of the depth function. The distortion, however, is such that the worse the motion estimate, the more likely we are to obtain depth estimates that are locally unsmooth, i.e., they vary more than the correct ones. Since local variability of depth is due either to the existence of a discontinuity or to a wrong 3D motion estimate, being able to differentiate between these two cases provides the correct motion, which yields the {\textquotedblleft}smoothest{\textquotedblright} estimated depth as well as the image location of scene discontinuities. Although no optic flow values are computed, we show that our algorithm is very much related to minimizing the epipolar constraint and we present a number of experimental results with real image sequences indicating the robustness of the method.}, isbn = {978-3-540-64569-6}, url = {http://dx.doi.org/10.1007/BFb0055677}, author = {Brodsk{\'y},Tom{\'a}{\v s} and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Burkhardt,Hans and Neumann,Bernd} } @article {18714, title = {Solution structure and dynamics of the bioactive retroviral M domain from rous sarcoma virus}, journal = {Journal of Molecular Biology}, volume = {279}, year = {1998}, month = {1998/06/19/}, pages = {921 - 928}, abstract = {A biologically active construct of the retroviral M domain from the avian Rous sarcoma virus is defined and its solution structure described. This M domain is fully active in budding and infectivity without myristylation. In spite of a sequence homology level that suggests no relationship among M domains and the family of matrix proteins in mammalian retroviruses, the conserved structural elements of a central core allow an M domain sequence motif to be described for all retroviruses. The surface of the M domain has a highly clustered positive patch comprised of sequentially distant residues. An analysis of the backbone dynamics, incorporating rotational anisotropy, is used to estimate the thermodynamics of proposed domain oligomerization.}, keywords = {heteronuclear NMR spectroscopy, protein dynamics, RSV matrix protein, sequence homology, three-dimensional structure}, isbn = {0022-2836}, doi = {10.1006/jmbi.1998.1788}, url = {http://www.sciencedirect.com/science/article/pii/S0022283698917880}, author = {McDonnell,James M and Fushman, David and Cahill,Sean M. and Zhou,Wenjun and Wolven,Amy and Wilson,Carol B and Nelle,Timothy D and Resh,Marilyn D and Wills,John and Cowburn,David} } @article {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} } @inbook {13718, title = {A Thematic Hierarchy for Efficient Generation from Lexical-Conceptual Structure}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {333 - 343}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes an implemented algorithm for syntactic realization of a target-language sentence from an interlingual representation called Lexical Conceptual Structure (LCS). We provide a mapping between LCS thematic roles and Abstract Meaning Representation (AMR) relations; these relations serve as input to an off-the-shelf generator (Nitrogen). There are two contributions of this work: (1) the development of a thematic hierarchy that provides ordering information for realization of arguments in their surface positions; (2) the provision of a diagnostic tool for detecting inconsistencies in an existing online LCS-based lexicon that allows us to enhance principles for thematic-role assignment.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_30}, author = {Dorr, Bonnie J and Habash,Nizar and Traum,David}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @book {13028, title = {Trends in the Early Careers of Life Scientists}, year = {1998}, month = {1998///}, publisher = {National Academy Press}, organization = {National Academy Press}, address = {Washington, DC}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @article {13029, title = {Trends in the early careers of life scientists - Preface and executive summary}, journal = {Mol Biol Cell}, volume = {9}, year = {1998}, month = {1998/11//}, pages = {3007 - 3015}, author = {Tilghman,S and Astin,HS and Brinkley,W and Chilton,MD and Cummings, Michael P. and Ehrenberg,RG and Fox,MF and Glenn,K and Green,PJ and Hans,S and Kelman,A and LaPidus,J and Levin,B and McIntosh,JR and Riecken,H and Stephen,PE} } @inbook {14268, title = {The Video Yardstick}, booktitle = {Modelling and Motion Capture Techniques for Virtual EnvironmentsModelling and Motion Capture Techniques for Virtual Environments}, series = {Lecture Notes in Computer Science}, volume = {1537}, year = {1998}, month = {1998///}, pages = {144 - 158}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Given uncalibrated video sequences, how can we recover rich descriptions of the scene content, beyond two-dimensional (2D) measurements such as color/texture or motion fields {\textemdash} descriptions of shape and three-dimensional (3D) motion? This is the well known structure from motion (SFM) problem. Up to now, SFM algorithms proceeded in two well defined steps, where the first and most important step is recovering the rigid transformation between two views, and the subsequent step is using this transformation to compute the structure of the scene in view. This paper introduces a novel approach to structure from motion in which both steps are accomplished in a synergistic manner. It deals with the classical structure from motion problem considering a calibrated camera as well as the extension to an uncalibrated optical device. Existing approaches to estimation of the viewing geometry are mostly based on the use of optic flow, which, however, poses a problem at the locations of depth discontinuities. If we knew where depth discontinuities were, we could (using a multitude of approaches based on smoothness constraints) accurately estimate flow values for image patches corresponding to smooth scene patches; but to know the discontinuities requires solving the structure from motion problem first. In the past this dilemma has been addressed by improving the estimation of flow through sophisticated optimization techniques, whose performance often depends on the scene in view. In this paper we follow a different approach. We directly utilize the image derivatives and employ constraints which involve the 3D motion and shape of the scene, leading to a geometric and statistical estimation problem. The main idea is based on the interaction between 3D motion and shape which allows us to estimate the 3D motion while at the same time segmenting the scene. If we use a wrong 3D motion estimate to compute depth, we obtain a distorted version of the depth function. The distortion, however, is such that the worse the motion estimate, the more likely we are to obtain depth estimates that are locally unsmooth, i.e., they vary more than the correct ones. Since local variability of depth is due either to the existence of a discontinuity or to a wrong 3D motion estimate, being able to differentiate between these two cases provides the correct motion, which yields the {\textquotedblleft}smoothest{\textquotedblright} estimated depth as well as the image locations of scene discontinuities. We analyze the new constraints introduced by our approach and show their relationship to the minimization of the epipolar constraint, which becomes a special case of our theory. Finally, we present a number of experimental results with real image sequences indicating the robustness of our method and the improvement over traditional methods. The resulting system is a video yardstick that can be applied to any video sequence to recover first the calibration parameters of the camera that captured the video and, subsequently, the structure of the scene.}, isbn = {978-3-540-65353-0}, url = {http://dx.doi.org/10.1007/3-540-49384-0_12}, author = {Brodsk{\'y},Tom{\'a}{\v s} and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Magnenat-Thalmann,Nadia and Thalmann,Daniel} } @inbook {14277, title = {What is computed by structure from motion algorithms?}, booktitle = {Computer Vision {\textemdash} ECCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1406}, year = {1998}, month = {1998///}, pages = {359 - 375}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In the literature we find two classes of algorithms which, on the basis of two views of a scene, recover the rigid transformation between the views and subsequently the structure of the scene. The first class contains techniques which require knowledge of the correspondence or the motion field between the images and are based on the epipolar constraint. The second class contains so-called direct algorithms which require knowledge about the value of the flow in one direction only and are based on the positive depth constraint. Algorithms in the first class achieve the solution by minimizing a function representing deviation from the epipolar constraint while direct algorithms find the 3D motion that, when used to estimate depth, produces a minimum number of negative depth values. This paper presents a stability analysis of both classes of algorithms. The formulation is such that it allows comparison of the robustness of algorithms in the two classes as well as within each class. Specifically, a general statistical model is employed to express the functions which measure the deviation from the epipolar constraint and the number of negative depth values, and these functions are studied with regard to their topographic structure, specifically as regards the errors in the 3D motion parameters at the places representing the minima of the functions. The analysis shows that for algorithms in both classes which estimate all motion parameters simultaneously, the obtained solution has an error such that the projections of the translational and rotational errors on the image plane are perpendicular to each other. Furthermore, the estimated projection of the translation on the image lies on a line through the origin and the projection of the real translation.}, isbn = {978-3-540-64569-6}, url = {http://dx.doi.org/10.1007/BFb0055678}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Burkhardt,Hans and Neumann,Bernd} } @conference {12047, title = {Which shape from motion?}, booktitle = {Sixth International Conference on Computer Vision, 1998}, year = {1998}, month = {1998/01/04/7}, pages = {689 - 695}, publisher = {IEEE}, organization = {IEEE}, abstract = {In a practical situation, the rigid transformation relating different views is recovered with errors. In such a case, the recovered depth of the scene contains errors, and consequently a distorted version of visual space is computed. What then are meaningful shape representations that can be computed from the images? The result presented in this paper states that if the rigid transformation between different views is estimated in a way that gives rise to a minimum number of negative depth values, then at the center of the image affine shape can be correctly computed. This result is obtained by exploiting properties of the distortion function. The distortion model turns out to be a very powerful tool in the analysis and design of 3D motion and shape estimation algorithms, and as a byproduct of our analysis we present a computational explanation of psychophysical results demonstrating human visual space distortion from motion information}, keywords = {3D motion estimation, affine shape, Algorithm design and analysis, Computer vision, distorted version, distortion function, human visual space distortion, HUMANS, Image motion analysis, image representation, Information analysis, Layout, Motion analysis, Motion estimation, motion information, Psychology, rigid transformation, SHAPE, shape estimation, shape representations, State estimation, visual space}, isbn = {81-7319-221-9}, doi = {10.1109/ICCV.1998.710792}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @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 {14264, title = {The confounding of translation and rotation in reconstruction from multiple views}, booktitle = {, 1997 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1997. Proceedings}, year = {1997}, month = {1997/06/17/19}, pages = {250 - 256}, publisher = {IEEE}, organization = {IEEE}, abstract = {If 3D rigid motion is estimated with some error a distorted version of the scene structure will in turn be computed. Of computational interest are these regions in space where the distortions are such that the depths become negative, because in order to be visible the scene has to lie in front of the image. The stability analysis for the structure-from-motion problem presented in this paper investigates the optimal relationship between the errors in the estimated translational and rotational parameters of a rigid motion, that results in the estimation of a minimum number of negative depth values. The input used is the value of the flow along some direction, which is more general than optic flow or correspondence. For a planar retina it is shown that the optimal configuration is achieved when the projections of the translational and rotational errors on the image plane are perpendicular. Furthermore, the projection of the actual and the estimated translation lie on a line passing through the image center. For a spherical retina given a rotational error, the optimal translation is the correct one, while given a translational error. The optimal rotational error is normal to the translational one at an equal distance from the real and estimated translations. The proofs, besides illuminating the confounding of translation and rotation in structure from motion, have an important application to ecological optics, explaining differences of planar and spherical eye or camera designs in motion and shape estimation}, keywords = {3D rigid motion, CAMERAS, ecological optics, Error correction, Image motion analysis, Image reconstruction, Layout, Motion analysis, Motion estimation, multiple views, Optical distortion, optimal configuration, optimal rotational error, planar retina, RETINA, rigid motion, ROTATION, scene structure, shape estimation, spherical retina, Stability analysis, structure-from-motion problem, translation}, isbn = {0-8186-7822-4}, doi = {10.1109/CVPR.1997.609328}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {12017, title = {DIRECT MOTION PERCEPTION}, journal = {Visual navigation: from biological systems to unmanned ground vehicles}, year = {1997}, month = {1997///}, pages = {135 - 135}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14473, title = {Effective redundant constraints for online scheduling}, journal = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, year = {1997}, month = {1997///}, pages = {302 - 307}, abstract = {The use of heuristics as a means to improve constraint solverperformance has been researched widely. However, most work has been on problem-independent heuristics (e.g., vari- able and value ordering), and has focused on offline prob- lems (e.g., one-shot constraint satisfaction). In this paper, we present an online scheduling problem for which we are developing a real-time scheduling algorithm. While we can and do use generic heuristics in the scheduler, here we fo- cus on the use of domain-specific redundant constraints to ef- fectively approximate optimal offline solutions. We present a taxonomy of redundant domain constraints, and examine their impact on the effectiveness of the scheduler. We also describe several techniques for generating redundant con- straints, which can be applied to a large class of job shop scheduling problems. }, author = {Getoor, Lise and Ottosson,G. and Fromherz,M. and Carlson,B.} } @article {14220, title = {Families of Stationary Patterns Producing Illusory Movement: Insights into the Visual System}, journal = {Proceedings of the Royal Society of London. Series B: Biological SciencesProc. R. Soc. Lond. B}, volume = {264}, year = {1997}, month = {1997/06/22/}, pages = {795 - 806}, abstract = {A computational explanation of the illusory movement experienced upon extended viewing of Enigma, a static figure painted by Leviant, is presented. The explanation relies on a model for the interpretation of three{\textendash}dimensional motion information contained in retinal motion measurements. This model shows that the Enigma figure is a special case of a larger class of figures exhibiting the same illusory movement and these figures are introduced here. Our explanation suggests that eye movements and/or accommodation changes cause weak retinal motion signals, which are interpreted by higher{\textendash}level processes in a way that gives rise to these illusions, and proposes a number of new experiments to unravel the functional structure of the motion pathway.}, isbn = {0962-8452, 1471-2954}, doi = {10.1098/rspb.1997.0112}, url = {http://rspb.royalsocietypublishing.org/content/264/1383/795}, author = {Ferm{\"u}ller, Cornelia and Pless,Robert and Aloimonos, 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 {14242, title = {On the Geometry of Visual Correspondence}, journal = {International Journal of Computer Vision}, volume = {21}, year = {1997}, month = {1997///}, pages = {223 - 247}, abstract = {Image displacement fields{\textemdash}optical flow fields, stereo disparity fields, normal flow fields{\textemdash}due to rigid motion possess a global geometric structure which is independent of the scene in view. Motion vectors of certain lengths and directions are constrained to lie on the imaging surface at particular loci whose location and form depends solely on the 3D motion parameters. If optical flow fields or stereo disparity fields are considered, then equal vectors are shown to lie on conic sections. Similarly, for normal motion fields, equal vectors lie within regions whose boundaries also constitute conics. By studying various properties of these curves and regions and their relationships, a characterization of the structure of rigid motion fields is given. The goal of this paper is to introduce a concept underlying the global structure of image displacement fields. This concept gives rise to various constraints that could form the basis of algorithms for the recovery of visual information from multiple views.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1023/A:1007951901001}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @inbook {14265, title = {The geometry of visual space distortion}, booktitle = {Algebraic Frames for the Perception-Action CycleAlgebraic Frames for the Perception-Action Cycle}, series = {Lecture Notes in Computer Science}, volume = {1315}, year = {1997}, month = {1997///}, pages = {249 - 277}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The encounter of perception and action happens at the intermediate representations of space-time. In many of the computational models employed in the past, it has been assumed that a metric representation of physical space can be derived by visual means. Psychophysical experiments, as well as computational considerations, can convince us that the perception of space and shape has a much more complicated nature, and that only a distorted version of actual, physical space can be computed. This paper develops a computational geometric model that explains why such distortion might take place. The basic idea is that, both in stereo and motion, we perceive the world from multiple views. Given the rigid transformation between the views and the properties of the image correspondence, the depth of the scene can be obtained. Even a slight error in the rigid transformation parameters causes distortion of the computed depth of the scene. The unified framework introduced here describes this distortion in computational terms. We characterize the space of distortions by its level sets, that is, we characterize the systematic distortion via a family of iso-distortion surfaces which describes the locus over which depths are distorted by some multiplicative factor. Clearly, functions of the distorted space exhibiting some sort of invariance, produce desirable representations for biological and artificial systems [13]. Given that humans{\textquoteright} estimation of egomotion or estimation of the extrinsic parameters of the stereo apparatus is likely to be imprecise, the framework is used to explain a number of psychophysical experiments on the perception of depth from motion or stereo.}, isbn = {978-3-540-63517-8}, url = {http://dx.doi.org/10.1007/BFb0017872}, author = {Ferm{\"u}ller, Cornelia and LoongFah Cheong and Aloimonos, J.}, editor = {Sommer,Gerald and Koenderink,Jan} } @conference {18321, title = {Learning parameterized models of image motion}, booktitle = {Computer Vision and Pattern Recognition, 1997. Proceedings., 1997 IEEE Computer Society Conference on}, year = {1997}, month = {1997/06//}, pages = {561 - 567}, abstract = {A framework for learning parameterized models of optical flow from image sequences is presented. A class of motions is represented by a set of orthogonal basis flow fields that are computed from a training set using principal component analysis. Many complex image motions can be represented by a linear combination of a small number of these basis flows. The learned motion models may be used for optical flow estimation and for model-based recognition. For optical flow estimation we describe a robust, multi-resolution scheme for directly computing the parameters of the learned flow models from image derivatives. As examples we consider learning motion discontinuities, non-rigid motion of human mouths, and articulated human motion}, keywords = {image motion, Image sequences, learning, learning (artificial intelligence), model-based recognition, Motion estimation, multi-resolution scheme, non-rigid motion, optical flow, optical flow estimation, parameterized models, Principal component analysis, training set}, doi = {10.1109/CVPR.1997.609381}, author = {Black,M. J and Yacoob,Yaser and Jepson,A. D and Fleet,D. J} } @article {14627, title = {Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model}, journal = {Journal of Computational Biology}, volume = {4}, year = {1997}, month = {1997/01//}, pages = {275 - 296}, abstract = {We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill (1985), which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail (1996a) gave approximation algorithms for folding proteins on the cubic lattice under the HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that the triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.1997.4.275}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.1997.4.275}, author = {Agarwala,Richa and Batzoglou,Serafim and Dan{\v c}{\'\i}K,Vlado and Decatur,Scott E. and Hannenhalli, Sridhar and Farach,Martin and Muthukrishnan,S. and Skiena,Steven} } @article {18722, title = {The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibration}, journal = {Journal of Molecular Biology}, volume = {266}, year = {1997}, month = {1997/02/14/}, pages = {173 - 194}, abstract = {The backbone dynamics of the pleckstrin homology (PH) domain from dynamin were studied by 15N NMR relaxation (R1 and R2) and steady state heteronuclear 15N {1H} nuclear Overhauser effect measurements at 500 and 600 MHz, at protein concentrations of 1.7 mM and 300 μM, and by molecular dynamics (MD) simulations. The analysis was performed using the model-free approach. The method was extended in order to account for observed partial (equilibrium) dimerization of the protein at NMR concentrations. A model is developed that takes into account both rapid monomer-dimer exchange and anisotropy of the over-all rotation of the dimer. The data show complex dynamics of the dynamin PH domain. Internal motions in elements of the secondary structure are restricted, as inferred from the high value of the order parameter (S2 \~{} 0.9) and from the local correlation time \<100 ps. Of the four extended loop regions that are disordered in the NMR-derived solution structure of the protein, loops β1/β2 and β5/β6 are involved in a large-amplitude (S2 down to 0.2 to 0.3) subnanosecond to nanosecond time-scale motion. Reorientation of the loops β3/β4 and β6/β7, in contrast, is restricted, characterized by the values of order parameter S2 \~{} 0.9 more typical of the protein core. These loops, however, are involved in much slower processes of motion resulting in a conformational exchange on a microsecond to submillisecond time scale. The motions of the terminal regions (residues 1 to 10, 122 to 125) are practically unrestricted (S2 down to 0.05, characteristic times in nanosecond time scale), suggesting that these parts of the sequence do not participate in the protein fold. The analysis shows a larger sensitivity of the 15N relaxation data to protein microdynamic parameters (S2, τloc) when protein molecular mass (τc) increases. The use of negative values of the steady state 15N{1H} NOEs as an indicator of the residues not belonging to the folded structure is suggested. The amplitudes of local motion observed in the MD simulation are in a good agreement with the NMR data for the amide NH groups located in the protein core.}, keywords = {dynamin, monomer/dimer equilibration, NMR relaxation, pleckstrin homology domain, protein dynamics}, isbn = {0022-2836}, doi = {10.1006/jmbi.1996.0771}, url = {http://www.sciencedirect.com/science/article/pii/S0022283696907718}, author = {Fushman, David and Cahill,Sean and Cowburn,David} } @article {15223, title = {A Network-Flow Technique for Finding Low-Weight Bounded-Degree Spanning Trees}, journal = {Journal of Algorithms}, volume = {24}, year = {1997}, month = {1997/08//}, pages = {310 - 324}, abstract = {Given a graph with edge weights satisfying the triangle inequality, and a degree bound for each vertex, the problem of computing a low-weight spanning tree such that the degree of each vertex is at most its specified bound is considered. In particular, modifying a given spanning treeTusingadoptionsto meet the degree constraints is considered. A novel network-flow-based algorithm for finding a good sequence of adoptions is introduced. The method yields a better performance guarantee than any previous algorithm. If the degree constraintd(v) for eachvis at least 2, the algorithm is guaranteed to find a tree whose weight is at most the weight of the given tree times 2\&$\#$xa0;-\&$\#$xa0;min{(d(v)\&$\#$xa0;-\&$\#$xa0;2)/(degT(v)\&$\#$xa0;-\&$\#$xa0;2)\&$\#$xa0;:\&$\#$xa0;degT(v)\&$\#$xa0;\>\&$\#$xa0;2}, where degT(v) is the initial degree ofv. Equally importantly, it takes this approach to the limit in the following sense: if any performance guarantee that is solely a function of the topology and edge weights of a given tree holds foranyalgorithm at all, then it also holds for the given algorithm. Examples are provided in which no lighter tree meeting the degree constraint exists. Linear-time algorithms are provided with the same worst-case performance guarantee. ChoosingTto be a minimum spanning tree yields approximation algorithms with factors less than 2 for the general problem on geometric graphs with distances induced by variousLpnorms. Finally, examples of Euclidean graphs are provided in which the ratio of the lengths of an optimal Traveling Salesman path and a minimum spanning tree can be arbitrarily close to 2.}, isbn = {0196-6774}, doi = {10.1006/jagm.1997.0862}, url = {http://www.sciencedirect.com/science/article/pii/S0196677497908622}, author = {Fekete,S{\'a}ndor P and Khuller, Samir and Klemmstein,Monika and Raghavachari,Balaji and Young,Neal} } @article {15796, title = {Regularization by Truncated Total Least Squares}, journal = {SIAM Journal on Scientific Computing}, volume = {18}, year = {1997}, month = {1997///}, pages = {1223 - 1241}, abstract = {The total least squares (TLS) method is a successful method for noise reduction in linear least squares problems in a number of applications. The TLS method is suited to problems in which both the coefficient matrix and the right-hand side are not precisely known. This paper focuses on the use of TLS for solving problems with very ill-conditioned coefficient matrices whose singular values decay gradually (so-called discrete ill-posed problems), where some regularization is necessary to stabilize the computed solution. We filter the solution by truncating the small singular values of the TLS matrix. We express our results in terms of the singular value decomposition (SVD) of the coefficient matrix rather than the augmented matrix. This leads to insight into the filtering properties of the truncated TLS method as compared to regularized least squares solutions. In addition, we propose and test an iterative algorithm based on Lanczos bidiagonalization for computing truncated TLS solutions.}, keywords = {bidiagonalization, discrete ill-posed problems, regularization, total least squares}, doi = {10.1137/S1064827594263837}, url = {http://link.aip.org/link/?SCE/18/1223/1}, author = {Fierro,R. D. and Golub, G. H and Hansen,P. C. and O{\textquoteright}Leary, Dianne P.} } @conference {12092, title = {A secure and reliable bootstrap architecture}, booktitle = {, 1997 IEEE Symposium on Security and Privacy, 1997. Proceedings}, year = {1997}, month = {1997/05/04/7}, pages = {65 - 71}, publisher = {IEEE}, organization = {IEEE}, abstract = {In a computer system, the integrity of lower layers is typically treated as axiomatic by higher layers. Under the presumption that the hardware comprising the machine (the lowest layer) is valid, the integrity of a layer can be guaranteed if and only if: (1) the integrity of the lower layers is checked and (2) transitions to higher layers occur only after integrity checks on them are complete. The resulting integrity {\textquotedblleft}chain{\textquotedblright} inductively guarantees system integrity. When these conditions are not met, as they typically are not in the bootstrapping (initialization) of a computer system, no integrity guarantees can be made, yet these guarantees are increasingly important to diverse applications such as Internet commerce, security systems and {\textquotedblleft}active networks{\textquotedblright}. In this paper, we describe the AEGIS architecture for initializing a computer system. It validates integrity at each layer transition in the bootstrap process. AEGIS also includes a recovery process for integrity check failures, and we show how this results in robust systems}, keywords = {active networks, AEGIS architecture, bootstrap architecture, Computer architecture, computer bootstrapping, data integrity, Distributed computing, Hardware, hardware validity, initialization, integrity chain, integrity check failures, Internet, Internet commerce, IP networks, Laboratories, lower-layer integrity, Microprogramming, Operating systems, recovery process, reliability, robust systems, Robustness, Security, security of data, software reliability, system integrity guarantees, system recovery, transitions, Virtual machining}, isbn = {0-8186-7828-3}, doi = {10.1109/SECPRI.1997.601317}, author = {Arbaugh, William A. and Farber,D. J and Smith,J. M} } @inbook {14269, title = {Toward motion picture grammars}, booktitle = {Computer Vision {\textemdash} ACCV{\textquoteright}98Computer Vision {\textemdash} ACCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1352}, year = {1997}, month = {1997///}, pages = {283 - 290}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We are interested in processing video data for the purpose of solving a variety of problems in video search, analysis, indexing, browsing and compression. Instead of concentrating on a particular problem, in this paper we present a framework for developing video applications. Our basic thesis is that video data can be represented at a higher level of abstraction as a string generated by a grammar, termed motion picture grammar. The rules of that grammar relate different spatiotemporal representations of the video content and, in particular, representations of action.}, isbn = {978-3-540-63931-2}, url = {http://dx.doi.org/10.1007/3-540-63931-4_228}, author = {Bolle,Ruud and Aloimonos, J. and Ferm{\"u}ller, Cornelia}, editor = {Chin,Roland and Pong,Ting-Chuen} } @conference {13696, title = {VideoTrails: Representing and Visualizing Structure in Video Sequences}, booktitle = {Proceedings of the ACMInternational Multimedia Conference}, year = {1997}, month = {1997///}, pages = {335 - 346}, author = {Kobla,V. and David Doermann and Faloutsos,C.} } @conference {17846, title = {The virtual microscope.}, booktitle = {Proceedings of the AMIA Annual Fall Symposium}, year = {1997}, month = {1997///}, pages = {449 - 449}, author = {Ferreira,R. and Moon,B. and Humphries,J. and Sussman, Alan and Saltz, J. and Miller,R. and Demarzo,A.} } @article {14275, title = {Visual space distortion}, journal = {Biological Cybernetics}, volume = {77}, year = {1997}, month = {1997///}, pages = {323 - 337}, abstract = {We are surrounded by surfaces that we perceive by visual means. Understanding the basic principles behind this perceptual process is a central theme in visual psychology, psychophysics, and computational vision. In many of the computational models employed in the past, it has been assumed that a metric representation of physical space can be derived by visual means. Psychophysical experiments, as well as computational considerations, can convince us that the perception of space and shape has a much more complicated nature, and that only a distorted version of actual, physical space can be computed. This paper develops a computational geometric model that explains why such distortion might take place. The basic idea is that, both in stereo and motion, we perceive the world from multiple views. Given the rigid transformation between the views and the properties of the image correspondence, the depth of the scene can be obtained. Even a slight error in the rigid transformation parameters causes distortion of the computed depth of the scene. The unified framework introduced here describes this distortion in computational terms. We characterize the space of distortions by its level sets, that is, we characterize the systematic distortion via a family of iso-distortion surfaces which describes the locus over which depths are distorted by some multiplicative factor. Given that humans{\textquoteright} estimation of egomotion or estimation of the extrinsic parameters of the stereo apparatus is likely to be imprecise, the framework is used to explain a number of psychophysical experiments on the perception of depth from motion or stereo.}, isbn = {0340-1200}, url = {http://dx.doi.org/10.1007/s004220050393}, author = {Ferm{\"u}ller, Cornelia and LoongFah Cheong and Aloimonos, J.} } @article {18305, title = {Visual surveillance of human activity}, journal = {Computer Vision{\textemdash}ACCV{\textquoteright}98}, year = {1997}, month = {1997///}, pages = {267 - 274}, author = {Davis, Larry S. and Fejes,S. and Harwood,D. and Yacoob,Yaser and Hariatoglu,I. and Black,M.} } @article {12177, title = {A zooming web browser}, journal = {Human Factors in Web Development}, year = {1997}, month = {1997///}, author = {Bederson, Benjamin B. and Hollan,J.D. and Stewart,J. and Rogers,D. and Druin, Allison and Vick,D. and Ring,L. and Grose,E. and Forsythe,C.} } @article {14194, title = {Algorithm-Independent Stability Analysis of Structure from Motion.}, year = {1996}, month = {1996///}, institution = {Computer Vision Lab, University of Maryland College Park}, abstract = {The stability analysis for the structure from motion problem presented in this paper investigates the optimal relationship between the errors in the estimated translational and rotational parameters of a rigid motion that results in the estimation of a minimum number of negative depth values. No particular estimators are used and no specific assumptions about the scene are made. The input used is the value of the flow along some direction, which is more general than optic flow or correspondence. For a planar retina it is shown that the optimal configuration is achieved when the projections of the translational and rotational errors on the image plane are perpendicular. For a spherical retina, given a rotational error, the optimal translation is the correct one, while given a translational error the optimal rotational error is normal to the translational one at an equal distance from the real and estimated translations. The proofs, besides illuminating the confounding of translation and rotation in structure from motion, have an important application to ecological optics. The same analysis provides a computational explanation of why it is much easier to estimate self-motion in the case of a spherical retina and why it is much easier to estimate shape in the case of a planar retina, thus suggesting that nature{\textquoteright}s design of compound eyes (or panoramic vision) for flying systems and camera-type eyes for primates (and other systems that perform manipulation) is optimal.}, author = {Ferm{\"u}ller, Cornelia} } @conference {16460, title = {Answering queries using OQL view expressions}, booktitle = {In Workshop on Materialized Views, in cooperation with ACM SIGMOD}, year = {1996}, month = {1996///}, author = {Florescu,D. and Raschid, Louiqa and Valduriez,P.} } @inbook {14213, title = {Directions of motion fields are hardly ever ambiguous}, booktitle = {Computer Vision {\textemdash} ECCV {\textquoteright}96Computer Vision {\textemdash} ECCV {\textquoteright}96}, series = {Lecture Notes in Computer Science}, volume = {1065}, year = {1996}, month = {1996///}, pages = {119 - 128}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Recent literature [7, 10, 11, 9, 13, 17] provides a number of results regarding uniqueness aspects of motion fields and exact image displacements due to 3-D rigid motion. Here instead of the full motion field we consider only the direction of the motion field due to a rigid motion and ask what can we say about the three-dimensional motion information contained in it. This paper provides a geometric analysis of this question based solely on the fact that the depth of the surfaces in view is positive (i.e. that the surface in view is in front of the camera). With this analysis we thus offer a theoretical foundation for image constraints employing only the sign of flow in various directions and provide a solid basis for their utilization in addressing 3D dynamic vision problems.}, isbn = {978-3-540-61123-3}, url = {http://dx.doi.org/10.1007/3-540-61123-1_132}, author = {Brodsky, Tomas and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Buxton,Bernard and Cipolla,Roberto} } @conference {15533, title = {Disjunctive deductive databases: Semantics, updates and architecture}, booktitle = {Proceedings of the 4th Bar-Ilan Symposium on Foundations of AI}, year = {1996}, month = {1996///}, pages = {256 - 274}, abstract = {The basic assumption in relational and deductive databases is that there are no gaps in our knowledge. That is, the database cannot store data that contain null values or data that is indefinite. In practical situations knowledge is not precise, and there are gaps in our knowledge. These gaps may be due to null values in the data, may arise when we combine several databases that lead to inconsistent theories, or may occur because information is indefinite in nature, such as in military or medical applications. In this paper we describe semantics for disjunctive deductive databases that extend the work in deductive databases, solve the view update problem, and permit indefinite data to be represented efficiently. Hierarchic, stratified, and normal stable models of disjunctive databases are described. An architecture is proposed for a disjunctive deductive database system and a class of theories for which the architecture will be effective is discussed.}, author = {Fernandez,J. A. and Gryz,J. and Minker, Jack} } @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 {14216, title = {Explaining Human Visual Space Distortion.}, year = {1996}, month = {1996///}, institution = {Computer Vision Lab, University of Maryland College Park}, abstract = {A number of experiments have recently been conducted to compare aspects of depth judgment due to stereoscopic and monocular motion perception. In these experiments, it has been shown that from stereo vision humans over-estimate depth (relative to fronto-parallel size) at near fixations and under-estimate it at far fixations, whereas human depth estimates from visual motion are not affected by the fixation point. On the other hand, the orientation of an object in space does not affect depth judgment in stereo vision while it has a strong effect in motion vision, for the class of motions tested. This paper develops a computational geometric model that explains why such distortion might take place. The basic idea is that, both in stereo and motion, we perceive the world from multiple views. Given the rigid transformation between the views and the properties of the image correspondence, the depth of the scene can be obtained. Even a slight error in the rigid transformation parameters causes distortion of the computed depth of the scene. The unified framework introduced here describes this distortion in computational terms, in order to explain a number of recent psychophysical experiments on the perception of depth from motion or stereo.}, author = {Ferm{\"u}ller, Cornelia} } @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} } @book {14225, title = {Interaction between 3D Shape and Motion: Theory and Applications}, year = {1996}, month = {1996/06//}, publisher = {Computer Vision Laboratory, University of Maryland}, organization = {Computer Vision Laboratory, University of Maryland}, abstract = {Research during the past few years has attempted to characterize the errors that arise in computing 3D motion (egomotion estimation) and in a scene{\textquoteright}s structure (structure from motion) from a sequence of images acquired by a moving sensor. This paper presents a new geometric framework that characterizes how the three-dimensional space recovered by a moving monocular observer, whose 3D motion is estimated with some error, is distorted. We characterize the space of distortions by its level sets, that is, by a family of iso-distortion surfaces, each of which describes the locus over which the depths of points in the scene are distorted by the same multiplicative factor. By analyzing the geometry of the regions where the distortion factor is negative, that is, where the visibility constraint is violated, we make explicit situations which are likely to give rise to ambiguities in motion estimation. We also apply our approach to a uniqueness analysis for 3D motion analysis from normal flow; we study the constraints on egomotion, object motion and depth for an independently moving object to be detectable by a moving observer; and we offer a quantitative account of the precision needed in an inertial sensor for accurate estimation of 3D motion.}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J. and Cheong,L.} } @article {16452, title = {A methodology for query reformulation in CIS using semantic knowledge}, journal = {International Journal of Cooperative Information Systems}, volume = {5}, year = {1996}, month = {1996///}, pages = {431 - 468}, author = {Florescu,D. and Raschid, Louiqa and Valduriez,P.} } @article {15534, title = {Model theoretic approach to view updates in deductive databases}, journal = {Journal of Automated Reasoning}, volume = {17}, year = {1996}, month = {1996///}, pages = {171 - 197}, abstract = {The view update problem for deductive databases has been defined as the problem of accomplishing the update of an intensional predicate by modifying appropriately the extensional database. A previous paper by Grant, Horty, Lobo, and Minker developed algorithms for the insertion and the deletion of an intensional predicate in certain important classes of stratified disjunctive deductive databases. This paper introduces a model theoretic approach which encompasses a wide class of Herbrand semantics, including the perfect model and stable model semantics, for disjunctive databases including negation. This generalizes the earlier results: now the intensional database may contain disjunctive and denial rules, and the database may be required to satisfy integrity constraints. As in the previous paper, the algorithms are proved to be correct and best according to the criterion of causing minimal change to the database, where the first priority is to minimize deletions.}, doi = {10.1007/BF00244495}, author = {Fernandez,J. A. and Grant,J. and Minker, Jack} } @article {14243, title = {Ordinal representations of visual space}, journal = {Proc. Image Understanding Workshop}, year = {1996}, month = {1996///}, pages = {897 - 904}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @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.} } @conference {14249, title = {Qualitative depth and FOE information via smoothed flow}, booktitle = {Proceedings of the 20th workshop of the Austrian Association for Pattern Recognition (OAGM/AAPR) on Pattern recognition 1996}, year = {1996}, month = {1996///}, pages = {207 - 213}, publisher = {R. Oldenbourg Verlag GmbH}, organization = {R. Oldenbourg Verlag GmbH}, address = {Munich, Germany, Germany}, isbn = {3-486-23865-5}, url = {http://dl.acm.org/citation.cfm?id=258081.258100}, author = {Shulman,David and Ferm{\"u}ller, Cornelia} } @inbook {14259, title = {Spatiotemporal representations for visual navigation}, booktitle = {Computer Vision {\textemdash} ECCV {\textquoteright}96Computer Vision {\textemdash} ECCV {\textquoteright}96}, series = {Lecture Notes in Computer Science}, volume = {1064}, year = {1996}, month = {1996///}, pages = {671 - 684}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The study of visual navigation problems requires the integration of visual processes with motor control. Most essential in approaching this integration is the study of appropriate spatio-temporal representations which the system computes from the imagery and which serve as interfaces to all motor activities. Since representations resulting from exact quantitative reconstruction have turned out to be very hard to obtain, we argue here for the necessity of representations which can be computed easily, reliably and in real time and which recover only the information about the 3D world which is really needed in order to solve the navigational problems at hand. In this paper we introduce a number of such representations capturing aspects of 3D motion and scene structure which are used for the solution of navigational problems implemented in visual servo systems. In particular, the following three problems are addressed: (a) to change the robot{\textquoteright}s direction of motion towards a fixed direction, (b) to pursue a moving target while keeping a certain distance from the target, and (c) to follow a wall-like perimeter. The importance of the introduced representations lies in the following: \&$\#$x96; They can be extracted using minimal visual information, in particular the sign of flow measurements or the the first order spatiotemporal derivatives of the image intensity function. In that sense they are direct representations needing no intermediate level of computation such as correspondence. \&$\#$x96; They are global in the sense that they represent how three-dimensional information is globally encoded in them. Thus, they are robust representations since local errors do not affect them. \&$\#$x96; Usually, from sequences of images, three-dimensional quantities such as motion and shape are computed and used as input to control processes. The representations discussed here are given directly as input to the control procedures, thus resulting in a real time solution.}, isbn = {978-3-540-61122-6}, url = {http://dx.doi.org/10.1007/BFb0015577}, author = {LoongFah Cheong and Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Buxton,Bernard and Cipolla,Roberto} } @article {11997, title = {The synthesis of vision and action}, journal = {Exploratory vision: the active eye}, year = {1996}, month = {1996///}, pages = {205 - 205}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @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} } @conference {12033, title = {3D motion representations in visual servo control}, booktitle = {Proceedings of International Symposium on Computer Vision, 1995}, year = {1995}, month = {1995/11/21/23}, pages = {61 - 66}, publisher = {IEEE}, organization = {IEEE}, abstract = {A new approach to visual servoing and vision-guided robotics is introduced. This approach uses visual information for autonomous behavior. It amounts to using robust, global spatiotemporal representations easily extracted from the dynamic imagery. Specifically, the geometrical patterns of normal flows are used as the input to the servo mechanism. It is shown that the positions of these patterns are related to the three dimensional motion parameters. By locating the positions of these patterns, we can solve a variety of navigational problems with little computational effort}, keywords = {3D motion representations, autonomous behavior, CAMERAS, computational effort, Computer vision, dynamic imagery, global spatiotemporal representations, image representation, Mobile robots, motion control, Navigation, navigational problems, Optical computing, Robot kinematics, Robot sensing systems, robot vision, Robot vision systems, Robotics and automation, servomechanisms, Servosystems, Spatiotemporal phenomena, vision-guided robotics, visual information, visual servo control, visual servoing}, isbn = {0-8186-7190-4}, doi = {10.1109/ISCV.1995.476978}, author = {Ferm{\"u}ller, Cornelia and LoongFah Cheong and Aloimonos, J.} } @article {15539, title = {Bottom-up computation of perfect models for disjunctive theories}, journal = {The Journal of logic programming}, volume = {25}, year = {1995}, month = {1995///}, pages = {33 - 51}, author = {Fern{\'a}ndez,J. A. and Minker, Jack} } @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.} } @article {14094, title = {Crystallization and preliminary X-ray investigation of the recombinant Trypanosoma brucei rhodesiense calmodulin}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {21}, year = {1995}, month = {1995///}, pages = {354 - 357}, author = {El-Sayed, Najib M. and Patton,C. L and Harkins,P. C and Fox,R. O and Anderson,K.} } @article {14212, title = {Direct Perception of Three-Dimensional Motion from Patterns of Visual Motion}, journal = {ScienceScience}, volume = {270}, year = {1995}, month = {1995/12/22/}, pages = {1973 - 1976}, abstract = {Measurements of retinal motion along a set of predetermined orientations on the retina of a moving system give rise to global patterns. Because the form and location of these patterns depend purely on three-dimensional (3D) motion, the effects of 3D motion and scene structure on image motion can be globally separated. The patterns are founded on easily derivable image measurements that depend only on the sign of image motion and do not require information about optical flow. The computational theory presented here explains how the self-motion of a system can be estimated by locating these patterns.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.270.5244.1973}, url = {http://www.sciencemag.org/content/270/5244/1973}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {14955, title = {Efficient Algorithms for Atmospheric Correction of Remotely Sensed Data}, booktitle = {Supercomputing, 1995. Proceedings of the IEEE/ACM SC95 Conference}, year = {1995}, month = {1995///}, pages = {12 - 12}, abstract = {Remotely sensed imagery has been used for developing and validating various studies regarding land cover dynamics. However, the large amounts of imagery collected by the satellites are largely contaminated by the effects of atmospheric particles. The objective of atmospheric correction is to retrieve the surface reflectance from remotely sensed imagery by removing the atmospheric effects. We introduce a number of computational techniques that lead to a substantial speedup of an atmospheric correction algorithm based on using look-up tables. Excluding I/O time, the previous known implementation processes one pixel at a time and requires about 2.63 seconds per pixel on a SPARC-10 machine, while our implementation is based on processing the whole image and takes about 4-20 microseconds per pixel on the same machine. We also develop a parallel version of our algorithm that is scalable in terms of both computation and I/O. Experimental results obtained show that a Thematic Mapper (TM) image (36 MB per band, 5 bands need to be corrected) can be handled in less than 4.3 minutes on a 32-node CM-5 machine, including I/O time.}, keywords = {Atmospheric, AVHRR;, computing;, correction;, high, I/O;, Parallel, performance, processing;, remote, scalable, sensing;, TM;}, doi = {10.1109/SUPERC.1995.242453}, author = {Fallah-Adl,H. and JaJa, Joseph F. and Liang,Shunlin and Kaufman,Y.J. and Townshend,J.} } @conference {13769, title = {Experimental investigation of high performance cognitive and interactive text filtering}, booktitle = {, IEEE International Conference on Systems, Man and Cybernetics, 1995. Intelligent Systems for the 21st Century}, volume = {5}, year = {1995}, month = {1995/10/22/25}, pages = {4398-4403 vol.5 - 4398-4403 vol.5}, publisher = {IEEE}, organization = {IEEE}, abstract = {Text filtering has become increasingly important as the volume of networked information has exploded in recent years. This paper reviews recent progress in that field and reports on the development of a testbed for experimental investigation of cognitive and interactive text selection based on a history of user evaluations. An interactive filtering system model is presented and a new cognitive filtering technique which the authors call the Gaussian User Model is described. Because development of analytic measures of text selection effectiveness has proven intractable, the authors have modified the Cornell SMART text retrieval system to create a flexible text filtering testbed for experimental determination of filtering effectiveness. The paper concludes with a description of the design of this testbed system}, keywords = {Cause effect analysis, Computer science, Contracts, Cornell SMART text retrieval system, Educational institutions, Gaussian User Model, high performance cognitive interactive text filtering, History, Information filtering, Information filters, Information retrieval, information retrieval system evaluation, Libraries, Matched filters, online front-ends, Query processing, System testing, text selection effectiveness, user evaluations, User interfaces, user modelling}, isbn = {0-7803-2559-1}, doi = {10.1109/ICSMC.1995.538486}, author = {Oard, Douglas and DeClaris,N. and Dorr, Bonnie J and Faloutsos,C. and Marchionini,G.} } @conference {14168, title = {Global rigidity constraints in image displacement fields}, booktitle = {, Fifth International Conference on Computer Vision, 1995. Proceedings}, year = {1995}, month = {1995/06/20/23}, pages = {245 - 250}, publisher = {IEEE}, organization = {IEEE}, abstract = {Image displacement fields-optical flow fields, stereo disparity fields, normal flow fields-due to rigid motion possess a global geometric structure which is independent of the scene in view. Motion vectors of certain lengths and directions are constrained to lie on the imaging surface at particular loci whose location and form depends solely on the 3D motion parameters. If optical flow fields or stereo disparity fields are considered, then equal vectors are shown to lie on conic sections. Similarly, for normal motion fields, equal vectors lie within regions whose boundaries also constitute conics. By studying various properties of these curves and regions and their relationships, a characterization of the structure of rigid motion fields is given. The goal of this paper is to introduce a concept underlying the global structure of image displacement fields. This concept gives rise to various constraints that could form the basis of algorithms for the recovery of visual information from multiple views}, keywords = {3D motion parameters, algorithms, Automation, Computer science, Computer vision, conic sections, curves, equal vectors, Fluid flow measurement, global geometric structure, global rigidity constraints, image displacement fields, Image motion analysis, Image segmentation, Image sequences, imaging surface, Laboratories, Layout, Motion estimation, Motion measurement, motion vectors, multiple views, normal flow fields, optical flow fields, regions, rigid motion, stereo disparity fields, Stereo vision, vectors, visual information recovery}, isbn = {0-8186-7042-8}, doi = {10.1109/ICCV.1995.466779}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {11982, title = {Global rigidity constraints in image displacement fields}, booktitle = {Proceedings of Fifth International Conference on Computer Vision, 1995}, year = {1995}, month = {1995/06/20/23}, pages = {245 - 250}, publisher = {IEEE}, organization = {IEEE}, abstract = {Image displacement fields-optical flow fields, stereo disparity fields, normal flow fields-due to rigid motion possess a global geometric structure which is independent of the scene in view. Motion vectors of certain lengths and directions are constrained to lie on the imaging surface at particular loci whose location and form depends solely on the 3D motion parameters. If optical flow fields or stereo disparity fields are considered, then equal vectors are shown to lie on conic sections. Similarly, for normal motion fields, equal vectors lie within regions whose boundaries also constitute conics. By studying various properties of these curves and regions and their relationships, a characterization of the structure of rigid motion fields is given. The goal of this paper is to introduce a concept underlying the global structure of image displacement fields. This concept gives rise to various constraints that could form the basis of algorithms for the recovery of visual information from multiple views}, keywords = {3D motion parameters, algorithms, Automation, Computer science, Computer vision, conic sections, curves, equal vectors, Fluid flow measurement, global geometric structure, global rigidity constraints, image displacement fields, Image motion analysis, Image segmentation, Image sequences, imaging surface, Laboratories, Layout, Motion estimation, Motion measurement, motion vectors, multiple views, normal flow fields, optical flow fields, regions, rigid motion, stereo disparity fields, Stereo vision, vectors, visual information recovery}, isbn = {0-8186-7042-8}, doi = {10.1109/ICCV.1995.466779}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {14171, title = {The information in the direction of image flow}, booktitle = {, International Symposium on Computer Vision, 1995. Proceedings}, year = {1995}, month = {1995/11/21/23}, pages = {461 - 466}, publisher = {IEEE}, organization = {IEEE}, abstract = {If instead of the full motion field, we consider only the direction of the motion field due to a rigid motion, what can we say about the information regarding the three-dimensional motion? In this paper it is shown that considering as the imaging surface the whole sphere, independently of the scene in view, two different rigid motions cannot give rise to the same directional motion field. If we restrict the image to half of a sphere (or an infinitely large image plane) two different rigid motions with instantaneous translational and rotational velocities (t1, ω1) and (t2, ω2) cannot give rise to the same directional motion field unless the plane through t1 and t2 is perpendicular to the plane through ω1 and ω2 (i.e., (t1{\texttimes}t2){\textperiodcentered}(ω1 {\texttimes}ω2)=0). In addition, in order to give a practical significance to these uniqueness results for the case of a limited field of view we also characterize the locations on the image where the motion vectors due to the different motions must have different directions. If (ω1{\texttimes}ω2){\textperiodcentered}(t1 {\texttimes}t2)=0 and certain additional constraints are met, then the two rigid motions could produce motion fields with the same direction. For this to happen the depth of each corresponding surface has to be within a certain range, defined by a second and a third order surface}, keywords = {Automation, CAMERAS, Computer vision, Educational institutions, image flow, Image motion analysis, Image sequences, imaging surface, Laboratories, Layout, Motion analysis, Motion estimation, motion field, motion vectors, Optical imaging, rigid motion, rigid motions, three-dimensional motion}, isbn = {0-8186-7190-4}, doi = {10.1109/ISCV.1995.477071}, author = {Brodsky, T. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14244, title = {Passive navigation as a pattern recognition problem}, journal = {International Journal of Computer Vision}, volume = {14}, year = {1995}, month = {1995///}, pages = {147 - 158}, abstract = {The most basic visual capabilities found in living organisms are based on motion. Machine vision, of course, does not have to copy animal vision, but the existence of reliably functioning vision modules in nature gives us some reason to believe that it is possible for an artificial system to work in the same or a similar way. In this article it is argued that many navigational capabilities can be formulated as pattern recognition problems. An appropriate retinotopic representation of the image would make it possible to extract the information necessary to solve motion-related tasks through the recognition of a set of locations on the retina. This argument is illustrated by introducing a representation of image motion by which an observer{\textquoteright}s egomotion could be derived from information globally encoded in the image-motion field. In the past, the problem of determining a system{\textquoteright}s own motion from dynamic imagery has been considered as one of the classical visual reconstruction problems, wherein local constraints have been employed to compute from exact 2-D image measurements (correspondence, optical flow) the relative 3-D motion and structure of the scene in view. The approach introduced here is based on new global constraints defined on local normal-flow measurements{\textemdash}the spatio-temporal derivatives of the image-intensity function. Classifications are based on orientations of normal-flow vectors, which allows selection of vectors that form global patterns in the image plane. The position of these patterns is related to the 3-D motion of the observer, and their localization provides the axis of rotation and the direction of translation. The constraints introduced are utilized in algorithmic procedures formulated as search techniques. These procedures are very stable, since they are not affected by small perturbations in the image measurements. As a matter of fact, the solution to the two directions of translation and rotation is not affected, as long as the measurement of the sign of the normal flow is correct.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1007/BF01418980}, author = {Ferm{\"u}ller, Cornelia} } @article {14245, title = {Perception of 3D Motion through Patterns of Visual Motion.}, year = {1995}, month = {1995/05//}, institution = {CENTER FOR AUTOMATION RESEARCH, UNIVERSITY OF MARYLAND COLLEGE PARK}, abstract = {Geometric considerations suggest that the problem of estimating a system{\textquoteright}s three-dimensional (3D) motion from a sequence of images, which has puzzled researchers in the fields of Computational Vision and Robotics as well as the Biological Sciences, can be addressed as a pattern recognition problem. Information for constructing the relevant patterns is found in spatial arrangements or gratings, that is, aggregations of orientations along which retinal motion information is estimated. The exact form of the gratings is defined by the shape of the retina or imaging surface; for a planar retina they are radial lines, concentric circles, as well as elliptic and hyperbolic curves, while for a spherical retina they become longitudinal and latitudinal circles for various axes. Considering retinal motion information computed normal to these gratings, patterns are found that have encoded in their shape and location on the retina subsets of the 3D motion parameters. The importance of these patterns is first that they depend only on the 3D motion and not on the scene in view, and second that they utilize only the sign of image motion along a set of directions defined by the gratings.}, author = {Ferm{\"u}ller, Cornelia} } @article {14250, title = {Qualitative egomotion}, journal = {International Journal of Computer Vision}, volume = {15}, year = {1995}, month = {1995///}, pages = {7 - 29}, abstract = {Due to the aperture problem, the only motion measurement in images, whose computation does not require any assumptions about the scene in view, is normal flow{\textemdash}the projection of image motion on the gradient direction. In this paper we show how a monocular observer can estimate its 3D motion relative to the scene by using normal flow measurements in a global and qualitative way. The problem is addressed through a search technique. By checking constraints imposed by 3D motion parameters on the normal flow field, the possible space of solutions is gradually reduced. In the four modules that comprise the solution, constraints of increasing restriction are considered, culminating in testing every single normal flow value for its consistency with a set of motion parameters. The fact that motion is rigid defines geometric relations between certain values of the normal flow field. The selected values form patterns in the image plane that are dependent on only some of the motion parameters. These patterns, which are determined by the signs of the normal flow values, are searched for in order to find the axes of translation and rotation. The third rotational component is computed from normal flow vectors that are only due to rotational motion. Finally, by looking at the complete data set, all solutions that cannot give rise to the given normal flow field are discarded from the solution space.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1007/BF01450848}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {14180, title = {Representations for active vision}, booktitle = {Proceedings of the 14th international joint conference on Artificial intelligence - Volume 1}, year = {1995}, month = {1995///}, pages = {20 - 26}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco, CA, USA}, isbn = {1-55860-363-8, 978-1-558-60363-9}, url = {http://dl.acm.org/citation.cfm?id=1625855.1625858}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14255, title = {Seeing and understanding: representing the visual world}, journal = {ACM Comput. Surv.}, volume = {27}, year = {1995}, month = {1995/09//}, pages = {307 - 309}, isbn = {0360-0300}, doi = {10.1145/212094.212101}, url = {http://doi.acm.org/10.1145/212094.212101}, author = {Aloimonos, J. and Ferm{\"u}ller, Cornelia and Rosenfeld, A.} } @conference {12176, title = {Space-scale diagrams: understanding multiscale interfaces}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {1995}, month = {1995///}, pages = {234 - 241}, author = {Furnas,G.W. and Bederson, Benjamin B.} } @article {14177, title = {Vision and action}, journal = {Image and Vision Computing}, volume = {13}, year = {1995}, month = {1995/12//}, pages = {725 - 744}, abstract = {Our work on active vision has recently focused on the computational modelling of navigational tasks, where our investigations were guided by the idea of approaching vision for behavioural systems in the form of modules that are directly related to perceptual tasks. These studies led us to branch in various directions and inquire into the problems that have to be addressed in order to obtain an overall understanding of perceptual systems. In this paper, we present our views about the architecture of vision systems, about how to tackle the design and analysis of perceptual systems, and promising future research directions. Our suggested approach for understanding behavioural vision to realize the relationships of perception and action builds on two earlier approaches, the Medusa philosophy1 and the Synthetic approach2. The resulting framework calls for synthesizing an artificial vision system by studying vision competences of increasing complexity and, at the same time, pursuing the integration of the perceptual components with action and learning modules. We expect that computer vision research in the future will progress in tight collaboration with many other disciplines that are concerned with empirical approaches to vision, i.e. the understanding of biological vision. Throughout the paper, we describe biological findings that motivate computational arguments which we believe will influence studies of computer vision in the near future.}, keywords = {active vision, perceptual system design and analysis, vision system architecture}, isbn = {0262-8856}, doi = {10.1016/0262-8856(95)98754-H}, url = {http://www.sciencedirect.com/science/article/pii/026288569598754H}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {12030, title = {Vision and action* 1}, journal = {Image and vision computing}, volume = {13}, year = {1995}, month = {1995///}, pages = {725 - 744}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {13837, title = {On automatic filtering of multilingual texts}, booktitle = {, 1994 IEEE International Conference on Systems, Man, and Cybernetics, 1994. {\textquoteright}Humans, Information and Technology{\textquoteright}}, volume = {2}, year = {1994}, month = {1994/10/02/5}, pages = {1645-1650 vol.2 - 1645-1650 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {An emerging requirement to sift through the increasing flood of text information has led to the rapid development of information filtering technology in the past five years. This study introduces novel approaches for filtering texts regardless of their source language. We begin with a brief description of related developments in text filtering and multilingual information retrieval. We then present three alternative approaches to selecting texts from a multilingual information stream which represent a logical evolution from existing techniques in related disciplines. Finally, a practical automated performance evaluation technique is proposed}, keywords = {automated performance evaluation, Business communication, Computer science, Discussion forums, Displays, Educational institutions, Floods, Government, Information filtering, Information filters, Information retrieval, multilingual information retrieval, multilingual text filtering, natural languages, performance evaluation}, isbn = {0-7803-2129-4}, doi = {10.1109/ICSMC.1994.400083}, author = {Oard, Douglas and DeClaris,N. and Dorr, Bonnie J and Faloutsos,C.} } @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} } @article {17337, title = {QUEST{\textemdash}Query Environment for Science Teaching}, journal = {Digital Libraries{\textquoteright} 94}, year = {1994}, month = {1994///}, abstract = {QUery Environment for Science Teaching (QUEST) is a proposed digital library implementation consisting of a set of research projects dealing with data capture and organization, content analysis, information seeking and visual interfaces.The QUEST team includes a large number of renown technical collaborators and prominent source collaborators, as well as a significant number of contributors in the University of Maryland, the central, co-ordinating agency.A large collection of multidisciplinary materials in visual and textual formats, made accessible to us by our source collaborators, will be organized to allow integrated access by users from the science education community, that is elementary school through college level teachers. QUEST will be structured so as to provide seamless access to widespread resources on disparate subjects. We intend to provide first-rate subject analysis and representation in order to provide ready access. QUEST will be accessible nationally by means of Mosaic. We propose to provide highly sophisticated querying, browsing and information investigation facilities which will handle integrated textual and visual materials without difficulty. They will be augmented by online reference and referral services, immediately accessible by the user. QUEST will provide a comprehensive information resource for science education accessible through a dynamic, visual user interface. }, author = {Shneiderman, Ben and Rosenfeld, A. and Marchioni,G. and Holliday,W. and Ricart, G. and Faloutsos,С. and Dick,J.} } @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.} } @article {14189, title = {A syntactic approach to scale-space-based corner description}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {16}, year = {1994}, month = {1994/07//}, pages = {748 - 751}, abstract = {Planar curves are described by information about corners integrated over various levels of resolution. The detection of corners takes place on a digital representation. To compensate for ambiguities arising from sampling problems due to the discreteness, results about the local behavior of curvature extrema in continuous scale-space are employed}, keywords = {Computer vision, corner detection, curvature extrema, edge detection, IMAGE PROCESSING, image resolution, Image segmentation, Laboratories, Large-scale systems, PARALLEL PROCESSING, pattern recognition, planar curves, resolution, Sampling methods, sampling problems, scale space based corner description, SHAPE, Smoothing methods, syntactic approach}, isbn = {0162-8828}, doi = {10.1109/34.297957}, author = {Ferm{\"u}ller, Cornelia and Kropatsch,W.} } @conference {15659, title = {Fast search algorithms with applications to split and multi-stage vector quantization of speech lsp parameters}, booktitle = {Speech Coding for Telecommunications, 1993. Proceedings., IEEE Workshop on}, year = {1993}, month = {1993///}, pages = {65 - 66}, doi = {10.1109/SCFT.1993.762341}, author = {Arya,S. and Phamdo,N. and Farvardin,N. and Mount, Dave} } @article {12784, title = {A generalized approach to real-time schedulability analysis}, journal = {IEEE Real-Time Systems Newsletter}, volume = {9}, year = {1993}, month = {1993///}, pages = {98 - 103}, author = {Fredette,A. N and Cleaveland, Rance} } @conference {14174, title = {Global 3D motion estimation}, booktitle = {, 1993 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1993. Proceedings CVPR {\textquoteright}93}, year = {1993}, month = {1993/06/15/17}, pages = {415 - 421}, publisher = {IEEE}, organization = {IEEE}, abstract = {It is shown how a monocular observer can estimate its 3D motion relative to the scene by using normal flow measurements in a global and qualitative way. It is proved that local normal flow measurements form global patterns in the image plane. The position of these patterns is related to the 3D motion parameters. By locating some of these patterns, which depend only on subsets of the motion parameters, through a simple search technique, the 3D motion parameters can be found. The proposed algorithmic procedure is very robust, since it is not affected by small perturbations in the normal flow measurements. The direction of translation and the axis of rotation can be estimated with up to 100\% error in the image measurements}, keywords = {3D motion parameters, Automation, axis of rotation, Computer vision, direction of translation, Educational institutions, Equations, Fluid flow measurement, global 3D motion estimation, Laboratories, Layout, monocular observer, Motion estimation, Motion measurement, normal flow measurements, Robustness, Rotation measurement, search problems, search technique, State estimation}, isbn = {0-8186-3880-X}, doi = {10.1109/CVPR.1993.341097}, author = {Ferm{\"u}ller, Cornelia} } @conference {13571, title = {Image based typographic analysis of documents}, booktitle = {Document Analysis and Recognition, 1993., Proceedings of the Second International Conference on}, year = {1993}, month = {1993/10//}, pages = {769 - 773}, abstract = {An approach to image based typographic analysis of documents is provided. The problem requires a spatial understanding of the document layout as well as knowledge of the proper syntax. The system performs a page synthesis from the stream of formatting commands defined in a DVI file. Since the two-dimensional relationships between document components are not explicit in the page language, the authors develop a representation which preserves the two-dimensional layout, the read-order and the attributes of document components. From this hierarchical representation of the page layout we extract and analyze relevant typographic features such as margins, line and character spacing, and figure placement}, keywords = {2D, analysis;, attributes;, based, character, commands;, component, data, description, document, DVI, extraction;, feature, figure, file;, formatting, hierarchical, image, language;, languages;, layout;, line, margins;, page, placement;, processing;, read-order;, relationships;, representation;, spacing;, spatial, structures;, syntax;, synthesis;, typographic, understanding;}, doi = {10.1109/ICDAR.1993.395624}, author = {David Doermann and Furuta,R.} } @conference {14176, title = {Motion constraint patterns}, booktitle = {, Proceedings of IEEE Workshop on Qualitative Vision, 1993}, year = {1993}, month = {1993/06/14/}, pages = {128 - 139}, publisher = {IEEE}, organization = {IEEE}, abstract = {The problem of egomotion recovery has been treated by using as input local image motion, with the published algorithms utilizing the geometric constraint relating 2-D local image motion (optical flow, correspondence, derivatives of the image flow) to 3-D motion and structure. Since it has proved very difficult to achieve accurate input (local image motion), a lot of effort has been devoted to the development of robust techniques. A new approach to the problem of egomotion estimation is taken, based on constraints of a global nature. It is proved that local normal flow measurements form global patterns in the image plane. The position of these patterns is related to the three dimensional motion parameters. By locating some of these patterns, which depend only on subsets of the motion parameters, through a simple search technique, the 3-D motion parameters can be found. The proposed algorithmic procedure is very robust, since it is not affected by small perturbations in the normal flow measurements. As a matter of fact, since only the sign of the normal flow measurement is employed, the direction of translation and the axis of rotation can be estimated with up to 100\% error in the image measurements}, keywords = {3D motion parameters, Automation, computational geometry, Computer vision, correspondence, Educational institutions, egomotion recovery, Fluid flow measurement, geometric constraint, Geometrical optics, Image motion analysis, image plane, Laboratories, local image motion, local normal flow measurements, Motion estimation, Motion measurement, motion parameters, optical flow, Rotation measurement}, isbn = {0-8186-3692-0}, doi = {10.1109/WQV.1993.262942}, author = {Ferm{\"u}ller, Cornelia} } @article {14252, title = {Recognizing 3-D Motion}, journal = {INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {13}, year = {1993}, month = {1993///}, pages = {1624 - 1624}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14266, title = {The role of fixation in visual motion analysis}, journal = {International Journal of Computer Vision}, volume = {11}, year = {1993}, month = {1993///}, pages = {165 - 186}, abstract = {How does the ability of humans and primates to fixate at environmental points in the presence of relative motion help their visual systems in solving various tasks? To state the question in a more formal setting, we investigate in this article the following problem: Suppose that we have an active vision system, that is, a camera resting on a platform and being controlled through motors by a computer that has access to the images sensed by the camera in real time. The platform can move freely in the environment. If this machine can fixate on targets being in relative motion with it, can it solve visual tasks in an efficient and robust manner? By restricting our attention to a set of navigational tasks, we find that such an active observer can solve the problems of 3-D motion estimation, egomotion recovery, and estimation of time-to-contact in a very efficient manner, using as input the spatiotemporal derivatives of the image-intensity function (or normal flow). Fixation over time changes the input (motion field) in a controlled way and from this change additional information is derived making the previously mentioned tasks easier to solve.}, isbn = {0920-5691}, url = {http://dx.doi.org/10.1007/BF01469227}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @conference {12796, title = {RTSL: a language for real-time schedulability analysis}, booktitle = {Real-Time Systems Symposium, 1993., Proceedings.}, year = {1993}, month = {1993/12/01/3}, pages = {274 - 283}, publisher = {IEEE}, organization = {IEEE}, abstract = {The paper develops a generalized approach to schedulability analysis that is mathematically founded in a process algebra called RTSL. Within RTSL one may describe the functional behavior, timing behavior, timing constraints (or deadlines), and scheduling discipline for real-time systems. The formal semantics of RTSL then allows the reachable state space of finite state systems to be automatically generated and searched for timing exceptions. We provide a generalized schedulability analysis technique to perform this state-based analysis}, keywords = {Algebra, Algorithm design and analysis, Dynamic scheduling, Failure analysis, finite state machines, finite state systems, formal logic, formal semantics, functional behavior, generalized approach, generalized schedulability analysis technique, Process algebra, Processor scheduling, reachable state space, Real time systems, real-time schedulability analysis, Real-Time Specification Language, real-time systems, RTSL, scheduling, Scheduling algorithm, scheduling discipline, Specification languages, state-based analysis, State-space methods, Time factors, Timing, timing behavior, timing constraints, timing exceptions}, isbn = {0-8186-4480-X}, doi = {10.1109/REAL.1993.393489}, author = {Fredette,A. N and Cleaveland, Rance} } @article {14199, title = {Behavioral Visual Motion Analysis,"}, journal = {Proceedings, DARPA Image Understanding Workshop}, year = {1992}, month = {1992///}, pages = {521 - 541}, author = {Aloimonos, J. and Duri{\c c},Z. and Ferm{\"u}ller, Cornelia and Huang, L. and Rivlin,E. and Sharma, R.} } @conference {14169, title = {Hierarchical curve representation}, booktitle = {, 11th IAPR International Conference on Pattern Recognition, 1992. Vol.III. Conference C: Image, Speech and Signal Analysis, Proceedings}, year = {1992}, month = {1992/09/30/Aug-3}, pages = {143 - 146}, publisher = {IEEE}, organization = {IEEE}, abstract = {Presents a robust method for describing planar curves in multiple resolution using curvature information. The method is developed by taking into account the discrete nature of digital images as well as the discrete aspect of a multiresolution structure (pyramid). The authors deal with the robustness of the technique, which is due to the additional information that is extracted from observing the behavior of corners in the pyramid. Furthermore the resulting algorithm is conceptually simple and easily parallelizable. They develop theoretical results, analyzing the curvature of continuous curves in scale-space, which show the behavior of curvature extrema under varying scale. These results are used to eliminate any ambiguities that might arise from sampling problems due to the discreteness of the representation. Finally, experimental results demonstrate the potential of the method}, keywords = {Automation, continuous curves, curvature, data mining, digital images, Educational institutions, Feature extraction, hierarchical curve representation, IMAGE PROCESSING, image recognition, image resolution, Image segmentation, multiresolution structure, Object recognition, planar curves, pyramid, Robustness, Sampling methods, Smoothing methods}, isbn = {0-8186-2920-7}, doi = {10.1109/ICPR.1992.201947}, author = {Ferm{\"u}ller, Cornelia and Kropatsch,W.} } @conference {14233, title = {Multi-resolution shape description by corners}, booktitle = {, 1992 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 1992. Proceedings CVPR {\textquoteright}92}, year = {1992}, month = {1992/06/15/18}, pages = {271 - 276}, publisher = {IEEE}, organization = {IEEE}, abstract = {A robust method for describing planar curves in multiple resolution using curvature information is presented. The method is developed by taking into account the discrete nature of digital images as well as the discrete aspect of a multiresolution structure (pyramid). The main contribution lies in the robustness of the technique, which is due to the additional information that is extracted from observing the behavior of corners in the whole pyramid. Furthermore, the resulting algorithm is conceptually simple and easily parallelizable. Theoretical results are developed analyzing the curvature of continuous curves in scale-space and showing the behavior of curvature extrema under varying scale. The results are used to eliminate any ambiguities that might arise from sampling problems due to the discreteness of the representation. Experimental results demonstrate the potential of the method}, keywords = {ambiguities, Automation, computational geometry, Computer vision, continuous curves, corners, curvature extrema, curvature information, curve fitting, digital images, Feature extraction, IMAGE PROCESSING, image resolution, Image segmentation, Laboratories, multiple resolution, multiresolution structure, parallelizable, planar curves, Robustness, Sampling methods, scale-space, SHAPE, Smoothing methods, varying scale}, isbn = {0-8186-2855-3}, doi = {10.1109/CVPR.1992.223264}, author = {Ferm{\"u}ller, Cornelia and Kropatsch,W.} } @conference {14246, title = {Perceptual computational advantages of tracking}, booktitle = {, 11th IAPR International Conference on Pattern Recognition, 1992. Vol.I. Conference A: Computer Vision and Applications, Proceedings}, year = {1992}, month = {1992/09/30/Aug-3}, pages = {599 - 602}, publisher = {IEEE}, organization = {IEEE}, abstract = {The paradigm of active vision advocates studying visual problems in the form of modules that are directly related to a visual task for observers that are active. It is argued that in many cases when an object is moving in an unrestricted manner (translation and rotation) in the 3D world only the motion{\textquoteright}s translational components are of interest. For a monocular observer, using only the normal flow-the spatiotemporal derivatives of the image intensity function-the authors solve the problem of computing the direction of translation. Their strategy uses fixation and tracking. Fixation simplifies much of the computation by placing the object at the center of the visual field, and the main advantage of tracking is the accumulation of information over time. The authors show how tracking is accomplished using normal flow measurements and use it for two different tasks in the solution process. First, it serves as a tool to compensate for the lack of existence of an optical flow field and thus to estimate the translation parallel to the image plane; and second, it gathers information about the motion component perpendicular to the image plane}, keywords = {active vision, Automation, Employment, fixation, image intensity function, Image motion analysis, IMAGE PROCESSING, Motion estimation, Nonlinear optics, Optical computing, Optical sensors, parameter estimation, pattern recognition, perceptual computational advantages, spatiotemporal derivatives, Spatiotemporal phenomena, tracking, unrestricted motion, visual flow measurements}, isbn = {0-8186-2910-X}, doi = {10.1109/ICPR.1992.201633}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {19000, title = {Splicing signals in Drosophila: intron size, information content, and consensus sequences}, journal = {Nucleic Acids ResearchNucl. Acids Res.}, volume = {20}, year = {1992}, month = {1992/08/25/}, pages = {4255 - 4262}, abstract = {A database of 209 Drosophila Introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger RNA splicing. A tight distribution of sizes was observed: while the smallest introns in the database are 51 nucleotides, more than half are less than 80 nucleotides in length, and most of these have lengths in the range of 59 {\textendash} 67 nucleotides. Drosophila splice sites found in large and small introns differ in only minor ways from each other and from those found in vertebrate Introns. However, larger introns have greater pyrimidlne-richness in the region between 11 and 21 nucleotides upstream of 3' splice sites. The Drosophila branchpoint consensus matrix resembles C T A A T (in which branch formation occurs at the underlined A), and differs from the corresponding mammalian signal in the absence of G at the position immediately preceding the branchpoint. The distribution of occurrences of this sequence suggests a minimum distance between 5' splice shies and branchpoints of about 38 nucleotides, and a minimum distance between 3' splice sites and branchpoints of 15 nucleotides. The methods we have used detect no information in exon sequences other than in the few nucleotides immediately adjacent to the splice sites. However, Drosophila resembles many other species in that there is a discontinuity in A + T content between exons and introns, which are A + T rich.}, isbn = {0305-1048, 1362-4962}, doi = {10.1093/nar/20.16.4255}, url = {http://nar.oxfordjournals.org/content/20/16/4255}, author = {Mount, Stephen M. and Burks,Christian and Herts,Gerald and Stormo,Gary D. and White,Owen and Fields,Chris} } @article {14270, title = {Tracking facilitates 3-D motion estimation}, journal = {Biological Cybernetics}, volume = {67}, year = {1992}, month = {1992///}, pages = {259 - 268}, abstract = {The recently emerging paradigm of Active Vision advocates studying visual problems in form of modules that are directly related to a visual task for observers that are active. Along these lines, we are arguing that in many cases when an object is moving in an unrestricted manner (translation and rotation) in the 3D world, we are just interested in the motion{\textquoteright}s translational components. For a monocular observer, using only the normal flow {\textemdash} the spatio-temporal derivatives of the image intensity function {\textemdash} we solve the problem of computing the direction of translation and the time to collision. We do not use optical flow since its computation is an ill-posed problem, and in the general case it is not the same as the motion field {\textemdash} the projection of 3D motion on the image plane. The basic idea of our motion parameter estimation strategy lies in the employment of fixation and tracking. Fixation simplifies much of the computation by placing the object at the center of the visual field, and the main advantage of tracking is the accumulation of information over time. We show how tracking is accomplished using normal flow measurements and use it for two different tasks in the solution process. First it serves as a tool to compensate for the lack of existence of an optical flow field and thus to estimate the translation parallel to the image plane; and second it gathers information about the motion component perpendicular to the image plane.}, isbn = {0340-1200}, url = {http://dx.doi.org/10.1007/BF00204399}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {12993, title = {Evolution of avocados as revealed by DNA restriction fragment variation}, journal = {J Hered}, volume = {81}, year = {1990}, month = {1990/06//May}, pages = {183 - 188}, abstract = {Individuals representing the genus {\i}t Persea, subgenus {\i}t Persea were assayed for restriction fragment length polymorphisms in their chloroplast genome, nuclear ribosomal DNA, and the genes coding for the enzyme cellulase. The subgenus {\i}t Persea appears to consist of {\i}t P. schiedeana and a separate taxon containing the remaining species. {\i}t P. americana does not appear to be a monophyletic group. If {\i}t P. americana is to be maintained as a species containing var. {\i}t americana, var. {\i}t drymifolia, and var. {\i}t guatemalensis, then our data suggest that it should also contain varieties corresponding to {\i}t P. floccosa, {\i}t P. nubigena, and {\i}t P. steyermarkii. {\i}t P. americana var. {\i}t guatemalensis appears to have originated as a hybrid between {\i}t P. steyermarkii and {\i}t P. nubigena. The root-rot-resistant cultivar G755A is a hybrid progeny of {\i}t P. schiedeana and {\i}t P. americana var. guatemalensis. The three varieties of {\i}t P. americana were all distinguished by mutations.}, author = {Furnier,GR and Cummings, Michael P. and Clegg,M. T} } @article {16234, title = {Automatically transforming regularly structured linear documents into hypertext.}, journal = {Electronic Publishing}, volume = {2}, year = {1989}, month = {1989///}, pages = {211 - 229}, abstract = {Fully automatic conversion of a paper-based document into hypertext can be achieved in manycases if the original document is naturally partitioned into a collection of small-sized pieces that are unambiguously and consistently structured. We describe the methodology that we have used successfully to design and implement several straightforward conversions from the original document{\textquoteright}s machine-readable markup. }, author = {Furuta,R. and Plaisant, Catherine and Shneiderman, Ben} } @article {16521, title = {Generating plausible diagnostic hypotheses with self-processing causal networks}, journal = {Journal of Experimental \& Theoretical Artificial Intelligence}, volume = {1}, year = {1989}, month = {1989///}, pages = {91 - 112}, author = {Wald,J. and Farach,M. and Tagamets,M. and Reggia, James A.} } @article {16235, title = {A spectrum of automatic hypertext constructions}, journal = {Hypermedia}, volume = {1}, year = {1989}, month = {1989///}, pages = {179 - 195}, abstract = {We describe our experiences with four separate conversions from paper documents into hypertext and discuss the lessons we have learned. The paper document{\textquoteright}s organization affects the ease with which it can be converted and the appropriateness of the resu lting hypertext. The form of the paper document{\textquoteright}s machine-readable {\textquoteleft}markup{\textquoteright} description affects the ability to transform the structure automatically. Designing the link structures that tie together the parts of the hypertext takes special care in automa ting, as badly-designed and incorrectly-formed links destroy the integrity of the hypertext. Overall, each of the conversions followed the same basic methodology, providing the handle for the development of {\textquoteleft}power tools{\textquoteright} that can be applied to simplify s ubsequent conversions.}, author = {Furuta,R. and Plaisant, Catherine and Shneiderman, Ben} } @inbook {18363, title = {A support tool for teaching computer programming}, booktitle = {Issues in software engineering educationIssues in software engineering education}, year = {1989}, month = {1989///}, pages = {139 - 167}, publisher = {Springer-Verlag New York, Inc.}, organization = {Springer-Verlag New York, Inc.}, address = {New York, NY, USA}, isbn = {0-387-96840-7}, url = {http://dl.acm.org/citation.cfm?id=73064.73074}, author = {Zelkowitz, Marvin V and Kowalchack,B. and Itkin,D. and Herman,L.}, editor = {Fairley,Richard and Freeman,Peter} } @article {16791, title = {An efficient pictorial database system for PSQL}, journal = {IEEE Transactions on Software Engineering}, volume = {14}, year = {1988}, month = {1988/05//}, pages = {639 - 650}, abstract = {Pictorial databases require efficient and direct spatial search based on the analog form of spatial objects and relationships instead of search based on some cumbersome alphanumeric encodings of the pictures. A description is given of PSQL, a query language that allows pictorial domains to be presented to the user in their analog form and allows him or her to do direct manipulation on the objects found on those domains. Direct spatial search and computation on the pictures is done using efficient data structures, R- and R+-trees (multidimensional B-trees), which are excellent devices for searching spatial objects and relationships found on pictures}, keywords = {alphanumeric encodings, Computer science, Data structures, Database languages, database management systems, Database systems, Encoding, Image coding, Image databases, multidimensional B-trees, Object oriented databases, pictorial database system, PSQL, query language, query languages, R+-trees, Relational databases, Spatial databases, spatial objects, spatial search, User interfaces}, isbn = {0098-5589}, doi = {10.1109/32.6141}, author = {Roussopoulos, Nick and Faloutsos,C. and Sellis,T.} } @article {16745, title = {Expert database systems: Efficient support for engineering environments}, journal = {Data \& Knowledge Engineering}, volume = {3}, year = {1988}, month = {1988/09//}, pages = {71 - 85}, abstract = {Manufacturing and Engineering processes use both large scale data and knowledge bases, and the use of expert systems in such environments has become a necessity. Expert Database Systems have evolved from conventional database systems to meet the requirements of current Artificial Intelligence applications. However, future Expert Database Systems will contain knowledge bases of significant size which makes main memory insufficient and the use of a database system a necessity. We propose an effective way of building High Performance Expert Database Systems to support manufacturing and engineering environments. These systems are based on Incremental Computation Models; such models utilize results of previous computations by merging them with newly derived results of computations on small increments representing changes in the database. Our system will be able to support very large knowledge bases by utilizing novel structures and access methods and by using a very sophisticated inference engine based on incremental computation models.}, keywords = {engineering databases, Expert database systems, high performance systems, incremental computation models}, isbn = {0169-023X}, doi = {16/0169-023X(88)90007-9}, url = {http://www.sciencedirect.com/science/article/pii/0169023X88900079}, author = {Sellis,T. and Roussopoulos, Nick and Mark,L. and Faloutsos,C.} } @article {16527, title = {Expert system development: letting the domain specialist directly author knowledge bases}, journal = {Expert systems: the user interface}, year = {1988}, month = {1988///}, pages = {37 - 56}, author = {Tuhrim,S. and Reggia, James A. and Floor,M.} } @book {17471, title = {User interface strategies {\textquoteright}88 (videotape)}, year = {1988}, month = {1988///}, publisher = {University of Maryland at College Park}, organization = {University of Maryland at College Park}, address = {College Park, MD, USA}, author = {Shneiderman, Ben and Malone,Thomas and Norman,Donald and Foley,James} } @article {16370, title = {ALEX-an Alexical Programming Language}, volume = {TR87-835}, year = {1987}, month = {1987///}, institution = {Cornell University}, abstract = {ALEX is an experimental language for high-level parallel programming. It is a testbed for exploring various non-traditional ways of expressing algorithmic ideas, making extensive use of high-resolution color graphics. The language itself is not a programming language in the traditional sense, since there is no lexical syntax. This paper discusses the basic design of the ALEX user interface.}, url = {http://hdl.handle.net/1813/6675}, author = {Kozen,D. and Teitelbaum,T. and Chen,W. Z and Field,J. H and Pugh, William and Vander Zanden,B. T} } @article {16757, title = {Analysis of object oriented spatial access methods}, journal = {ACM SIGMOD Record}, volume = {16}, year = {1987}, month = {1987///}, pages = {426 - 439}, author = {Faloutsos,C. and Sellis,T. and Roussopoulos, Nick} } @article {16726, title = {The R+-tree: A dynamic index for multi-dimensional data}, journal = {Proceedings of VLDB 1987}, year = {1987}, month = {1987///}, pages = {507 - 518}, author = {Sellis,T. and Roussopoulos, Nick and Faloutsos,C.} } @article {16628, title = {A comparative analysis of methods for expert systems}, journal = {International journal of man-machine studies}, volume = {24}, year = {1986}, month = {1986///}, pages = {475 - 499}, author = {Ramsey,C. L and Reggia, James A. and Nau, Dana S. and Ferrentino,A.} } @article {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} } @article {14998, title = {On the relationship between the biconnectivity augmentation and traveling salesman problem}, journal = {Theoretical Computer Science}, volume = {19}, year = {1982}, month = {1982///}, pages = {189 - 201}, author = {Fredrickson,G. N. and JaJa, Joseph F.} } @article {15975, title = {A re-evaluation of story grammars*}, journal = {Cognitive Science}, volume = {5}, year = {1981}, month = {1981///}, pages = {79 - 86}, author = {Frisch,A. M and Perlis, Don} } @conference {17051, title = {Database Program Conversion: A Framework For Research}, booktitle = {Fifth International Conference on Very Large Data Bases, 1979}, year = {1979}, month = {1979/10/03/5}, pages = {299 - 312}, publisher = {IEEE}, organization = {IEEE}, keywords = {Application software, Costs, Data conversion, Data structures, Databases, Delay, Prototypes, Technology planning, US Government, Writing}, doi = {10.1109/VLDB.1979.718145}, author = {Taylor,R. W and Fry,J. P and Shneiderman, Ben and Smith,D. C.P and Su,S. Y.W} } @book {11937, title = {A guide to major job accounting systems: the Logger system of the UNIVAC 1100 series operating system}, year = {1978}, month = {1978///}, publisher = {U.S. Dept. of Commerce, National Bureau of Standards : for sale by the Supt. of Docs., U.S. Govt. Print. Off.}, organization = {U.S. Dept. of Commerce, National Bureau of Standards : for sale by the Supt. of Docs., U.S. Govt. Print. Off.}, keywords = {Accounting, Business \& Economics / Accounting / General, Electronic digital computers, EXEC 8 (Electronic computer system), Reference / Questions \& Answers, Univac 1100 series (Computer), Univac computer}, author = {Mohr,Jeffrey Myron and Agrawala, Ashok K. and Flannagan,J. F.} } @book {11940, title = {The EXEC-8 Log System: Error Analysis}, year = {1976}, month = {1976///}, publisher = {University of Maryland, Dept. of Computer Science}, organization = {University of Maryland, Dept. of Computer Science}, author = {Mohr,J. M and Agrawala, Ashok K. and Flanagan,J. F. and Science,University of Maryland. Dept. of Computer} }