@article {19692, title = {Evaluating Regularized Anchor Words}, journal = {mimno.infosci.cornell.edu}, year = {Submitted}, abstract = {Abstract We perform a comprehensive examination of the recently proposed anchor method for topic model inference using topic interpretability and held-out likelihood measures. After measuring the sensitivity to the anchor selection process, we incorporate L2 and Beta ...}, url = {http://mimno.infosci.cornell.edu/nips2013ws/nips2013tm_submission_27.pdf}, author = {Nguyen, T and Hu, Y and Jordan Boyd-Graber} } @article {19693, title = {Tree-based Label Dependency Topic Models}, journal = {cs.umd.edu}, year = {Submitted}, abstract = {Abstract Multi-labeled corpora, where each document is tagged with a set of labels, are ubiquitous. When the number of unique labels in the dataset is large, there are naturally some dependencies among the labels. In this paper, we propose TREELAD{\textemdash}a ...}, url = {http://www.cs.umd.edu/~vietan/2013_l2h.pdf}, author = {Nguyen, V A and Jordan Boyd-Graber and Chang, J and Resnik, P} } @article {20295, title = {Biofilms Comprise a Component of the Annual Cycle of Vibrio cholerae in the Bay of Bengal Estuary}, journal = {mBio}, year = {2018}, month = {Feb-05-2018}, pages = {e00483-18}, abstract = {Vibrio cholerae, an estuarine bacterium, is the causative agent of cholera, a severe diarrheal disease that demonstrates seasonal incidence in Bangladesh. In an extensive study of V. cholerae occurrence in a natural aquatic environment, water and plankton samples were collected biweekly between December 2005 and November 2006 from Mathbaria, an estuarine village of Bangladesh near the mangrove forests of the Sundarbans. Toxigenic V. cholerae exhibited two seasonal growth peaks, one in spring (March to May) and another in autumn (September to November), corresponding to the two annual seasonal outbreaks of cholera in this region. The total numbers of bacteria determined by heterotrophic plate count (HPC), representing culturable bacteria, accounted for 1\% to 2.7\% of the total numbers obtained using acridine orange direct counting (AODC). The highest bacterial culture counts, including toxigenic V. cholerae, were recorded in the spring. The direct fluorescent antibody (DFA) assay was used to detect V. cholerae O1 cells throughout the year, as free-living cells, within clusters, or in association with plankton. V. cholerae O1 varied significantly in morphology, appearing as distinctly rod-shaped cells in the spring months, while small coccoid cells within thick clusters of biofilm were observed during interepidemic periods of the year, notably during the winter months. Toxigenic V. cholerae O1 was culturable in natural water during the spring when the temperature rose sharply. The results of this study confirmed biofilms to be a means of persistence for bacteria and an integral component of the annual life cycle of toxigenic V. cholerae in the estuarine environment of Bangladesh.}, doi = {10.1128/mBio.00483-18}, url = {https://mbio.asm.org/content/9/2/e00483-18}, author = {Sultana, Marzia and Nusrin, Suraia and Hasan, Nur A. and Sadique, Abdus and Ahmed, Kabir U. and Islam, Atiqul and Hossain, Anwar and Longini, Ira and Nizam, Azhar and Huq, Anwar and Siddique, Abul K. and Sack, David A. and Sack, Richard B. and Rita R Colwell and Alam, Munirul}, editor = {Vidaver, Anne K.} } @article {20293, title = {Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments}, journal = {Frontiers in Microbiology}, year = {2018}, month = {Jan-06-2020}, doi = {10.3389/fmicb.2018.01361}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.01361/full}, author = {Hourigan, Suchitra K. and Subramanian, Poorani and Hasan, Nur A. and Ta, Allison and Klein, Elisabeth and Chettout, Nassim and Huddleston, Kathi and Deopujari, Varsha and Levy, Shira and Baveja, R and Clemency, Nicole C. and Baker, Robin L. and Niederhuber, John E. and Rita R Colwell} } @article {20252, title = {Deep-learning-assisted Volume Visualization}, journal = {IEEE Transactions on Visualization and Computer Graphics}, year = {2018}, month = {Jan-01-2018}, pages = {1 - 1}, issn = {1077-2626}, doi = {10.1109/TVCG.2018.2796085}, url = {http://ieeexplore.ieee.org/document/8265023/http://xplorestaging.ieee.org/ielx7/2945/4359476/08265023.pdf?arnumber=8265023}, author = {Cheng, Hsueh-Chien and Cardone, Antonio and Jain, Somay and Krokos, Eric and Narayan, Kedar and Subramaniam, Sriram and Varshney, Amitabh} } @article {20289, title = {Environmental and hydroclimatic factors influencing Vibrio populations in the estuarine zone of the Bengal delta}, journal = {Environmental Monitoring and Assessment}, year = {2018}, month = {Jan-10-2018}, abstract = {The objective of this study was to determine environmental parameters driving Vibrio populations in the estuarine zone of the Bengal delta. Spatio-temporal data were collected at river estuary, mangrove, beach, pond, and canal sites. Effects of salinity, tidal amplitude, and a cyclone and tsunami were included in the study. Vibrio population shifts were found to be correlated with tide-driven salinity and suspended particulate matter (SPM). Increased abundance of Vibrio spp. in surface water was observed after a cyclone, attributed to re-suspension of benthic particulate organic carbon (POC), and increased availability of chitin and dissolved organic carbon (DOC). Approximately a two log10 increase in the (p < 0.05) number of Vibrio spp. was observed in < 20 μm particulates, compared with microphytoplankton (20{\textendash}60 μm) and zooplankton > 60 μm fractions. Benthic and suspended sediment comprised a major reservoir of Vibrio spp. Results of microcosm experiments showed enhanced growth of vibrios was related to concentration of organic matter in SPM. It is concluded that SPM, POC, chitin, and salinity significantly influence abundance and distribution of vibrios in the Bengal delta estuarine zone. Keywords Vibrio Salinity Cyclone Tide Chitin Sediment dynamics }, issn = {0167-6369}, doi = {10.1007/s10661-018-6925-7}, url = {https://link.springer.com/article/10.1007\%2Fs10661-018-6925-7}, author = {Neogi, Sucharit and Rubin, Lara and Alam, Munirul and Harder, Jens and Yamasaki, Shinji and Rita R Colwell} } @article {20300, title = {High-Throughput DNA Sequencing To Profile Microbial Water Quality Of Potable Reuse}, year = {2018}, url = {https://www.wateronline.com/doc/high-throughput-dna-sequencing-to-profile-microbial-water-quality-of-potable-reuse-0001}, author = {Menu B. Leddy and Megan H. Plumlee and Rose S. Kantor and Kara L. Nelson and Scott E. Miller and Lauren C. Kennedy and Blake W. Stamps and John R. Spear and Nur A. Hasan and Rita R Colwell} } @article {20311, title = {Comparative Genomics of Escherichia coli Isolated from Skin and Soft Tissue and Other Extraintestinal Infections}, journal = {mBio}, year = {2017}, month = {Jun-09-2017}, abstract = {Escherichia coli, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs), meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs), and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic E. coli (ExPEC). It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive. In the study reported here, ExPEC E. coli isolated from SSTIs was characterized, including virulence and drug resistance profiles, and compared with isolates from patients suffering either pyelonephritis or septicemia. Results revealed that the majority of the isolates belonged to two pathogenic phylogroups, B2 and D. Approximately 67\% of the isolates were multidrug resistant (MDR), with 85\% producing extended-spectrum beta-lactamase (ESBL) and 6\% producing metallo-beta-lactamase (MBL). The blaCTX-M-15 genotype was observed in at least 70\% of the E. coli isolates in each category, conferring resistance to an extended range of beta-lactam antibiotics. Whole-genome sequencing and comparative genomics of the ExPEC isolates revealed that two of the four isolates from SSTIs, NA633 and NA643, belong to pandemic sequence type ST131, whereas functional characteristics of three of the ExPEC pathotypes revealed that they had equal capabilities to form biofilm and were resistant to human serum. Overall, the isolates from a variety of ExPEC infections demonstrated similar resistomes and virulomes and did not display any disease-specific functional or genetic coordinates. IMPORTANCE Infections caused by extraintestinal pathogenic E. coli (ExPEC) are of global concern as they result in significant costs to health care facilities management. The recent emergence of a multidrug-resistant pandemic clone, Escherichia coli ST131, is of primary concern as a global threat. In developing countries, such as India, skin and soft tissue infections (SSTIs) associated with E. coli are marginally addressed. In this study, we employed both genomic analysis and phenotypic assays to determine relationships, if any, among the ExPEC pathotypes. Similarity between antibiotic resistance and virulence profiles was observed, ST131 isolates from SSTIs were reported, and genomic similarities among strains isolated from different disease conditions were detected. This study provides functional molecular infection epidemiology insight into SSTI-associated E. coli compared with ExPEC pathotypes.}, doi = {10.1128/mBio.01070-17}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.01070-17}, author = {Ranjan, Amit and Shaik, Sabiha and Nandanwar, Nishant and Hussain, Arif and Tiwari, Sumeet K. and Semmler, Torsten and Jadhav, Savita and Wieler, Lothar H. and Alam, Munirul and Rita R Colwell and Ahmed, Niyaz}, editor = {Cossart, Pascale F.} } @article {20322, title = {Hydroclimatic sustainability assessment of changing climate on cholera in the Ganges-Brahmaputra basin}, journal = {Advances in Water Resources}, volume = {108}, year = {2017}, month = {Jan-10-2017}, pages = {332 - 344}, abstract = {The association of cholera and climate has been extensively documented. However, determining the effects of changing climate on the occurrence of disease remains a challenge. Bimodal peaks of cholera in Bengal Delta are hypothesized to be linked to asymmetric flow of the Ganges and Brahmaputra rivers. Spring cholera is related to intrusion of bacteria-laden coastal seawater during low flow seasons, while autumn cholera results from cross-contamination of water resources when high flows in the rivers cause massive inundation. Coarse resolution of General Circulation Model (GCM) output (usually at 100 {\textendash} 300 km)cannot be used to evaluate variability at the local scale(10{\textendash}20 km),hence the goal of this study was to develop a framework that could be used to understand impacts of climate change on occurrence of cholera. Instead of a traditional approach of downscaling precipitation, streamflow of the two rivers was directly linked to GCM outputs, achieving reasonable accuracy (R2 = 0.89 for the Ganges and R2 = 0.91 for the Brahmaputra)using machine learning algorithms (Support Vector Regression-Particle Swarm Optimization). Copula methods were used to determine probabilistic risks of cholera under several discharge conditions. Key results, using model outputs from ECHAM5, GFDL, andHadCM3for A1B and A2 scenarios, suggest that the combined low flow of the two rivers may increase in the future, with high flows increasing for first half of this century, decreasing thereafter. Spring and autumn cholera, assuming societal conditions remain constant e.g., at the current rate, may decrease. However significant shifts were noted in the magnitude of river discharge suggesting that cholera dynamics of the delta may well demonstrate an uncertain predictable pattern of occurrence over the next century.}, issn = {03091708}, doi = {10.1016/j.advwatres.2016.11.018}, url = {https://linkinghub.elsevier.com/retrieve/pii/S030917081630728X}, author = {Nasr-Azadani, Fariborz and Khan, Rakibul and Rahimikollu, Javad and Unnikrishnan, Avinash and Akanda, Ali and Alam, Munirul and Huq, Anwar and Jutla, Antarpreet and Rita R Colwell} } @article {20343, title = {Downscaling river discharge to assess the effects of climate change on cholera outbreaks in the Bengal Delta}, journal = {Climate Research}, volume = {64}, year = {2015}, month = {Jul-08-2017}, pages = {257 - 274}, abstract = {Endemic cholera in the Bengal Delta region of South Asia has been associated with asymmetric and episodic variability of river discharge. Spring cholera was found to be related to intrusion of bacteria-laden coastal seawater during low flow seasons. Autumn cholera was hypothesized to result from cross-contamination of water resources when high river discharge causes massive inland inundation. The effect of climate change on diarrheal diseases has not been explored, because of the difficulties in establishing linkages between coarse-resolution global climate model outputs with localized disease outbreaks. Since rivers act as corridors for transport of cholera bacteria, the first step is to understand the discharge variability that may occur with climate change and whether it is linked to cholera. Here, we present a framework for downscaling precipitation from global climate models for river discharge in the Ganges-Brahmaputra-Meghna basin. Using a data-mining method that includes particle swarm optimization-based support vector regression, precipitation was downscaled for a statistical multiple regressive model to estimate river discharge in the basin. Key results from an ensemble of HadCM3, GFDL, and ECHAM5 models indicated 8 and 7.5\% increase in flows for the IPCC A1B and A2 scenarios, respectively. The majority of the changes are attributable to increases in flows from February through August for both scenarios, with little to no change in seasonality of high and low flows during the next century. The probability of spring and autumn cholera is likely to increase steadily in the endemic region of the Bengal Delta. }, issn = {0936-577X}, doi = {10.3354/cr01310}, url = {http://www.int-res.com/abstracts/cr/v64/n3/p257-274/}, author = {Nasr-Azadani, F and Unnikrishnan, A and Akanda, A and Islam, S and Alam, M and Huq, A and Jutla, A and Rita R Colwell} } @article {20347, title = {Hybrid Vibrio~cholerae El Tor Lacking SXT Identified as the Cause of a Cholera Outbreak in the Philippines}, journal = {mBio}, year = {2015}, month = {Jan-05-2015}, abstract = {Cholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died. Vibrio cholerae O1 was confirmed as the etiological agent. Source attribution is critical in cholera outbreaks for proper management of the disease, as well as to control spread. In this study, three V. cholerae O1 isolates from a Philippines cholera outbreak were sequenced and their genomes analyzed to determine phylogenetic relatedness to V. cholerae O1 isolates from recent outbreaks of cholera elsewhere. The Philippines V. cholerae O1 isolates were determined to be V. cholerae O1 hybrid El Tor belonging to the seventh-pandemic clade. They clustered tightly, forming a monophyletic clade closely related to V. cholerae O1 hybrid El Tor from Asia and Africa. The isolates possess a unique multilocus variable-number tandem repeat analysis (MLVA) genotype (12-7-9-18-25 and 12-7-10-14-21) and lack SXT. In addition, they possess a novel 15-kb genomic island (GI-119) containing a predicted type I restriction-modification system. The CTXΦ-RS1 array of the Philippines isolates was similar to that of V. cholerae O1 MG116926, a hybrid El Tor strain isolated in Bangladesh in 1991. Overall, the data indicate that the Philippines V. cholerae O1 isolates are unique, differing from recent V. cholerae O1 isolates from Asia, Africa, and Haiti. Furthermore, the results of this study support the hypothesis that the Philippines isolates of V. cholerae O1 are indigenous and exist locally in the aquatic ecosystem of the Philippines.}, doi = {10.1128/mBio.00047-15}, url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.00047-15}, author = {Klinzing, David C. and Choi, Seon Young and Hasan, Nur A. and Matias, Ronald R. and Tayag, Enrique and Geronimo, Josefina and Skowronski, Evan and Rashed, Shah M. and Kawashima, Kent and Rosenzweig, C. Nicole and Gibbons, Henry S. and Torres, Brian C. and Liles, Veni and Alfon, Alicia C. and Juan, Maria Luisa and Natividad, Filipinas F. and Cebula, Thomas A. and Rita R Colwell} } @article {20334, title = {Occurrence in Mexico, 1998{\textendash}2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage}, journal = {Proceedings of the National Academy of Sciences}, volume = {111}, year = {2014}, month = {Aug-07-2014}, pages = {9917 - 9922}, issn = {0027-8424}, doi = {10.1073/pnas.1323408111}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1323408111}, author = {Alam, Munirul and Rashed, Shah M and Mannan, Shahnewaj Bin and Islam, Tarequl and Lizarraga-Partida, Marcial L. and Delgado, Gabriela and Morales-Espinosa, Rosario and Mendez, Jose Luis and Navarro, Armando and Watanabe, Haruo and Ohnishi, Makoto and Hasan, Nur A. and Huq, Anwar and Sack, R. Bradley and Rita R Colwell and Cravioto, Alejandro} } @article {19684, title = {Argviz: Interactive Visualization of Topic Dynamics in Multi-party Conversations}, journal = {Human Language Technologies: The 2013 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, year = {2013}, month = {2013/00/01}, abstract = {Abstract We introduce an efficient, interactive framework{\textemdash}Argviz{\textemdash}for experts to analyze the dynamic topical structure of multi-party conversations. Users inject their needs, expertise, and insights into models via iterative topic refinement. The refined topics feed into a ...}, url = {https://www.aclweb.org/anthology-new/N/N13/N13-3.pdf$\#$page=42}, author = {Nguyen, V A and Hu, Y and Jordan Boyd-Graber} } @article {19160, title = {Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space}, journal = {Journal of Computational Biology}, volume = {20}, number = {1}, year = {2013}, abstract = {The Dirichlet process is used to model probability distributions that are mixtures of an unknown number of components. Amino acid frequencies at homologous positions within related proteins have been fruitfully modeled by Dirichlet mixtures, and we use the Dirichlet process to derive such mixtures with an unbounded number of components. This application of the method requires several technical innovations to sample an unbounded number of Dirichlet-mixture components. The resulting Dirichlet mixtures model multiple-alignment data substantially better than do previously derived ones. They consist of over 500 components, in contrast to fewer than 40 previously, and provide a novel perspective on the structure of proteins. Individual protein positions should be seen not as falling into one of several categories, but rather as arrayed near probability ridges winding through amino acid multinomial space.}, keywords = {ALIGNMENT, computational molecular biology, dynamic programming, multiple alignment, sequence analysis}, doi = {10.1089/cmb.2012.0244}, author = {Nguyen,Viet-An and Jordan Boyd-Graber and Altschul, Stephen F.} } @article {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 {20364, title = {Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments}, journal = {Aquatic Biosystems}, volume = {9}, year = {2013}, month = {Jan-01-2013}, pages = {17}, abstract = {Background The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10{\textdegree}30' N, 64{\textdegree}40' W), B (10{\textdegree}40' N, 64{\textdegree}45' W) and D (10{\textdegree}43{\textquoteright}N, 64{\textdegree}32{\textquoteright}W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands. Results DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability. Conclusions In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.}, issn = {2046-9063}, doi = {10.1186/2046-9063-9-17}, url = {http://aquaticbiosystems.biomedcentral.com/articles/10.1186/2046-9063-9-17}, author = {Bozo-Hurtado, Lorelei and Garc{\'\i}a-Amado, M and Chistoserdov, Andrei and Varela, Ramon and Narvaez, J and Rita R Colwell and Su{\'a}rez, Paula} } @article {19700, title = {Improving public transit accessibility for blind riders by crowdsourcing bus stop landmark locations with Google street view}, journal = {The 15th International ACM SIGACCESS Conference}, year = {2013}, month = {2013/00/21}, pages = {16 - 8}, publisher = {SIGACCESS, ACM Special Interest Group on Accessible ComputingACM}, address = {New York, New York, USA}, abstract = {Abstract Low-vision and blind bus riders often rely on known physical landmarks to help locate and verify bus stop locations (eg., by searching for a shelter, bench, newspaper bin). However, there are currently few, if any, methods to determine this information a priori via ...}, isbn = {9781450324052}, doi = {10.1145/2513383.2513448}, url = {http://dl.acm.org/citation.cfm?doid=2513383.2513448}, author = {Hara, Kotaro and Azenkot, Shiri and Campbell, Megan and Bennett, Cynthia L and Le, Vicki and Pannella, Sean and Moore, Robert and Minckler, Kelly and Ng, Rochelle H and Jon Froehlich} } @article {19687, title = {Lexical and Hierarchical Topic Regression}, year = {2013}, month = {2013/00/01}, pages = {1106 - 1114}, abstract = {Abstract Inspired by a two-level theory that unifies agenda setting and ideological framing, we propose supervised hierarchical latent Dirichlet allocation (SHLDA) which jointly captures documents{\textquoteright} multi-level topic structure and their polar response variables. Our ...}, url = {http://papers.nips.cc/paper/5163-lexical-and-hierarchical-topic-regression}, author = {Nguyen, Viet-An and Jordan Boyd-Graber and Resnik, Philip} } @article {19686, title = {Modeling topic control to detect influence in conversations using nonparametric topic models}, journal = {Machine Learning}, year = {2013}, month = {2013/00/01}, pages = {1 - 41}, publisher = {Springer US}, abstract = {Abstract Identifying influential speakers in multi-party conversations has been the focus of research in communication, sociology, and psychology for decades. It has been long acknowledged qualitatively that controlling the topic of a conversation is a sign of ...}, doi = {10.1007/s10994-013-5417-9/fulltext.html}, url = {http://link.springer.com/article/10.1007/s10994-013-5417-9/fulltext.html}, author = {Nguyen, Viet-An and Jordan Boyd-Graber and Resnik, Philip and Cai, Deborah A and Midberry, Jennifer E and Wang, Yuanxin} } @article {20373, title = {Species composition of limnetic zooplankton from the southern coastal areas (Mathbaria and Bakerganj) in Bangladesh}, journal = {Journal of the Asiatic Society of Bangladesh, Science}, volume = {38}, year = {2013}, month = {Apr-06-2014}, abstract = {We studied the coastal zooplankton community structure of six waterbodies of Mathbaria and Bakerganj from January 2008 to June 2009. In total 35 zooplankton species were identified under 26 genera under 20 families under 8 orders from Mathbaria. Among them 6 were protozoans, 24 were rotifers, 3 were copepods, 1 was cladocerans and 1 was ostracods. From Bakergonj a total of 42 zooplankton species were identified under 23 genera under 17 Families under 7 orders. Among them 3 were protozoans, 25 were rotifers, 7 were copepods, 6 were cladocerans and 1 was ostracods. Results showed that abundance of rotifera group from both area was higher in Mathbaria (64.86\%) and Bakerganj (60.98\%) than other groups while abundance of ostracoda of Bakerganj area was lowest.}, issn = {1016-6947}, doi = {10.3329/jasbs.v38i1.15326}, url = {http://banglajol.info/index.php/JASBS/article/view/15326}, author = {Mozumder, Pronob K and Nahar, Samsun and Naser, M Niamul and Alam, Munirul and Huq, Anwar and Sack, R Bradley and Rita R Colwell} } @inbook {19613, title = {Streaming Authenticated Data Structures}, booktitle = {Advances in Cryptology {\textendash} EUROCRYPT 2013}, series = {Lecture Notes in Computer Science}, year = {2013}, month = {2013/01/01/}, pages = {353 - 370}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {We consider the problem of streaming verifiable computation, where both a verifier and a prover observe a stream of n elements x 1,x 2,{\textellipsis},x n and the verifier can later delegate some computation over the stream to the prover. The prover must return the output of the computation, along with a cryptographic proof to be used for verifying the correctness of the output. Due to the nature of the streaming setting, the verifier can only keep small local state (e.g., logarithmic) which must be updatable in a streaming manner and with no interaction with the prover. Such constraints make the problem particularly challenging and rule out applying existing verifiable computation schemes. We propose streaming authenticated data structures, a model that enables efficient verification of data structure queries on a stream. Compared to previous work, we achieve an exponential improvement in the prover{\textquoteright}s running time: While previous solutions have linear prover complexity (in the size of the stream), even for queries executing in sublinear time (e.g., set membership), we propose a scheme with O(logM logn)O(\log M\ log n) prover complexity, where n is the size of the stream and M is the size of the universe of elements. Our schemes support a series of expressive queries, such as (non-)membership, successor, range search and frequency queries, over an ordered universe and even in higher dimensions. The central idea of our construction is a new authentication tree, called generalized hash tree. We instantiate our generalized hash tree with a hash function based on lattices assumptions, showing that it enjoys suitable algebraic properties that traditional Merkle trees lack. We exploit such properties to achieve our results.}, keywords = {Algorithm Analysis and Problem Complexity, Data Encryption, Discrete Mathematics in Computer Science, Systems and Data Security}, isbn = {978-3-642-38347-2, 978-3-642-38348-9}, url = {http://link.springer.com/chapter/10.1007/978-3-642-38348-9_22}, author = {Charalampos Papamanthou and Shi, Elaine and Tamassia, Roberto and Yi, Ke}, editor = {Johansson, Thomas and Nguyen, Phong Q.} } @article {19485, title = {A study of unpredictability in fault-tolerant middleware}, journal = {Computer Networks}, volume = {57}, year = {2013}, month = {2013/02/26/}, pages = {682 - 698}, abstract = {In enterprise applications relying on fault-tolerant middleware, it is a common engineering practice to establish service-level agreements (SLAs) based on the 95th or the 99th percentiles of the latency, to allow a margin for unexpected variability. However, the extent of this unpredictability has not been studied systematically. We present an extensive empirical study of unpredictability in 16 distributed systems, ranging from simple transport protocols to fault-tolerant, middleware-based enterprise applications, and we show that the inherent unpredictability in the systems examined arises from at most 1\% of the remote invocations. In the normal, fault-free operating mode most remote invocations have a predictable end-to-end latency, but the maximum latency follows unpredictable trends and is comparable with the time needed to recover from a fault. The maximum latency is not influenced by the system{\textquoteright}s workload, cannot be regulated through configuration parameters and is not correlated with the system{\textquoteright}s resource consumption. The high-latency outliers (up to three orders of magnitude higher than the average latency) have multiple causes and may originate in any component of the system. However, after filtering out 1\% of the invocations with the highest recorded response-times, the latency becomes bounded with high statistical confidence (p \< 0.01). We have verified this result on different operating systems (Linux 2.4, Linux 2.6, Linux-rt, TimeSys), middleware platforms (CORBA and EJB), programming languages (C, C++ and Java), replication styles (active and warm passive) and applications (e-commerce and online gaming). Moreover, this phenomenon occurs at all the layers of middleware-based systems, from the communication protocols to the business logic.}, keywords = {Fault tolerance, latency, Middleware, Remote procedure call, Unpredictability}, isbn = {1389-1286}, url = {http://www.sciencedirect.com/science/article/pii/S1389128612003696}, author = {Tudor Dumitras and Narasimhan, Priya} } @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 {12853, title = {Conversion of viable but nonculturable enteric bacteria to culturable by co-culture with eukaryotic cells}, journal = {Microbiology and Immunology}, volume = {56}, year = {2012}, month = {2012/04/27/}, pages = {342 - 345}, abstract = {Viable but nonculturable (VBNC) Vibrio cholerae non-O1/non-O139, V. parahaemolyticus, enterohemorrhagic Escherichia coli, enterotoxigenic E. coli, enteropathogenic E. coli, Shigella flexneri, and Salmonella enterica were converted to the culturable state by co-culture with selected eukaryotic cells, e.g., HT-29, Caco-2, T84, HeLa, Intestine 407, and CHO cells.}, keywords = {conversion to culturability, enteric bacteria, viable but nonculturable}, isbn = {1348-0421}, doi = {10.1111/j.1348-0421.2012.00440.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2012.00440.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Senoh,Mitsutoshi and Ghosh-Banerjee,Jayeeta and Ramamurthy,Thandavarayan and Rita R Colwell and Miyoshi,Shin-ichi and Nair,G. Balakrish and Takeda,Yoshifumi} } @article {19658, title = {Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size}, journal = {Nature Cell Biology}, volume = {14}, year = {2012}, month = {2012/05//}, pages = {518 - 525}, abstract = {Networks of epithelial and endothelial tubes are essential for the function of organs such as the lung, kidney and vascular system. The sizes and shapes of these tubes are highly regulated to match their individual functions. Defects in tube size can cause debilitating diseases such as polycystic kidney disease and ischaemia. It is therefore critical to understand how tube dimensions are regulated. Here we identify the tyrosine kinase Src as an instructive regulator of epithelial-tube length in the Drosophila tracheal system. Loss-of-function Src42 mutations shorten tracheal tubes, whereas Src42 overexpression elongates them. Surprisingly, Src42 acts distinctly from known tube-size pathways and regulates both the amount of apical surface growth and, with the conserved formin dDaam, the direction of growth. Quantitative three-dimensional image analysis reveals that Src42- and dDaam-mutant tracheal cells expand more in the circumferential than the axial dimension, resulting in tubes that are shorter in length{\textemdash}but larger in diameter{\textemdash}than wild-type tubes. Thus, Src42 and dDaam control tube dimensions by regulating the direction of anisotropic growth, a mechanism that has not previously been described.}, isbn = {1465-7392}, url = {http://www.nature.com/ncb/journal/v14/n5/abs/ncb2467.html}, author = {Nelson, Kevin S. and Zia Khan and Moln{\'a}r, Imre and Mih{\'a}ly, J{\'o}zsef and Kaschube, Matthias and Beitel, Greg J.} } @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.} } @article {20387, title = {Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)}, journal = {Applied and Environmental Microbiology}, year = {2012}, month = {Mar-10-2013}, pages = {7249 - 7257}, abstract = {Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.}, issn = {0099-2240}, doi = {10.1128/AEM.01296-12}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.01296-12}, author = {Johnson, Crystal N. and Bowers, John C. and Griffitt, Kimberly J. and Molina, Vanessa and Clostio, Rachel W. and Pei, Shaofeng and Laws, Edward and Paranjpye, Rohinee N. and Strom, Mark S. and Chen, Arlene and Hasan, Nur A. and Huq, Anwar and Noriea, Nicholas F. and Grimes, D. Jay and Rita R Colwell} } @article {19612, title = {Efficient Verification of Web-content Searching Through Authenticated Web Crawlers}, journal = {Proc. VLDB Endow.}, volume = {5}, year = {2012}, month = {2012/06//}, pages = {920 - 931}, abstract = {We consider the problem of verifying the correctness and completeness of the result of a keyword search. We introduce the concept of an authenticated web crawler and present its design and prototype implementation. An authenticated web crawler is a trusted program that computes a specially-crafted signature over the web contents it visits. This signature enables (i) the verification of common Internet queries on web pages, such as conjunctive keyword searches---this guarantees that the output of a conjunctive keyword search is correct and complete; (ii) the verification of the content returned by such Internet queries---this guarantees that web data is authentic and has not been maliciously altered since the computation of the signature by the crawler. In our solution, the search engine returns a cryptographic proof of the query result. Both the proof size and the verification time are proportional only to the sizes of the query description and the query result, but do not depend on the number or sizes of the web pages over which the search is performed. As we experimentally demonstrate, the prototype implementation of our system provides a low communication overhead between the search engine and the user, and fast verification of the returned results by the user.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=2336664.2336666}, author = {Goodrich, Michael T. and Charalampos Papamanthou and Nguyen, Duy and Tamassia, Roberto and Lopes, Cristina Videira and Ohrimenko, Olga and Triandopoulos, Nikos} } @article {19131, title = {A framework for human microbiome research}, journal = {Nature}, volume = {486}, year = {2012}, month = {2012}, pages = {215 - 221}, abstract = {A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.}, author = {Meth{\'e}, B.A. and Nelson,K. E and Pop, Mihai and Creasy, H.H. and Giglio, M.G. and Huttenhower, C. and Gevers, D. and Petrosino, J.F. and Abubucker, S. and Badger, J.H.} } @article {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 {19129, title = {Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli}, journal = {Infection and immunity}, volume = {80}, year = {2012}, month = {2012}, pages = {2791 - 2801}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea, mainly in developing countries. Although there are 25 different ETEC adhesins described in strains affecting humans, between 15\% and 50\% of the clinical isolates from different geographical regions are negative for these adhesins, suggesting that additional unidentified adhesion determinants might be present. Here, we report the discovery of Coli Surface Antigen 23 (CS23), a novel adhesin expressed by an ETEC serogroup O4 strain (ETEC 1766a), which was negative for the previously known ETEC adhesins, albeit it has the ability to adhere to Caco-2 cells. CS23 is encoded by an 8.8-kb locus which contains 9 open reading frames (ORFs), 7 of them sharing significant identity with genes required for assembly of K88-related fimbriae. This gene locus, named aal (adhesion-associated locus), is required for the adhesion ability of ETEC 1766a and was able to confer this adhesive phenotype to a nonadherent E. coli HB101 strain. The CS23 major structural subunit, AalE, shares limited identity with known pilin proteins, and it is more closely related to the CS13 pilin protein CshE, carried by human ETEC strains. Our data indicate that CS23 is a new member of the diverse adhesin repertoire used by ETEC strains.}, author = {Del Canto, F. and Botkin, D.J. and Valenzuela, P. and Popov, V. and Ruiz-Perez, F. and Nataro, J.P. and Levine, M.M. and Stine, O.C. and Pop, Mihai and Torres, A.G. and others} } @article {19721, title = {InterPro in 2011: new developments in the family and domain prediction database.}, journal = {Nucleic Acids Res}, volume = {40}, year = {2012}, month = {2012 Jan}, pages = {D306-12}, abstract = {

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

}, keywords = {Databases, Protein, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, software, Terminology as Topic, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkr948}, author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F and Rivoire, Catherine and Sangrador-Vegas, Amaia and Jeremy D Selengut and Sigrist, Christian J A and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D and Wu, Cathy H and Yeats, Corin and Yong, Siew-Yit} } @article {12854, title = {Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico}, journal = {Journal of Clinical Microbiology}, year = {2012}, month = {04/2012}, abstract = {Vibrio cholerae O1 Classical (CL) biotype caused the 5th and 6th, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the 7th pandemic in Asia in the 1970{\textquoteright}s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia, and it had never been reported from Latin America, V. cholerae CL and ET biotypes, including hybrid ET were found associated with endemic cholera in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from endemic cholera in Mexico, between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits, and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and bio-typing data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim/sulfamethoxazole, furazolidone, ampicillin, and gentamycin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all the CL biotype strains, although the Mexican strains differed with the Bangladeshi strains in 1-2 DNA bands. The difference may be subtle, but consistent, as confirmed by the sub-clustering patterns in the PFGE-based dendrogram, and can serve as regional signature, suggesting pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from that of Asia.}, isbn = {0095-1137, 1098-660X}, doi = {10.1128/JCM.00189-12}, url = {http://jcm.asm.org/content/early/2012/04/12/JCM.00189-12}, author = {Alam,Munirul and Islam,M. Tarequl and Rashed,Shah Manzur and Johura,Fatema-Tuz and Bhuiyan,Nurul A. and Delgado,Gabriela and Morales,Rosario and Mendez,Jose Luis and Navarro,Armando and Watanabe,Haruo and Hasan,Nur-A. and Rita R Colwell and Cravioto,Alejandro} } @conference {13585, title = {Local Segmentation of Touching Characters using Contour based Shape Decomposition}, booktitle = {Document Analysis Systems}, year = {2012}, month = {2012///}, abstract = {We propose a contour based shape decomposition approach that provides local segmentation of touching characters. The shape contour is linearized into edgelets and edgelets are merged into boundary fragments. Connection cost between boundary fragments is obtained by considering local smoothness, connection length and a stroke-level property Similar Stroke Rate. Samples of connections among boundary fragments are randomly generated and the one with the minimum global cost is selected to produce optimal segmentation of the shape. To obtain a binary segmentation using this approach, we make an iterative search for the parameters that yields two components on a shape. Experimental results on a number of synthetic shape images and the LTP dataset showed that this contour based shape decomposition technique is promising and it is effective on providing local segmentation of touching characters.}, author = {Kang,Le and David Doermann and Cao,Huiagu and Prasad,Rohit and Natarajan,Prem} } @conference {17630, title = {Networking lessons: From computers to water}, booktitle = {2012 Fourth International Conference on Communication Systems and Networks (COMSNETS)}, year = {2012}, month = {2012/01/03/7}, pages = {1 - 6}, publisher = {IEEE}, organization = {IEEE}, abstract = {As an instance of using IT to green non-IT domains, we consider the question whether lessons from computer networking can be applied in water distribution networks to improve their energy footprint and/or efficiency. Our contributions in this work are: (i) we identify several areas where principles from computer networking can be used to better water distribution; (ii) we focus on a specific infrastructure enhancement problem caused by increasing demands on a water utility network and present solutions (similar to those used in computer networks) that optimize both operational expenditure and total cost of ownership. We validate our solutions through simulations and compare their efficacy against techniques that are traditionally used in enhancing water networks. Our results show that lessons from computer networks can help in enhancing water networks.}, keywords = {Biological cells, computer networking, Computer networks, COMPUTERS, energy footprint, Genetic algorithms, green nonIT domains, infrastructure enhancement problem, Internet, network theory (graphs), networking lessons, planning, pricing, water distribution networks, water supply, water utility network}, isbn = {978-1-4673-0296-8}, doi = {10.1109/COMSNETS.2012.6151373}, author = {Narayanan,I. and Sarangan,V. and Vasan, A. and Srinivasan, Aravind and Sivasubramaniam,A.} } @article {12857, title = {Occurrence of protozoans \& their limnological relationships in some ponds of Mathbaria, Bangladesh}, journal = {University Journal of Zoology, Rajshahi University}, volume = {29}, year = {2012}, month = {2012///}, pages = {69 - 71}, isbn = {1023-6104}, url = {http://journals.sfu.ca/bd/index.php/UJZRU}, author = {Mozumder,P. K. and Banu,M. A. and Naser,M. N. and Ali,M. S. and Alam,M. and Sack,R. B. and Rita R Colwell and Huq,A.} } @article {14415, title = {Organizing User Search Histories}, journal = {Knowledge and Data Engineering, IEEE Transactions on}, volume = {24}, year = {2012}, month = {2012/05//}, pages = {912 - 925}, abstract = {Users are increasingly pursuing complex task-oriented goals on the web, such as making travel arrangements, managing finances, or planning purchases. To this end, they usually break down the tasks into a few codependent steps and issue multiple queries around these steps repeatedly over long periods of time. To better support users in their long-term information quests on the web, search engines keep track of their queries and clicks while searching online. In this paper, we study the problem of organizing a user{\textquoteright}s historical queries into groups in a dynamic and automated fashion. Automatically identifying query groups is helpful for a number of different search engine components and applications, such as query suggestions, result ranking, query alterations, sessionization, and collaborative search. In our approach, we go beyond approaches that rely on textual similarity or time thresholds, and we propose a more robust approach that leverages search query logs. We experimentally study the performance of different techniques, and showcase their potential, especially when combined together.}, keywords = {alteration;query, analysis;user, engines;search, engines;text, goal;textual, group, historical, History, identification;query, information, interfaces;, log;sessionization;task-oriented, organization;query, processing;search, query, query;user, quest;query, ranking;search, search, search;long-term, similarity;time, suggestion;result, threshold;user, Web;collaborative}, isbn = {1041-4347}, doi = {10.1109/TKDE.2010.251}, author = {Hwang,Heasoo and Lauw,H. W and Getoor, Lise and Ntoulas,A.} } @article {12855, title = {Role of Shrimp Chitin in the Ecology of Toxigenic Vibrio cholerae and Cholera Transmission}, journal = {Frontiers in Microbiology}, volume = {2:260}, year = {2012}, month = {01/2012}, abstract = {Seasonal plankton blooms correlate with occurrence of cholera in Bangladesh, although the mechanism of how dormant Vibrio cholerae, enduring interepidemic period in biofilms and plankton, initiates seasonal cholera is not fully understood. In this study, laboratory microcosms prepared with estuarine Mathbaria water (MW) samples supported active growth of toxigenic V. cholerae O1 up to 7 weeks as opposed to 6 months when microcosms were supplemented with dehydrated shrimp chitin chips (CC) as the single source of nutrient. Bacterial counting and detection of wbe and ctxA genes were done employing culture, direct fluorescent antibody (DFA) assay, and multiplex-polymerase chain reaction methods. In MW microcosm, the aqueous phase became clear as the non-culturable cells settled, whereas the aqueous phase of the MW{\textendash}CC microcosm became turbid from bacterial growth stimulated by chitin. Bacterial chitin degradation and biofilm formation proceeded from an initial steady state to a gradually declining bacterial culturable count. V. cholerae within the microenvironments of chitin and chitin-associated biofilms remained metabolically active even in a high acidic environment without losing either viability or virulence. It is concluded that the abundance of chitin that occurs during blooms plays an important role in the aquatic life cycle of V. cholerae and, ultimately, in the seasonal transmission of cholera.}, isbn = {1664-302X}, doi = {10.3389/fmicb.2011.00260}, author = {Nahar,Shamsun and Sultana,Marzia and Naser,M. Niamul and Nair,Gopinath B. and Watanabe,Haruo and Ohnishi,Makoto and Yamamoto,Shouji and Endtz,Hubert and Cravioto,Alejandro and Sack,R. Bradley and Hasan,Nur A. and Sadique,Abdus and Huq,Anwar and Rita R Colwell and Alam,Munirul} } @article {12421, title = {SITS: A Hierarchical Nonparametric Model using Speaker Identity for Topic Segmentation in Multiparty Conversations}, journal = {Association for Computational Linguistics}, year = {2012}, month = {2012///}, abstract = {One of the key tasks for analyzing conversa- tional data is segmenting it into coherent topic segments. However, most models of topic segmentation ignore the social aspect of con- versations, focusing only on the words used. We introduce a hierarchical Bayesian nonpara- metric model, Speaker Identity for Topic Seg- mentation (SITS), that discovers (1) the top- ics used in a conversation, (2) how these top- ics are shared across conversations, (3) when these topics shift, and (4) a person-specific tendency to introduce new topics. We eval- uate against current unsupervised segmenta- tion models to show that including person- specific information improves segmentation performance on meeting corpora and on po- litical debates. Moreover, we provide evidence that SITS captures an individual{\textquoteright}s tendency to introduce new topics in political contexts, via analysis of the 2008 US presidential debates and the television program Crossfire.}, author = {Nguyen,Viet-An and Jordan Boyd-Graber and Resnik, Philip} } @conference {19374, title = {Sub-cellular feature detection and automated extraction of collocalized actin and myosin regions}, booktitle = {the 2nd ACM SIGHIT symposiumProceedings of the 2nd ACM SIGHIT symposium on International health informatics - IHI {\textquoteright}12}, year = {2012}, pages = {399}, publisher = {ACM Press}, organization = {ACM Press}, address = {Miami, Florida, USANew York, New York, USA}, isbn = {9781450307819}, doi = {10.1145/211036310.1145/2110363.2110409}, author = {Martineau, Justin and Mokashi,Ronil and Chapman, David and Grasso, Michael and Brady,Mary and Yesha,Yelena and Yesha,Yaacov and Cardone, Antonio and Dima, Alden} } @article {19618, title = {Verifying Search Results Over Web Collections}, journal = {arXiv:1204.5446 [cs]}, year = {2012}, month = {2012/04/24/}, abstract = {Searching accounts for one of the most frequently performed computations over the Internet as well as one of the most important applications of outsourced computing, producing results that critically affect users{\textquoteright} decision-making behaviors. As such, verifying the integrity of Internet-based searches over vast amounts of web contents is essential. We provide the first solution to this general security problem. We introduce the concept of an authenticated web crawler and present the design and prototype implementation of this new concept. An authenticated web crawler is a trusted program that computes a special "signature" $s$ of a collection of web contents it visits. Subject to this signature, web searches can be verified to be correct with respect to the integrity of their produced results. This signature also allows the verification of complicated queries on web pages, such as conjunctive keyword searches. In our solution, along with the web pages that satisfy any given search query, the search engine also returns a cryptographic proof. This proof, together with the signature $s$, enables any user to efficiently verify that no legitimate web pages are omitted from the result computed by the search engine, and that no pages that are non-conforming with the query are included in the result. An important property of our solution is that the proof size and the verification time both depend solely on the sizes of the query description and the query result, but not on the number or sizes of the web pages over which the search is performed. Our authentication protocols are based on standard Merkle trees and the more involved bilinear-map accumulators. As we experimentally demonstrate, the prototype implementation of our system gives a low communication overhead between the search engine and the user, and allows for fast verification of the returned results on the user side.}, keywords = {Computer Science - Cryptography and Security}, url = {http://arxiv.org/abs/1204.5446}, author = {Goodrich, Michael T. and Nguyen, Duy and Ohrimenko, Olga and Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikos and Lopes, Cristina Videira} } @conference {14496, title = {Active Surveying: A Probabilistic Approach for Identifying Key Opinion Leaders}, booktitle = {Twenty-Second International Joint Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, abstract = {Opinion leaders play an important role in influenc- ing people{\textquoteright}s beliefs, actions and behaviors. Al- though a number of methods have been proposed for identifying influentials using secondary sources of information, the use of primary sources, such as surveys, is still favored in many domains. In this work we present a new surveying method which combines secondary data with partial knowl- edge from primary sources to guide the information gathering process. We apply our proposed active surveying method to the problem of identifying key opinion leaders in the medical field, and show how we are able to accurately identify the opinion lead- ers while minimizing the amount of primary data required, which results in significant cost reduction in data acquisition without sacrificing its integrity.}, author = {Sharara,H. and Getoor, Lise and Norton,M.} } @conference {19489, title = {Cloud software upgrades: Challenges and opportunities}, booktitle = {2011 International Workshop on the Maintenance and Evolution of Service-Oriented and Cloud-Based Systems (MESOCA) }, year = {2011}, month = {2011///}, pages = {1 - 10}, abstract = {The fast evolution pace for cloud computing software is on a collision course with our growing reliance on cloud computing. On one hand, cloud software must have the agility to evolve rapidly, in order to remain competitive; on the other hand, more and more critical services become dependent on the cloud and demand high availability through firm Service Level Agreements (SLAs) for cloud infrastructures. This race between the needs to increase both the cloud upgrade frequency and the service availability is unsustainable. In this paper we highlight challenges and opportunities for upgrades in the cloud. We survey the release histories of several cloud applications to analyze their evolution pace, and we discuss the shortcomings with current cloud upgrade mechanisms. We outline several solutions for sustaining this evolution while improving availability, by focusing on the novel characteristics of cloud computing. By discussing several promising directions for realizing this vision, we propose a research agenda for the future of software upgrades in the cloud.}, keywords = {Availability, Cloud computing, cloud computing software, cloud upgrade frequency, collision course, Electronic publishing, Encyclopedias, service level agreement, service-oriented architecture}, author = {Neamtiu, I. and Tudor Dumitras} } @conference {14447, title = {Collective graph identification}, booktitle = {Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining}, series = {KDD {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {87 - 95}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Data describing networks (communication networks, transaction networks, disease transmission networks, collaboration networks, etc.) is becoming increasingly ubiquitous. While this observational data is useful, it often only hints at the actual underlying social or technological structures which give rise to the interactions. For example, an email communication network provides useful insight but is not the same as the "real" social network among individuals. In this paper, we introduce the problem of graph identification, i.e., the discovery of the true graph structure underlying an observed network. We cast the problem as a probabilistic inference task, in which we must infer the nodes, edges, and node labels of a hidden graph, based on evidence provided by the observed network. This in turn corresponds to the problems of performing entity resolution, link prediction, and node labeling to infer the hidden graph. While each of these problems have been studied separately, they have never been considered together as a coherent task. We present a simple yet novel approach to address all three problems simultaneously. Our approach, called C3, consists of Coupled Collective Classifiers that are iteratively applied to propagate information among solutions to the problems. We empirically demonstrate that C3 is superior, in terms of both predictive accuracy and runtime, to state-of-the-art probabilistic approaches on three real-world problems.}, keywords = {collective classification, entity resolution, link prediction, semi-supervised learning}, isbn = {978-1-4503-0813-7}, doi = {10.1145/2020408.2020429}, url = {http://doi.acm.org/10.1145/2020408.2020429}, author = {Namata,Galileo Mark and Kok,Stanley and Getoor, Lise} } @article {15698, title = {A Constraint-Reduced Variant of Mehrotra{\textquoteright}s Predictor-Corrector Algorithm}, journal = {Computational Optimization and Applications}, year = {2011}, month = {2011/01/19/36 pa}, doi = {DOI: 10.1007/s10589-010-9389-4}, author = {Winternitz,Luke B. and Nicholls,Stacey O. and Tits,Andr\&$\#$x65;\&$\#$x0301; and O{\textquoteright}Leary, Dianne P.} } @conference {13362, title = {Declarative analysis of noisy information networks}, booktitle = {2011 IEEE 27th International Conference on Data Engineering Workshops (ICDEW)}, year = {2011}, month = {2011/04/11/16}, pages = {106 - 111}, publisher = {IEEE}, organization = {IEEE}, abstract = {There is a growing interest in methods for analyzing data describing networks of all types, including information, biological, physical, and social networks. Typically the data describing these networks is observational, and thus noisy and incomplete; it is often at the wrong level of fidelity and abstraction for meaningful data analysis. This has resulted in a growing body of work on extracting, cleaning, and annotating network data. Unfortunately, much of this work is ad hoc and domain-specific. In this paper, we present the architecture of a data management system that enables efficient, declarative analysis of large-scale information networks. We identify a set of primitives to support the extraction and inference of a network from observational data, and describe a framework that enables a network analyst to easily implement and combine new extraction and analysis techniques, and efficiently apply them to large observation networks. The key insight behind our approach is to decouple, to the extent possible, (a) the operations that require traversing the graph structure (typically the computationally expensive step), from (b) the operations that do the modification and update of the extracted network. We present an analysis language based on Datalog, and show how to use it to cleanly achieve such decoupling. We briefly describe our prototype system that supports these abstractions. We include a preliminary performance evaluation of the system and show that our approach scales well and can efficiently handle a wide spectrum of data cleaning operations on network data.}, keywords = {Cleaning, Data analysis, data cleaning operations, data management system, data mining, Databases, Datalog, declarative analysis, graph structure, information networks, Noise measurement, noisy information networks, Prediction algorithms, semantics, Syntactics}, isbn = {978-1-4244-9195-7}, doi = {10.1109/ICDEW.2011.5767619}, author = {Moustafa,W. E and Namata,G. and Deshpande, Amol and Getoor, Lise} } @conference {13433, title = {Educational advances in artificial intelligence}, booktitle = {Proceedings of the 42nd ACM technical symposium on Computer science education}, series = {SIGCSE {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {81 - 82}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In 2010 a new annual symposium on Educational Advances in Artificial Intelligence (EAAI) was launched as part of the AAAI annual meeting. The event was held in cooperation with ACM SIGCSE and has many similar goals related to broadening and disseminating work in computer science education. EAAI has a particular focus, however, as the event is specific to educational work in Artificial Intelligence and collocated with a major research conference (AAAI) to promote more interaction between researchers and educators in that domain. This panel seeks to introduce participants to EAAI as a way of fostering more interaction between educational communities in computing. Specifically, the panel will discuss the goals of EAAI, provide an overview of the kinds of work presented at the symposium, and identify potential synergies between that EAAI and SIGCSE as a way of better linking the two communities going forward.}, keywords = {artificial intelligence education, model AI assignments}, isbn = {978-1-4503-0500-6}, doi = {10.1145/1953163.1953189}, url = {http://doi.acm.org/10.1145/1953163.1953189}, author = {Sahami,Mehran and desJardins, Marie and Dodds,Zachary and Neller,Todd} } @article {14691, title = {Evolution in Action: Using Active Networking to Evolve Network Support for Mobility}, journal = {IFIP Lecture Notes in Computer Science (LNCS)}, volume = {2546}, year = {2011}, month = {2011///}, pages = {146 - 161}, abstract = {key early objective of Active Networking (AN) was to support on-the-fly network evolution. Although AN has been used relatively extensively to build application-customized protocols and even whole networking systems, demonstrations of evolution have been limited.}, author = {Hicks, Michael W. and Nettles,S. and Seong-Kyu,S. and Shannon,S.} } @article {12440, title = {Example-Driven Manifold Priors for Image Deconvolution}, journal = {Image Processing, IEEE Transactions on}, volume = {20}, year = {2011}, month = {2011/11//}, pages = {3086 - 3096}, abstract = {Image restoration methods that exploit prior information about images to be estimated have been extensively studied, typically using the Bayesian framework. In this paper, we consider the role of prior knowledge of the object class in the form of a patch manifold to address the deconvolution problem. Specifically, we incorporate unlabeled image data of the object class, say natural images, in the form of a patch-manifold prior for the object class. The manifold prior is implicitly estimated from the given unlabeled data. We show how the patch-manifold prior effectively exploits the available sample class data for regularizing the deblurring problem. Furthermore, we derive a generalized cross-validation (GCV) function to automatically determine the regularization parameter at each iteration without explicitly knowing the noise variance. Extensive experiments show that this method performs better than many competitive image deconvolution methods.}, keywords = {Bayesian, cross-validation, data;Bayes, deconvolution;image, determination;deblurring, estimation;, framework;GCV, function;automatic, function;image, image, image;patch-manifold, manifold, method;iteration, method;natural, methods;deconvolution;image, methods;natural, parameter, prior;generalized, prior;unlabeled, problem, regularization, regularization;example-driven, restoration, restoration;iterative, scenes;parameter}, isbn = {1057-7149}, doi = {10.1109/TIP.2011.2145386}, author = {Ni,Jie and Turaga,P. and Patel, Vishal M. and Chellapa, Rama} } @conference {14497, title = {G-PARE: A visual analytic tool for comparative analysis of uncertain graphs}, booktitle = {Visual Analytics Science and Technology (VAST), 2011 IEEE Conference on}, year = {2011}, month = {2011///}, pages = {61 - 70}, author = {Sharara,H. and Sopan,A. and Namata,G. and Getoor, Lise and Singh,L.} } @article {16273, title = {Hawkeye and AMOS: Visualizing and Assessing the Quality of Genome Assemblies}, journal = {Briefings in Bioinformatics}, year = {2011}, month = {2011/12/23/}, abstract = {Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second- and now third-generation sequencing. This review describes the major components of AMOS in light of these challenges, with an emphasis on methods for assessing assembly quality and the visual analytics capabilities of Hawkeye. These interactive graphical aspects are essential for navigating and understanding the complexities of a genome assembly, from the overall genome structure down to individual bases. Hawkeye and AMOS are available open source at http://amos.sourceforge.net.}, keywords = {assembly forensics, DNA Sequencing, genome assembly, visual analytics}, isbn = {1467-5463, 1477-4054}, doi = {10.1093/bib/bbr074}, url = {http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074}, author = {Schatz,Michael C and Phillippy,Adam M and Sommer,Daniel D and Delcher,Arthur L. and Puiu,Daniela and Narzisi,Giuseppe and Salzberg,Steven L. and Pop, Mihai} } @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} } @book {19360, title = {Image Registration for Remote Sensing}, year = {2011}, month = {2011}, pages = {515}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, abstract = {Image registration is a digital image processing discipline that studies how to bring two or more digital images into precise alignment for analysis and comparison. Accurate registration algorithms are essential for creating mosaics of satellite images and tracking changes on the planet{\textquoteright}s surface over time. Bringing together invited contributions from 36 distinguished researchers, the book presents a detailed overview of current research and practice in the application of image registration to remote sensing imagery. Chapters cover the problem definition, theoretical issues in accuracy and efficiency, fundamental algorithms, and real-world case studies of image registration software applied to imagery from operational satellite systems. This book provides a comprehensive and practical overview for Earth and space scientists, presents image processing researchers with a summary of current research, and can be used for specialized graduate courses.}, keywords = {Science / Astronomy, Science / Earth Sciences / General, Technology \& Engineering / Environmental / General, Technology \& Engineering / Remote Sensing \& Geographic Information Systems}, isbn = {9781139494373}, author = {LeMoigne,Jacqueline and Netanyahu,Nathan S. and Eastman,Roger D.} } @inbook {19034, title = {Implicit Authentication through Learning User Behavior}, booktitle = {Information Security}, series = {Lecture Notes in Computer Science}, volume = {6531}, year = {2011}, month = {2011}, pages = {99 - 113}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Users are increasingly dependent on mobile devices. However, current authentication methods like password entry are significantly more frustrating and difficult to perform on these devices, leading users to create and reuse shorter passwords and pins, or no authentication at all. We present implicit authentication - authenticating users based on behavior patterns. We describe our model for performing implicit authentication and assess our techniques using more than two weeks of collected data from over 50 subjects.}, keywords = {Computer science}, isbn = {978-3-642-18177-1}, url = {http://www.springerlink.com/content/m57u551u3133475m/abstract/}, author = {Elaine Shi and Niu, Yuan and Jakobsson, Markus and Chow, Richard}, editor = {Burmester, Mike and Tsudik, Gene and Magliveras, Spyros and Ilic, Ivana} } @article {16814, title = {An incremental Hausdorff distance calculation algorithm}, journal = {Proceedings of the VLDB Endowment}, volume = {4}, year = {2011}, month = {2011/05//}, pages = {506 - 517}, abstract = {The Hausdorff distance is commonly used as a similarity measure between two point sets. Using this measure, a set X is considered similar to Y iff every point in X is close to at least one point in Y. Formally, the Hausdorff distance HausDist(X, Y) can be computed as the Max-Min distance from X to Y, i.e., find the maximum of the distance from an element in X to its nearest neighbor (NN) in Y. Although this is similar to the closest pair and farthest pair problems, computing the Hausdorff distance is a more challenging problem since its Max-Min nature involves both maximization and minimization rather than just one or the other. A traditional approach to computing HausDist(X, Y) performs a linear scan over X and utilizes an index to help compute the NN in Y for each x in X. We present a pair of basic solutions that avoid scanning X by applying the concept of aggregate NN search to searching for the element in X that yields the Hausdorff distance. In addition, we propose a novel method which incrementally explores the indexes of the two sets X and Y simultaneously. As an example application of our techniques, we use the Hausdorff distance as a measure of similarity between two trajectories (represented as point sets). We also use this example application to compare the performance of our proposed method with the traditional approach and the basic solutions. Experimental results show that our proposed method outperforms all competitors by one order of magnitude in terms of the tree traversal cost and total response time.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=2002974.2002978}, author = {Nutanong,Sarana and Jacox,Edwin H. and Samet, Hanan} } @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 {18922, title = {The Life Game: Cognitive Strategies for Repeated Stochastic Games}, year = {2011}, month = {2011/10//}, pages = {95 - 102}, abstract = {Standard models in bio-evolutionary game theory involve repetitions of a single stage game (e.g., the Prisoner{\textquoteright}s Dilemma or the Stag Hunt); but it is clear that repeatedly playing the same stage game is not an accurate model of most individuals{\textquoteright} lives. Rather, individuals{\textquoteright} interactions with others correspond to many different kinds of stage games. In this work, we concentrate on discovering behavioral strategies that are successful for the life game, in which the stage game is chosen stochastically at each iteration. We present a cognitive agent model based on Social Value Orientation (SVO) theory. We provide extensive evaluations of our model{\textquoteright}s performance, both against standard agents from the game theory literature and against a large set of life-game agents written by students in two different countries. Our empirical results suggest that for life-game strategies to be successful in environments with such agents, it is important (i) to be unforgiving with respect to trust behavior and (ii) to use adaptive, fine-grained opponent models of the other agents.}, keywords = {adaptive model, behavioral strategy, bioevolutionary game theory, cognitive agent model, fine-grained opponent model, game theory, iteration, iterative methods, life game, prisoner{\textquoteright}s dilemma, repeated stochastic games, social value orientation theory, stag hunt, stage game, Stochastic processes, trust behavior}, doi = {10.1109/PASSAT/SocialCom.2011.62}, author = {Cheng,Kan-Leung and Zuckerman,I. and Nau, Dana S. and Golbeck,J.} } @conference {19035, title = {Link prediction by de-anonymization: How We Won the Kaggle Social Network Challenge}, year = {2011}, month = {2011}, pages = {1825 - 1834}, abstract = {This paper describes the winning entry to the IJCNN 2011 Social Network Challenge run by Kaggle.com. The goal of the contest was to promote research on real-world link prediction, and the dataset was a graph obtained by crawling the popular Flickr social photo sharing website, with user identities scrubbed. By de-anonymizing much of the competition test set using our own Flickr crawl, we were able to effectively game the competition. Our attack represents a new application of de-anonymization to gaming machine learning contests, suggesting changes in how future competitions should be run. We introduce a new simulated annealing-based weighted graph matching algorithm for the seeding step of de-anonymization. We also show how to combine de-anonymization with link prediction-the latter is required to achieve good performance on the portion of the test set not de-anonymized-for example by training the predictor on the de-anonymized portion of the test set, and combining probabilistic predictions from de-anonymization and link prediction.}, keywords = {deanonymization, Flickr social photo sharing Website, graph theory, IJCNN 2011 social network challenge, Kaggle social network challenge, learning (artificial intelligence), machine learning, realworld link prediction, Simulated annealing, simulated annealing-based weighted graph matching algorithm, social networking (online)}, author = {Narayanan, A. and Elaine Shi and Rubinstein, B.I.P.} } @article {17980, title = {A Low-Overhead Asynchronous Interconnection Network for GALS Chip Multiprocessors}, journal = {Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on}, volume = {30}, year = {2011}, month = {2011/04//}, pages = {494 - 507}, abstract = {A new asynchronous interconnection network is introduced for globally-asynchronous locally-synchronous (GALS) chip multiprocessors. The network eliminates the need for global clock distribution, and can interface multiple synchronous timing domains operating at unrelated clock rates. In particular, two new highly-concurrent asynchronous components are introduced which provide simple routing and arbitration/merge functions. Post-layout simulations in identical commercial 90 nm technology indicate that comparable recent synchronous router nodes have 5.6-10.7 more energy per packet and 2.8-6.4 greater area than the new asynchronous nodes. Under random traffic, the network provides significantly lower latency and identical throughput over the entire operating range of the 800 MHz network and through mid-range traffic rates for the 1.36 GHz network, but with degradation at higher traffic rates. Preliminary evaluations are also presented for a mixed-timing (GALS) network in a shared-memory parallel architecture, running both random traffic and parallel benchmark kernels, as well as directions for further improvement.}, keywords = {1.36, 800, 90, architecture;size, architectures;shared, asynchronous, benchmark, chip, chips;multiprocessor, distribution, distribution;frequency, GALS, GHz;frequency, interconnection, kernel;post-layout, layout;clock, locally-synchronous, memory, MHz;globally-asynchronous, multiple, multiprocessor;clock, multiprocessor;interface, network;mixed-timing, network;network, networks;microprocessor, networks;network, nm;circuit, Parallel, routing;network-on-chip;parallel, routing;parallel, simulation;random, synchronous, systems;, timing;low-overhead, traffic;shared-memory}, isbn = {0278-0070}, doi = {10.1109/TCAD.2011.2114970}, author = {Horak,M.N. and Nowick,S.M. and Carlberg,M. and Vishkin, Uzi} } @conference {13454, title = {Model AI Assignments 2011}, booktitle = {Second AAAI Symposium on Educational Advances in Artificial Intelligence}, year = {2011}, month = {2011/04/08/}, abstract = {The Model AI Assignments session seeks to gather and disseminate the best assignment designs of the Artificial Intelligence (AI) Education community. Recognizing that assignments form the core of student learning experience, we here present abstracts of three AI assignments from the 2011 session that are easily adoptable, playfully engaging, and flexible for a variety of instructor needs.}, url = {http://www.aaai.org/ocs/index.php/EAAI/EAAI11/paper/viewPaper/3452}, author = {Neller,Todd William and desJardins, Marie and Oates,Tim and Taylor,Matthew E} } @conference {18891, title = {Real-Time Planning for Covering an Initially-Unknown Spatial Environment}, year = {2011}, month = {2011///}, abstract = {We consider the problem of planning, on the fly, a path whereby a robotic vehicle will cover every point in an ini- tially unknown spatial environment. We describe four strate- gies (Iterated WaveFront, Greedy-Scan, Delayed Greedy- Scan and Closest-First Scan) for generating cost-effective coverage plans in real time for unknown environments. We give theorems showing the correctness of our planning strate- gies. Our experiments demonstrate that some of these strate- gies work significantly better than others, and that the best ones work very well; e.g., in environments having an average of 64,000 locations for the robot to cover, the best strategy re- turned plans with less than 6\% redundant coverage, and took only an average of 0.1 milliseconds per action.}, url = {http://www.aaai.org/ocs/index.php/FLAIRS/FLAIRS11/paper/download/2566/2992}, author = {Shivashankar,V. and Jain, R. and Kuter,U. and Nau, Dana S.} } @article {12434, title = {Remote identification of faces: Problems, prospects, and progress}, journal = {Pattern Recognition Letters}, year = {2011}, month = {2011/12//}, abstract = {Face recognition in unconstrained acquisition conditions is one of the most challenging problems that has been actively researched in recent years. It is well known that many state-of-the-art still face recognition algorithms perform well, when constrained (frontal, well illuminated, high-resolution, sharp, and full) face images are acquired. However, their performance degrades significantly when the test images contain variations that are not present in the training images. In this paper, we highlight some of the key issues in remote face recognition. We define the remote face recognition as one where faces are several tens of meters (10{\textendash}250\&$\#$xa0;m) from the cameras. We then describe a remote face database which has been acquired in an unconstrained outdoor maritime environment. Recognition performance of a subset of existing still image-based face recognition algorithms is evaluated on the remote face data set. Further, we define the remote re-identification problem as matching a subject at one location with candidate sets acquired at a different location and over time in remote conditions. We provide preliminary experimental results on remote re-identification. It is demonstrated that in addition to applying a good classification algorithm, finding features that are robust to variations mentioned above and developing statistical models which can account for these variations are very important for remote face recognition.}, keywords = {Blur, illumination, low-resolution, pose variation, Re-identification, Remote face recognition}, isbn = {0167-8655}, doi = {10.1016/j.patrec.2011.11.020}, url = {http://www.sciencedirect.com/science/article/pii/S0167865511004107}, author = {Chellapa, Rama and Ni,Jie and Patel, Vishal M.} } @article {12861, title = {Role of Zooplankton Diversity in Vibrio Cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans}, journal = {Applied and Environmental Microbiology}, volume = {77}, year = {2011}, month = {09/2011}, pages = {6125 - 6132}, abstract = {Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries. V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenic V. cholerae strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.01472-10}, url = {http://aem.asm.org/content/77/17/6125}, author = {De Magny,Guillaume Constantin and Mozumder,Pronob K. and Grim,Christopher J. and Hasan,Nur A. and Naser,M. Niamul and Alam,Munirul and Sack,R. Bradley and Huq,Anwar and Rita R Colwell} } @conference {13643, title = {Shape Codebook based Handwritten and Machine Printed Text Zone Extraction}, booktitle = {Document Recognition and Retrieval}, year = {2011}, month = {2011/01//}, pages = {7874:1-8 - 7874:1-8}, address = {San Francisco}, abstract = {We present a novel method for extracting handwritten and printed text zones from noisy document images with mixed content. We use Triple-Adjacent-Segment (TAS) based features which encode local shape characteristics of text in a consistent manner. We first construct two different codebooks of the shape features extracted from a set of handwritten and printed text documents. In the next step, we compute the normalized histogram of codewords for each segmented zone and use it to train Support Vector Machine (SVM) classifier. Due to a codebook based approach, our method is robust to the background noise present in the image. The TAS features used are invariant to translation, scale and rotation of text. In our experimental results, we show that a pixel-weighted zone classification accuracy of 98\% can be achieved for noisy Arabic documents. Further, we demonstrate the effectiveness of our method for document page classification and show that a high precision can be achieved for machine printed documents. The proposed method is robust to the size of zones, which may contain text content at word, line or paragraph level.}, author = {Kumar,Jayant and Prasad,Rohit and Cao,Huiagu and Abd-Almageed, Wael and David Doermann and Natarajan,Prem} } @article {15907, title = {Sparsity-motivated automatic target recognition}, journal = {Applied OpticsAppl. Opt.}, volume = {50}, year = {2011}, month = {2011/04/01/}, pages = {1425 - 1433}, abstract = {We present an automatic target recognition algorithm using the recently developed theory of sparse representations and compressive sensing. We show how sparsity can be helpful for efficient utilization of data for target recognition. We verify the efficacy of the proposed algorithm in terms of the recognition rate and confusion matrices on the well known Comanche (Boeing{\textendash}Sikorsky, USA) forward-looking IR data set consisting of ten different military targets at different orientations.}, keywords = {IMAGE PROCESSING, Image recognition, algorithms and filters, pattern recognition, Vision - patterns and recognition}, doi = {10.1364/AO.50.001425}, url = {http://ao.osa.org/abstract.cfm?URI=ao-50-10-1425}, author = {Patel, Vishal M. and Nasrabadi,Nasser M. and Chellapa, Rama} } @inbook {17378, title = {Speeding Up Network Layout and Centrality Measures for Social Computing Goals}, booktitle = {Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction}, series = {Lecture Notes in Computer Science}, volume = {6589}, year = {2011}, month = {2011///}, pages = {244 - 251}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents strategies for speeding up calculation of graph metrics and layout by exploiting the parallel architecture of modern day Graphics Processing Units (GPU), specifically Compute Unified Device Architecture ( CUDA ) by Nvidia . Graph centrality metrics like Eigenvector , Betweenness , Page Rank and layout algorithms like Fruchterman - Rheingold are essential components of Social Network Analysis ( SNA ). With the growth in adoption of SNA in different domains and increasing availability of huge networked datasets for analysis, social network analysts require faster tools that are also scalable. Our results, using NodeXL, show up to 802 times speedup for a Fruchterman-Rheingold graph layout and up to 17,972 times speedup for Eigenvector centrality metric calculations on a 240 core CUDA-capable GPU.}, isbn = {978-3-642-19655-3}, url = {http://dx.doi.org/10.1007/978-3-642-19656-0_35}, author = {Sharma,Puneet and Khurana,Udayan and Shneiderman, Ben and Scharrenbroich,Max and Locke,John}, editor = {Salerno,John and Yang,Shanchieh and Nau, Dana S. and Chai,Sun-Ki} } @inbook {16046, title = {Temporal Visualization of Social Network Dynamics: Prototypes for Nation of Neighbors}, booktitle = {Social Computing, Behavioral-Cultural Modeling and PredictionSocial Computing, Behavioral-Cultural Modeling and Prediction}, series = {Lecture Notes in Computer Science}, volume = {6589}, year = {2011}, month = {2011///}, pages = {309 - 316}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Information visualization is a powerful tool for analyzing the dynamic nature of social communities. Using Nation of Neighbors community network as a testbed, we propose five principles of implementing temporal visualizations for social networks and present two research prototypes: NodeXL and TempoVis. Three different states are defined in order to visualize the temporal changes of social networks. We designed the prototypes to show the benefits of the proposed ideas by letting users interactively explore temporal changes of social networks.}, isbn = {978-3-642-19655-3}, url = {http://dx.doi.org/10.1007/978-3-642-19656-0_43}, author = {Ahn,Jae-wook and Taieb-Maimon,Meirav and Sopan,Awalin and Plaisant, Catherine and Shneiderman, Ben}, editor = {Salerno,John and Yang,Shanchieh and Nau, Dana S. and Chai,Sun-Ki} } @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 {17484, title = {Visual Analysis of Temporal Trends in Social Networks Using Edge Color Coding and Metric Timelines}, 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 = {549 - 554}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present Net EvViz, a visualization tool for analysis and exploration of a dynamic social network. There are plenty of visual social network analysis tools but few provide features for visualization of dynamically changing networks featuring the addition or deletion of nodes or edges. Our tool extends the code base of the Node XL template for Microsoft Excel, a popular network visualization tool. The key features of this work are (1) The ability of the user to specify and edit temporal annotations to the network components in an Excel sheet, (2) See the dynamics of the network with multiple graph metrics plotted over the time span of the graph, called the Timeline, and (3) Temporal exploration of the network layout using an edge coloring scheme and a dynamic Time slider. The objectives of the new features presented in this paper are to let the data analysts, computer scientists and others to observe the dynamics or evolution in a network interactively. We presented Net EvViz to five users of Node XL and received positive responses.}, keywords = {Color, computer scientists, data analysts, data visualisation, Data visualization, dynamic social network, dynamic timeslider, edge color coding, excel sheet, Image coding, image colour analysis, Layout, measurement, metric timelines, Microsoft excel, multiple graph metrics, Net EvViz, network components, network layout, network visualization tool, NodeXL template, social networking (online), temporal trends, Twitter, Visualization}, isbn = {978-1-4577-1931-8}, doi = {10.1109/PASSAT/SocialCom.2011.212}, author = {Khurana,U. and Nguyen,Viet-An and Hsueh-Chien Cheng and Ahn,Jae-wook and Chen,Xi and Shneiderman, Ben} } @inbook {15424, title = {Advances in Automated Model-Based System Testing of Software Applications with a GUI Front-End}, booktitle = {Advances in ComputersAdvances in Computers}, volume = {Volume 80}, year = {2010}, month = {2010///}, pages = {121 - 162}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {Despite the ubiquity of software applications that employ a graphical-user interface (GUI) front-end, functional system testing of these applications has remained, until recently, an understudied research area. During {\textquotedblleft}GUI testing,{\textquotedblright} test cases, modeled as sequences of user input events, are created and executed on the software by exercising the GUI{\textquoteright}s widgets. Because each possible sequence of user events may potentially be a test case and today{\textquoteright}s GUIs offer enormous flexibility to end-users, in principle, GUI testing requires a prohibitively large number of test cases. Any practical test-case generation technique must sample the vast GUI input space. Existing techniques are largely manual, and hence extremely resource intensive. Several new automated model-based techniques have been developed in the past decade. All these techniques develop, either manually or automatically, a model of the GUI and employ it to generate test cases. This chapter presents the first detailed taxonomy of these techniques. A small GUI application is used as a running example to demonstrate each technique and illustrate its relative strengths and weaknesses.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245810800038}, author = {Memon, Atif M. and Nguyen,Bao N.}, editor = {Zelkowitz, Marvin V} } @article {16242, title = {Alignment and clustering of phylogenetic markers - implications for microbial diversity studies}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010/03/24/}, pages = {152 - 152}, abstract = {Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved marker genes (primarily 16S rRNA) to characterize the taxonomic composition and diversity of these communities. To date, however, there exists significant variability in analysis methods employed in these studies.}, isbn = {1471-2105}, doi = {10.1186/1471-2105-11-152}, url = {http://www.biomedcentral.com/1471-2105/11/152}, author = {White,James R and Navlakha,Saket and Nagarajan,Niranjan and Ghodsi,Mohammad-Reza and Kingsford, Carl and Pop, Mihai} } @conference {19026, title = {Authentication in the clouds: a framework and its application to mobile users}, series = {CCSW {\textquoteright}10}, year = {2010}, month = {2010}, pages = {1 - 6}, publisher = {ACM}, organization = {ACM}, abstract = {Cloud computing is a natural fit for mobile security. Typical handsets have input constraints and practical computational and power limitations, which must be respected by mobile security technologies in order to be effective. We describe how cloud computing can address these issues. Our approach is based on a flexible framework for supporting authentication decisions we call TrustCube (to manage the authentication infrastructure) and on a behavioral authentication approach referred to as implicit authentication (to translate user behavior into authentication scores). The combination results in a new authentication paradigm for users of mobile technologies, one where an appropriate balance between usability and trust can be managed through flexible policies and dynamic tuning.}, keywords = {Authentication, Cloud computing, Mobile computing}, isbn = {978-1-4503-0089-6}, url = {http://doi.acm.org/10.1145/1866835.1866837}, author = {Chow, Richard and Jakobsson, Markus and Masuoka, Ryusuke and Molina,Jesus and Niu, Yuan and Elaine Shi and Song,Zhexuan} } @conference {12471, title = {Automatic target recognition based on simultaneous sparse representation}, booktitle = {Image Processing (ICIP), 2010 17th IEEE International Conference on}, year = {2010}, month = {2010/09//}, pages = {1377 - 1380}, abstract = {In this paper, an automatic target recognition algorithm is presented based on a framework for learning dictionaries for simultaneous sparse signal representation and feature extraction. The dictionary learning algorithm is based on class supervised simultaneous orthogonal matching pursuit while a matching pursuit-based similarity measure is used for classification. We show how the proposed framework can be helpful for efficient utilization of data, with the possibility of developing real-time, robust target classification. We verify the efficacy of the proposed algorithm using confusion matrices on the well known Comanche forward-looking infrared data set consisting of ten different military targets at different orientations.}, keywords = {(artificial, algorithm;feature, based, classification;iterative, classification;learning, Comanche, data, dictionary;matching, extraction;image, forward-looking, infrared, intelligence);military, learning, MATCHING, matrix;dictionary, measure;military, methods;learning, orthogonal, pursuit, pursuit;confusion, recognition;class, recognition;target, representation;feature, representation;sparse, set;automatic, signal, similarity, simultaneous, sparse, supervised, systems;object, target, target;simultaneous, tracking;}, doi = {10.1109/ICIP.2010.5652306}, author = {Patel, Vishal M. and Nasrabadi,N.M. and Chellapa, Rama} } @article {12881, title = {Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae}, journal = {BMC Microbiology}, volume = {10}, year = {2010}, month = {2010///}, abstract = {In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study. Results Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15\% divergence (88 to 85\% ANI and 92 to 91\% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95\% and AAI <96\% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59\%) and 2058 ORFs (56\%) with the published core genome of V. cholerae and 2956 (82\%) and 3048 ORFs (84\%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81\% Vibrio sp. RC341 and 81\% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp. Conclusions Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.}, author = {Bradd,H. and Christopher,G. and Nur,H. and Seon-Young,C. and Jongsik,C. and Thomas,B. and David,B. and Jean,C. and Chris,D. J. and Cliff,H. and Rita R Colwell} } @article {14509, title = {Context-Aware Query Recommendations}, volume = {12/408,726}, year = {2010}, month = {2010/09/23/}, abstract = {Described is a search-related technology in which context information regarding a user{\textquoteright}s prior search actions is used in making query recommendations for a current user action, such as a query or click. To determine whether each set or subset of context information is relevant to the user action, data obtained from a query log is evaluated. More particularly, a query transition (query-query) graph and a query click (query-URL) graph are extracted from the query log; vectors are computed for the current action and each context/sub-context and evaluated against vectors in the graphs to determine current action-to-context similarity. Also described is using similar context to provide the query recommendations, using parameters to control the similarity strictness, and/or whether more recent context information is more relevant than less recent context information, and using context information to distinguish between user sessions.}, url = {http://www.google.com/patents?id=nubWAAAAEBAJ}, author = {Ntoulas,Alexandros and Hwang,Heasoo and Getoor, Lise and Paparizos,Stelios and Lauw,Hady Wirawan}, editor = {Microsoft Corporation} } @article {12873, title = {Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co-culture with eukaryotic cells}, journal = {Microbiology and Immunology}, volume = {54}, year = {2010}, month = {2010/06/14/}, pages = {502 - 507}, abstract = {VBNC Vibrio cholerae O139 VC-280 obtained by incubation in 1\% solution of artificial sea water IO at 4{\textdegree}C for 74 days converted to the culturable state when co-cultured with CHO cells. Other eukaryotic cell lines, including HT-29, Caco-2, T84, HeLa, and Intestine 407, also supported conversion of VBNC cells to the culturable state. Conversion of VBNC V. cholerae O1 N16961 and V. cholerae O139 VC-280/pG13 to the culturable state, under the same conditions, was also confirmed. When VBNC V. cholerae O139 VC-280 was incubated in 1\% IO at 4{\textdegree}C for up to 91 days, the number of cells converted by co-culture with CHO cells declined with each additional day of incubation and after 91 days conversion was not observed.}, keywords = {conversion to culturability, co-culture, eukaryotic cell, viable but nonculturable (VBNC) Vibrio cholerae}, isbn = {1348-0421}, doi = {10.1111/j.1348-0421.2010.00245.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2010.00245.x/full}, author = {Senoh,Mitsutoshi and Ghosh-Banerjee,Jayeeta and Ramamurthy,Thandavarayan and Hamabata,Takashi and Kurakawa,Takashi and Takeda,Makoto and Rita R Colwell and Nair,G. Balakrish and Takeda,Yoshifumi} } @conference {18940, title = {Crowdsourcing the evaluation of a domain-adapted named entity recognition system}, series = {HLT {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {345 - 348}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Named entity recognition systems sometimes have difficulty when applied to data from domains that do not closely match the training data. We first use a simple rule-based technique for domain adaptation. Data for robust validation of the technique is then generated, and we use crowdsourcing techniques to show that this strategy produces reliable results even on data not seen by the rule designers. We show that it is possible to extract large improvements on the target data rapidly at low cost using these techniques.}, isbn = {1-932432-65-5}, url = {http://dl.acm.org/citation.cfm?id=1857999.1858050}, author = {Sayeed,Asad B. and Meyer,Timothy J. and Nguyen,Hieu C. and Buzek,Olivia and Weinberg, Amy} } @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 {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.} } @conference {18902, title = {Emergence of cooperative societies in evolutionary games}, series = {GECCO {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1793 - 1800}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We utilize evolutionary game theory to study the evolution of cooperative societies and the behaviors of individual agents (i.e., players) in it. We present a novel player model based upon empirical evidence from the social and behavioral sciences, stating that: (1) an individual{\textquoteright}s behavior may often be motivated not only by self-interest but also by the consequences for the others, and (2) individuals vary in their interpersonal social tendencies, which reflect stable personal orientations that influence their choices. Alongside the formal player model we provide an analysis that considers possible interactions between different types of individuals. We present series of evolutionary simulations that ratify previous findings on evolution of cooperation, and provide new insights on the evolutionary process of cooperative behavior in a society as well as on the emergence of cooperative societies. Our main experimental result demonstrate that in contrast to previous common knowledge, increasing the value of mutual Reward or increasing mutual Punishment in the Prisoner{\textquoteright}s dilemma game do not result in the same type of cooperative society: while increasing R does result in a more cooperative society, increasing P does not.}, keywords = {evolutionary game theory, social orientations}, isbn = {978-1-4503-0073-5}, doi = {10.1145/1830761.1830805}, url = {http://doi.acm.org/10.1145/1830761.1830805}, author = {Cheng,Kan-Leung and Zuckerman,Inon and Kuter,Ugur and Nau, Dana S.} } @conference {12472, title = {Evaluation of state-of-the-art algorithms for remote face recognition}, booktitle = {Image Processing (ICIP), 2010 17th IEEE International Conference on}, year = {2010}, month = {2010/09//}, pages = {1581 - 1584}, abstract = {In this paper, we describe a remote face database which has been acquired in an unconstrained outdoor environment. The face images in this database suffer from variations due to blur, poor illumination, pose, and occlusion. It is well known that many state-of-the-art still image-based face recognition algorithms work well, when constrained (frontal, well illuminated, high-resolution, sharp, and complete) face images are presented. In this paper, we evaluate the effectiveness of a subset of existing still image-based face recognition algorithms for the remote face data set. We demonstrate that in addition to applying a good classification algorithm, consistent detection of faces with fewer false alarms and finding features that are robust to variations mentioned above are very important for remote face recognition. Also setting up a comprehensive metric to evaluate the quality of face images is necessary in order to reject images that are of low quality.}, keywords = {alarm;feature, algorithm;still, classification;image, classification;visual, database;remote, databases;, extraction;hidden, extraction;image, Face, feature, image-based, image;false, quality;occlusion;remote, recognition;face, recognition;feature, recognition;state-of-the-art, removal;image}, doi = {10.1109/ICIP.2010.5652608}, author = {Ni,Jie and Chellapa, Rama} } @article {18903, title = {Evolution of state-dependent risk preferences}, journal = {ACM Transactions on Intelligent Systems and Technology (TIST)}, volume = {1}, year = {2010}, month = {2010/10//}, pages = {6:1{\textendash}6:21 - 6:1{\textendash}6:21}, abstract = {Researchers have invested much effort in constructing models of the state-dependent (sometimes risk-averse and sometimes risk-prone) nature of human decision making. An important open question is how state-dependent risk behavior can arise and remain prominent in populations. We believe that one part of the answer is the interplay between risk-taking and sequentiality of choices in populations subject to evolutionary population dynamics. To support this hypothesis, we provide simulation and analytical results for evolutionary lottery games, including results on evolutionary stability. We consider a parameterized class of imitation dynamics in which the parameter 0 <= α <= 1 yields the replicator dynamic with α = 1 and the imitate-the-better dynamic with α = 0. Our results demonstrate that for every population dynamic in this class except for the replicator dynamic, the interplay between risk-taking and sequentiality of choices allows state-dependent risk behavior to have an evolutionary advantage over expected-value maximization.}, keywords = {decision theory, Evolutionary games, Population Dynamics, risk}, isbn = {2157-6904}, doi = {10.1145/1858948.1858954}, url = {http://doi.acm.org/10.1145/1858948.1858954}, author = {Roos,Patrick and Carr,J. Ryan and Nau, Dana S.} } @conference {15267, title = {Exploring Biological Network Dynamics with Ensembles of Graph Partitions}, booktitle = {Proceedings of the PSB Pacific Symposium on Biocomputing}, volume = {15}, year = {2010}, month = {2010///}, pages = {166 - 177}, author = {Navlakha,S. and Kingsford, Carl} } @conference {18943, title = {Expresses-an-opinion-about: using corpus statistics in an information extraction approach to opinion mining}, series = {COLING {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {1095 - 1103}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We present a technique for identifying the sources and targets of opinions without actually identifying the opinions themselves. We are able to use an information extraction approach that treats opinion mining as relation mining; we identify instances of a binary "expresses-an-opinion-about" relation. We find that we can classify source-target pairs as belonging to the relation at a performance level significantly higher than two relevant baselines. This technique is particularly suited to emerging approaches in corpus-based social science which focus on aggregating interactions between sources to determine their effects on socio-economically significant targets. Our application is the analysis of information technology (IT) innovations. This is an example of a more general problem where opinion is expressed using either sub- or supersets of expressive words found in newswire. We present an annotation scheme and an SVM-based technique that uses the local context as well as the corpus-wide frequency of a source-target pair as data to determine membership in "expresses-an-opinion-about". While the presence of conventional subjectivity keywords appears significant in the success of this technique, we are able to find the most domain-relevant keywords without sacrificing recall.}, url = {http://dl.acm.org/citation.cfm?id=1944566.1944692}, author = {Sayeed,Asad B. and Nguyen,Hieu C. and Meyer,Timothy J. and Weinberg, Amy} } @article {16264, title = {Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information}, journal = {Journal of Computational Biology}, volume = {17}, year = {2010}, month = {2010/03//}, pages = {503 - 516}, abstract = {Hierarchical clustering is a popular method for grouping together similar elements based on a distance measure between them. In many cases, annotations for some elements are known beforehand, which can aid the clustering process. We present a novel approach for decomposing a hierarchical clustering into the clusters that optimally match a set of known annotations, as measured by the variation of information metric. Our approach is general and does not require the user to enter the number of clusters desired. We apply it to two biological domains: finding protein complexes within protein interaction networks and identifying species within metagenomic DNA samples. For these two applications, we test the quality of our clusters by using them to predict complex and species membership, respectively. We find that our approach generally outperforms the commonly used heuristic methods.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.2009.0173}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0173}, author = {Navlakha,Saket and White,James and Nagarajan,Niranjan and Pop, Mihai and Kingsford, Carl} } @article {16265, title = {Finishing genomes with limited resources: lessons from an ensemble of microbial genomes}, journal = {BMC Genomics}, volume = {11}, year = {2010}, month = {2010/04/16/}, pages = {242 - 242}, abstract = {While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.}, isbn = {1471-2164}, doi = {10.1186/1471-2164-11-242}, url = {http://www.biomedcentral.com/1471-2164/11/242}, author = {Nagarajan,Niranjan and Cook,Christopher and Di Bonaventura,Maria Pia and Ge,Hong and Richards,Allen and Bishop-Lilly,Kimberly A and DeSalle,Robert and Read,Timothy D. and Pop, Mihai} } @article {12871, title = {Genome Sequence of Hybrid Vibrio Cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. Cholerae}, journal = {Journal of BacteriologyJ. Bacteriol.}, volume = {192}, year = {2010}, month = {2010/07/01/}, pages = {3524 - 3533}, abstract = {The genomes of Vibrio cholerae O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33, and altered O1 El Tor CIRS101 were sequenced. All three strains were found to belong to the phylocore group 1 clade of V. cholerae, which includes the 7th-pandemic O1 El Tor and serogroup O139 isolates, despite displaying certain characteristics of the classical biotype. All three strains were found to harbor a hybrid variant of CTXΦ and an integrative conjugative element (ICE), leading to their establishment as successful clinical clones and the displacement of prototypical O1 El Tor. The absence of strain- and group-specific genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most likely factor in the recent establishment of dominance of V. cholerae CIRS101 over the other two hybrid strains.}, isbn = {0021-9193, 1098-5530}, doi = {10.1128/JB.00040-10}, url = {http://jb.asm.org/content/192/13/3524}, author = {Grim,Christopher J. and Hasan,Nur A. and Taviani,Elisa and Haley,Bradd and Jongsik Chun and Brettin,Thomas S. and Bruce,David C. and Detter,J. Chris and Han,Cliff S. and Chertkov,Olga and Challacombe,Jean and Huq,Anwar and Nair,G. Balakrish and Rita R Colwell} } @article {19094, title = {Genomic characterization of the Yersinia genus}, journal = {Genome biology}, volume = {11}, year = {2010}, month = {2010}, author = {Chen, P.E. and Cook, C. and Stewart, A.C. and Nagarajan,N. and Sommer, D.D. and Pop, Mihai and Thomason, B. and Thomason, M.P.K. and Lentz, S. and Nolan, N. and others} } @article {14510, title = {Identifying Modifiers in Web Queries Over Structured Data}, volume = {12/473,286}, year = {2010}, month = {2010/12/02/}, abstract = {Described is using modifiers in online search queries for queries that map to a database table. A modifier (e.g., an adjective or a preposition) specifies the intended meaning of a target, in which the target maps to a column in that table. The modifier thus corresponds to one or more functions that determine which rows of data in the column match the query, e.g., {\textquotedblleft}cameras under $400{\textquotedblright} maps to a camera (or product) table, and {\textquotedblleft}under{\textquotedblright} is the modifier that represents a function (less than) that is used to evaluate a {\textquotedblleft}price{\textquotedblright} target/data column. Also described are different classes of modifiers, and generating the dictionaries for a domain (corresponding to a table) via query log mining.}, url = {http://www.google.com/patents?id=gQTkAAAAEBAJ}, author = {Paparizos,Stelios and Joshi,Amrula Sadanand and Getoor, Lise and Ntoulas,Alexandros}, editor = {Microsoft Corporation} } @inbook {17635, title = {On k-Column Sparse Packing Programs}, booktitle = {Integer Programming and Combinatorial OptimizationInteger Programming and Combinatorial Optimization}, series = {Lecture Notes in Computer Science}, volume = {6080}, year = {2010}, month = {2010///}, pages = {369 - 382}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We consider the class of packing integer programs (PIPs) that are column sparse, where there is a specified upper bound k on the number of constraints that each variable appears in. We give an improved (ek + o(k))-approximation algorithm for k-column sparse PIPs. Our algorithm is based on a linear programming relaxation, and involves randomized rounding combined with alteration. We also show that the integrality gap of our LP relaxation is at least 2k - 1; it is known that even special cases of k-column sparse PIPs are (klogk)-hard to approximate.We generalize our result to the case of maximizing monotone submodular functions over k-column sparse packing constraints, and obtain an e2ke-1+o(k) -approximation algorithm. In obtaining this result, we prove a new property of submodular functions that generalizes the fractionally subadditive property, which might be of independent interest. }, isbn = {978-3-642-13035-9}, url = {http://dx.doi.org/10.1007/978-3-642-13036-6_28}, author = {Bansal,Nikhil and Korula,Nitish and Nagarajan,Viswanath and Srinivasan, Aravind}, editor = {Eisenbrand,Friedrich and Shepherd,F.} } @conference {12223, title = {Maranello: practical partial packet recovery for 802.11}, booktitle = {Proceedings of the 7th USENIX conference on Networked systems design and implementation}, series = {NSDI{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {14 - 14}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Partial packet recovery protocols attempt to repair corrupted packets instead of retransmitting them in their entirety. Recent approaches have used physical layer confidence estimates or additional error detection codes embedded in each transmission to identify corrupt bits, or have applied forward error correction to repair without such explicit knowledge. In contrast to these approaches, our goal is a practical design that simultaneously: (a) requires no extra bits in correct packets, (b) reduces recovery latency, except in rare instances, (c) remains compatible with existing 802.11 devices by obeying timing and backoff standards, and (d) can be incrementally deployed on widely available access points and wireless cards. In this paper, we design, implement, and evaluate Maranello, a novel partial packet recovery mechanism for 802.11. In Maranello, the receiver computes checksums over blocks in corrupt packets and bundles these checksums into a negative acknowledgment sent when the sender expects to receive an acknowledgment. The sender then retransmits only those blocks for which the checksum is incorrect, and repeats this partial retransmission until it receives an acknowledgment. Successful transmissions are not burdened by additional bits and the receiver needs not infer which bits were corrupted. We implemented Maranello using OpenFWWF (open source firmware for Broadcom wireless cards) and deployed it in a small testbed. We compare Maranello to alternative recovery protocols using a trace-driven simulation and to 802.11 using a live implementation under various channel conditions. To our knowledge, Maranello is the first partial packet recovery design to be implemented in commonly available firmware.}, url = {http://dl.acm.org/citation.cfm?id=1855711.1855725}, author = {Han,Bo and Schulman,Aaron and Gringoli,Francesco and Spring, Neil and Bhattacharjee, Bobby and Nava,Lorenzo and Ji,Lusheng and Lee,Seungjoon and Miller,Robert} } @conference {18589, title = {Network I/O fairness in virtual machines}, booktitle = {Proceedings of the second ACM SIGCOMM workshop on Virtualized infrastructure systems and architectures}, series = {VISA {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {73 - 80}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present a mechanism for achieving network I/O fairness in virtual machines, by applying flexible rate limiting mechanisms directly to virtual network interfaces. Conventional approaches achieve this fairness by implementing rate limiting either in the virtual machine monitor or hypervisor, which generates considerable CPU interrupt and instruction overhead for forwarding packets. In contrast, our design pushes per-VM rate limiting as close as possible to the physical hardware themselves, effectively implementing per-virtual interface rate limiting in hardware. We show that this design reduces CPU overhead (both interrupts and instructions) by an order of magnitude. Our design can be applied either to virtual servers for cloud-based services, or to virtual routers}, keywords = {netfpga, network virtualization, xen}, isbn = {978-1-4503-0199-2}, doi = {10.1145/1851399.1851412}, url = {http://doi.acm.org/10.1145/1851399.1851412}, author = {Anwer,Muhammad Bilal and Nayak,Ankur and Feamster, Nick and Liu,Ling} } @inbook {15597, title = {New Approaches to Robust, Point-Based Image Registration}, booktitle = {Image Registration for Remote SensingImage Registration for Remote Sensing}, year = {2010}, month = {2010///}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, abstract = {We consider various algorithmic solutions to image registration based on thealignment of a set of feature points. We present a number of enhancements to a branch-and-bound algorithm introduced by Mount, Netanyahu, and Le Moigne (Pattern Recognition, Vol. 32, 1999, pp. 17{\textendash}38), which presented a registration algorithm based on the partial Hausdorff distance. Our enhance- ments include a new distance measure, the discrete Gaussian mismatch, and a number of improvements and extensions to the above search algorithm. Both distance measures are robust to the presence of outliers, that is, data points from either set that do not match any point of the other set. We present experimental studies, which show that the new distance measure considered can provide significant improvements over the partial Hausdorff distance in instances where the number of outliers is not known in advance. These experiments also show that our other algorithmic improvements can offer tangible improvements. We demonstrate the algorithm{\textquoteright}s efficacy by considering images involving different sensors and different spectral bands, both in a traditional framework and in a multiresolution framework. }, isbn = {9780521516112}, author = {Mount, Dave and Netanyahu,N. S and Ratanasanya,S.}, editor = {LeMoigne,Jacqueline and Netanyahu,Nathan S. and Eastman,Roger D.} } @conference {12481, title = {Object Dependent Manifold Priors for Image Deconvolution}, booktitle = {Digital Image Processing and Analysis}, series = {OSA Technical Digest (CD)}, year = {2010}, month = {2010/06/07/}, pages = {DMC2 - DMC2}, publisher = {Optical Society of America}, organization = {Optical Society of America}, abstract = {In this paper we propose a manifold based deconvolution algorithm by estimating a manifold from a set of natural images that exploits the availability of the sample class data for regularizing the deblurring problem.}, keywords = {Deconvolution, IMAGE PROCESSING, Inverse problems}, url = {http://www.opticsinfobase.org/abstract.cfm?URI=DIPA-2010-DMC2}, author = {Ni,Jie and Turaga,Pavan and M.Patel,Vishal and Chellapa, Rama} } @conference {19023, title = {One experience collecting sensitive mobile data}, year = {2010}, month = {2010}, abstract = {We report on our efforts to collect behavioral data basedon activities recorded by phones. We recruited Android de- vice owners and offered entry into a raffle for participants. Our application was distributed from the Android Market, and its placement there unexpectedly helped us find par- ticipants from casual users browsing for free applications. We collected data from 267 total participants who gave us varying amounts of data. }, url = {http://www2.parc.com/csl/members/eshi/docs/users.pdf}, author = {Niu, Y. and Elaine Shi and Chow, R. and Golle, P. and Jakobsson, M.} } @article {15270, title = {The power of protein interaction networks for associating genes with diseases}, journal = {Bioinformatics}, volume = {26}, year = {2010}, month = {2010///}, pages = {1057 - 1057}, author = {Navlakha,S. and Kingsford, Carl} } @article {12877, title = {The pre-seventh pandemic Vibrio cholerae BX 330286 El Tor genome: evidence for the environment as a genome reservoir}, journal = {Environmental Microbiology Reports}, volume = {2}, year = {2010}, month = {2010/02/01/}, pages = {208 - 216}, abstract = {Vibrio cholerae O1 El Tor BX 330286 was isolated from a water sample in Australia in 1986, 9 years after an indigenous outbreak of cholera occurred in that region. This environmental strain encodes virulence factors highly similar to those of clinical strains, suggesting an ability to cause disease in humans. We demonstrate its high similarity in gene content and genome-wide nucleotide sequence to clinical V. cholerae strains, notably to pre-seventh pandemic O1 El Tor strains isolated in 1910 (V. cholerae NCTC 8457) and 1937 (V. cholerae MAK 757), as well as seventh pandemic strains isolated after 1960 globally. Here we demonstrate that this strain represents a transitory clone with shared characteristics between pre-seventh and seventh pandemic strains of V. cholerae. Interestingly, this strain was isolated 25 years after the beginning of the seventh pandemic, suggesting the environment as a genome reservoir in areas where cholera does not occur in sporadic, endemic or epidemic form.}, isbn = {1758-2229}, doi = {10.1111/j.1758-2229.2010.00141.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00141.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Haley,Bradd J. and Grim,Christopher J. and Hasan,Nur A. and Taviani,Elisa and Jongsik Chun and Brettin,Thomas S. and Bruce,David C. and Challacombe,Jean F. and Detter,J. Chris and Han,Cliff S. and Huq,Anwar and Nair,G. Balakrish and Rita R Colwell} } @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 {12487, title = {Sparsity inspired automatic target recognition}, journal = {Proceedings of SPIE}, volume = {7696}, year = {2010}, month = {2010/04/23/}, pages = {76960Q-76960Q-8 - 76960Q-76960Q-8}, abstract = {In this paper, we develop a framework for using only the needed data for automatic target recognition (ATR) algorithms using the recently developed theory of sparse representations and compressive sensing (CS). We show how sparsity can be helpful for efficient utilization of data, with the possibility of developing real-time, robust target classification. We verify the efficacy of the proposed algorithm in terms of the recognition rate on the well known Comanche forward-looking infrared (FLIR) data set consisting of ten different military targets at different orientations.}, isbn = {0277786X}, doi = {doi:10.1117/12.850533}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/7696/1/76960Q_1?isAuthorized=no}, author = {Patel, Vishal M. and Nasrabadi,Nasser M. and Chellapa, Rama} } @conference {18864, title = {Strategy generation in multi-agent imperfect-information pursuit games}, series = {AAMAS {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {947 - 954}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {We describe a formalism and algorithms for game-tree search in partially-observable Euclidean space, and implementation and tests in a scenario where a multi-agent team, called tracking agents, pursues a target agent that wants to evade the tracking agents. Our contributions include--- {\textbullet} A formalism that combines geometric elements (agents{\textquoteright} locations and trajectories and observable regions, and obstacles that restrict mobility and observability) with game-theoretic elements (information sets, utility functions, and strategies). {\textbullet} A recursive formula for information-set minimax values based on our formalism, and a implementation of the formula in a game-tree search algorithm. {\textbullet} A heuristic evaluation function for use at the leaf nodes of the game-tree search. It works by doing a quick lookahead search of its own, in a relaxed version of the problem. {\textbullet} Experimental results in 500 randomly generated trials. With the strategies generated by our heuristic, the tracking agents were more than twice as likely to know the target agent{\textquoteright}s location at the end of the game than with the strategies generated by heuristics that compute estimates of the target{\textquoteright}s possible locations.}, keywords = {game tree search, multi-agent planning, visibility-based pursuit-evasion games}, isbn = {978-0-9826571-1-9}, url = {http://dl.acm.org/citation.cfm?id=1838206.1838333}, author = {Raboin,Eric and Nau, Dana S. and Kuter,Ugur and Gupta, Satyandra K. and Svec,Petr} } @article {14417, title = {A survey of link mining tasks for analyzing noisy and incomplete networks}, journal = {Link Mining: Models, Algorithms, and Applications}, year = {2010}, month = {2010///}, pages = {107 - 133}, abstract = {Many data sets of interest today are best described as networks or graphs of interlinked entities. Examples include Web and text collections, social networks and social media sites, information, transaction and communication networks, and all manner of scientific networks, including biological networks. Unfortunately, often the data collection and extraction process for gathering these network data sets is imprecise, noisy, and/or incomplete. In this chapter, we review a collection of link mining algorithms that are well suited to analyzing and making inferences about networks, especially in the case where the data is noisy or missing.}, doi = {10.1007/978-1-4419-6515-8_4}, author = {Namata,G.M. and Sharara,H. and Getoor, Lise} } @conference {19506, title = {To Upgrade or Not to Upgrade: Impact of Online Upgrades Across Multiple Administrative Domains}, booktitle = {OOPSLA{\textquoteright}10 Proceedings of the ACM International Conference on Object Oriented Programming Systems Languages and Applications}, series = {OOPSLA {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {865 - 876}, publisher = {ACM}, organization = {ACM}, abstract = {Online software upgrades are often plagued by runtime behaviors that are poorly understood and difficult to ascertain. For example, the interactions among multiple versions of the software expose the system to race conditions that can introduce latent errors or data corruption. Moreover, industry trends suggest that online upgrades are currently needed in large-scale enterprise systems, which often span multiple administrative domains (e.g., Web 2.0 applications that rely on AJAX client-side code or systems that lease cloud-computing resources). In such systems, the enterprise does not control all the tiers of the system and cannot coordinate the upgrade process, making existing techniques inadequate to prevent mixed-version races. In this paper, we present an analytical framework for impact assessment, which allows system administrators to directly compare the risk of following an online-upgrade plan with the risk of delaying or canceling the upgrade. We also describe an executable model that implements our formal impact assessment and enables a systematic approach for deciding whether an online upgrade is appropriate. Our model provides a method of last resort for avoiding undesirable program behaviors, in situations where mixed-version races cannot be avoided through other technical means.}, keywords = {mixed-version race, multiple administrative domains, online upgrade, risk assessment}, isbn = {978-1-4503-0203-6}, url = {http://doi.acm.org/10.1145/1869459.1869530}, author = {Tudor Dumitras and Narasimhan, Priya and Tilevich, Eli} } @conference {12480, title = {Tracking via object reflectance using a hyperspectral video camera}, booktitle = {2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)}, year = {2010}, month = {2010/06/13/18}, pages = {44 - 51}, publisher = {IEEE}, organization = {IEEE}, abstract = {Recent advances in electronics and sensor design have enabled the development of a hyperspectral video camera that can capture hyperspectral datacubes at near video rates. The sensor offers the potential for novel and robust methods for surveillance by combining methods from computer vision and hyperspectral image analysis. Here, we focus on the problem of tracking objects through challenging conditions, such as rapid illumination and pose changes, occlusions, and in the presence of confusers. A new framework that incorporates radiative transfer theory to estimate object reflectance and the mean shift algorithm to simultaneously track the object based on its reflectance spectra is proposed. The combination of spectral detection and motion prediction enables the tracker to be robust against abrupt motions, and facilitate fast convergence of the mean shift tracker. In addition, the system achieves good computational efficiency by using random projection to reduce spectral dimension. The tracker has been evaluated on real hyperspectral video data.}, keywords = {Computer vision, electronic design, hyperspectral datacubes, hyperspectral image analysis, Hyperspectral imaging, Hyperspectral sensors, hyperspectral video camera, Image motion analysis, Image sensors, lighting, Motion estimation, motion prediction, Object detection, object reflectance tracking, random projection, Reflectivity, robust methods, Robustness, sensor design, spectral detection, Surveillance, tracking, Video surveillance}, isbn = {978-1-4244-7029-7}, doi = {10.1109/CVPRW.2010.5543780}, author = {Nguyen,Hien Van and Banerjee, A. and Chellapa, Rama} } @conference {18890, title = {Using a Social Orientation Model for the Evolution of Cooperative Societies}, year = {2010}, month = {2010///}, pages = {431 - 438}, abstract = {We utilize evolutionary game theory to studythe evolution of cooperative societies and the behaviors of individual agents (i.e., players) in such societies. We present a novel player model based upon empirical evidence from the social and behavioral sciences stating that: (1) an individual{\textquoteright}s behavior may often be motivated not only by self-interest but also by the consequences for others, and (2) individuals vary in their interpersonal social tendencies, which reflect stable personal orientations that influence their choices. Alongside the formal player model we provide an analysis that considers possible interactions between different types of individuals and identifies five general steady-state behavioral patterns. We present evolutionary simulations that ratify previous findings on evolution of cooperation, and provide new insights on the evolutionary process of cooperative behavior in a society as well as on the emergence of cooperative societies. Our main experimental result demonstrates that in contrast to previous common knowledge, increasing mutual reward or mutual punishment in the Prisoner{\textquoteright}s dilemma game does not result in the same type of cooperative society: while increasing reward does increase the society{\textquoteright}s cooperativeness level, increasing mutual punishment does not. }, url = {http://www.ariel.ac.il/sites/inon/papers/iat10Kan.pdf}, author = {Cheng,K. L. and Zuckerman,I. and Kuter,U. and Nau, Dana S.} } @conference {15496, title = {Using methods \& measures from network analysis for gui testing}, booktitle = {Software Testing, Verification, and Validation Workshops (ICSTW), 2010 Third International Conference on}, year = {2010}, month = {2010/04//}, pages = {240 - 246}, abstract = {Graphical user interfaces (GUIs) for today{\textquoteright}s applications are extremely large. Moreover, they provide many degrees of freedom to the end-user, thus allowing the user to perform a very large number of event sequences on the GUI. The large sizes and degrees of freedom create severe problems for GUI quality assurance, including GUI testing. In this paper, we leverage methods and measures from network analysis to analyze and study GUIs, with the goal of aiding GUI testing activities. We apply these methods and measures on the event-flow graph model of GUIs. Results of a case study show that "network centrality measures" are able to identify the most important events in the GUI as well as the most important sequences of events. These events and sequences are good candidates for test prioritization. In addition, the "betweenness clustering" method is able to partition the GUI into regions that can be tested separately.}, keywords = {betweenness clustering method, event sequences, event-flow graph model, Graphical user interfaces, GUI quality assurance, GUI testing, network analysis, network centrality measures, program testing, Software quality}, doi = {10.1109/ICSTW.2010.61}, author = {Elsaka,E. and Moustafa,W. E and Nguyen,Bao and Memon, Atif M.} } @article {18925, title = {When is it better not to look ahead?}, journal = {Artificial Intelligence}, volume = {174}, year = {2010}, month = {2010/11//}, pages = {1323 - 1338}, abstract = {In situations where one needs to make a sequence of decisions, it is often believed that looking ahead will help produce better decisions. However, it was shown 30 years ago that there are {\textquotedblleft}pathological{\textquotedblright} situations in which looking ahead is counterproductive. Two long-standing open questions are (a) what combinations of factors have the biggest influence on whether lookahead pathology occurs, and (b) whether it occurs in real-world decision-making.This paper includes simulation results for several synthetic game-tree models, and experimental results for three well-known board games: two chess endgames, kalah (with some modifications to facilitate experimentation), and the 8-puzzle. The simulations show the interplay between lookahead pathology and several factors that affect it; and the experiments confirm the trends predicted by the simulation models. The experiments also show that lookahead pathology is more common than has been thought: all three games contain situations where it occurs. }, keywords = {Game-tree search, Lookahead pathology, minimax}, isbn = {0004-3702}, doi = {10.1016/j.artint.2010.08.002}, url = {http://www.sciencedirect.com/science/article/pii/S0004370210001402}, author = {Nau, Dana S. and Lu{\v s}trek,Mitja and Parker,Austin and Bratko,Ivan and Gams,Matja{\v z}} } @conference {18613, title = {Wide-area route control for distributed services}, booktitle = {Proceedings of the 2010 USENIX conference on USENIX annual technical conference}, series = {USENIXATC{\textquoteright}10}, year = {2010}, month = {2010///}, pages = {2 - 2}, publisher = {USENIX Association}, organization = {USENIX Association}, address = {Berkeley, CA, USA}, abstract = {Many distributed services would benefit from control over the flow of traffic to and from their users, to offer better performance and higher reliability at a reasonable cost. Unfortunately, although today{\textquoteright}s cloud-computing platforms offer elastic computing and bandwidth resources, they do not give services control over wide-area routing. We propose replacing the data center{\textquoteright}s border router with a Transit Portal (TP) that gives each service the illusion of direct connectivity to upstream ISPs, without requiring each service to deploy hardware, acquire IP address space, or negotiate contracts with ISPs. Our TP prototype supports many layer-two connectivity mechanisms, amortizes memory and message overhead over multiple services, and protects the rest of the Internet from misconfigured and malicious applications. Our implementation extends and synthesizes open-source software components such as the Linux kernel and the Quagga routing daemon. We also implement a management plane based on the GENI control framework and couple this with our four-site TP deployment and Amazon EC2 facilities. Experiments with an anycast DNS application demonstrate the benefits the TP offers to distributed services.}, url = {http://dl.acm.org/citation.cfm?id=1855840.1855842}, author = {Valancius,Vytautas and Feamster, Nick and Rexford,Jennifer and Nakao,Akihiro} } @article {15278, title = {2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates}, journal = {PLoS ONEPLoS ONE}, volume = {4}, year = {2009}, month = {2009/07/28/}, pages = {e6402 - e6402}, abstract = {In April 2009, novel swine-origin influenza viruses (S-OIV) were identified in patients from Mexico and the United States. The viruses were genetically characterized as a novel influenza A (H1N1) strain originating in swine, and within a very short time the S-OIV strain spread across the globe via human-to-human contact.We conducted a comprehensive computational search of all available sequences of the surface proteins of H1N1 swine influenza isolates and found that a similar strain to S-OIV appeared in Thailand in 2000. The earlier isolates caused infections in pigs but only one sequenced human case, A/Thailand/271/2005 (H1N1). Differences between the Thai cases and S-OIV may help shed light on the ability of the current outbreak strain to spread rapidly among humans. }, doi = {10.1371/journal.pone.0006402}, url = {http://dx.doi.org/10.1371/journal.pone.0006402}, author = {Kingsford, Carl and Nagarajan,Niranjan and Salzberg,Steven L.} } @inbook {18894, title = {Artificial Intelligence and Automation}, booktitle = {Springer Handbook of Automation}, year = {2009}, month = {2009///}, pages = {249 - 268}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Artificial intelligence (AI) focuses on getting machines to do things that we would call intelligent behavior. Intelligence {\textendash} whether artificial or otherwise {\textendash} does not have a precise definition, but there are many activities and behaviors that are considered intelligent when exhibited by humans and animals. Examples include seeing, learning, using tools, understanding human speech, reasoning, making good guesses, playing games, and formulating plans and objectives. AI focuses on how to get machines or computers to perform these same kinds of activities, though not necessarily in the same way that humans or animals might do them.}, keywords = {engineering}, isbn = {978-3-540-78831-7}, url = {http://www.springerlink.com/content/q7051r251p38p51h/abstract/}, author = {Nau, Dana S.}, editor = {Nof,Shimon Y.} } @conference {12399, title = {Better vocabularies for assistive communication aids: connecting terms using semantic networks and untrained annotators}, booktitle = {Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility}, series = {Assets {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {171 - 178}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The difficulties of navigating vocabulary in an assistive communication device are exacerbated for individuals with lexical access disorders like those due to aphasia. We present the design and implementation of a vocabulary network based on WordNet, a resource that attempts to model human semantic memory, that enables users to find words easily. To correct for the sparsity of links among words, we augment WordNet with additional connections derived from human judgments of semantic similarity collected in an online experiment. We evaluate the resulting system, the visual vocabulary for aphasia (ViVA), and describe its potential to adapt to a user{\textquoteright}s profile and enable faster search and improved navigation.}, keywords = {adaptive tools, aphasia, assistive communication, semantic networks, visual vocabularies}, isbn = {978-1-60558-558-1}, doi = {10.1145/1639642.1639673}, url = {http://doi.acm.org/10.1145/1639642.1639673}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Fellbaum,Christiane and Cook,Perry} } @inbook {14493, title = {Collective classification for text classification}, booktitle = {Text Mining: Classification, Clustering, and ApplicationsText Mining: Classification, Clustering, and Applications}, year = {2009}, month = {2009///}, pages = {51 - 69}, author = {Namata,G. and Sen,P. and Bilgic,M. and Getoor, Lise} } @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} } @conference {12416, title = {The design of ViVA: a mixed-initiative visual vocabulary for aphasia}, booktitle = {Proceedings of the 27th international conference extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {4015 - 4020}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we present the design of ViVA, a visual vocabulary for aphasia. Aphasia is an acquired language disorder that causes variability of impairments affecting individual{\textquoteright}s ability to speak, comprehend, read and write. Existing communication aids lack flexibility and adequate customization functionality failing to address this variability and to satisfy individual user needs. We tackle these shortcomings by incorporating adaptive and adaptable capabilities in ViVA which is designed to assist communication for users suffering from aphasia. The visual vocabulary for aphasia implements a novel approach that organizes the words in the vocabulary according to user preferences, word usage and certain semantic measures, thus continuously tailoring the tool to the user{\textquoteright}s profile.}, keywords = {adaptive and adaptable interfaces, assistive communication tools, multi-modal interfaces}, isbn = {978-1-60558-247-4}, doi = {10.1145/1520340.1520610}, url = {http://doi.acm.org/10.1145/1520340.1520610}, author = {Nikolova,Sonya and Jordan Boyd-Graber and Cook,Perry R.} } @article {16404, title = {The emergence of zoning policy games in exurban jurisdictions: Informing collective action theory}, journal = {Land Use Policy}, volume = {26}, year = {2009}, month = {2009/04//}, pages = {356 - 367}, abstract = {Theoretical urban policy literature predicts the likelihood of free riding in the management of common goods such as forested open space; such outcome is often characterized as a Prisoner{\textquoteright}s Dilemma game. Numerous cases exist in which neighboring jurisdictions cooperate to maintain public goods, challenging the expected results, yet theoretical explanations of these cases have not been fully developed. In this paper, we use an agent-based model to explore how underlying micro-behaviors affect the payoffs obtained by two neighboring municipalities in a hypothetical exurban area. Payoffs are measured in terms of regional forested space and of local tax revenue at the end of the agent-based simulations; the municipalities affect these payoffs through their choice of residential zoning policies and the spillover effect between the neighboring jurisdictions. Zoning restrictions influence the conversion of farmland into residential subdivisions of different types, and consequently the location of heterogeneous residential households in the region. Developers and residents respond to the changing landscape characteristics, thus establishing a feedback between early and future land-use patterns. The structure of the simulated payoffs is analyzed using standard game theory. Our analysis shows that a variety of games, in addition to Prisoner{\textquoteright}s Dilemma, can emerge between the neighboring jurisdictions. Other games encourage coordination or subsidization, offering some explanations for the unexpected observations. The game realized in any given context depends on the initial characteristics of the landscape, the value given to the objectives each township seeks to maximize, and the income distribution of the population.}, keywords = {Agent-based modeling, game theory, Land-use policy, Local government cooperation, Scale interaction}, isbn = {0264-8377}, doi = {10.1016/j.landusepol.2008.04.004}, url = {http://www.sciencedirect.com/science/article/pii/S0264837708000604}, author = {Zellner,Moira L. and Page,Scott E. and Rand, William and Brown,Daniel G. and Robinson,Derek T. and Nassauer,Joan and Low,Bobbi} } @article {12997, title = {Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development}, journal = {Sci Transl Med}, volume = {1}, year = {2009}, month = {2009/10//}, pages = {2ra5 - 2ra5}, abstract = {Vaccines directed against the blood stages of Plasmodium falciparum malaria are intended to prevent the parasite from invading and replicating within host cells. No blood-stage malaria vaccine has shown clinical efficacy in humans. Most malaria vaccine antigens are parasite surface proteins that have evolved extensive genetic diversity, and this diversity could allow malaria parasites to escape vaccine-induced immunity. We examined the extent and within-host dynamics of genetic diversity in the blood-stage malaria vaccine antigen apical membrane antigen-1 in a longitudinal study in Mali. Two hundred and fourteen unique apical membrane antigen-1 haplotypes were identified among 506 human infections, and amino acid changes near a putative invasion machinery binding site were strongly associated with the development of clinical symptoms, suggesting that these residues may be important to consider in designing polyvalent apical membrane antigen-1 vaccines and in assessing vaccine efficacy in field trials. This extreme diversity may pose a serious obstacle to an effective polyvalent recombinant subunit apical membrane antigen-1 vaccine.}, doi = {10.1126/scitranslmed.3000257}, author = {Takala,S. L and Coulibaly,D. and Thera,M. A and Batchelor,A. H and Cummings, Michael P. and Escalante,A. A and Ouattara,A. and Traor{\'e},K. and Niangaly,A. and Djimd{\'e},A. A and Doumbo,OK and Plowe,CV} } @article {15276, title = {Finding Biologically Accurate Clusterings in Hierarchical Decompositions Using the Variation of Information}, journal = {Lecture Notes in Computer Science: Research in Computational Molecular Biology}, volume = {5541}, year = {2009}, month = {2009///}, pages = {400 - 417}, author = {Navlakha,S. and White,J. R. and Nagarajan,N. and Pop, Mihai and Kingsford, Carl} } @inbook {16263, title = {Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information}, booktitle = {Research in Computational Molecular Biology}, series = {Lecture Notes in Computer Science}, volume = {5541}, year = {2009}, month = {2009///}, pages = {400 - 417}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Hierarchical clustering is a popular method for grouping together similar elements based on a distance measure between them. In many cases, annotations for some elements are known beforehand, which can aid the clustering process. We present a novel approach for decomposing a hierarchical clustering into the clusters that optimally match a set of known annotations, as measured by the variation of information metric. Our approach is general and does not require the user to enter the number of clusters desired. We apply it to two biological domains: finding protein complexes within protein interaction networks and identifying species within metagenomic DNA samples. For these two applications, we test the quality of our clusters by using them to predict complex and species membership, respectively. We find that our approach generally outperforms the commonly used heuristic methods.}, isbn = {978-3-642-02007-0}, url = {http://dx.doi.org/10.1007/978-3-642-02008-7_29}, author = {Navlakha,Saket and White,James and Nagarajan,Niranjan and Pop, Mihai and Kingsford, Carl}, editor = {Batzoglou,Serafim} } @conference {14451, title = {Identifying graphs from noisy and incomplete data}, booktitle = {Proceedings of the 1st ACM SIGKDD Workshop on Knowledge Discovery from Uncertain Data}, series = {U {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {23 - 29}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {There is a growing wealth of data describing networks of various types, including social networks, physical networks such as transportation or communication networks, and biological networks. At the same time, there is a growing interest in analyzing these networks, in order to uncover general laws that govern their structure and evolution, and patterns and predictive models to develop better policies and practices. However, a fundamental challenge in dealing with this newly available observational data describing networks is that the data is often of dubious quality -- it is noisy and incomplete -- and before any analysis method can be applied, the data must be cleaned, and missing information inferred. In this paper, we introduce the notion of graph identification, which explicitly models the inference of a "cleaned" output network from a noisy input graph. It is this output network that is appropriate for further analysis. We present an illustrative example and use the example to explore the types of inferences involved in graph identification, as well as the challenges and issues involved in combining those inferences. We then present a simple, general approach to combining the inferences in graph identification and experimentally show the utility of our combined approach and how the performance of graph identification is sensitive to the inter-dependencies among these inferences.}, keywords = {classification, data mining, entity resolution, link prediction, social networks, statistical relational learning}, isbn = {978-1-60558-675-5}, doi = {10.1145/1610555.1610559}, url = {http://doi.acm.org/10.1145/1610555.1610559}, author = {Namata,Jr.,Galileo Mark S. and Getoor, Lise} } @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 {19500, title = {No Downtime for Data Conversions: Rethinking Hot Upgrades (CMU-PDL-09-106)}, journal = {Parallel Data Laboratory}, year = {2009}, month = {2009/07/01/}, url = {http://repository.cmu.edu/pdl/74}, author = {Tudor Dumitras and Narasimhan, Priya} } @conference {14456, title = {Opinion graphs for polarity and discourse classification}, booktitle = {Proceedings of the 2009 Workshop on Graph-based Methods for Natural Language Processing}, series = {TextGraphs-4}, year = {2009}, month = {2009///}, pages = {66 - 74}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This work shows how to construct discourse-level opinion graphs to perform a joint interpretation of opinions and discourse relations. Specifically, our opinion graphs enable us to factor in discourse information for polarity classification, and polarity information for discourse-link classification. This inter-dependent framework can be used to augment and improve the performance of local polarity and discourse-link classifiers.}, isbn = {978-1-932432-54-1}, url = {http://dl.acm.org/citation.cfm?id=1708124.1708138}, author = {Somasundaran,Swapna and Namata,Galileo and Getoor, Lise and Wiebe,Janyce} } @article {16281, title = {Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing}, journal = {Journal of Computational Biology}, volume = {16}, year = {2009}, month = {2009/07//}, pages = {897 - 908}, abstract = {In recent years, a flurry of new DNA sequencing technologies have altered the landscape of genomics, providing a vast amount of sequence information at a fraction of the costs that were previously feasible. The task of assembling these sequences into a genome has, however, still remained an algorithmic challenge that is in practice answered by heuristic solutions. In order to design better assembly algorithms and exploit the characteristics of sequence data from new technologies, we need an improved understanding of the parametric complexity of the assembly problem. In this article, we provide a first theoretical study in this direction, exploring the connections between repeat complexity, read lengths, overlap lengths and coverage in determining the {\textquotedblleft}hard{\textquotedblright} instances of the assembly problem. Our work suggests at least two ways in which existing assemblers can be extended in a rigorous fashion, in addition to delineating directions for future theoretical investigations.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.2009.0005}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0005}, author = {Nagarajan,Niranjan and Pop, Mihai} } @inbook {18916, title = {Planning for Interactions among Autonomous Agents}, booktitle = {Programming Multi-Agent Systems}, series = {Lecture Notes in Computer Science}, volume = {5442}, year = {2009}, month = {2009///}, pages = {1 - 23}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {AI planning research has traditionally focused on offline pl- anning for static single-agent environments. In environments where an agent needs to plan its interactions with other autonomous agents, planning is much more complicated, because the actions of the other agents can induce a combinatorial explosion in the number of contingencies that the planner will need to consider. This paper discusses several ways to alleviate the combinatorial explosion, and illustrates their use in several different kinds of multi-agent planning domains.}, keywords = {Computer science}, isbn = {978-3-642-03277-6}, url = {http://www.springerlink.com/content/j258015ux2p38383/abstract/}, author = {Au,Tsz-Chiu and Kuter,Ugur and Nau, Dana S.}, editor = {Hindriks,Koen and Pokahr,Alexander and Sardina,Sebastian} } @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 {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 {15274, title = {Revealing biological modules via graph summarization}, journal = {Journal of Computational Biology}, volume = {16}, year = {2009}, month = {2009///}, pages = {253 - 264}, author = {Navlakha,S. and Schatz,M. C and Kingsford, Carl} } @article {14730, title = {Safe and timely updates to multi-threaded programs}, journal = {SIGPLAN Not.}, volume = {44}, year = {2009}, month = {2009/06//}, pages = {13 - 24}, abstract = {Many dynamic updating systems have been developed that enable a program to be patched while it runs, to fix bugs or add new features. This paper explores techniques for supporting dynamic updates to multi-threaded programs, focusing on the problem of applying an update in a timely fashion while still producing correct behavior. Past work has shown that this tension of safety versus timeliness can be balanced for single-threaded programs. For multi-threaded programs, the task is more difficult because myriad thread interactions complicate understanding the possible program states to which a patch could be applied. Our approach allows the programmer to specify a few program points (e.g., one per thread) at which a patch may be applied, which simplifies reasoning about safety. To improve timeliness, a combination of static analysis and run-time support automatically expands these few points to many more that produce behavior equivalent to the originals. Experiments with thirteen realistic updates to three multi-threaded servers show that we can safely perform a dynamic update within milliseconds when more straightforward alternatives would delay some updates indefinitely.}, keywords = {dynamic software updating, multi-threading, update safety, update timeliness}, isbn = {0362-1340}, doi = {10.1145/1543135.1542479}, url = {http://doi.acm.org/10.1145/1543135.1542479}, author = {Neamtiu,Iulian and Hicks, Michael W.} } @conference {19502, title = {Second ACM Workshop on Hot Topics in Software Upgrades (HotSWUp 2009)}, series = {OOPSLA {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {705 - 706}, publisher = {ACM}, organization = {ACM}, abstract = {The goal of HotSWUp is to identify cutting-edge research ideas for implementing software upgrades. In the presence of modified user requirements, deployment environments, and bug fixes, actively-used software must be upgraded continuously to ensure its utility and safety. The upgrades incorporate changes to the structure, behavior, configuration, data, or topology of a computer system. Whether applied offline or directly to a live system, such upgrades may have a significant impact on the performance and reliability of the software. Indeed, recent studies and a large body of anecdotal evidence suggest that, in practice, upgrades are failure-prone and can lead to outages, data corruption or latent errors. These problems not only inconvenience end users - they create a significant burden for organizations due to the associated downtime and high administrative costs.}, keywords = {software, upgrades}, isbn = {978-1-60558-768-4}, url = {http://doi.acm.org/10.1145/1639950.1639974}, author = {Tudor Dumitras and Neamtiu, Iulian and Tilevich, Eli} } @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.} } @article {12882, title = {Serogroup, Virulence, and Genetic Traits of Vibrio Parahaemolyticus in the Estuarine Ecosystem of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {75}, year = {2009}, month = {2009/10/01/}, pages = {6268 - 6274}, abstract = {Forty-two strains of Vibrio parahaemolyticus were isolated from Bay of Bengal estuaries and, with two clinical strains, analyzed for virulence, phenotypic, and molecular traits. Serological analysis indicated O8, O3, O1, and K21 to be the major O and K serogroups, respectively, and O8:K21, O1:KUT, and O3:KUT to be predominant. The K antigen(s) was untypeable, and pandemic serogroup O3:K6 was not detected. The presence of genes toxR and tlh were confirmed by PCR in all but two strains, which also lacked toxR. A total of 18 (41\%) strains possessed the virulence gene encoding thermostable direct hemolysin (TDH), and one had the TDH-related hemolysin (trh) gene, but not tdh. Ten (23\%) strains exhibited Kanagawa phenomenon that surrogates virulence, of which six, including the two clinical strains, possessed tdh. Of the 18 tdh-positive strains, 17 (94\%), including the two clinical strains, had the seromarker O8:K21, one was O9:KUT, and the single trh-positive strain was O1:KUT. None had the group-specific or ORF8 pandemic marker gene. DNA fingerprinting employing pulsed-field gel electrophoresis (PFGE) of SfiI-digested DNA and cluster analysis showed divergence among the strains. Dendrograms constructed using PFGE (SfiI) images from a soft database, including those of pandemic and nonpandemic strains of diverse geographic origin, however, showed that local strains formed a cluster, i.e., {\textquotedblleft}clonal cluster,{\textquotedblright} as did pandemic strains of diverse origin. The demonstrated prevalence of tdh-positive and diarrheagenic serogroup O8:K21 strains in coastal villages of Bangladesh indicates a significant human health risk for inhabitants.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00266-09}, url = {http://aem.asm.org/content/75/19/6268}, author = {Alam,Munirul and Chowdhury,Wasimul B. and Bhuiyan,N. A. and Islam,Atiqul and Hasan,Nur A. and Nair,G. Balakrish and Watanabe,H. and Siddique,A. K. and Huq,Anwar and Sack,R. Bradley and Akhter,M. Z. and Grim,Christopher J. and Kam,K.-M. and Luey,C. K. Y. and Endtz,Hubert P. and Cravioto,Alejandro and Rita R Colwell} } @conference {12414, title = {Speaking through pictures: images vs. icons}, booktitle = {Proceedings of the 11th international ACM SIGACCESS conference on Computers and accessibility}, series = {Assets {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {163 - 170}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {People with aphasia, a condition that impairs the ability to understand or generate written or spoken language, are aided by assistive technology that helps them communicate through a vocabulary of icons. These systems are akin to language translation systems, translating icon arrangements into spoken or written language and vice versa. However, these icon-based systems have little vocabulary breadth or depth, making it difficult for people with aphasia to apply their usage to multiple real world situations. Pictures from the web are numerous, varied, and easily accessible and thus, could potentially address the small size issues of icon-based systems. We present results from two studies that investigate this potential and demonstrate that images can be as effective as icons when used as a replacement for English language communication. The first study uses elderly subjects to investigate the efficacy of images vs. icons in conveying word meaning; the second study examines the retention of word-level meaning by both images and icons with a population of aphasics. We conclude that images collected from the web are as functional as icons in conveying information and thus, are feasible to use in assistive technology that supports people with aphasia.}, keywords = {aphasia, computerized visual communication (C-VIC), visual communication (VIC)}, isbn = {978-1-60558-558-1}, doi = {10.1145/1639642.1639672}, url = {http://doi.acm.org/10.1145/1639642.1639672}, author = {Ma,Xiaojuan and Jordan Boyd-Graber and Nikolova,Sonya and Cook,Perry R.} } @article {16287, title = {Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples}, journal = {PLoS Comput Biology}, volume = {5}, year = {2009}, month = {2009/04/10/}, pages = {e1000352 - e1000352}, abstract = {The emerging field of metagenomics aims to understand the structure and function of microbial communities solely through DNA analysis. Current metagenomics studies comparing communities resemble large-scale clinical trials with multiple subjects from two general populations (e.g. sick and healthy). To improve analyses of this type of experimental data, we developed a statistical methodology for detecting differentially abundant features between microbial communities, that is, features that are enriched or depleted in one population versus another. We show our methods are applicable to various metagenomic data ranging from taxonomic information to functional annotations. We also provide an assessment of taxonomic differences in gut microbiota between lean and obese humans, as well as differences between the functional capacities of mature and infant gut microbiomes, and those of microbial and viral metagenomes. Our methods are the first to statistically address differential abundance in comparative metagenomics studies with multiple subjects, and we hope will give researchers a more complete picture of how exactly two environments differ.}, doi = {10.1371/journal.pcbi.1000352}, url = {UR - http://dx.doi.org/10.1371/journal.pcbi.1000352,http://dx.doi.org/10.1371/journal.pcbi.1000352}, author = {White,James Robert and Nagarajan,Niranjan and Pop, Mihai} } @conference {14455, title = {Supervised and unsupervised methods in employing discourse relations for improving opinion polarity classification}, booktitle = {Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1 - Volume 1}, series = {EMNLP {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {170 - 179}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This work investigates design choices in modeling a discourse scheme for improving opinion polarity classification. For this, two diverse global inference paradigms are used: a supervised collective classification framework and an unsupervised optimization framework. Both approaches perform substantially better than baseline approaches, establishing the efficacy of the methods and the underlying discourse scheme. We also present quantitative and qualitative analyses showing how the improvements are achieved.}, isbn = {978-1-932432-59-6}, url = {http://dl.acm.org/citation.cfm?id=1699510.1699533}, author = {Somasundaran,Swapna and Namata,Galileo and Wiebe,Janyce and Getoor, Lise} } @article {18921, title = {Task decomposition on abstract states, for planning under nondeterminism}, journal = {Artificial Intelligence}, volume = {173}, year = {2009}, month = {2009/04//}, pages = {669 - 695}, abstract = {Although several approaches have been developed for planning in nondeterministic domains, solving large planning problems is still quite difficult. In this work, we present a new planning algorithm, called Yoyo, for solving planning problems in fully observable nondeterministic domains. Yoyo combines an HTN-based mechanism for constraining its search and a Binary Decision Diagram (BDD) representation for reasoning about sets of states and state transitions.We provide correctness theorems for Yoyo, and an experimental comparison of it with MBP and ND-SHOP2, the two previously-best algorithms for planning in nondeterministic domains. In our experiments, Yoyo could easily deal with problem sizes that neither MBP nor ND-SHOP2 could scale up to, and could solve problems about 100 to 1000 times faster than MBP and ND-SHOP2. }, keywords = {Binary decision diagrams, Hierarchical task-network (HTN) planning, Planning in nondeterministic domains}, isbn = {0004-3702}, doi = {10.1016/j.artint.2008.11.012}, url = {http://www.sciencedirect.com/science/article/pii/S0004370208001987}, author = {Kuter,Ugur and Nau, Dana S. and Pistore,Marco and Traverso,Paolo} } @article {19726, title = {Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.}, journal = {Appl Environ Microbiol}, volume = {75}, year = {2009}, month = {2009 Apr}, pages = {2046-56}, abstract = {

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

}, keywords = {Anti-Bacterial Agents, bacteria, Biological Transport, Carbohydrate Metabolism, Cyanobacteria, DNA, Bacterial, Fungi, Genome, Bacterial, Macrolides, Molecular Sequence Data, Nitrogen, Phylogeny, Proteobacteria, Sequence Analysis, DNA, sequence homology, Soil Microbiology}, issn = {1098-5336}, doi = {10.1128/AEM.02294-08}, author = {Ward, Naomi L and Challacombe, Jean F and Janssen, Peter H and Henrissat, Bernard and Coutinho, Pedro M and Wu, Martin and Xie, Gary and Haft, Daniel H and Sait, Michelle and Badger, Jonathan and Barabote, Ravi D and Bradley, Brent and Brettin, Thomas S and Brinkac, Lauren M and Bruce, David and Creasy, Todd and Daugherty, Sean C and Davidsen, Tanja M and DeBoy, Robert T and Detter, J Chris and Dodson, Robert J and Durkin, A Scott and Ganapathy, Anuradha and Gwinn-Giglio, Michelle and Han, Cliff S and Khouri, Hoda and Kiss, Hajnalka and Kothari, Sagar P and Madupu, Ramana and Nelson, Karen E and Nelson, William C and Paulsen, Ian and Penn, Kevin and Ren, Qinghu and Rosovitz, M J and Jeremy D Selengut and Shrivastava, Susmita and Sullivan, Steven A and Tapia, Roxanne and Thompson, L Sue and Watkins, Kisha L and Yang, Qi and Yu, Chunhui and Zafar, Nikhat and Zhou, Liwei and Kuske, Cheryl R} } @conference {19508, title = {Toward Upgrades-as-a-service in Distributed Systems}, booktitle = {Middleware{\textquoteright}09 Proceedings of the 10th ACM/IFIP/USENIX International Conference on Middleware}, series = {Middleware {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {29:1 - 29:2}, publisher = {Springer-Verlag New York, Inc.}, organization = {Springer-Verlag New York, Inc.}, abstract = {Unavailability in distributed enterprise systems is usually the result of planned events, such as upgrades, rather than failures. Major system upgrades entail complex data conversions that are difficult to perform on the fly, in the face of live workloads. Minimizing the downtime imposed by such conversions is a time-intensive and error-prone manual process. We propose upgrades-as-a-service, a novel approach that can eliminate all the causes of planned downtime recorded during the upgrade history of one of the ten most popular websites. Building on the lessons learned from past research on live upgrades in middleware systems, upgrades-as-a-service trade off a need for additional hardware resources during the upgrade for the ability to perform end-to-end upgrades online, with minimal application-specific knowledge.}, url = {http://dl.acm.org/citation.cfm?id=1656980.1657019}, author = {Tudor Dumitras and Narasimhan, Priya} } @conference {18884, title = {Translating HTNs to PDDL: A small amount of domain knowledge can go a long way}, year = {2009}, month = {2009///}, pages = {1629 - 1634}, abstract = {We show how to translate HTN domain descrip- tions (if they satisfy certain restrictions) into PDDL so that they can be used by classical planners. We provide correctness results for our translation al- gorithm, and show that it runs in linear time and space. We also show that even small and incom- plete amounts of HTN knowledge, when translated into PDDL using our algorithm, can greatly im- prove a classical planner{\textquoteright}s performance. In ex- periments on several thousand randomly gener- ated problems in three different planning domains, such knowledge speeded up the well-known Fast- Forward planner by several orders of magnitude, and enabled it to solve much larger problems than it could otherwise solve.}, url = {https://www.aaai.org/ocs/index.php/IJCAI/IJCAI-09/paper/download/573/853}, author = {Alford,R. and Kuter,U. and Nau, Dana S.} } @article {12233, title = {Understanding the design tradeoffs for cooperative streaming multicast}, year = {2009}, month = {2009///}, institution = {Technical report MPI-SWS-2009-002, Max Planck Institute for Software Systems}, abstract = {Video streaming over the Internet is rapidly increasing in popular-ity, but the availability and quality of the content is limited by the high bandwidth cost for server-based solutions. Cooperative end- system multicast (CEM) has emerged as a promising paradigm for content distribution in the Internet, because the bandwidth over- head of disseminating content is shared among the participants of the CEM overlay network. Several CEM systems have been pro- posed and deployed, but the tradeoffs inherent in the different de- signs are not well understood. In this work, we provide a common framework in which different CEM design choices can be empirically and systematically evalu- ated. Our results show that all CEM protocols are inherently lim- ited in certain aspects of their performance. We distill our observa- tions into a novel model that explains the inherent tradeoffs of CEM design choices and provides bounds on the practical performance limits of any future CEM protocol. In particular, the model conjec- tures that no CEM design can simultaneously achieve all three of low overhead, low lag, and high streaming quality. }, author = {Nandi,A. and Bhattacharjee, Bobby and Druschel,P.} } @article {12225, title = {What a mesh: understanding the design tradeoffs for streaming multicast}, journal = {SIGMETRICS Perform. Eval. Rev.}, volume = {37}, year = {2009}, month = {2009/10//}, pages = {85 - 86}, abstract = {Cooperative end-system multicast (CEM) is a promising paradigm for Internet video distribution. Several CEM systems have been proposed and deployed, but the tradeoffs inherent in the different designs are not well understood. In this work, we provide a common framework in which different CEM design choices can be empirically and systematically evaluated. Based on our results, we conjecture that all CEM systems must abide by a set of fundamental design constraints, which we express in a simple model. By necessity, existing system implementations couple the data- and control-planes and often use different transport protocols.}, isbn = {0163-5999}, doi = {10.1145/1639562.1639598}, url = {http://doi.acm.org/10.1145/1639562.1639598}, author = {Nandi,Animesh and Bhattacharjee, Bobby and Druschel,Peter} } @conference {19510, title = {Why Do Upgrades Fail and What Can We Do About It?: Toward Dependable, Online Upgrades in Enterprise System}, booktitle = {Middleware{\textquoteright}09 Proceedings of the 10th ACM/IFIP/USENIX International Conference on Middleware}, series = {Middleware {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {18:1 - 18:20}, publisher = {Springer-Verlag New York, Inc.}, organization = {Springer-Verlag New York, Inc.}, abstract = {Enterprise-system upgrades are unreliable and often produce downtime or data-loss. Errors in the upgrade procedure, such as broken dependencies, constitute the leading cause of upgrade failures. We propose a novel upgrade-centric fault model, based on data from three independent sources, which focuses on the impact of procedural errors rather than software defects. We show that current approaches for upgrading enterprise systems, such as rolling upgrades, are vulnerable to these faults because the upgrade is not an atomic operation and it risks breaking hidden dependencies among the distributed system-components. We also present a mechanism for tolerating complex procedural errors during an upgrade. Our system, called Imago, improves availability in the fault-free case, by performing an online upgrade, and in the faulty case, by reducing the risk of failure due to breaking hidden dependencies. Imago performs an end-to-end upgrade atomically and dependably, by dedicating separate resources to the new version and by isolating the old version from the upgrade procedure. Through fault injection, we show that Imago is more reliable than online-upgrade approaches that rely on dependency-tracking and that create system states with mixed versions.}, url = {http://dl.acm.org/citation.cfm?id=1656980.1657005}, author = {Tudor Dumitras and Narasimhan, Priya} } @conference {18926, title = {Within epsilon of optimal play in the cultaptation social learning game}, series = {AAMAS {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1327 - 1328}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {Social learning, in which members of a society learn by observing the behavior of others, is an important foundation for human culture, and is observed in many other species as well. It seems natural to assume that social learning evolved due to the inherent superiority of copying others{\textquoteright} success rather than learning on one{\textquoteright}s own via trial-and-error innovation. However, there has also been substantial work questioning this intuition [3, 5, 1, 6, 4]. For example, blindly copying information from others is not useful if the information is wrong---or if it once was right but has since become outdated. Under what conditions does social learning outperform trial-and-error learning, and what kinds of social-learning strategies are likely to perform well?}, isbn = {978-0-9817381-7-8}, url = {http://dl.acm.org/citation.cfm?id=1558109.1558276}, author = {Carr,Ryan and Raboin,Eric and Parker,Austin and Nau, Dana S.} } @conference {19483, title = {1st ACM workshop on hot topics in software upgrades (HotSWUp 2008)}, booktitle = {OOPSLA Companion{\textquoteright}08 Companion to the 23rd ACM SIGPLAN Conference on Object-Oriented Programming Systems Languages and Applications}, series = {OOPSLA Companion {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {837 - 838}, publisher = {ACM}, organization = {ACM}, abstract = {The goal of HotSWUp is to identify cutting-edge research ideas for implementing software upgrades. Actively-used software is upgraded regularly to incorporate bug fixes and security patches or to keep up with the evolving requirements. Whether upgrades are applied offline or online, they significantly impact the software{\textquoteright}s performance and reliability. Recently-introduced commercial products aim to address various aspects of this problem, e.g., programing language/framework/middleware support for online upgrade, large-scale dissemination of fine-grained updates, live data migration in storage-area networks. However, recent studies and a large body of anecdotal evidence suggest that, in practice, upgrades are failure-prone, tedious, and expensive.}, keywords = {software, upgrades}, isbn = {978-1-60558-220-7}, url = {http://doi.acm.org/10.1145/1449814.1449877}, author = {Tudor Dumitras and Dig, Danny and Neamtiu, Iulian} } @article {13979, title = {Audio Camera Using Microphone Arrays for Real Time Capture of Audio Images ...}, volume = {12/127,451}, year = {2008}, month = {2008/05//}, abstract = {Spherical microphone arrays provide an ability to compute the acoustical intensity corresponding to different spatial directions in a given frame of audio data. These intensities may be exhibited as an image and these images are generated at a high frame rate to achieve a video image if the data capture and intensity computations can be performed sufficiently quickly, thereby creating a frame-rate audio camera. A description is provided herein regarding how such a camera is built and the processing done sufficiently quickly using graphics processors. The joint processing of and captured frame-rate audio and video images enables applications such as visual identification of noise sources, beamforming and noise-suppression in video conferenceing and others, by accounting for the spatial differences in the location of the audio and the video cameras. Based on the recognition that the spherical array can be viewed as a central projection camera, such joint analysis can be performed.}, url = {http://www.google.com/patents?id=gWKzAAAAEBAJ}, author = {Duraiswami, Ramani and O{\textquoteright}donovan,Adam and Neumann, Jan and Gumerov, Nail A.} } @article {14375, title = {Collective Classification in Network Data}, journal = {AI Magazine}, volume = {29}, year = {2008}, month = {2008/09/06/}, pages = {93 - 93}, abstract = {Collective Classification in Network Data}, isbn = {0738-4602}, doi = {10.1609/aimag.v29i3.2157}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/2157}, author = {Sen,Prithviraj and Namata,Galileo and Bilgic,Mustafa and Getoor, Lise and Galligher,Brian and Eliassi-Rad,Tina} } @conference {18898, title = {Combining Domain-Independent Planning and HTN Planning: The Duet Planner}, year = {2008}, month = {2008///}, pages = {573 - 577}, publisher = {IOS Press}, organization = {IOS Press}, address = {Amsterdam, The Netherlands, The Netherlands}, abstract = {Despite the recent advances in planning for classical domains, the question of how to use domain knowledge in planning is yet to be completely and clearly answered. Some of the existing planners use domain-independent search heuristics, and some others depend on intensively-engineered domain-specific knowledge to guide the planning process. In this paper, we describe an approach to combine ideas from both of the above schools of thought. We present Duet, our planning system that incorporates the ability of using hierarchical domain knowledge in the form of Hierarchical Task Networks (HTNs) as in SHOP2 [14] and using domain-independent local search techniques as in LPG [8]. In our experiments, Duet was able to solve much larger problems than LPG could solve, with only minimal domain knowledge encoded in HTNs (much less domain knowledge than SHOP2 needed to solve those problems by itself).}, isbn = {978-1-58603-891-5}, url = {http://dl.acm.org/citation.cfm?id=1567281.1567406}, author = {Gerevini,Alfonso and Kuter,Ugur and Nau, Dana S. and Saetti,Alessandro and Waisbrot,Nathaniel} } @article {18899, title = {Computational Cultural Dynamics}, journal = {Intelligent Systems, IEEE}, volume = {23}, year = {2008}, month = {2008/08//july}, pages = {18 - 19}, abstract = {Computational cultural dynamics blends the behavioral and social sciences - fields such as political science, psychology, journalism, anthropology, and sociology - with technological fields such as computer science, computational linguistics, game theory, statistical modeling, and operations research.}, keywords = {anthropology, behavioral science, behavioural sciences computing, computational cultural dynamics, computational linguistics, Computer science, game theory, journalism, operations research, political science, Psychology, social sciences, social sciences computing, sociology, statistical modeling}, isbn = {1541-1672}, doi = {10.1109/MIS.2008.61}, author = {Nau, Dana S. and Wilkenfeld,J.} } @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} } @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} } @conference {15585, title = {Enhancements in robust feature matching}, booktitle = {Electrical Engineering/Electronics, Computer, Telecommunications and Information Technology, 2008. ECTI-CON 2008. 5th International Conference on}, volume = {1}, year = {2008}, month = {2008/05//}, pages = {505 - 508}, abstract = {We present in this paper a number of new enhancements to a branch-and-bound algorithm given by Mount, Netanyahu, and Le Moigne [8] for feature matching. We introduce a new distance measure, which is more robust to the presence of outliers than the previously used measure, as well as a new variant of the search algorithm and a new search strategy. We also present experimental results, which show that these enhancements offer significant tangible improvements in performance.}, keywords = {branch-and-bound algorithm, distance measure, Image Enhancement, Image matching, robust feature matching, tree searching}, doi = {10.1109/ECTICON.2008.4600481}, author = {Ratanasanya,S. and Mount, Dave and Netanyahu,N. S and Achalakul,T.} } @inbook {12117, title = {An Environment for Conducting Families of Software Engineering Experiments}, booktitle = {Software Development}, volume = {Volume 74}, year = {2008}, month = {2008///}, pages = {175 - 200}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. Understanding how to run such experiments, developing procedures to collect accurate data, and collecting data that is consistent across multiple studies are major problems. This paper describes an environment, the Experiment Manager that simplifies the process of collecting, managing, and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages in the high-performance computing domain on programmer productivity at multiple universities across the United States.}, isbn = {0065-2458}, url = {http://www.sciencedirect.com/science/article/pii/S0065245808006050}, author = {Hochstein, Lorin and Nakamura,Taiga and Shull, Forrest and Zazworka, Nico and Basili, Victor R. and Zelkowitz, Marvin V}, editor = {Zelkowitz, Marvin V} } @article {12913, title = {Environmental signatures associated with cholera epidemics}, journal = {Proceedings of the National Academy of Sciences}, volume = {105}, year = {2008}, month = {2008///}, pages = {17676 - 17676}, abstract = {The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998{\textendash}2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.ecology epidemiology microbiology remote sensing }, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0809654105}, url = {http://www.pnas.org/content/105/46/17676}, author = {Constantin de Magny,G. and Murtugudde,R. and Sapiano,M. R. P. and Nizam,A. and Brown,C. W. and Busalacchi,A. J. and Yunus,M. and Nair,G. B. and Gil,A. I. and Lanata,C. F. and Rita R Colwell} } @article {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 {16396, title = {Exurbia from the bottom-up: Confronting empirical challenges to characterizing a complex system}, journal = {Geoforum}, volume = {39}, year = {2008}, month = {2008/03//}, pages = {805 - 818}, abstract = {We describe empirical results from a multi-disciplinary project that support modeling complex processes of land-use and land-cover change in exurban parts of Southeastern Michigan. Based on two different conceptual models, one describing the evolution of urban form as a consequence of residential preferences and the other describing land-cover changes in an exurban township as a consequence of residential preferences, local policies, and a diversity of development types, we describe a variety of empirical data collected to support the mechanisms that we encoded in computational agent-based models. We used multiple methods, including social surveys, remote sensing, and statistical analysis of spatial data, to collect data that could be used to validate the structure of our models, calibrate their specific parameters, and evaluate their output. The data were used to investigate this system in the context of several themes from complexity science, including have (a) macro-level patterns; (b) autonomous decision making entities (i.e., agents); (c) heterogeneity among those entities; (d) social and spatial interactions that operate across multiple scales and (e) nonlinear feedback mechanisms. The results point to the importance of collecting data on agents and their interactions when producing agent-based models, the general validity of our conceptual models, and some changes that we needed to make to these models following data analysis. The calibrated models have been and are being used to evaluate landscape dynamics and the effects of various policy interventions on urban land-cover patterns.}, keywords = {Ecological effects, Land-cover change, Land-use change, spatial modeling, Urban sprawl}, isbn = {0016-7185}, doi = {10.1016/j.geoforum.2007.02.010}, url = {http://www.sciencedirect.com/science/article/pii/S0016718507000371}, author = {Brown,Daniel G. and Robinson,Derek T. and An,Li and Nassauer,Joan I. and Zellner,Moira and Rand, William and Riolo,Rick and Page,Scott E. and Low,Bobbi and Wang,Zhifang} } @article {19484, title = {A Fault Model for Upgrades in Distributed Systems (CMU-PDL-08-115)}, journal = {Parallel Data Laboratory}, year = {2008}, month = {2008/12/01/}, url = {http://repository.cmu.edu/pdl/10}, author = {Tudor Dumitras and Kavulya, Soila and Narasimhan, Priya} } @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} } @article {12975, title = {A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE}, journal = {Evolution}, volume = {62}, year = {2008}, month = {2008/09/01/}, pages = {2411 - 2422}, abstract = {We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than FST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.}, keywords = {Ancestral polymorphism, congruence, exclusivity, genealogy, lineage sorting, monophyly, paraphyly, Phylogeny, polyphyly, speciation, species}, isbn = {1558-5646}, doi = {10.1111/j.1558-5646.2008.00442.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2008.00442.x/abstract}, author = {Cummings, Michael P. and Neel,Maile C and Shaw,Kerry L} } @article {16271, title = {Genome-Wide Analysis of Repetitive Elements in Papaya}, journal = {Tropical Plant Biology}, volume = {1}, year = {2008}, month = {2008///}, pages = {191 - 201}, abstract = {Papaya ( Carica papaya L.) is an important fruit crop cultivated in tropical and subtropical regions worldwide. A first draft of its genome sequence has been recently released. Together with Arabidopsis , rice, poplar, grapevine and other genomes in the pipeline, it represents a good opportunity to gain insight into the organization of plant genomes. Here we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes. These repetitive sequences account for \~{}56\% of the papaya genome with TEs being the most abundant at 52\%, tandem repeats at 1.3\% and high copy number genes at 3\%. Most common types of TEs are represented in the papaya genome with retrotransposons being the dominant class, accounting for 40\% of the genome. The most prevalent retrotransposons are Ty3-gypsy (27.8\%) and Ty1-copia (5.5\%). Among the tandem repeats, microsatellites are the most abundant in number, but represent only 0.19\% of the genome. Minisatellites and satellites are less abundant, but represent 0.68\% and 0.43\% of the genome, respectively, due to greater repeat length. Despite an overall smaller gene repertoire in papaya than many other angiosperms, a significant fraction of genes (\>2\%) are present in large gene families with copy number greater than 20. This repeat database clarified a major part of the papaya genome organization and partly explained the lower gene repertoire in papaya than in Arabidopsis .}, isbn = {1935-9756}, url = {http://dx.doi.org/10.1007/s12042-008-9015-0}, author = {Nagarajan,Niranjan and Navajas-P{\'e}rez,Rafael and Pop, Mihai and Alam,Maqsudul and Ming,Ray and Paterson,Andrew and Salzberg,Steven} } @conference {12240, title = {Integrating categorical resource types into a P2P desktop grid system}, booktitle = {Grid Computing, 2008 9th IEEE/ACM International Conference on}, year = {2008}, month = {2008/10/29/1}, pages = {284 - 291}, abstract = {We describe and evaluate a set of protocols that implement a distributed, decentralized desktop grid. Incoming jobs are matched with system nodes through proximity in an N-dimensional resource space. This work improves on prior work by (1) efficiently accommodating node and job characterizations that include both continuous and categorical resource types, and (2) scaling gracefully to large system sizes even with highly non-uniform distributions of job and node types. We use extensive simulation results to show that the resulting system handles both continuous and categorical constraints efficiently, and that the new scalability techniques are effective.}, keywords = {computing;peer-to-peer, computing;protocols;, computing;protocols;scalability, desktop, Grid, grid;distributed, grid;peer-to-peer, N-dimensional, resource, space;P2P, system;categorical, technique;grid, types;decentralized}, doi = {10.1109/GRID.2008.4662810}, author = {Kim,Jik-Soo and Nam,Beomseok and Marsh,M. and Keleher,P. and Bhattacharjee, Bobby and Sussman, Alan} } @article {14921, title = {The Maryland Large-Scale Integrated Neurocognitive Architecture}, year = {2008}, month = {2008/03//}, institution = {University of Maryland College Park}, abstract = {Recent progress in neural computation, high performance computing, neuroscience and cognitive science suggests that an effort to produce a general-purpose, adaptive machine intelligence is likely to yield a qualitatively more powerful system than those currently existing. Here we outline our progress in developing a framework for creating such a large-scale machine intelligence, or neurocognitive architecture that is based on the modularity, dynamics and plasticity of the human brain. We successfully implemented three intermediate-scale parts of such a system, and these are described. Based on this experience, we concluded that for the short term, optimal results would be obtained by using a hybrid design including neural, symbolic AI, and artificial life methods. We propose a three-tiered architecture that integrates these different methods, and describe a prototype mini-Roboscout that we implemented and evaluated based on this architecture. We also examined, via computational experiments, the effectiveness of genetic programming as a design tool for recurrent neural networks, and the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for proceeding.}, keywords = {*COMPUTATIONS, *HYBRID SYSTEMS, *NEURAL NETS, *NEUROCOGNITIVE ARCHITECTURE, ADAPTIVE SYSTEMS, Artificial intelligence, BRAIN, Cognition, COMPUTER PROGRAMMING, COMPUTER PROGRAMMING AND SOFTWARE, HYBRID AI, Machine intelligence, MECHANICAL ORGANS, MODULAR CONSTRUCTION, NERVOUS SYSTEM, PE61101E, PLASTIC PROPERTIES, PROCESSING EQUIPMENT, RECURRENT NEURAL NETWORK}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA481261}, author = {Reggia, James A. and Tagamets,M. and Contreras-Vidal,J. and Jacobs, David W. and Weems,S. and Naqvi,W. and Yang,C.} } @conference {12244, title = {Matchmaking and implementation issues for a P2P desktop grid}, booktitle = {Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on}, year = {2008}, month = {2008/04//}, pages = {1 - 5}, abstract = {We present some recent and ongoing work in our decentralized desktop computing grid project. Specifically, we discuss matching jobs with compute nodes in a peer-to-peer grid of heterogeneous platforms, and the implementation of our algorithms in a concrete system.}, keywords = {computing, computing;, computing;peer-to-peer, desktop, grid;decentralized, grid;grid, grid;peer-to-peer, P2P}, doi = {10.1109/IPDPS.2008.4536388}, author = {Marsh,M. and Kim,Jik-Soo and Nam,Beomseok and Jaehwan Lee and Ratanasanya,S. and Bhattacharjee, Bobby and Keleher,P. and Richardson,D. and Wellnitz,D.} } @article {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.} } @conference {15851, title = {Resolving personal names in email using context expansion}, booktitle = {Association for Computational Linguistics (ACL)}, year = {2008}, month = {2008///}, author = {Elsayed,T. and Oard, Douglas and Namata,G.} } @article {16282, title = {Scaffolding and Validation of Bacterial Genome Assemblies Using Optical Restriction Maps}, journal = {Bioinformatics}, volume = {24}, year = {2008}, month = {2008/05/15/}, pages = {1229 - 1235}, abstract = {Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of mate-pair information. In this article we propose methods to overcome such limitations by incorporating information from optical restriction maps.Results: We demonstrate the robustness of our methods to sequencing and assembly errors using extensive experiments on simulated datasets. We then present the results obtained by applying our algorithms to data generated from two bacterial genomes Yersinia aldovae and Yersinia kristensenii. The resulting assemblies contain a single scaffold covering a large fraction of the respective genomes, suggesting that the careful use of optical maps can provide a cost-effective framework for the assembly of genomes. Availability: The tools described here are available as an open-source package at ftp://ftp.cbcb.umd.edu/pub/software/soma Contact: mpop@umiacs.umd.edu }, isbn = {1367-4803, 1460-2059}, doi = {10.1093/bioinformatics/btn102}, url = {http://bioinformatics.oxfordjournals.org/content/24/10/1229}, author = {Nagarajan,Niranjan and Read,Timothy D. and Pop, Mihai} } @article {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} } @conference {18920, title = {Synthesis of strategies from interaction traces}, series = {AAMAS {\textquoteright}08}, year = {2008}, month = {2008///}, pages = {855 - 862}, publisher = {International Foundation for Autonomous Agents and Multiagent Systems}, organization = {International Foundation for Autonomous Agents and Multiagent Systems}, address = {Richland, SC}, abstract = {We describe how to take a set of interaction traces produced by different pairs of players in a two-player repeated game, and combine them into a composite strategy. We provide an algorithm that, in polynomial time, can generate the best such composite strategy. We describe how to incorporate the composite strategy into an existing agent, as an enhancement of the agent{\textquoteright}s original strategy. We provide experimental results using interaction traces from 126 agents (most of them written by students as class projects) for the Iterated Prisoner{\textquoteright}s Dilemma, Iterated Chicken Game, and Iterated Battle of the Sexes. We compared each agent with the enhanced version of that agent produced by our algorithm. The enhancements improved the agents{\textquoteright} scores by about 5\% in the IPD, 11\% in the ICG, and 26\% in the IBS, and improved their rank by about 12\% in the IPD, 38\% in the ICG, and 33\% in the IBS.}, keywords = {agents, interaction, learning, multi-agent systems, prisoner{\textquoteright}s dilemma, repeated games}, isbn = {978-0-9817381-1-6}, url = {http://dl.acm.org/citation.cfm?id=1402298.1402343}, author = {Au,Tsz-Chiu and Kraus,Sarit and Nau, Dana S.} } @article {12243, title = {Trade-offs in matching jobs and balancing load for distributed desktop grids}, journal = {Future Generation Computer Systems}, volume = {24}, year = {2008}, month = {2008/05//}, pages = {415 - 424}, abstract = {Desktop grids~can achieve tremendous computing power at low cost through opportunistic sharing of resources. However, traditional client{\textendash}server Grid architectures do not deal with all types of failures, and do not always cope well with very dynamic environments. This paper describes the design of a desktop grid implemented over a modified Peer-to-Peer (P2P) architecture. The underlying P2P system is decentralized and inherently adaptable, giving the Grid robustness, scalability, and the ability to cope with dynamic environments, while still efficiently mapping application instances to available resources throughout the system.We use simulation to compare three different types of matching algorithms under differing workloads. Overall, the P2P approach produces significantly lower wait times than prior approaches, while adapting efficiently to the dynamic environment. }, keywords = {Desktop grid, load balancing, Matchmaking, peer-to-peer computing, Resource discovery}, isbn = {0167-739X}, doi = {10.1016/j.future.2007.07.007}, url = {http://www.sciencedirect.com/science/article/pii/S0167739X07001240}, author = {Kim,Jik-Soo and Nam,Beomseok and Keleher,Peter and Marsh,Michael and Bhattacharjee, Bobby and Sussman, Alan} } @conference {15271, title = {Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques}, booktitle = {IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM {\textquoteright}08}, year = {2008}, month = {2008/11/03/5}, pages = {223 - 230}, publisher = {IEEE}, organization = {IEEE}, abstract = {The evolutionary histories of viral genomes have received significant recent attention due to their importance in understanding virulence and the corresponding ramifications to public health. We present a novel framework to detect reassortment events in influenza based on the comparison of two distributions of phylogenetic trees, rather than a pair of, possibly unreliable, consensus trees. We show how to detect all high-probability inconsistencies between two distributions of trees by enumerating maximal bicliques within a defined incompatibility graph. In the process, we give the first quadratic delay algorithm for enumerating maximal bicliques within general bipartite graphs. We demonstrate the utility of our approach by applying it to several sets of influenza genomes (both human- and avian-hosted) and successfully identify all known reassortment events and a few novel candidate reassortments. In addition, on simulated datasets, our approach correctly finds implanted reassortments and rarely detects reassortments where none were introduced.}, keywords = {avian hosted influenza genome, Bioinformatics, Capacitive sensors, Delay, diseases, Event detection, general bipartite graphs, genomic reassortments, Genomics, graph theory, high probability inconsistencies, History, human hosted influenza genome, incompatibility graph, Influenza, influenza strain, maximal biclique, maximal biclique enumeration, microorganisms, phylogenetic trees, Phylogeny, Public healthcare, quadratic delay algorithm, reassortment, reassortment event detection, Tree graphs, viral genome evolutionary history, virulence}, isbn = {978-0-7695-3452-7}, doi = {10.1109/BIBM.2008.78}, author = {Nagarajan,N. and Kingsford, Carl} } @article {15706, title = {A Weighted GCV Method for Lanczos Hybrid Regularization}, journal = {Electronic Transactions on Numerical Analysis}, volume = {28}, year = {2008}, month = {2008///}, pages = {149 - 167}, url = {http://etna.mcs.kent.edu/vol.28.2007-2008/pp149-167.dir/pp149-167.pdfhttp://etna.mcs.kent.edu/vol.28.2007-2008/pp149-167.dir/pp149-167.pdf}, author = {Chung,Julianne and Nagy,James G. and O{\textquoteright}Leary, Dianne P.} } @article {12981, title = {Biased data reduce efficiency and effectiveness of conservation reserve networks}, journal = {Ecology Letters}, volume = {10}, year = {2007}, month = {2007/05/01/}, pages = {364 - 374}, abstract = {Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as {\textquoteleft}complete{\textquoteright}, we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1{\textendash}5\% of species, and resulted in reserve networks that were 9{\textendash}17\% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data.}, keywords = {Bias, biodiversity conservation, complementarity, efficiency, marxan, rarity, reserve networks, reserve selection algorithms, species detection}, isbn = {1461-0248}, doi = {10.1111/j.1461-0248.2007.01025.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2007.01025.x/abstract}, author = {Grand,Joanna and Cummings, Michael P. and Rebelo,Tony G and Ricketts,Taylor H and Neel,Maile C} } @conference {13146, title = {Bilattice-based Logical Reasoning for Human Detection}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {The capacity to robustly detect humans in video is a critical component of automated visual surveillance systems. This paper describes a bilattice based logical reasoning approach that exploits contextual information and knowledge about interactions between humans, and augments it with the output of different low level detectors for human detection. Detections from low level parts-based detectors are treated as logical facts and used to reason explicitly about the presence or absence of humans in the scene. Positive and negative information from different sources, as well as uncertainties from detections and logical rules, are integrated within the bilattice framework. This approach also generates proofs or justifications for each hypothesis it proposes. These justifications (or lack thereof) are further employed by the system to explain and validate, or reject potential hypotheses. This allows the system to explicitly reason about complex interactions between humans and handle occlusions. These proofs are also available to the end user as an explanation of why the system thinks a particular hypothesis is actually a human. We employ a boosted cascade of gradient histograms based detector to detect individual body parts. We have applied this framework to analyze the presence of humans in static images from different datasets.}, keywords = {automated, detection;parts-based, detectors;static, histograms;human, images;formal, interactions;gradient, logic;image, logical, mechanisms;surveillance;video, processing;, reasoning;complex, recognition;inference, signal, Surveillance, systems;bilattice-based, visual}, doi = {10.1109/CVPR.2007.383133}, author = {Shet,V. D and Neumann, J. and Ramesh,V. and Davis, Larry S.} } @article {18897, title = {CARA: A Cultural-Reasoning Architecture}, journal = {IEEE Intelligent Systems}, volume = {22}, year = {2007}, month = {2007///}, pages = {12 - 16}, abstract = {The Cognitive Architecture for Reasoning about Adversaries supports methods to gather data about different cultural groups and learn the intensity of those groups{\textquoteright} opinions on various topics. It also lets users build and extract models of those groups{\textquoteright} behavior and continuously refine those models through shared multiperson learning experiences. Researchers have applied the architecture to develop cultural-reasoning applications for example, a game that teaches soldiers about cultural norms in an Afghan village.}, keywords = {cultural reasoning, opinion extraction, opponent modeling}, isbn = {1541-1672}, author = {V.S. Subrahmanian and Albanese,Massimiliano and Martinez,Mar?a Vanina and Nau, Dana S. and Reforgiato,Diego and Simari,Gerardo I. and Sliva,Amy and Udrea,Octavian and Wilkenfeld,Jonathan} } @conference {14388, title = {Combining Collective Classification and Link Prediction}, booktitle = {Data Mining Workshops, 2007. ICDM Workshops 2007. Seventh IEEE International Conference on}, year = {2007}, month = {2007/10//}, pages = {381 - 386}, abstract = {The problems of object classification (labeling the nodes of a graph) and link prediction (predicting the links in a graph) have been largely studied independently. Commonly, object classification is performed assuming a complete set of known links and link prediction is done assuming a fully observed set of node attributes. In most real world domains, however, attributes and links are often missing or incorrect. Object classification is not provided with all the links relevant to correct classification and link prediction is not provided all the labels needed for accurate link prediction. In this paper, we propose an approach that addresses these two problems by interleaving object classification and link prediction in a collective algorithm. We investigate empirically the conditions under which an integrated approach to object classification and link prediction improves performance, and find that performance improves over a wide range of network types, and algorithm settings.}, keywords = {algorithm;link, classification;, classification;graph, collective, prediction;object, theory;pattern}, doi = {10.1109/ICDMW.2007.35}, author = {Bilgic,M. and Namata,G.M. and Getoor, Lise} } @article {18900, title = {Computing most probable worlds of action probabilistic logic programs: scalable estimation for 10^30,000 worlds}, journal = {Annals of Mathematics and Artificial Intelligence}, volume = {51}, year = {2007}, month = {2007///}, pages = {295 - 331}, abstract = {The semantics of probabilistic logic programs (PLPs) is usually given through a possible worlds semantics. We propose a variant of PLPs called action probabilistic logic programs or -programs that use a two-sorted alphabet to describe the conditions under which certain real-world entities take certain actions. In such applications, worlds correspond to sets of actions these entities might take. Thus, there is a need to find the most probable world (MPW) for -programs. In contrast, past work on PLPs has primarily focused on the problem of entailment. This paper quickly presents the syntax and semantics of -programs and then shows a naive algorithm to solve the MPW problem using the linear program formulation commonly used for PLPs. As such linear programs have an exponential number of variables, we present two important new algorithms, called and to solve the MPW problem exactly. Both these algorithms can significantly reduce the number of variables in the linear programs. Subsequently, we present a {\textquotedblleft}binary{\textquotedblright} algorithm that applies a binary search style heuristic in conjunction with the Naive, and algorithms to quickly find worlds that may not be {\textquotedblleft}most probable.{\textquotedblright} We experimentally evaluate these algorithms both for accuracy (how much worse is the solution found by these heuristics in comparison to the exact solution) and for scalability (how long does it take to compute). We show that the results of are very accurate and also very fast: more than 10 30,000 worlds can be handled in a few minutes. Subsequently, we develop parallel versions of these algorithms and show that they provide further speedups.}, keywords = {Computer science}, isbn = {1012-2443}, doi = {10.1007/s10472-008-9089-2}, url = {http://www.springerlink.com/content/t70g873h613273pu/abstract/}, author = {Khuller, Samir and Martinez,M. and Nau, Dana S. and Sliva,Amy and Simari,Gerardo and Subrahmanian,V.} } @conference {18879, title = {Conditionalization: Adapting forward-chaining planners to partially observable environments}, year = {2007}, month = {2007///}, abstract = {We provide a general way to take forward-chainingplanners for classical planning domains and condition- alize them, i.e., adapt them to generate policies for partially observable planning domains. For domain-configurable planners such as SHOP2, TLPlan, and TALplanner, our generalization tech- nique preserves the ability to use domain knowledge to achieve highly efficient planning. We demonstrate this experimentally in two problem domains. The experi- ments compare PKS and MBP (two existing planners for partially observable planning) and CondSHOP2, a version of the HTN planner SHOP2 created by apply- ing our conditionalization method. To our surprise, PKS and MBP could solve only the simplest problems in our test domains. In contrast, CondSHOP2 solved all of the test problems quite eas- ily. This suggests that the ability to use domain knowl- edge may be not just desirable but indeed essential for solving large problems in partially observable domains. }, url = {http://www.cs.umd.edu/~nau/papers/kuter2007conditionalization.pdf}, author = {Kuter,U. and Nau, Dana S. and Reisner,E. and Goldman,R.} } @conference {12252, title = {Creating a Robust Desktop Grid using Peer-to-Peer Services}, booktitle = {Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International}, year = {2007}, month = {2007/03//}, pages = {1 - 7}, abstract = {The goal of the work described in this paper is to design and build a scalable infrastructure for executing grid applications on a widely distributed set of resources. Such grid infrastructure must be decentralized, robust, highly available, and scalable, while efficiently mapping application instances to available resources in the system. However, current desktop grid computing platforms are typically based on a client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. Fortunately, these problems can be addressed through the capabilities promised by new techniques and approaches in peer-to-peer (P2P) systems. By employing P2P services, our system allows users to submit jobs to be run in the system and to run jobs submitted by other users on any resources available in the system, essentially allowing a group of users to form an ad-hoc set of shared resources. The initial target application areas for the desktop grid system are in astronomy and space science simulation and data analysis.}, keywords = {allocation;, architecture;load, balancing;peer-to-peer, client-server, computing;peer-to-peer, computing;resource, desktop, grid;scalable, infrastructure;client-server, system;robust, systems;grid}, doi = {10.1109/IPDPS.2007.370505}, author = {Kim,J.-S. and Nam,B. and Marsh,M. and Keleher,P. and Bhattacharjee, Bobby and Richardson,D. and Wellnitz,D. and Sussman, Alan} } @article {18901, title = {Current Trends in Automated Planning}, journal = {AI Magazine}, volume = {28}, year = {2007}, month = {2007/12/15/}, pages = {43 - 43}, abstract = {Current Trends in Automated Planning}, isbn = {0738-4602}, doi = {10.1609/aimag.v28i4.2067}, url = {http://www.aaai.org/ojs/index.php/aimagazine/article/view/2067}, author = {Nau, Dana S.} } @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 {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} } @conference {14477, title = {A dual-view approach to interactive network visualization}, booktitle = {Proceedings of the sixteenth ACM conference on Conference on information and knowledge management}, series = {CIKM {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {939 - 942}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Visualizing network data, from tree structures to arbitrarily connected graphs, is a difficult problem in information visualization. A large part of the problem is that in network data, users not only have to visualize the attributes specific to each data item, but also the links specifying how those items are connected to each other. Past approaches to resolving these difficulties focus on zooming, clustering, filtering and applying various methods of laying out nodes and edges. Such approaches, however, focus only on optimizing a network visualization in a single view, limiting the amount of information that can be shown and explored in parallel. Moreover, past approaches do not allow users to cross reference different subsets or aspects of large, complex networks. In this paper, we propose an approach to these limitations using multiple coordinated views of a given network. To illustrate our approach, we implement a tool called DualNet and evaluate the tool with a case study using an email communication network. We show how using multiple coordinated views improves navigation and provides insight into large networks with multiple node and link properties and types.}, keywords = {coordinated views, Information Visualization, interactive graph visualization, social networks}, isbn = {978-1-59593-803-9}, doi = {10.1145/1321440.1321580}, url = {http://doi.acm.org/10.1145/1321440.1321580}, author = {Namata,Galileo Mark and Staats,Brian and Getoor, Lise and Shneiderman, Ben} } @inbook {19491, title = {Ecotopia: An Ecological Framework for Change Management in Distributed Systems}, booktitle = {Architecting Dependable Systems IV}, series = {Lecture Notes in Computer Science}, year = {2007}, month = {2007/01/01/}, pages = {262 - 286}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Dynamic change management in an autonomic, service-oriented infrastructure is likely to disrupt the critical services delivered by the infrastructure. Furthermore, change management must accommodate complex real-world systems, where dependability and performance objectives are managed across multiple distributed service components and have specific criticality/value models. In this paper, we present Ecotopia, a framework for change management in complex service-oriented architectures (SOA) that is ecological in its intent: it schedules change operations with the goal of minimizing the service-delivery disruptions by accounting for their impact on the SOA environment. The change-planning functionality of Ecotopia is split between multiple objective-advisors and a system-level change-orchestrator component. The objective advisors assess the change-impact on service delivery by estimating the expected values of the Key Performance Indicators (KPIs), during and after change. The orchestrator uses the KPI estimations to assess the per-objective and overall business-value changes over a long time-horizon and to identify the scheduling plan that maximizes the overall business value. Ecotopia handles both external change requests, like software upgrades, and internal changes requests, like fault-recovery actions. We evaluate the Ecotopia framework using two realistic change-management scenarios in distributed enterprise systems.}, keywords = {Autonomic Computing, Dynamic Change Management, Fault-Tolerant Architecture, Operating systems, Performability, Service Orchestration, software engineering}, isbn = {978-3-540-74033-9, 978-3-540-74035-3}, url = {http://link.springer.com/chapter/10.1007/978-3-540-74035-3_12}, author = {Tudor Dumitras and Ro{\c s}u, Daniela and Dan, Asit and Narasimhan, Priya}, editor = {Lemos, Rog{\'e}rio de and Gacek, Cristina and Romanovsky, Alexander} } @article {12118, title = {An Environment of Conducting Families of Software Engineering Experiments}, year = {2007}, month = {2007/05//}, institution = {University of Maryland, College Park}, abstract = {The classroom is a valuable resource for conducting software engineering experiments. However, coordinating a family of experiments in classroom environments presents a number of challenges to researchers. This paper describes an environment that simplifies the process of collecting, managing and sanitizing data from classroom experiments, while minimizing disruption to natural subject behavior. We have successfully used this environment to study the impact of parallel programming languages on programmer productivity at multiple universities across the United States.}, keywords = {collecting data, managing data, parallel programming languages, sanitizing data, software engineering experiments, universities}, url = {http://drum.lib.umd.edu/handle/1903/7545}, author = {Hochstein, Lorin and Nakamura,Taiga and Shull, Forrest and Zazworka, Nico and Voelp,Martin and Zelkowitz, Marvin V and Basili, Victor R.} } @article {16261, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007/11/08/}, pages = {203 - 218}, abstract = {Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.}, isbn = {0028-0836}, doi = {10.1038/nature06341}, url = {http://www.nature.com/nature/journal/v450/n7167/full/nature06341.html}, author = {Clark,Andrew G. and Eisen,Michael B. and Smith,Douglas R. and Bergman,Casey M. and Oliver,Brian and Markow,Therese A. and Kaufman,Thomas C. and Kellis,Manolis and Gelbart,William and Iyer,Venky N. and Pollard,Daniel A. and Sackton,Timothy B. and Larracuente,Amanda M. and Singh,Nadia D. and Abad,Jose P. and Abt,Dawn N. and Adryan,Boris and Aguade,Montserrat and Akashi,Hiroshi and Anderson,Wyatt W. and Aquadro,Charles F. and Ardell,David H. and Arguello,Roman and Artieri,Carlo G. and Barbash,Daniel A. and Barker,Daniel and Barsanti,Paolo and Batterham,Phil and Batzoglou,Serafim and Begun,Dave and Bhutkar,Arjun and Blanco,Enrico and Bosak,Stephanie A. and Bradley,Robert K. and Brand,Adrianne D. and Brent,Michael R. and Brooks,Angela N. and Brown,Randall H. and Butlin,Roger K. and Caggese,Corrado and Calvi,Brian R. and Carvalho,A. Bernardo de and Caspi,Anat and Castrezana,Sergio and Celniker,Susan E. and Chang,Jean L. and Chapple,Charles and Chatterji,Sourav and Chinwalla,Asif and Civetta,Alberto and Clifton,Sandra W. and Comeron,Josep M. and Costello,James C. and Coyne,Jerry A. and Daub,Jennifer and David,Robert G. and Delcher,Arthur L. and Delehaunty,Kim and Do,Chuong B. and Ebling,Heather and Edwards,Kevin and Eickbush,Thomas and Evans,Jay D. and Filipski,Alan and Findei|[szlig]|,Sven and Freyhult,Eva and Fulton,Lucinda and Fulton,Robert and Garcia,Ana C. L. and Gardiner,Anastasia and Garfield,David A. and Garvin,Barry E. and Gibson,Greg and Gilbert,Don and Gnerre,Sante and Godfrey,Jennifer and Good,Robert and Gotea,Valer and Gravely,Brenton and Greenberg,Anthony J. and Griffiths-Jones,Sam and Gross,Samuel and Guigo,Roderic and Gustafson,Erik A. and Haerty,Wilfried and Hahn,Matthew W. and Halligan,Daniel L. and Halpern,Aaron L. and Halter,Gillian M. and Han,Mira V. and Heger,Andreas and Hillier,LaDeana and Hinrichs,Angie S. and Holmes,Ian and Hoskins,Roger A. and Hubisz,Melissa J. and Hultmark,Dan and Huntley,Melanie A. and Jaffe,David B. and Jagadeeshan,Santosh and Jeck,William R. and Johnson,Justin and Jones,Corbin D. and Jordan,William C. and Karpen,Gary H. and Kataoka,Eiko and Keightley,Peter D. and Kheradpour,Pouya and Kirkness,Ewen F. and Koerich,Leonardo B. and Kristiansen,Karsten and Kudrna,Dave and Kulathinal,Rob J. and Kumar,Sudhir and Kwok,Roberta and Lander,Eric and Langley,Charles H. and Lapoint,Richard and Lazzaro,Brian P. and Lee,So-Jeong and Levesque,Lisa and Li,Ruiqiang and Lin,Chiao-Feng and Lin,Michael F. and Lindblad-Toh,Kerstin and Llopart,Ana and Long,Manyuan and Low,Lloyd and Lozovsky,Elena and Lu,Jian and Luo,Meizhong and Machado,Carlos A. and Makalowski,Wojciech and Marzo,Mar and Matsuda,Muneo and Matzkin,Luciano and McAllister,Bryant and McBride,Carolyn S. and McKernan,Brendan and McKernan,Kevin and Mendez-Lago,Maria and Minx,Patrick and Mollenhauer,Michael U. and Montooth,Kristi and Mount, Stephen M. and Mu,Xu and Myers,Eugene and Negre,Barbara and Newfeld,Stuart and Nielsen,Rasmus and Noor,Mohamed A. F. and O{\textquoteright}Grady,Patrick and Pachter,Lior and Papaceit,Montserrat and Parisi,Matthew J. and Parisi,Michael and Parts,Leopold and Pedersen,Jakob S. and Pesole,Graziano and Phillippy,Adam M and Ponting,Chris P. and Pop, Mihai and Porcelli,Damiano and Powell,Jeffrey R. and Prohaska,Sonja and Pruitt,Kim and Puig,Marta and Quesneville,Hadi and Ram,Kristipati Ravi and Rand,David and Rasmussen,Matthew D. and Reed,Laura K. and Reenan,Robert and Reily,Amy and Remington,Karin A. and Rieger,Tania T. and Ritchie,Michael G. and Robin,Charles and Rogers,Yu-Hui and Rohde,Claudia and Rozas,Julio and Rubenfield,Marc J. and Ruiz,Alfredo and Russo,Susan and Salzberg,Steven L. and Sanchez-Gracia,Alejandro and Saranga,David J. and Sato,Hajime and Schaeffer,Stephen W. and Schatz,Michael C and Schlenke,Todd and Schwartz,Russell and Segarra,Carmen and Singh,Rama S. and Sirot,Laura and Sirota,Marina and Sisneros,Nicholas B. and Smith,Chris D. and Smith,Temple F. and Spieth,John and Stage,Deborah E. and Stark,Alexander and Stephan,Wolfgang and Strausberg,Robert L. and Strempel,Sebastian and Sturgill,David and Sutton,Granger and Sutton,Granger G. and Tao,Wei and Teichmann,Sarah and Tobari,Yoshiko N. and Tomimura,Yoshihiko and Tsolas,Jason M. and Valente,Vera L. S. and Venter,Eli and Venter,J. Craig and Vicario,Saverio and Vieira,Filipe G. and Vilella,Albert J. and Villasante,Alfredo and Walenz,Brian and Wang,Jun and Wasserman,Marvin and Watts,Thomas and Wilson,Derek and Wilson,Richard K. and Wing,Rod A. and Wolfner,Mariana F. and Wong,Alex and Wong,Gane Ka-Shu and Wu,Chung-I and Wu,Gabriel and Yamamoto,Daisuke and Yang,Hsiao-Pei and Yang,Shiaw-Pyng and Yorke,James A. and Yoshida,Kiyohito and Zdobnov,Evgeny and Zhang,Peili and Zhang,Yu and Zimin,Aleksey V. and Baldwin,Jennifer and Abdouelleil,Amr and Abdulkadir,Jamal and Abebe,Adal and Abera,Brikti and Abreu,Justin and Acer,St Christophe and Aftuck,Lynne and Alexander,Allen and An,Peter and Anderson,Erica and Anderson,Scott and Arachi,Harindra and Azer,Marc and Bachantsang,Pasang and Barry,Andrew and Bayul,Tashi and Berlin,Aaron and Bessette,Daniel and Bloom,Toby and Blye,Jason and Boguslavskiy,Leonid and Bonnet,Claude and Boukhgalter,Boris and Bourzgui,Imane and Brown,Adam and Cahill,Patrick and Channer,Sheridon and Cheshatsang,Yama and Chuda,Lisa and Citroen,Mieke and Collymore,Alville and Cooke,Patrick and Costello,Maura and D{\textquoteright}Aco,Katie and Daza,Riza and Haan,Georgius De and DeGray,Stuart and DeMaso,Christina and Dhargay,Norbu and Dooley,Kimberly and Dooley,Erin and Doricent,Missole and Dorje,Passang and Dorjee,Kunsang and Dupes,Alan and Elong,Richard and Falk,Jill and Farina,Abderrahim and Faro,Susan and Ferguson,Diallo and Fisher,Sheila and Foley,Chelsea D. and Franke,Alicia and Friedrich,Dennis and Gadbois,Loryn and Gearin,Gary and Gearin,Christina R. and Giannoukos,Georgia and Goode,Tina and Graham,Joseph and Grandbois,Edward and Grewal,Sharleen and Gyaltsen,Kunsang and Hafez,Nabil and Hagos,Birhane and Hall,Jennifer and Henson,Charlotte and Hollinger,Andrew and Honan,Tracey and Huard,Monika D. and Hughes,Leanne and Hurhula,Brian and Husby,M Erii and Kamat,Asha and Kanga,Ben and Kashin,Seva and Khazanovich,Dmitry and Kisner,Peter and Lance,Krista and Lara,Marcia and Lee,William and Lennon,Niall and Letendre,Frances and LeVine,Rosie and Lipovsky,Alex and Liu,Xiaohong and Liu,Jinlei and Liu,Shangtao and Lokyitsang,Tashi and Lokyitsang,Yeshi and Lubonja,Rakela and Lui,Annie and MacDonald,Pen and Magnisalis,Vasilia and Maru,Kebede and Matthews,Charles and McCusker,William and McDonough,Susan and Mehta,Teena and Meldrim,James and Meneus,Louis and Mihai,Oana and Mihalev,Atanas and Mihova,Tanya and Mittelman,Rachel and Mlenga,Valentine and Montmayeur,Anna and Mulrain,Leonidas and Navidi,Adam and Naylor,Jerome and Negash,Tamrat and Nguyen,Thu and Nguyen,Nga and Nicol,Robert and Norbu,Choe and Norbu,Nyima and Novod,Nathaniel and O{\textquoteright}Neill,Barry and Osman,Sahal and Markiewicz,Eva and Oyono,Otero L. and Patti,Christopher and Phunkhang,Pema and Pierre,Fritz and Priest,Margaret and Raghuraman,Sujaa and Rege,Filip and Reyes,Rebecca and Rise,Cecil and Rogov,Peter and Ross,Keenan and Ryan,Elizabeth and Settipalli,Sampath and Shea,Terry and Sherpa,Ngawang and Shi,Lu and Shih,Diana and Sparrow,Todd and Spaulding,Jessica and Stalker,John and Stange-Thomann,Nicole and Stavropoulos,Sharon and Stone,Catherine and Strader,Christopher and Tesfaye,Senait and Thomson,Talene and Thoulutsang,Yama and Thoulutsang,Dawa and Topham,Kerri and Topping,Ira and Tsamla,Tsamla and Vassiliev,Helen and Vo,Andy and Wangchuk,Tsering and Wangdi,Tsering and Weiand,Michael and Wilkinson,Jane and Wilson,Adam and Yadav,Shailendra and Young,Geneva and Yu,Qing and Zembek,Lisa and Zhong,Danni and Zimmer,Andrew and Zwirko,Zac and Jaffe,David B. and Alvarez,Pablo and Brockman,Will and Butler,Jonathan and Chin,CheeWhye and Gnerre,Sante and Grabherr,Manfred and Kleber,Michael and Mauceli,Evan and MacCallum,Iain} } @article {15606, title = {A fast implementation of the ISODATA clustering algorithm}, journal = {International Journal of Computational Geometry and Applications}, volume = {17}, year = {2007}, month = {2007///}, pages = {71 - 103}, abstract = {Clustering is central to many image processing and remote sensing applications. isodatais one of the most popular and widely used clustering methods in geoscience applications, but it can run slowly, particularly with large data sets. We present a more efficient approach to isodata clustering, which achieves better running times by storing the points in a kd-tree and through a modification of the way in which the algorithm estimates the dispersion of each cluster. We also present an approximate version of the algorithm which allows the user to further improve the running time, at the expense of lower fidelity in computing the nearest cluster center to each point. We provide both theoretical and empirical justification that our modified approach produces clusterings that are very similar to those produced by the standard isodata approach. We also provide empirical studies on both synthetic data and remotely sensed Landsat and MODIS images that show that our approach has significantly lower running times. }, author = {Memarsadeghi,N. and Mount, Dave and Netanyahu,N. S and Le Moigne,J. and de Berg,M.} } @inbook {18904, title = {Finding Most Probable Worlds of Probabilistic Logic Programs}, booktitle = {Scalable Uncertainty Management}, series = {Lecture Notes in Computer Science}, volume = {4772}, year = {2007}, month = {2007///}, pages = {45 - 59}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Probabilistic logic programs have primarily studied the problem of entailment of probabilistic atoms. However, there are some interesting applications where we are interested in finding a possible world that is most probable. Our first result shows that the problem of computing such {\textquotedblright}maximally probable worlds{\textquotedblright} (MPW) is intractable. We subsequently show that we can often greatly reduce the size of the linear program used in past work (by Ng and Subrahmanian) and yet solve the problem exactly. However, the intractability results still make computational efficiency quite impossible. We therefore also develop several heuristics to solve the MPW problem and report extensive experimental results on the accuracy and efficiency of such heuristics.}, keywords = {Computer science}, isbn = {978-3-540-75407-7}, url = {http://www.springerlink.com/content/e4463p4rv4k01u93/abstract/}, author = {Khuller, Samir and Martinez,Vanina and Nau, Dana S. and Simari,Gerardo and Sliva,Amy and Subrahmanian,V.}, editor = {Prade,Henri and Subrahmanian,V.} } @article {15255, title = {Finding most probable worlds of probabilistic logic programs}, journal = {Scalable Uncertainty Management}, year = {2007}, month = {2007///}, pages = {45 - 59}, abstract = {Probabilistic logic programs have primarily studied the problem of entailment of probabilistic atoms. However, there are some interesting applications where we are interested in finding a possible world that is most probable. Our first result shows that the problem of computing such {\textquotedblright}maximally probable worlds{\textquotedblright} (MPW) is intractable. We subsequently show that we can often greatly reduce the size of the linear program used in past work (by Ng and Subrahmanian) and yet solve the problem exactly. However, the intractability results still make computational efficiency quite impossible. We therefore also develop several heuristics to solve the MPW problem and report extensive experimental results on the accuracy and efficiency of such heuristics.}, doi = {10.1007/978-3-540-75410-7_4}, author = {Khuller, Samir and Martinez,V. and Nau, Dana S. and Simari,G. and Sliva,A. and Subrahmanian,V.} } @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 {19495, title = {Got Predictability?: Experiences with Fault-tolerant Middleware}, booktitle = {MC{\textquoteright}07 Proceedings of the 2007 ACM/IFIP/USENIX International Conference on Middleware Companion}, series = {MC {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {20:1 - 20:22}, publisher = {ACM}, organization = {ACM}, abstract = {Unpredictability in COTS-based systems often manifests as occasional instances of uncontrollably-high response times. A particular category of COTS systems, fault-tolerant (FT) middleware, is used in critical enterprise and embedded applications where predictability is of paramount importance. Our prior empirical study, which used a client-server microbenchmark, suggested that hard bounds for the maximum latency are hard to establish a priori, but that the unpredictability may be confined to less than 1\% of the requests. In this paper, we present empirical data, from 7 different three-tier, FT-middleware applications, that shows strong evidence supporting this "magical 1\%" hypothesis. We conducted a controlled experiment with 7 teams of students from a graduate-level course at Carnegie Mellon University. Each team, starting from a common three-tier architecture, independently implemented and evaluated an original application using middleware (either CORBA or EJB) and a custom-implemented fault-tolerance mechanism (relying on either state-machine or primary-backup replication) for the middle-tier server. This experiment shows that unpredictability may not be avoidable, even in the absence of faults, and that, in some cases, the random latency outliers are larger than the time needed to recover from a fault. The data also reveals a statistically-significant result that, across all 7 applications, unpredictability is confined to the highest 1\% of the recorded end-to-end latencies and is not correlated with the request rate, the size of messages exchanged or the number of clients. This suggests that strict predictability is hard to achieve in FT-middleware systems and that developers of critical FT applications should focus on guaranteeing bounds for statistical measures, such as the 99th percentile of the latency.}, isbn = {978-1-59593-935-7}, url = {http://doi.acm.org/10.1145/1377943.1377957}, author = {Tudor Dumitras and Narasimhan, Priya} } @conference {13348, title = {A graph-based approach to vehicle tracking in traffic camera video streams}, booktitle = {Proceedings of the 4th workshop on Data management for sensor networks: in conjunction with 33rd International Conference on Very Large Data Bases}, series = {DMSN {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {19 - 24}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Vehicle tracking has a wide variety of applications from law enforcement to traffic planning and public safety. However, the image resolution of the videos available from most traffic camera systems, make it difficult to track vehicles based on unique identifiers like license plates. In many cases, vehicles with similar attributes are indistinguishable from one another due to image quality issues. Often, network bandwidth and power constraints limit the frame rate, as well. In this paper, we discuss the challenges of performing vehicle tracking queries over video streams from ubiquitous traffic cameras. We identify the limitations of tracking vehicles individually in such conditions and provide a novel graph-based approach using the identity of neighboring vehicles to improve the performance. We evaluate our approach using streaming video feeds from live traffic cameras available on the Internet. The results show that vehicle tracking is feasible, even for low quality and low frame rate traffic cameras. Additionally, exploitation of the attributes of neighboring vehicles significantly improves the performance.}, isbn = {978-159593-911-1}, doi = {10.1145/1286380.1286386}, url = {http://doi.acm.org/10.1145/1286380.1286386}, author = {Shahri,Hamid Haidarian and Namata,Galileo and Navlakha,Saket and Deshpande, Amol and Roussopoulos, Nick} } @article {14491, title = {Inferring organizational titles in online communication}, journal = {Statistical Network Analysis: Models, Issues, and New Directions}, year = {2007}, month = {2007///}, pages = {179 - 181}, abstract = {There is increasing interest in the storage, retrieval, and analysis of email communications. One active area of research focuses on the inference of properties of the underlying social network giving rise to the email communications[1,2]. Email communication between individuals implies some type of relationship, whether it is formal, such as a manager-employee relationship, or informal, such as friendship relationships. Understanding the nature of these observed relationships can be problematic given there is a shared context among the individuals that isn{\textquoteright}t necessarily communicated. This provides a challenge for analysts that wish to explore and understand email archives for legal or historical research.}, doi = {10.1007/978-3-540-73133-7_15}, author = {Namata,G. and Getoor, Lise and Diehl,C.} } @conference {13991, title = {Microphone Arrays as Generalized Cameras for Integrated Audio Visual Processing}, booktitle = {Computer Vision and Pattern Recognition, 2007. CVPR {\textquoteright}07. IEEE Conference on}, year = {2007}, month = {2007/06//}, pages = {1 - 8}, abstract = {Combinations of microphones and cameras allow the joint audio visual sensing of a scene. Such arrangements of sensors are common in biological organisms and in applications such as meeting recording and surveillance where both modalities are necessary to provide scene understanding. Microphone arrays provide geometrical information on the source location, and allow the sound sources in the scene to be separated and the noise suppressed, while cameras allow the scene geometry and the location and motion of people and other objects to be estimated. In most previous work the fusion of the audio-visual information occurs at a relatively late stage. In contrast, we take the viewpoint that both cameras and microphone arrays are geometry sensors, and treat the microphone arrays as generalized cameras. We employ computer-vision inspired algorithms to treat the combined system of arrays and cameras. In particular, we consider the geometry introduced by a general microphone array and spherical microphone arrays. The latter show a geometry that is very close to central projection cameras, and we show how standard vision based calibration algorithms can be profitably applied to them. Experiments are presented that demonstrate the usefulness of the considered approach.}, keywords = {algorithms;generalized, arrays;scene, arrays;sensor, audio, audio-visual, cameras;geometrical, fusion;, fusion;computer-vision, geometry;sound, information, information;geometry, inspired, location;acoustic, processing;array, processing;audio-visual, processing;microphone, sensors;integrated, signal, sources;source, systems;cameras;computer, vision;geometry;microphone, visual}, doi = {10.1109/CVPR.2007.383345}, author = {O{\textquoteright}Donovan,A. and Duraiswami, Ramani and Neumann, J.} } @article {14711, title = {Mutatis Mutandis: Safe and predictable dynamic software updating}, journal = {ACM Trans. Program. Lang. Syst.}, volume = {29}, year = {2007}, month = {2007/08//}, abstract = {This article presents Proteus, a core calculus that models dynamic software updating, a service for fixing bugs and adding features to a running program. Proteus permits a program{\textquoteright}s type structure to change dynamically but guarantees the updated program remains type-correct by ensuring a property we call con-freeness. We show how con-freeness can be enforced dynamically, and how it can be approximated via a novel static analysis. This analysis can be used to assess the implications of a program{\textquoteright}s structure on future updates in order to make update success more predictable. We have implemented Proteus for C, and briefly discuss our implementation which we have tested on several well-known programs.}, keywords = {capability, dynamic software updating, proteus, Type inference, updateability analysis}, isbn = {0164-0925}, doi = {10.1145/1255450.1255455}, url = {http://doi.acm.org/10.1145/1255450.1255455}, author = {Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Sewell,Peter and Neamtiu,Iulian} } @article {14919, title = {Object recognition using linear subspaces}, volume = {EP20010117763}, year = {2007}, month = {2007/01/17/}, abstract = {Abstract of EP1204069A method for choosing an image from a plurality of three-dimensional models which is most similar to an input image is provided. The method includes the steps of: (a) providing a database of the plurality of three-dimensional models; (b) providing an input image; (c) positioning each three-dimensional model relative to the input image; (d) for each three-dimensional model, determining a rendered image that is most similar to the input image by: (d)(i) computing a linear subspace that describes an approximation to the set of all possible rendered images that each three-dimensional model can produce under all possible lighting conditions where each point in the linear subspace represents a possible image; and one of(d)(ii) finding the point on the linear subspace that is closest to the input image or finding a rendered image in a subset of the linear subspace obtained by projecting the set of images that are generated by positive lights onto the linear subspace; (e) computing a measure of similarly between the input image and each rendered image; and (f) selecting the three-dimensional model corresponding to the rendered image whose measure of similarity is most similar to the input image. Step (d) is preferably repeated for each of a red, green, and blue color component for each three-dimensional model. The linear subspace is preferably either four-dimensional or nine-dimensional.}, url = {http://www.freepatentsonline.com/EP1204069.html}, author = {Jacobs, David W. and Basri,Ronen The Weizmann Institute}, editor = {NEC Laboratories America, Inc. (4 Independence Way, Princeton, New Jersey 08540, US)} } @article {15572, title = {A practical approximation algorithm for the LMS line estimator}, journal = {Computational Statistics \& Data Analysis}, volume = {51}, year = {2007}, month = {2007/02/01/}, pages = {2461 - 2486}, abstract = {The problem of fitting a straight line to a finite collection of points in the plane is an important problem in statistical estimation. Robust estimators are widely used because of their lack of sensitivity to outlying data points. The least median-of-squares (LMS) regression line estimator is among the best known robust estimators. Given a set of n points in the plane, it is defined to be the line that minimizes the median squared residual or, more generally, the line that minimizes the residual of any given quantile q, where 0 \< q ⩽ 1 . This problem is equivalent to finding the strip defined by two parallel lines of minimum vertical separation that encloses at least half of the points.The best known exact algorithm for this problem runs in O ( n 2 ) time. We consider two types of approximations, a residual approximation, which approximates the vertical height of the strip to within a given error bound ε r ⩾ 0 , and a quantile approximation, which approximates the fraction of points that lie within the strip to within a given error bound ε q ⩾ 0 . We present two randomized approximation algorithms for the LMS line estimator. The first is a conceptually simple quantile approximation algorithm, which given fixed q and ε q \> 0 runs in O ( n log n ) time. The second is a practical algorithm, which can solve both types of approximation problems or be used as an exact algorithm. We prove that when used as a quantile approximation, this algorithm{\textquoteright}s expected running time is O ( n log 2 n ) . We present empirical evidence that the latter algorithm is quite efficient for a wide variety of input distributions, even when used as an exact algorithm. }, keywords = {Approximation algorithms, least median-of-squares regression, line arrangements, line fitting, randomized algorithms, robust estimation}, isbn = {0167-9473}, doi = {10.1016/j.csda.2006.08.033}, url = {http://www.sciencedirect.com/science/article/pii/S0167947306002921}, author = {Mount, Dave and Netanyahu,Nathan S. and Romanik,Kathleen and Silverman,Ruth and Wu,Angela Y.} } @article {12795, title = {Priority and abstraction in process algebra}, journal = {Information and Computation}, volume = {205}, year = {2007}, month = {2007/09//}, pages = {1426 - 1458}, abstract = {More than 15 years ago, Cleaveland and Hennessy proposed an extension of the process algebra CCS in which some actions may take priority over others. The theory was equipped with a behavioral congruence based on strong bisimulation.This article gives a full account of the challenges in, and the solutions employed for, defining a semantic theory of observation congruence for this process algebra. A full-abstraction result is presented whose proof relies on a novel approach based on successive approximations for identifying the largest congruence contained in an intuitive but na{\~A}{\textasciimacron}ve equivalence. Prioritized observation congruence is also characterized equationally for the class of finite processes, while its utility for system verification is demonstrated by an illustrative example. }, keywords = {Axiomatization, Bisimulation, Full abstraction, Observation congruence, Priority, Process algebra}, isbn = {0890-5401}, doi = {10.1016/j.ic.2007.05.001}, url = {http://www.sciencedirect.com/science/article/pii/S0890540107000624}, author = {Cleaveland, Rance and L{\~A}{\textonequarter}ttgen,Gerald and Natarajan,V.} } @conference {18886, title = {Probabilistic go theories}, year = {2007}, month = {2007///}, abstract = {There are numerous cases where we need to rea- son about vehicles whose intentions and itineraries are not known in advance to us. For example, Coast Guard agents tracking boats don{\textquoteright}t always know where they are headed. Likewise, in drug en- forcement applications, it is not always clear where drug-carrying airplanes (which do often show up on radar) are headed, and how legitimate planes with an approved flight manifest can avoid them. Likewise, traffic planners may want to understand how many vehicles will be on a given road at a given time. Past work on reasoning about vehi- cles (such as the {\textquotedblleft}logic of motion{\textquotedblright} by Yaman et. al. [Yaman et al., 2004]) only deals with vehicles whose plans are known in advance and don{\textquoteright}t cap- ture such situations. In this paper, we develop a for- mal probabilistic extension of their work and show that it captures both vehicles whose itineraries are known, and those whose itineraries are not known. We show how to correctly answer certain queries against a set of statements about such vehicles. A prototype implementation shows our system to work efficiently in practice.}, url = {http://www.aaai.org/Papers/IJCAI/2007/IJCAI07-079.pdf}, author = {Parker,A. and Yaman,F. and Nau, Dana S. and V.S. Subrahmanian} } @inbook {17646, title = {Randomized Algorithms and Probabilistic Analysis in Wireless Networking}, booktitle = {Stochastic Algorithms: Foundations and ApplicationsStochastic Algorithms: Foundations and Applications}, series = {Lecture Notes in Computer Science}, volume = {4665}, year = {2007}, month = {2007///}, pages = {54 - 57}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Devices connected wirelessly, in various forms including computers, hand-held devices, ad hoc networks, and embedded systems, are expected to become ubiquitous all around us. Wireless networks pose interesting new challenges, some of which do not arise in standard (wired) networks. This survey discusses some key probabilistic notions {\textendash} both randomized algorithms and probabilistic analysis {\textendash} in wireless networking.}, isbn = {978-3-540-74870-0}, url = {http://dx.doi.org/10.1007/978-3-540-74871-7_5}, author = {Srinivasan, Aravind}, editor = {Hromkovic,Juraj and Kr{\'a}lovic,Richard and Nunkesser,Marc and Widmayer,Peter} } @conference {18919, title = {Reactive Query Policies: A Formalism for Planning with Volatile External Information}, year = {2007}, month = {2007/04/01/5}, pages = {243 - 250}, abstract = {To generate plans for collecting data for data mining, an important problem is information volatility during planning: the information needed by the planning system may change or expire during the planning process, as changes occur in the data being collected. In such situations, the planning system faces two challenges: how to generate plans despite these changes, and how to guarantee that a plan returned by the planner will remain valid for some period of time after the planning ends. The focus of our work is to address both of the above challenges. In particular, we provide: 1) A formalism for reactive query policies, a class of strategies for deciding when to reissue queries for information that has changed during the planning process. This class includes all query management strategies that have yet been developed. 2) A new reactive query policy called the presumptive strategy. In our experiments, the presumptive strategy ran exponentially faster than the lazy strategy, the best previously known query management strategy. In the hardest set of problems we tested, the presumptive strategy took 4.7\% as much time and generated 6.9\% as many queries as the lazy strategy}, keywords = {data collection, data mining, information volatility, planning (artificial intelligence), planning system, presumptive strategy, query management, Query processing, reactive query policies, volatile external information}, doi = {10.1109/CIDM.2007.368880}, author = {Au,Tsz-Chiu and Nau, Dana S.} } @article {14476, title = {Relationship identification for social network discovery}, journal = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {22}, year = {2007}, month = {2007///}, pages = {546 - 546}, abstract = {In recent years, informal, online communication has trans- formed the ways in which we connect and collaborate with friends and colleagues. With millions of individuals commu- nicating online each day, we have a unique opportunity to ob- serve the formation and evolution of roles and relationships in networked groups and organizations. Yet a number of chal- lenges arise when attempting to infer the underlying social network from data that is often ambiguous, incomplete and context-dependent. In this paper, we consider the problem of collaborative network discovery from domains such as intel- ligence analysis and litigation support where the analyst is at- tempting to construct a validated representation of the social network. We specifically address the challenge of relation- ship identification where the objective is to identify relevant communications that substantiate a given social relationship type. We propose a supervised ranking approach to the prob- lem and assess its performance on a manager-subordinate re- lationship identification task using the Enron email corpus. By exploiting message content, the ranker routinely cues the analyst to relevant communications relationships and mes- sage traffic that are indicative of the social relationship.}, author = {Diehl,C. P and Namata,G. and Getoor, Lise} } @article {15476, title = {Reliable Effects Screening: A Distributed Continuous Quality Assurance Process for Monitoring Performance Degradation in Evolving Software Systems}, journal = {Software Engineering, IEEE Transactions on}, volume = {33}, year = {2007}, month = {2007/02//}, pages = {124 - 141}, abstract = {Developers of highly configurable performance-intensive software systems often use in-house performance-oriented "regression testing" to ensure that their modifications do not adversely affect their software{\textquoteright}s performance across its large configuration space. Unfortunately, time and resource constraints can limit in-house testing to a relatively small number of possible configurations, followed by unreliable extrapolation from these results to the entire configuration space. As a result, many performance bottlenecks escape detection until systems are fielded. In our earlier work, we improved the situation outlined above by developing an initial quality assurance process called "main effects screening". This process 1) executes formally designed experiments to identify an appropriate subset of configurations on which to base the performance-oriented regression testing, 2) executes benchmarks on this subset whenever the software changes, and 3) provides tool support for executing these actions on in-the-field and in-house computing resources. Our initial process had several limitations, however, since it was manually configured (which was tedious and error-prone) and relied on strong and untested assumptions for its accuracy (which made its use unacceptably risky in practice). This paper presents a new quality assurance process called "reliable effects screening" that provides three significant improvements to our earlier work. First, it allows developers to economically verify key assumptions during process execution. Second, it integrates several model-driven engineering tools to make process configuration and execution much easier and less error prone. Third, we evaluate this process via several feasibility studies of three large, widely used performance-intensive software frameworks. Our results indicate that reliable effects screening can detect performance degradation in large-scale systems more reliably and with significantly less resources than conventional t- echniques}, keywords = {configuration subset, distributed continuous quality assurance process, evolving software systems, in house testing, main effects screening, performance bottlenecks, performance degradation monitoring, performance intensive software systems, process configuration, process execution, program testing, regression testing, reliable effects screening, software benchmarks, Software performance, software performance evaluation, Software quality, software reliability, tool support}, isbn = {0098-5589}, doi = {10.1109/TSE.2007.20}, author = {Yilmaz,C. and Porter, Adam and Krishna,A. S and Memon, Atif M. and Schmidt,D. C and Gokhale,A.S. and Natarajan,B.} } @article {12255, title = {SAAR: A shared control plane for overlay multicast}, journal = {Proceedings of 4th USENIX Symposium on Networked Systems Design \& Implementation}, year = {2007}, month = {2007///}, pages = {57 - 72}, abstract = {Many cooperative overlay multicast systems of diverse designs have been implemented and deployed. In this paper, we explore a new architecture for overlay multicast: we factor out the control plane into a separate overlay that provides a single primitive: a configurable anycast for peer selection. This separation of control and data overlays has several advantages. Data overlays can be optimized for efficient content delivery, while the control overlay can be optimized for flexible and efficient peer selection. Several data channels can share a control plane for fast switching among content channels, which is particularly important for IPTV. And, the control overlay can be reused in multicast systems with different data plane organizations.We designed and evaluated a decentralized control overlay for endsystem multicast. The overlay proactively aggregates system state and implements a powerful anycast primitive for peer selection. We demonstrate that SAAR{\textquoteright}s efficiency in locating peers reduces channel switching time, improves the quality of content delivery, and reduces overhead, even under dynamic conditions and at scale. An experimental evaluation demonstrates that the system can efficiently support single-tree, multi-tree and block-based multicast systems. }, author = {Nandi,A. and Ganjam,A. and Druschel,P. and Ng,T. S.E and Stoica,I. and Zhang,H. and Bhattacharjee, Bobby} } @conference {12591, title = {Simulation and Analysis of Human Walking Motion}, booktitle = {Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on}, volume = {1}, year = {2007}, month = {2007/04//}, pages = {I-797 -I-800 - I-797 -I-800}, abstract = {Simulation and analysis of human walking motion has applications in surveillance and healthcare. In this paper we discuss an approach for modeling human walking motion using a mechanical model in the form of a kinematic chain consisting of rigid links and revolute joints. Our goal is to discriminate different types of walking motions using information such as joint torque and angle sequences extracted from the model. The angle sequences are initially extracted using 3D geometry. From these angle sequences we extract the torque sequences using a recursive Newton Euler inverse dynamics algorithm. Time series models and dynamic time warping of the torque and angle sequences are used to characterize and discriminate different walking patterns. A forward dynamics algorithm is also presented for synthesizing different walking sequences like limping from a normal walking torque sequence}, keywords = {3D, algorithm;revolute, analysis;image, chain;mechanical, DYNAMICS, Euler, extraction;image, geometry;angle, inverse, joints;rigid, links;surveillance;time, method;feature, model;recursive, models;torque, MOTION, motion;kinematic, Newton, patterns;Newton, problems;time, sequences;dynamic, sequences;inverse, sequences;walking, series, series;time, simulation;torque;, TIME, walking, warp, warping;healthcare;human}, doi = {10.1109/ICASSP.2007.366028}, author = {Nandy, K. and Chellapa, Rama} } @article {15475, title = {Skoll: A Process and Infrastructure for Distributed Continuous Quality Assurance}, journal = {Software Engineering, IEEE Transactions on}, volume = {33}, year = {2007}, month = {2007/08//}, pages = {510 - 525}, abstract = {Software engineers increasingly emphasize agility and flexibility in their designs and development approaches. They increasingly use distributed development teams, rely on component assembly and deployment rather than green field code writing, rapidly evolve the system through incremental development and frequent updating, and use flexible product designs supporting extensive end-user customization. While agility and flexibility have many benefits, they also create an enormous number of potential system configurations built from rapidly changing component implementations. Since today{\textquoteright}s quality assurance (QA) techniques do not scale to handle highly configurable systems, we are developing and validating novel software QA processes and tools that leverage the extensive computing resources of user and developer communities in a distributed, continuous manner to improve software quality significantly. This paper provides several contributions to the study of distributed, continuous QA (DCQA). First, it shows the structure and functionality of Skoll, which is an environment that defines a generic around-the-world, around-the-clock QA process and several sophisticated tools that support this process. Second, it describes several novel QA processes built using the Skoll environment. Third, it presents two studies using Skoll: one involving user testing of the Mozilla browser and another involving continuous build, integration, and testing of the ACE+TAO communication software package. The results of our studies suggest that the Skoll environment can manage and control distributed continuous QA processes more effectively than conventional QA processes. For example, our DCQA processes rapidly identified problems that had taken the ACE+TAO developers much longer to find and several of which they had not found. Moreover, the automatic analysis of QA results provided developers information that enabled them to quickly find the root causes of problems}, keywords = {ACE+TAO communication software package, component assembly, component deployment, distributed continuous quality assurance, distributed development teams, distributed processing, end-user customization, flexible product design, incremental development, object-oriented programming, Skoll, software engineering, Software quality, systems analysis}, isbn = {0098-5589}, doi = {10.1109/TSE.2007.70719}, author = {Porter, Adam and Yilmaz,C. and Memon, Atif M. and Schmidt,D. C and Natarajan,B.} } @article {16078, title = {Special Issue in Honor of Ben Shneiderman{\textquoteright}s 60th Birthday: Reflections on Human-Computer Interaction}, journal = {International Journal of Human-Computer Interaction}, volume = {23}, year = {2007}, month = {2007///}, pages = {195 - 204}, isbn = {1044-7318}, doi = {10.1080/10447310701702766}, url = {http://www.tandfonline.com/doi/abs/10.1080/10447310701702766}, author = {Plaisant, Catherine and North,Chris} } @conference {16449, title = {Using annotations from controlled vocabularies to find meaningful associations}, booktitle = {Proceedings of the 4th international conference on Data integration in the life sciences}, year = {2007}, month = {2007///}, pages = {247 - 263}, author = {Lee,W. J and Raschid, Louiqa and Srinivasan,P. and Shah,N. and Rubin,D. and Noy,N.} } @article {12923, title = {Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission}, journal = {Proceedings of the National Academy of Sciences}, volume = {104}, year = {2007}, month = {2007///}, pages = {17801 - 17801}, abstract = {Vibrio cholerae persists in aquatic environments predominantly in a nonculturable state. In this study coccoid, nonculturable V. cholerae O1 in biofilms maintained for 495 days in Mathbaria, Bangladesh, pond water became culturable upon animal passage. Culturability, biofilm formation, and the wbe, ctxA, and rstR2 genes were monitored by culture, direct fluorescent antibody (DFA), and multiplex PCR. DFA counts were not possible after formation of biofilm. Furthermore, wbe, but not ctxA, were amplifiable, even after incubation for 54 and 68 days at room temperature (≈25{\textdegree}C) and 4{\textdegree}C, respectively, when no growth was detectable. Slower biofilm formation and extended culturability were observed for cultures incubated at 4{\textdegree}C, compared with ≈25{\textdegree}C, suggesting biofilm production to be temperature dependent and linked to loss of culturability. Small colonies appearing after incubation in microcosms for 54 and 68 days at 25{\textdegree}C and 4{\textdegree}C, respectively, were wbe positive and ctxA and rstR2 negative, indicating loss of bacteriophage CTXΦ. The coccoid V. cholerae O1 observed as free cells in microcosms incubated for 495 days could not be cultured, but biofilms in the same microcosms yielded culturable cells. It is concluded that biofilms can act as a reservoir for V. cholerae O1 between epidemics because of its long-term viability in biofilms. In contrast to biofilms produced in Mathbaria pond water, V. cholerae O1 in biofilms present in cholera stools and incubated under identical conditions as the Mathbaria pond water biofilms could not be cultured after 2 months, indicating that those V. cholerae cells freshly discharged into the environment are significantly less robust than cells adapted to environmental conditions.Bangladesh bacteriophage CTXΦ DFA multiplex-PCR ctxA }, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0705599104}, url = {http://www.pnas.org/content/104/45/17801}, author = {Alam,M. and Sultana,M. and Nair,G. B. and Siddique,A. K. and Hasan,N. A. and Sack,R. B. and Sack,D. A. and Ahmed,K. U. and Sadique,A. and Watanabe,H. and Rita R Colwell} } @conference {18880, title = {Accident or intention: That is the question (in the noisy iterated prisoner{\textquoteright}s dilemma)}, year = {2006}, month = {2006///}, pages = {561 - 568}, abstract = {This paper focuses on the Noisy Iterated Prisoner{\textquoteright}sDilemma, a version of the Iterated Prisoner{\textquoteright}s Dilemma (IPD) in which there is a nonzero probability that a {\textquotedblleft}co- operate{\textquotedblright} action will accidentally be changed into a {\textquotedblleft}defect{\textquotedblright} action and vice versa. Tit-For-Tat and other strategies that do quite well in the ordinary (non-noisy) IPD can do quite badly in the Noisy IPD. This paper presents a technique called symbolic noise de- tection, for detecting whether anomalies in player{\textquoteright}s behavior are deliberate or accidental. The key idea is to construct a model of the other agent{\textquoteright}s behavior, and watch for any de- viation from this model. If the other agent{\textquoteright}s next action is inconsistent with this model, the inconsistency can be due either to noise or to a genuine change in their behavior; and we can often distinguish between two cases by waiting to see whether this inconsistency persists in next few moves. We entered several different versions of our strategy in the 2005 Iterated Prisoner{\textquoteright}s Dilemma competition, in Cat- egory 2 (noisy environments). Out of the 165 contestants in this category, our programs consistently ranked among top ten. The best of our programs ranked third, and it was beaten only by two {\textquotedblleft}master-slave strategy{\textquotedblright} programs that each had a large number of {\textquotedblleft}slave{\textquotedblright} programs feeding points to them. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.120.7640\&rep=rep1\&type=pdf}, author = {Au,T. C and Nau, Dana S.} } @inbook {19624, title = {Applications of Parameterized st-Orientations in Graph Drawing Algorithms}, booktitle = {Graph Drawing}, series = {Lecture Notes in Computer Science}, year = {2006}, month = {2006/01/01/}, pages = {355 - 367}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Many graph drawing algorithms use st-numberings (st-orien-tations or bipolar orientations) as a first step. An st-numbering of a biconnected undirected graph defines a directed graph with no cycles, one single source s and one single sink t. As there exist exponentially many st-numberings that correspond to a certain undirected graph G, using different st-numberings in various graph drawing algorithms can result in aesthetically different drawings with different area bounds. In this paper, we present results concerning new algorithms for parameterized st-orientations, their impact on graph drawing algorithms and especially in visibility representations.}, keywords = {Algorithm Analysis and Problem Complexity, Computer Graphics, Data structures, Discrete Mathematics in Computer Science}, isbn = {978-3-540-31425-7, 978-3-540-31667-1}, url = {http://link.springer.com/chapter/10.1007/11618058_32}, author = {Charalampos Papamanthou and Tollis, Ioannis G.}, editor = {Healy, Patrick and Nikolov, Nikola S.} } @article {18874, title = {Automatic web services composition using Shop2}, year = {2006}, month = {2006///}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {Semantic markup of Web services will enable the automation of various kinds of tasks, including discovery, composition, and execution of Web services. We describe how an AI planning system (SHOP2) can be used with DAML-S Web service descriptions to automatically compose Web services.}, url = {http://www.stormingmedia.us/96/9697/A969744.html}, author = {Hendler,J. and Nau, Dana S. and Parsia,B. and Sirin,E. and Wu,D.} } @article {16866, title = {Building and querying a P2P virtual world}, journal = {Geoinformatica}, volume = {10}, year = {2006}, month = {2006///}, pages = {91 - 116}, abstract = {Peer-to-Peer (P2P) systems are known to provide excellent scalability in a networked environment. One peer is introduced to the system by each participant. However current P2P applications can only provide file sharing and other forms of relatively simple data communications, and, in this paper, we demonstrate how this limitation can be bridged by indexing and querying a 3D virtual-world on a dynamic distributed network. We present an algorithm for 3D range queries as well as an algorithm for nearest neighbor queries. We also show how to build such a complex application from the ground level of a P2P routing algorithm.}, doi = {10.1007/s10707-005-4887-8}, author = {Tanin,E. and Harwood,A. and Samet, Hanan and Nayar,D. and Nutanong,S.} } @article {14924, title = {Cast shadows and linear subspaces for object recognition}, volume = {10/085,750}, year = {2006}, month = {2006/02/28/}, abstract = {The present invention is a method of deriving a reflectance function that analytically approximates the light reflected from an object model in terms of the spherical harmonic components of light. The reflectance function depends upon the intensity of light incident at each point on the model, but excludes light originating from below a local horizon, therefore not contributing to the reflectance because of the cast shadows. This reflectance function is used in the process of machine vision, by allowing a machine to optimize the reflectance function and arrive at an optimal rendered image of the object model, relative to an input image. Therefore, the recognition of an image produced under variable lighting conditions is more robust. The reflectance function of the present invention also has applicability in other fields, such as computer graphics.}, url = {http://www.google.com/patents?id=io54AAAAEBAJ}, author = {Thornber,Karvel K and Jacobs, David W.}, editor = {NEC Laboratories America, Inc.} } @conference {18888, title = {Controlled search over compact state representations, in nondeterministic planning domains and beyond}, volume = {21}, year = {2006}, month = {2006///}, pages = {1638 - 1638}, abstract = {Two of the most efficient planners for planning in nondeter- ministic domains are MBP and ND-SHOP2. MBP achieves its efficiency by using Binary Decision Diagrams (BDDs) to represent sets of states that share some common properties, so it can plan for all of these states simultaneously. ND-SHOP2 achieves its efficiency by using HTN task decomposition to focus the search. In some environments, ND-SHOP2 runs exponentially faster than MBP, and in others the reverse is true. In this paper, we discuss the following:{\textbullet} We describe how to combine ND-SHOP2{\textquoteright}s HTNs with MBP{\textquoteright}s BDDs. Our new planning algorithm, YoYo, per- forms task decompositions over classes of states that are represented as BDDs. In our experiments, YoYo easily outperformed both MBP and ND-SHOP2, often by sev- eral orders of magnitude. {\textbullet} HTNsarejustoneofseveraltechniquesthatareoriginally developed for classical planning domains and that can be adapted to work in nondeterministic domains. By combin- ing those techniques with a BDD representation, it should be possible to get great speedups just as we did here. {\textbullet} We discuss how these same ideas can be generalized for use in several other research areas, such as planning with Markov Decision Processes, synthesizing controllers for hybrid systems, and composing Semantic Web Services. }, url = {https://www.aaai.org/Papers/AAAI/2006/AAAI06-269.pdf}, author = {Kuter,U. and Nau, Dana S.} } @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} } @book {15740, title = {Deblurring Images: Matrices, Spectra, and Filtering}, year = {2006}, month = {2006///}, publisher = {SIAM Press}, organization = {SIAM Press}, address = {Philadelphia}, author = {Hansen,Per Christian and Nagy,James G. and O{\textquoteright}Leary, Dianne P.} } @inbook {12925, title = {Detection, Isolation, and Identification of Vibrio cholerae from the Environment}, booktitle = {Current Protocols in MicrobiologyCurrent Protocols in Microbiology}, year = {2006}, month = {2006/09/01/}, pages = {6A.5.1-6A.5.38 - 6A.5.1-6A.5.38}, publisher = {John Wiley \& Sons, Inc.}, organization = {John Wiley \& Sons, Inc.}, keywords = {culturable, DETECTION, Environment, identification, isolation, nonculturable, viable, Vibrio cholerae}, isbn = {9780471729259}, url = {http://onlinelibrary.wiley.com/doi/10.1002/9780471729259.mc06a05s02/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Huq,Anwar and Grim,Christopher and Rita R Colwell and Nair,G. Balakrish} } @article {14920, title = {Development of a Large-Scale Integrated Neurocognitive Architecture - Part 2: Design and Architecture}, volume = {UMIACS-TR-2006-43}, year = {2006}, month = {2006/10//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In Part 1 of this report, we outlined a framework for creating an intelligent agentbased upon modeling the large-scale functionality of the human brain. Building on those results, we begin Part 2 by specifying the behavioral requirements of a large-scale neurocognitive architecture. The core of our long-term approach remains focused on creating a network of neuromorphic regions that provide the mechanisms needed to meet these requirements. However, for the short term of the next few years, it is likely that optimal results will be obtained by using a hybrid design that also includes symbolic methods from AI/cognitive science and control processes from the field of artificial life. We accordingly propose a three-tiered architecture that integrates these different methods, and describe an ongoing computational study of a prototype {\textquoteright}mini-Roboscout{\textquoteright} based on this architecture. We also examine the implications of some non-standard computational methods for developing a neurocognitive agent. This examination included computational experiments assessing the effectiveness of genetic programming as a design tool for recurrent neural networks for sequence processing, and experiments measuring the speed-up obtained for adaptive neural networks when they are executed on a graphical processing unit (GPU) rather than a conventional CPU. We conclude that the implementation of a large-scale neurocognitive architecture is feasible, and outline a roadmap for achieving this goal. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/3957}, author = {Reggia, James A. and Tagamets,M. and Contreras-Vidal,J. and Jacobs, David W. and Weems,S. and Naqvi,W. and Winder,R. and Chabuk,T. and Jung,J. and Yang,C.} } @conference {17877, title = {DiST: fully decentralized indexing for querying distributed multidimensional datasets}, booktitle = {Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International}, year = {2006}, month = {2006/04//}, publisher = {IEEE}, organization = {IEEE}, abstract = {Grid computing and peer-to-peer (P2P) systems are emerging as new paradigms for managing large scale distributed resources across wide area networks. While grid computing focuses on managing heterogeneous resources and relies on centralized managers for resource and data discovery, P2P systems target scalable, decentralized methods for publishing and searching for data. In large distributed systems, a centralized resource manager is a potential performance bottleneck and decentralization can help avoid this bottleneck, as is done in P2P systems. However, the query functionality provided by most existing P2P systems is very rudimentary, and is not directly applicable to grid resource management. In this paper, we propose a fully decentralized multidimensional indexing structure, called DiST, that operates in a fully distributed environment with no centralized control. In DiST, each data server only acquires information about data on other servers from executing and routing queries. We describe the DiST algorithms for maintaining the decentralized network of data servers, including adding and deleting servers, the query routing algorithm, and failure recovery algorithms. We also evaluate the performance of the decentralized scheme against a more structured hierarchical indexing scheme that we have previously shown to perform well in distributed grid environments}, keywords = {Computer network management, distributed multidimensional dataset querying, failure recovery, fault tolerant computing, fully decentralized multidimensional indexing, grid computing, Indexing, large scale distributed resource management, Large-scale systems, Multidimensional systems, Network servers, P2P systems, Peer to peer computing, peer-to-peer computing, peer-to-peer systems, Publishing, Query processing, query routing, resource allocation, Resource management, telecommunication network routing, wide area networks}, isbn = {1-4244-0054-6}, doi = {10.1109/IPDPS.2006.1639280}, author = {Nam,Beomseok and Sussman, Alan} } @inbook {12634, title = {Early Recognition Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {35 - 43}, abstract = {The earliest approaches concerned recognition within small populations, with the volume of data limited largely by the computational resources available then. As illustrated by Fig. 4.1, many sought to derive a human silhouette from an image and, as common in pattern recognition, and then to derive a description which can be associated with the identity of the subject. This gives a {\textquoteleft}statistical{\textquoteright} approach to automatic gait recognition wherein the image sequence is described as a whole, and neither by a model- nor by a motion-based approach, but one which describes the motion content. Given that techniques to separate a moving object from its background have been developed for many years (especially in surveillance) there existed a selection of approaches to derive the silhouette of the moving subject, an example silhouette extraction from the image of Fig. 4.1(a) is shown in Fig. 4.1(b). What was then needed was approaches to process the sequence of silhouettes so as to derive a gait signature {\textemdash} a set of numbers to represent a subject{\textquoteright}s identity. A selection of signatures is shown in Fig. 4.1(c) which are displayed in a 3-dimensional space for visualization purposes only (the signature usually has more dimensions than this). These signatures represent ten of walking subjects with four instances of each subject. In this case the signatures derived from the four instances mostly cluster well, representing a good recognition rate. Accordingly, the target of the early approaches was to process video data of the form of Fig. 4.1(a) to obtain silhouettes of the form of Fig. 4.1(b) so as to derive signatures for recognition performance analysis.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @article {12930, title = {Effect of transport at ambient temperature on detection and isolation of Vibrio cholerae from environmental samples}, journal = {Applied and environmental microbiology}, volume = {72}, year = {2006}, month = {2006///}, pages = {2185 - 2190}, abstract = {It has long been assumed that prolonged holding of environmental samples at the ambient air temperature prior to bacteriological analysis is detrimental to isolation and detection of Vibrio cholerae, the causative agent of pandemic cholera. The present study was aimed at understanding the effect of transporting environmental samples at the ambient air temperature on isolation and enumeration of V. cholerae. For water and plankton samples held at ambient temperatures ranging from 31{\textdegree}C to 35{\textdegree}C for 20 h, the total counts did not increase significantly but the number of culturable V. cholerae increased significantly compared to samples processed within 1 h of collection, as measured by culture, acridine orange direct count, direct fluorescent-antibody-direct viable count (DFA-DVC), and multiplex PCR analyses. For total coliform counts, total bacterial counts, and DFA-DVC counts, the numbers did not increase significantly, but the culturable plate counts for V. cholerae increased significantly after samples were held at the ambient temperature during transport to the laboratory for analysis. An increase in the recovery of V. cholerae O1 and improved detection of V. cholerae O1 rfb and ctxA also occurred when samples were enriched after they were kept for 20 h at the ambient temperature during transport. Improved detection and isolation of toxigenic V. cholerae from freshwater ecosystems can be achieved by holding samples at the ambient temperature, an observation that has significant implications for tracking this pathogen in diverse aquatic environments.}, author = {Alam,M. and Sadique,A. and Bhuiyan,N. A. and Nair,G. B. and Siddique,A. K. and Sack,D. A. and Ahsan,S. and Huq,A. and Sack,R. B. and Rita R Colwell and others} } @article {12135, title = {Experiments to understand HPC time to development}, journal = {CTWatch Quarterly}, year = {2006}, month = {2006///}, abstract = {In order to understand how high performance computing (HPC) programs are developed, a series of experiments, using students in graduate level HPC classes, have been conducted at many universities in the US. In this paper we discuss the general process of conducting those experiments, give some of the early results of those experiments, and describe a web-based process we are developing that will allow us to run additional experiments at other universities and laboratories that will be easier to conduct and generate results that more accurately reflect the process of building HPC programs.}, keywords = {hackystat, HPC, publications-journals}, url = {http://csdl.ics.hawaii.edu/techreports/06-08/06-08.pdf}, author = {Hochstein, Lorin and Nakamura,Taiga and Basili, Victor R. and Asgari, Sima and Zelkowitz, Marvin V and Hollingsworth, Jeffrey K and Shull, Forrest and Carver,Jeffrey and Voelp,Martin and Zazworka, Nico and Johnson,Philip} } @conference {19493, title = {Eye of the Beholder: Phone-Based Text-Recognition for the Visually-Impaired}, booktitle = {2006 10th IEEE International Symposium on Wearable Computers}, year = {2006}, month = {2006///}, pages = {145 - 146}, abstract = {Blind and visually-impaired people cannot access essential information in the form of written text in our environment (e.g., on restaurant menus, street signs, door labels, product names and instructions, expiration dates). In this paper, we present and evaluate a mobile text-recognition system capable of extracting written information from a wide variety of sources and communicating it on-demand to the user. The user needs no additional hardware except an ordinary, Internet- enabled mobile camera-phone - a device that many visually-impaired individuals already own. This approach fills a gap in assistive technologies for the visually- impaired because it makes users aware of textual information not available to them through any other means.}, keywords = {CAMERAS, data mining, handicapped aids, Hardware, Image quality, Internet, Land mobile radio cellular systems, Mobile computing, mobile handsets, mobile text-recognition system, Optical character recognition software, phone-based text-recognition, Product safety, Text recognition, visually-impaired}, author = {Tudor Dumitras and Lee, M. and Quinones, P. and Smailagic, A. and Siewiorek, Dan and Narasimhan, P.} } @inbook {12635, title = {Further Gait Developments}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {135 - 149}, abstract = {Human gait characteristics are best analyzed when presented in its canonical view (side view). The dynamics behind an individual{\textquoteright}s gait, the quasi-periodicity of an individual{\textquoteright}s gait etc. which contribute significantly towards establishing his/her identity are more evident when the canonical view of human gait is presented. Thus, the availability of such a canonical view is crucial to the success of many gait recognition systems. We observe that in surveillance applications a non-canonical view of an individual{\textquoteright}s gait is captured more often and this necessitates developing gait recognition algorithms that are view invariant. When individuals walk at an angle oblique to the camera, the performance of gait recognition systems suffers due to the gradual change in the individual{\textquoteright}s height and stride length as captured by the camera.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @inbook {12631, title = {Future Challenges}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {151 - 170}, abstract = {Although a large number of gait recognition algorithms have been reported, it should be noted that gait recognition is still in its infancy. This is because previous work was mainly implemented under some simplified and controlled conditions, e.g., no occlusion during human walking, relatively plain background, the lack of view generality except [142, 103, 102], etc (see Table 8.1). Although reporting good recognition performance, most existing algorithms were usually evaluated on a small and non-realistic database. Further, recognition rates have not yet far reached a possible upper bound even under the above two conditions.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @inbook {12632, title = {Gait Databases}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {17 - 34}, abstract = {Naturally, the success and evolution of a new application relies largely on the dataset used for evaluation. The early gait databases were collected about 10 years before the time of writing. Then, computers had little power and memory costs were comparatively high. Clearly, this was before digital video and acquisition was based on analogue camcorder technology which resulted in frames being digitized individually. Since techniques were in their infancy, as in face recognition, early databases only had few subjects. The idea then was to determine whether recognition could be achieved at all {\textemdash} or not. At that stage we were not interested in the ramifications of recognition. There were two early databases which were developed independently: the UCSD data was recorded outdoors and the Southampton data was indoors, with subjects wearing special trousers. The current databases are considerably more advanced, but certainly benefited in their development for the early approaches.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @book {12628, title = {Human identification based on gait}, year = {2006}, month = {2006///}, publisher = {Springer Science \& Business}, organization = {Springer Science \& Business}, abstract = {Biometrics now affect many people{\textquoteright}s lives, and is the focus of much academic research and commercial development. Gait is one of the most recent biometrics, with its own unique advantages. Gait recognizes people by the way they walk and run, analyzes movement, which in turn implies analyzing sequences of images. This professional book introduces developments from the laboratories of very distinguished researchers within this relatively new area of biometrics and clearly establishes human gait as a biometric. Human Identification Based on Gait provides a snapshot of all the biometric work in human identification by gait (all major centers for research are indicated in this book). To complete the picture, studies are included from medicine, psychology and other areas wherein we find not only justification for the use of gait as a biometric, but also pointers to techniques and to analysis. Human Identification Based on Gait is designed for a professional audience, composed of researchers and practitioners in industry. This book is also suitable as a secondary text for graduate-level students in computer science.}, keywords = {Biometric identification, Computers / Computer Graphics, Computers / Computer Science, Computers / Computer Vision \& Pattern Recognition, Computers / General, Computers / Information Technology, Computers / Programming / Software Development, Computers / Software Development \& Engineering / Systems Analysis \& Design, Gait in humans, Medical / Physiology, Social Science / Anthropology / Physical}, isbn = {9780387244242}, author = {Nixon,Mark S. and Tan,Tieniu and Chellapa, Rama} } @conference {12137, title = {Identifying domain-specific defect classes using inspections and change history}, booktitle = {Proceedings of the 2006 ACM/IEEE international symposium on Empirical software engineering}, series = {ISESE {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {346 - 355}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We present an iterative, reading-based methodology for analyzing defects in source code when change history is available. Our bottom-up approach can be applied to build knowledge of recurring defects in a specific domain, even if other sources of defect data such as defect reports and change requests are unavailable, incomplete or at the wrong level of abstraction for the purposes of the defect analysis. After defining the methodology, we present the results of an empirical study where our method was applied to analyze defects in parallel programs which use the MPI (Message Passing Interface) library to express parallelism. This library is often used in the domain of high performance computing, where there is much discussion but little empirical data about the frequency and severity of defect types. Preliminary results indicate the methodology is feasible and can provide insights into the nature of real defects. We present the results, derived hypothesis, and lessons learned.}, keywords = {change history, code reading, domain specific defects, Inspection}, isbn = {1-59593-218-6}, doi = {10.1145/1159733.1159785}, url = {http://doi.acm.org/10.1145/1159733.1159785}, author = {Nakamura,Taiga and Hochstein, Lorin and Basili, Victor R.} } @conference {15543, title = {Image Registration and Fusion Studies for the Integration of Multiple Remote Sensing Data}, booktitle = {Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on}, volume = {5}, year = {2006}, month = {2006/05//}, pages = {V - V}, abstract = {The future of remote sensing will see the development of spacecraft formations, and with this development will come a number of complex challenges such as maintaining precise relative position and specified attitudes. At the same time, there will be increasing needs to understand planetary system processes and build accurate prediction models. One essential technology to accomplish these goals is the integration of multiple source data. For this integration, image registration and fusion represent the first steps and need to be performed with very high accuracy. In this paper, we describe studies performed in both image registration and fusion, including a modular framework that was built to describe registration algorithms, a Web-based image registration toolbox, and the comparison of several image fusion techniques using data from the EO-1/ALI and Hyperion sensors}, keywords = {ALI, EO-1, fusion studies, geophysical signal processing, Hyperion sensors, image registration, Internet, multiple remote sensing data, multiple source data, Remote sensing, Web-based image registration toolbox}, doi = {10.1109/ICASSP.2006.1661494}, author = {Le Moigne,J. and Cole-Rhodes,A. and Eastman,R. and Jain,P. and Joshua,A. and Memarsadeghi,N. and Mount, Dave and Netanyahu,N. and Morisette,J. and Uko-Ozoro,E.} } @article {18885, title = {The incompleteness of planning with volatile external information}, journal = {FRONTIERS IN ARTIFICIAL INTELLIGENCE AND APPLICATIONS}, volume = {141}, year = {2006}, month = {2006///}, pages = {839 - 839}, abstract = {In many real-world planning environments, someof the information about the world is both external (the planner must request it from external information sources) and volatile (it changes before the planning process completes). In such en- vironments, a planner faces two challenges: how to generate plans despite changes in the external information during plan- ning, and how to guarantee that a plan returned by the plan- ner will remain valid for some period of time after the plan- ning ends. Previous works on planning with volatile informa- tion have addressed the first challenge, but not the second one. This paper provides a general model for planning with volatile external information in which the planner offers a guar- antee of how long the solution will remain valid after it is re- turned, and an incompleteness theorem showing that there is no planner that can succeed in solving all solvable planning prob- lems in which there is volatile external information. }, url = {http://www.cs.umd.edu/~nau/papers/au2006incompleteness.pdf}, author = {Au,T. and Nau, Dana S.} } @article {14440, title = {Inferring formal titles in organizational email archives}, journal = {Proc. of the ICML Workshop on Statistical Network Analysis}, year = {2006}, month = {2006///}, abstract = {In the social network of large groups of people, such as companiesand organizations, formal hierarchies with titles and lines of authority are established to define the responsibilities and order of power within that group. Although this information may be readily available for individuals within that group, the context this hierarchy provides in communications is not available to those outside the group. In this paper, we define the problem of inferring this formal hierarchy in the context of organizational email archives. We present a new dataset for the widely used Enron email dataset, for use with analysis of the Enron social network hierarchy. We then provide some preliminary results on the problem of classifying individuals to their formal titles using standard classification algorithms. }, author = {Namata,G.M. and Getoor, Lise and Diehl,C.} } @inbook {12637, title = {Integrating Video Information over Time. Example: Face Recognition from Video}, booktitle = {Cognitive Vision SystemsCognitive Vision Systems}, series = {Lecture Notes in Computer Science}, volume = {3948}, year = {2006}, month = {2006///}, pages = {127 - 144}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The ability to integrate information over time in order to come to a conclusion is a strength of cognitive systems. It allows the system, e.g., to 1 verify insecure observations: This is the case when data is noisy or of low-quality, or if conditions in general are non-optimal. 2 exploit general knowledge about spatio-temporal relations: This allows the system to exploit the specific dynamics of an object as an additional feature for, e.g., recognition, interpretation and prediction of actions of other agents. 3 In general, using dynamics allows the system to recursively generate and verify hypotheses for object and scene interpretation and to generate warnings when {\textquoteleft}implausible{\textquoteright} hypotheses occur or to circumvent them altogether. We have studied the effectiveness of temporal integration for recognition purposes by using the face recognition as an example study case. Face recognition is a prominent problem and has been studied more extensively than almost any other recognition problem. An observation is that face recognition works well in ideal conditions. If those conditions, however, are not met, then all present algorithms break down disgracefully. This problem appears to be general to all vision techniques that intend to extract visual information out of low-SNR image data. It is exactly a strength of cognitive systems that they are able to cope with non-ideal situations. In this chapter we will deal with this problem.}, isbn = {978-3-540-33971-7}, url = {http://dx.doi.org/10.1007/11414353_9}, author = {Kr{\"u}ger,Volker and Zhou,Shaohua and Chellapa, Rama}, editor = {Christensen,Henrik and Nagel,Hans-Hellmut} } @inbook {12639, title = {Key Frame-Based Activity Representation Using Antieigenvalues}, booktitle = {Computer Vision {\textendash} ACCV 2006Computer Vision {\textendash} ACCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3852}, year = {2006}, month = {2006///}, pages = {499 - 508}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Many activities may be characterized by a sequence of key frames that are related to important changes in motion rather than dominant characteristics that persist over a long sequence of frames. To detect such changes, we define a transformation operator at every time instant, which relates the past to the future states. One of the useful quantities associated with numerical range of an operator is the eigenvalue. In the literature, eigenvalue-based approaches have been studied extensively for many modeling tasks. These rely on gross properties of the data and are not suitable to detect subtle changes. We propose an antieigenvalue {\textendash} based measure to detect key frames. Antieigenvalues depend critically on the turning of the operator, whereas eigenvalues represent the amount of dilation along the eigenvector directions aligned with the direction of maximum variance. We demonstrate its application to activity modeling and recognition using two datasets: a motion capture dataset and the UCF human action dataset.}, isbn = {978-3-540-31244-4}, url = {http://dx.doi.org/10.1007/11612704_50}, author = {Cuntoor,Naresh and Chellapa, Rama}, editor = {Narayanan,P. and Nayar,Shree and Shum,Heung-Yeung} } @conference {18877, title = {Learning to do HTN planning}, year = {2006}, month = {2006///}, pages = {390 - 393}, abstract = {We describe HDL, an algorithm that learns HTN do- main descriptions by examining plan traces produced by an expert problem-solver. Prior work on learning HTN methods requires that all the methods{\textquoteright} informa- tion except for their preconditions be given in advance so that the learner can learn the preconditions. In con- trast, HDL has no prior information about the methods. In our experiments, in most cases HDL converged fully with no more than about 200 plan traces. Furthermore, even when HDL was given only half the plan traces it required to fully converge, it usually was able to pro- duce HTN methods that were sufficient to solve more than 3/4 of the planning problems in the test set.}, url = {https://www.aaai.org/Papers/ICAPS/2006/ICAPS06-048.pdf}, author = {Ilghami,O. and Nau, Dana S. and Munoz-Avila,H.} } @conference {18889, title = {Maintaining cooperation in noisy environments}, volume = {21}, year = {2006}, month = {2006///}, pages = {1561 - 1561}, abstract = {To prevent or alleviate conflicts in multi-agent environ- ments, it is important to distinguish between situations where another agent has misbehaved intentionally and situations where the misbehavior was accidental. One situation where this problem arises is the Noisy Iterated Prisoner{\textquoteright}s Dilemma, a version of the Iterated Prisoner{\textquoteright}s Dilemma (IPD) in which there is a nonzero probability that a {\textquotedblleft}cooperate{\textquotedblright} action will accidentally be changed into a {\textquotedblleft}defect{\textquotedblright} action and vice versa. Tit-For-Tat and other strategies that do quite well in the ordi- nary (non-noisy) IPD can do quite badly in the Noisy IPD.This paper presents a technique called symbolic noise detec- tion, for detecting whether anomalies in player{\textquoteright}s behavior are deliberate or accidental. This idea to use player{\textquoteright}s determin- istic behavior to tell whether an action has been affected by noise. We also present DBS, an algorithm that uses symbolic noise detection in the Noisy IPD. DBS constructs a model of the other agent{\textquoteright}s deterministic behavior, and watches for any deviation from this model. If the other agent{\textquoteright}s next ac- tion is inconsistent with this model, the inconsistency can be due either to noise or to a genuine change in their behavior; and DBS can often distinguish between two cases by waiting to see whether this inconsistency persists in next few moves. This technique is effective because many IPD players often have clear deterministic patterns of behavior. We entered several different implementations of DBS in the 2005 Iterated Prisoner{\textquoteright}s Dilemma competition, in Category 2 (noisy environments). Out of the 165 contestants in this cate- gory, most of DBS implementations ranked among top ten. The best one ranked third, and it was beaten only by two {\textquotedblleft}master-and-slaves strategy{\textquotedblright} programs that each had a large number of {\textquotedblleft}slave{\textquotedblright} programs feeding points to them. }, url = {https://www.aaai.org/Papers/AAAI/2006/AAAI06-250.pdf}, author = {Au,T. C and Nau, Dana S.} } @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.} } @article {16933, title = {A model for computer frustration: the role of instrumental and dispositional factors on incident, session, and post-session frustration and mood}, journal = {Computers in Human Behavior}, volume = {22}, year = {2006}, month = {2006/11//}, pages = {941 - 961}, abstract = {Frustration is almost universally accepted as the emotional outcome of a negative computing experience. Despite the wide use of the term, however, it has not been rigorously conceptualized as a factor in the study of the human{\textendash}computer interface. This project sets out to explicate frustration as a pre-emotional state generated by the user{\textquoteright}s appraisal of the interface as an impediment to goal attainment, and looks at how user characteristics, such as self-efficacy, relate to it. This project employed episode report methodology to capture data from 144 computer users{\textquoteright} reports of actual frustrating events as they took place. Diaries taken as users worked at their everyday tasks yield detailed data about the problems they encountered and included information about session length and an estimate of the time lost due to the experiences. Outcomes were measured as either situational or dispositional factors. Situational factors, having to do with specific events, predicted incident frustration. However, disposition variables, especially user self-efficacy, were much stronger, predicting incident and session frustration, and post-session mood. One surprising outcome was the failure of demographic variables as predictors of frustration.}, keywords = {Efficacy, Emotion, Frustration, Mood, problem solving, usability}, isbn = {0747-5632}, doi = {10.1016/j.chb.2004.03.015}, url = {http://www.sciencedirect.com/science/article/pii/S0747563204000615}, author = {Bessi{\`e}re,Katie and Newhagen,John E. and Robinson,John P. and Shneiderman, Ben} } @inbook {12633, title = {Model-Based Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {107 - 133}, abstract = {The model based approaches aim to derive the movement of the torso and/or the legs. The distinction of a structural approach is one which uses static parameters illustrated in Fig. 6.1(a) whereas a model can be the (relative) motion of the angles (α, β, and ϕ) between the limbs, shown in Fig. 6.1(b). As earlier, these angles can also be measured relative to vertical.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @inbook {12624, title = {Multi-camera Tracking of Articulated Human Motion Using Motion and Shape Cues}, booktitle = {Computer Vision {\textendash} ACCV 2006Computer Vision {\textendash} ACCV 2006}, series = {Lecture Notes in Computer Science}, volume = {3852}, year = {2006}, month = {2006///}, pages = {131 - 140}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present a framework and algorithm for tracking articulated motion for humans. We use multiple calibrated cameras and an articulated human shape model. Tracking is performed using motion cues as well as image-based cues (such as silhouettes and {\textquotedblleft}motion residues{\textquotedblright} hereafter referred to as spatial cues,) as opposed to constructing a 3D volume image or visual hulls. Our algorithm consists of a predictor and corrector: the predictor estimates the pose at the t + 1 using motion information between images at t and t + 1. The error in the estimated pose is then corrected using spatial cues from images at t + 1. In our predictor, we use robust multi-scale parametric optimisation to estimate the pixel displacement for each body segment. We then use an iterative procedure to estimate the change in pose from the pixel displacement of points on the individual body segments. We present a method for fusing information from different spatial cues such as silhouettes and {\textquotedblleft}motion residues{\textquotedblright} into a single energy function. We then express this energy function in terms of the pose parameters, and find the optimum pose for which the energy is minimised.}, isbn = {978-3-540-31244-4}, url = {http://dx.doi.org/10.1007/11612704_14}, author = {Sundaresan,Aravind and Chellapa, Rama}, editor = {Narayanan,P. and Nayar,Shree and Shum,Heung-Yeung} } @conference {17852, title = {Multiple range query optimization with distributed cache indexing}, booktitle = {Proceedings of the 2006 ACM/IEEE conference on Supercomputing}, year = {2006}, month = {2006///}, pages = {100{\textendash}es - 100{\textendash}es}, author = {Nam,B. and Andrade,H. and Sussman, Alan} } @article {14483, title = {Name reference resolution in organizational email archives}, journal = {SIAM International Conference on Data Mining}, year = {2006}, month = {2006///}, pages = {20 - 22}, author = {Diehl,C. P and Getoor, Lise and Namata,G.} } @article {17309, title = {Nuclear Envelope Dystrophies Show a Transcriptional Fingerprint Suggesting Disruption of Rb{\textendash}MyoD Pathways in Muscle Regeneration}, journal = {BrainBrain}, volume = {129}, year = {2006}, month = {2006/04/01/}, pages = {996 - 1013}, abstract = {Mutations of lamin A/C (LMNA) cause a wide range of human disorders, including progeria, lipodystrophy, neuropathies and autosomal dominant Emery{\textendash}Dreifuss muscular dystrophy (EDMD). EDMD is also caused by X-linked recessive loss-of-function mutations of emerin, another component of the inner nuclear lamina that directly interacts with LMNA. One model for disease pathogenesis of LMNA and emerin mutations is cell-specific perturbations of the mRNA transcriptome in terminally differentiated cells. To test this model, we studied 125 human muscle biopsies from 13 diagnostic groups (125 U133A, 125 U133B microarrays), including EDMD patients with LMNA and emerin mutations. A Visual and Statistical Data Analyzer (VISDA) algorithm was used to statistically model cluster hierarchy, resulting in a tree of phenotypic classifications. Validations of the diagnostic tree included permutations of U133A and U133B arrays, and use of two probe set algorithms (MAS5.0 and MBEI). This showed that the two nuclear envelope defects (EDMD LMNA, EDMD emerin) were highly related disorders and were also related to fascioscapulohumeral muscular dystrophy (FSHD). FSHD has recently been hypothesized to involve abnormal interactions of chromatin with the nuclear envelope. To identify disease-specific transcripts for EDMD, we applied a leave-one-out (LOO) cross-validation approach using LMNA patient muscle as a test data set, with reverse transcription{\textendash}polymerase chain reaction (RT{\textendash}PCR) validations in both LMNA and emerin patient muscle. A high proportion of top-ranked and validated transcripts were components of the same transcriptional regulatory pathway involving Rb1 and MyoD during muscle regeneration (CRI-1, CREBBP, Nap1L1, ECREBBP/p300), where each was specifically upregulated in EDMD. Using a muscle regeneration time series (27 time points) we develop a transcriptional model for downstream consequences of LMNA and emerin mutations. We propose that key interactions between the nuclear envelope and Rb and MyoD fail in EDMD at the point of myoblast exit from the cell cycle, leading to poorly coordinated phosphorylation and acetylation steps. Our data is consistent with mutations of nuclear lamina components leading to destabilization of the transcriptome in differentiated cells.}, keywords = {EDMD = Emery{\textendash}Dreifuss muscular dystrophy, emerin, Emery-Dreifuss muscular dystrophy, FSHD = fascioscapulohumeral muscular dystrophy, IDG = individual discriminatory genes, JDG = jointly discriminatory genes, lamin A/C, LGMD = limb-girdle muscular dystrophy, LOO = leave-one-out, RT{\textendash}PCR = reverse transcription{\textendash}polymerase chain reaction; VISDA = Visual and Statistical Data Analyzer, Skeletal muscle, wFC = weighted Fisher criterion}, isbn = {0006-8950, 1460-2156}, doi = {10.1093/brain/awl023}, url = {http://brain.oxfordjournals.org/content/129/4/996}, author = {Bakay,Marina and Wang,Zuyi and Melcon,Gisela and Schiltz,Louis and Xuan,Jianhua and Zhao,Po and Sartorelli,Vittorio and Seo,Jinwook and Pegoraro,Elena and Angelini,Corrado and Shneiderman, Ben and Escolar,Diana and Chen,Yi-Wen and Winokur,Sara T and Pachman,Lauren M and Fan,Chenguang and Mandler,Raul and Nevo,Yoram and Gordon,Erynn and Zhu,Yitan and Dong,Yibin and Wang,Yue and Hoffman,Eric P} } @article {12150, title = {Observations about software development for high end computing}, journal = {CTWatch Quarterly}, volume = {2}, year = {2006}, month = {2006///}, pages = {33 - 38}, abstract = {In this paper, we have summarized our findings from a series of case studies conducted with ten ASC and MP Codes as a series of observations. Due to different environments in which each code is developed, some of the observations are consistent across code teams while others vary across code teams. Overall, we found high consistency among the ASC Codes and the MP Codes. Due to the different environments and foci of these projects, this result is both surprising and positive. In addition, despite the fact that a large majority of the developers on these teams have little or no formal training in software engineering, they have been able to make use of some basic software engineering principles. Further education and motivation could increase the use of these principles and further increase the quality of scientific and engineering software that has already demonstrated its value.Based on the positive results thus far, we have plans to conduct additional case studies to gather more data in support of or in contradiction to the observations presented in this paper. In future case studies, we will strive to investigate codes from additional domains, thereby allowing broader, more inclusive conclusions to be drawn. }, author = {Carver, J. C and Hochstein, L. M and Kendall,R. P and Nakamura, T. and Zelkowitz, Marvin V and Basili, Victor R. and Post,D. E} } @conference {17786, title = {Overconfidence or paranoia? search in imperfect-information games}, booktitle = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {21}, year = {2006}, month = {2006///}, pages = {1045 - 1045}, abstract = {We derive a recursive formula for expected utility valuesin imperfect- information game trees, and an imperfect- information game tree search algorithm based on it. The for- mula and algorithm are general enough to incorporate a wide variety of opponent models. We analyze two opponent mod- els. The {\textquotedblleft}paranoid{\textquotedblright} model is an information-set analog of the minimax rule used in perfect-information games. The {\textquotedblleft}over- confident{\textquotedblright} model assumes the opponent moves randomly. Our experimental tests in the game of kriegspiel chess (an imperfect-information variant of chess) produced surpris- ing results: (1) against each other, and against one of the kriegspiel algorithms presented at IJCAI-05, the overconfi- dent model usually outperformed the paranoid model; (2) the performance of both models depended greatly on how well the model corresponded to the opponent{\textquoteright}s behavior. These re- sults suggest that the usual assumption of perfect-information game tree search{\textemdash}that the opponent will choose the best pos- sible move{\textemdash}isn{\textquoteright}t as useful in imperfect-information games. }, url = {http://www.aaai.org/Papers/AAAI/2006/AAAI06-164.pdf}, author = {Parker,A. and Nau, Dana S. and V.S. Subrahmanian} } @conference {12410, title = {Participatory design with proxies: developing a desktop-PDA system to support people with aphasia}, booktitle = {Proceedings of the SIGCHI conference on Human Factors in computing systems}, series = {CHI {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {151 - 160}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In this paper, we describe the design and preliminary evaluation of a hybrid desktop-handheld system developed to support individuals with aphasia, a disorder which impairs the ability to speak, read, write, or understand language. The system allows its users to develop speech communication through images and sound on a desktop computer and download this speech to a mobile device that can then support communication outside the home. Using a desktop computer for input addresses some of this population{\textquoteright}s difficulties interacting with handheld devices, while the mobile device addresses stigma and portability issues. A modified participatory design approach was used in which proxies, that is, speech-language pathologists who work with aphasic individuals, assumed the role normally filled by users. This was done because of the difficulties in communicating with the target population and the high variability in aphasic disorders. In addition, the paper presents a case study of the proxy-use participatory design process that illustrates how different interview techniques resulted in different user feedback.}, keywords = {aphasia, assistive technology, multi-modal interfaces, participatory design}, isbn = {1-59593-372-7}, doi = {10.1145/1124772.1124797}, url = {http://doi.acm.org/10.1145/1124772.1124797}, author = {Jordan Boyd-Graber and Nikolova,Sonya S. and Moffatt,Karyn A. and Kin,Kenrick C. and Lee,Joshua Y. and Mackey,Lester W. and Tremaine,Marilyn M. and Klawe,Maria M.} } @article {14724, title = {Practical dynamic software updating for C}, journal = {SIGPLAN Not.}, volume = {41}, year = {2006}, month = {2006/06//}, pages = {72 - 83}, abstract = {Software updates typically require stopping and restarting an application, but many systems cannot afford to halt service, or would prefer not to. Dynamic software updating (DSU) addresses this difficulty by permitting programs to be updated while they run. DSU is appealing compared to other approaches for on-line upgrades because it is quite general and requires no redundant hardware. The challenge is in making DSU practical: it should be flexible, and yet safe, efficient, and easy to use.In this paper, we present Ginseng, a DSU implementation for C that aims to meet this challenge. We compile programs specially so that they can be dynamically patched, and generate most of a dynamic patch automatically. Ginseng performs a series of analyses that when combined with some simple runtime support ensure that an update will not violate type-safety while guaranteeing that data is kept up-to-date. We have used Ginseng to construct and dynamically apply patches to three substantial open-source server programs---Very Secure FTP daemon, OpenSSH sshd daemon, and GNU Zebra. In total, we dynamically patched each program with three years{\textquoteright} worth of releases. Though the programs changed substantially, the majority of updates were easy to generate. Performance experiments show that all patches could be applied in less than 5 ms, and that the overhead on application throughput due to updating support ranged from 0 to at most 32\%.}, keywords = {dynamic software updating, function indirection, loop extraction, type wrapping}, isbn = {0362-1340}, doi = {10.1145/1133255.1133991}, url = {http://doi.acm.org/10.1145/1133255.1133991}, author = {Neamtiu,Iulian and Hicks, Michael W. and Stoyle,Gareth and Oriol,Manuel} } @article {15245, title = {Query planning in the presence of overlapping sources}, journal = {Advances in Database Technology-EDBT 2006}, year = {2006}, month = {2006///}, pages = {811 - 828}, abstract = {Navigational queries on Web-accessible life science sources pose unique query optimization challenges. The objects in these sources are interconnected to objects in other sources, forming a large and complex graph, and there is an overlap of objects in the sources. Answering a query requires the traversal of multiple alternate paths through these sources. Each path can be associated with the benefit or the cardinality of the target object set (TOS) of objects reached in the result. There is also an evaluation cost of reaching the TOS.We present dual problems in selecting the best set of paths. The first problem is to select a set of paths that satisfy a constraint on the evaluation cost while maximizing the benefit (number of distinct objects in the TOS). The dual problem is to select a set of paths that satisfies a threshold of the TOS benefit with minimal evaluation cost. The two problems can be mapped to the budgeted maximum coverage problem and the maximal set cover with a threshold. To solve these problems, we explore several solutions including greedy heuristics, a randomized search, and a traditional IP/LP formulation with bounds. We perform experiments on a real-world graph of life sciences objects from NCBI and report on the computational overhead of our solutions and their performance compared to the optimal solution. }, doi = {10.1007/11687238_48}, author = {Bleiholder,J. and Khuller, Samir and Naumann,F. and Raschid, Louiqa and Wu,Y.} } @article {16469, title = {Query planning in the presence of overlapping sources}, journal = {Advances in Database Technology-EDBT 2006}, year = {2006}, month = {2006///}, pages = {811 - 828}, author = {Bleiholder,J. and Khuller, Samir and Naumann,F. and Raschid, Louiqa and Wu,Y.} } @conference {12275, title = {Resource Discovery Techniques in Distributed Desktop Grid Environments}, booktitle = {Proceedings of the 7th IEEE/ACM International Conference on Grid Computing}, series = {GRID {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {9 - 16}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, abstract = {Desktop grids use opportunistic sharing to exploit large collections of personal computers and workstations across the Internet, achieving tremendous computing power at low cost. Traditional desktop grid systems are typically based on a client-server architecture, which has inherent shortcomings with respect to robustness, reliability and scalability. In this paper, we propose a decentralized, robust, highly available, and scalable infrastructure to match incoming jobs to available resources. Through a comparative analysis on the experimental results obtained via simulation of three different types of matchmaking algorithms under different workload scenarios, we show the trade-offs between effcient matchmaking and good load balancing in a fully decentralized, heterogeneous computational environment.}, isbn = {1-4244-0343-X}, doi = {10.1109/ICGRID.2006.310992}, url = {http://dx.doi.org/10.1109/ICGRID.2006.310992}, author = {Kim,Jik-Soo and Nam,Beomseok and Keleher,Peter and Marsh,Michael and Bhattacharjee, Bobby and Sussman, Alan} } @article {14069, title = {Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: Sixteen new members and a novel subfamily}, journal = {Gene}, volume = {366}, year = {2006}, month = {2006/02/01/}, pages = {303 - 315}, abstract = {Nuclear receptors (NRs) are important transcriptional modulators in metazoans. Sixteen new NRs were identified in the Platyhelminth trematode, Schistosoma mansoni. Three were found to possess novel tandem DNA-binding domains that identify a new subfamily of NR. Two NRs are homologues of the thyroid hormone receptor that previously were thought to be restricted to chordates. This study brings the total number of identified NR in S. mansoni to 21. Phylogenetic and comparative genomic analyses demonstrate that S. mansoni NRs share an evolutionary lineage with that of arthropods and vertebrates. Phylogenic analysis shows that more than half of the S. mansoni nuclear receptors evolved from a second gene duplication. As the second gene duplication of NRs was thought to be specific to vertebrates, our data challenge the current theory of NR evolution.}, keywords = {Nuclear receptors, Schistosoma mansoni}, isbn = {0378-1119}, doi = {16/j.gene.2005.09.013}, url = {http://www.sciencedirect.com/science/article/pii/S0378111905005871}, author = {Wu,Wenjie and Niles,Edward G. and El-Sayed, Najib M. and Berriman,Matthew and LoVerde,Philip T.} } @article {12926, title = {Seasonal Cholera Caused by Vibrio Cholerae Serogroups O1 and O139 in the Coastal Aquatic Environment of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {72}, year = {2006}, month = {2006/06/01/}, pages = {4096 - 4104}, abstract = {Since Vibrio cholerae O139 first appeared in 1992, both O1 El Tor and O139 have been recognized as the epidemic serogroups, although their geographic distribution, endemicity, and reservoir are not fully understood. To address this lack of information, a study of the epidemiology and ecology of V. cholerae O1 and O139 was carried out in two coastal areas, Bakerganj and Mathbaria, Bangladesh, where cholera occurs seasonally. The results of a biweekly clinical study (January 2004 to May 2005), employing culture methods, and of an ecological study (monthly in Bakerganj and biweekly in Mathbaria from March 2004 to May 2005), employing direct and enrichment culture, colony blot hybridization, and direct fluorescent-antibody methods, showed that cholera is endemic in both Bakerganj and Mathbaria and that V. cholerae O1, O139, and non-O1/non-O139 are autochthonous to the aquatic environment. Although V. cholerae O1 and O139 were isolated from both areas, most noteworthy was the isolation of V. cholerae O139 in March, July, and September 2004 in Mathbaria, where seasonal cholera was clinically linked only to V. cholerae O1. In Mathbaria, V. cholerae O139 emerged as the sole cause of a significant outbreak of cholera in March 2005. V. cholerae O1 reemerged clinically in April 2005 and established dominance over V. cholerae O139, continuing to cause cholera in Mathbaria. In conclusion, the epidemic potential and coastal aquatic reservoir for V. cholerae O139 have been demonstrated. Based on the results of this study, the coastal ecosystem of the Bay of Bengal is concluded to be a significant reservoir for the epidemic serogroups of V. cholerae.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.00066-06}, url = {http://aem.asm.org/content/72/6/4096}, author = {Alam,Munirul and Hasan,Nur A. and Sadique,Abdus and Bhuiyan,N. A. and Ahmed,Kabir U. and Nusrin,Suraia and Nair,G. Balakrish and Siddique,A. K. and Sack,R. Bradley and Sack,David A. and Huq,Anwar and Rita R Colwell} } @inbook {12629, title = {Silhouette-Based Approaches}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {45 - 105}, abstract = {Of the current approaches, most are based on analysis of silhouettes. This is like the earlier analysis which concerned abstracting a walking subject from the background and then deriving set of measurements that describe the shape and motion of that silhouette in a sequence of images. This is similar in approach the classic computer vision approach to recognize objects by using shape descriptions of objects derived, say, by optimal thresholding.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @conference {17785, title = {A stochastic language for modelling opponent agents}, booktitle = {Proceedings of the fifth international joint conference on Autonomous agents and multiagent systems}, year = {2006}, month = {2006///}, pages = {244 - 246}, abstract = {There are numerous cases where a reasoning agent needs toreason about the behavior of an opponent agent. In this pa- per, we propose a hybrid probabilistic logic language within which we can express what actions an opponent may take in a given situation. We present the syntaxis and semantics of the language, and the concept of a Maximally Probable Course of Action. }, author = {Simari,G. and Sliva,A. and Nau, Dana S. and V.S. Subrahmanian} } @inbook {12630, title = {Subjects Allied to Gait}, booktitle = {Human Identification Based on GaitHuman Identification Based on Gait}, year = {2006}, month = {2006///}, pages = {5 - 15}, abstract = {There is considerable support for the notion that each person{\textquoteright}s gait is unique. As we shall see, it has been observed in literature that people can be recognized by the way they walk. The same notion has been observed in medicine and biomechanics, though not in the context of biometrics but more as an assertion of individuality. Perhaps driven by these notions, though without reference to them, there has been work in psychology on the human ability to recognize each other by using gait. Those suffering myopia often state that they can use gait as a way of recognizing people. There is other evidence too, which suggests that each person{\textquoteright}s gait is unique. People have also studied walking from medical and biomechanical perspectives, and this gives insight into how its properties can change which is of general interest in any biometrie deployment. We shall start with literature, with definitions of meaning.}, author = {Nixon, M.S. and Tan, T. and Chellapa, Rama} } @article {12927, title = {Toxigenic Vibrio Cholerae in the Aquatic Environment of Mathbaria, Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {72}, year = {2006}, month = {2006/04/01/}, pages = {2849 - 2855}, abstract = {Toxigenic Vibrio cholerae, rarely isolated from the aquatic environment between cholera epidemics, can be detected in what is now understood to be a dormant stage, i.e., viable but nonculturable when standard bacteriological methods are used. In the research reported here, biofilms have proved to be a source of culturable V. cholerae, even in nonepidemic periods. Biweekly environmental surveillance for V. cholerae was carried out in Mathbaria, an area of cholera endemicity adjacent to the Bay of Bengal, with the focus on V. cholerae O1 and O139 Bengal. A total of 297 samples of water, phytoplankton, and zooplankton were collected between March and December 2004, yielding eight V. cholerae O1 and four O139 Bengal isolates. A combination of culture methods, multiplex-PCR, and direct fluorescent antibody (DFA) counting revealed the Mathbaria aquatic environment to be a reservoir for V. cholerae O1 and O139 Bengal. DFA results showed significant clumping of the bacteria during the interepidemic period for cholera, and the fluorescent micrographs revealed large numbers of V. cholerae O1 in thin films of exopolysaccharides (biofilm). A similar clumping of V. cholerae O1 was also observed in samples collected from Matlab, Bangladesh, where cholera also is endemic. Thus, the results of the study provided in situ evidence for V. cholerae O1 and O139 in the aquatic environment, predominantly as viable but nonculturable cells and culturable cells in biofilm consortia. The biofilm community is concluded to be an additional reservoir of cholera bacteria in the aquatic environment between seasonal epidemics of cholera in Bangladesh.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.72.4.2849-2855.2006}, url = {http://aem.asm.org/content/72/4/2849}, author = {Alam,Munirul and Sultana,Marzia and Nair,G. Balakrish and Sack,R. Bradley and Sack,David A. and Siddique,A. K. and Ali,Afsar and Huq,Anwar and Rita R Colwell} } @inbook {16090, title = {Visualizing Graphs as Trees: Plant a Seed and Watch it Grow}, booktitle = {Graph DrawingGraph Drawing}, series = {Lecture Notes in Computer Science}, volume = {3843}, year = {2006}, month = {2006///}, pages = {516 - 518}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {TreePlus is a graph browsing technique based on a tree-style layout. It shows the missing graph structure using interaction techniques and enables users to start with a specific node and incrementally explore the local structure of graphs. We believe that it supports particularly well tasks that require rapid reading of labels.}, isbn = {978-3-540-31425-7}, url = {http://dx.doi.org/10.1007/11618058_50}, author = {Lee,Bongshin and Parr,Cynthia and Plaisant, Catherine and Bederson, Benjamin B.}, editor = {Healy,Patrick and Nikolov,Nikola} } @article {18893, title = {Applications of SHOP and SHOP2}, journal = {Intelligent Systems, IEEE}, volume = {20}, year = {2005}, month = {2005/04//march}, pages = {34 - 41}, abstract = {We design the simple hierarchical ordered planner (SHOP) and its successor, SHOP2, with two goals in mind: to investigate research issues in automated planning and to provide some simple, practical planning tools. SHOP and SHOP2 are based on a planning formalism called hierarchical task network planning. SHOP and SHOP2 use a search-control strategy called ordered task decomposition, which breaks tasks into subtasks and generates the plan{\textquoteright}s actions in the same order that the plan executor executes them. So, throughout the planning process, the planner can tell what the state of the world at each step of the plan.}, keywords = {automated planning, hierarchical task network planning, ordered task decomposition, planning (artificial intelligence), problem solving, search-control strategy, simple hierarchical ordered planner, trees (mathematics), uncertainty handling}, isbn = {1541-1672}, doi = {10.1109/MIS.2005.20}, author = {Nau, Dana S. and Au,T.-C. and Ilghami,O. and Kuter,U. and Wu,D. and Yaman,F. and Munoz-Avila,H. and Murdock,J. W.} } @inbook {19486, title = {Architecting and Implementing Versatile Dependability}, booktitle = {Architecting Dependable Systems III}, series = {Lecture Notes in Computer Science}, year = {2005}, month = {2005/01/01/}, pages = {212 - 231}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Distributed applications must often consider and select the appropriate trade-offs among three important aspects {\textendash} fault-tolerance, performance and resources. We introduce a novel concept, called versatile dependability, that provides a framework for analyzing and reasoning about these trade-offs in dependable software architectures. We present the architecture of a middleware framework that implements versatile dependability by providing the appropriate {\textquotedblright}knobs{\textquotedblright} to tune and re-calibrate the trade-offs. Our framework can adjust the properties and the behavior of the system at development-time, at deployment-time, and throughout the application{\textquoteright}s life-cycle. This renders the versatile dependability approach useful both to applications that require static fault-tolerance configurations supporting the loss/addition of resources and changing workloads, as well as to applications that evolve in terms of their dependability requirements. Through a couple of specific examples, one on adapting the replication style at runtime and the other on tuning the system scalability under given constraints, we demonstrate concretely how versatile dependability can provide an extended coverage of the design space of dependable distributed systems.}, keywords = {Operating systems, software engineering}, isbn = {978-3-540-28968-5, 978-3-540-31648-0}, url = {http://link.springer.com/chapter/10.1007/11556169_10}, author = {Tudor Dumitras and Srivastava, Deepti and Narasimhan, Priya}, editor = {Lemos, Rog{\'e}rio de and Gacek, Cristina and Romanovsky, Alexander} } @article {15445, title = {Automating regression testing for evolving GUI software}, journal = {Journal of Software Maintenance and Evolution: Research and Practice}, volume = {17}, year = {2005}, month = {2005///}, pages = {27 - 64}, abstract = {With the widespread deployment of broadband connections worldwide, software development and maintenance are increasingly being performed by multiple engineers, often working around-the-clock to maximize code churn rates. To ensure rapid quality assurance of such software, techniques such as {\textquoteleft}nightly/daily building and smoke testing{\textquoteright} have become widespread since they often reveal bugs early in the software development process. During these builds, a development version of the software is checked out from the source code repository tree, compiled, linked, and (re)tested with the goal of (re)validating its basic functionality. Although successful for conventional software, smoke tests are difficult to develop and automatically re-run for software that has a graphical user interface (GUI). In this paper, we describe a framework called DART (Daily Automated Regression Tester) that addresses the needs of frequent and automated re-testing of GUI software. The key to our success is automation: DART automates everything from structural GUI analysis, smoke-test-case generation, test-oracle creation, to code instrumentation, test execution, coverage evaluation, regeneration of test cases, and their re-execution. Together with the operating system{\textquoteright}s task scheduler, DART can execute frequently with little input from the developer/tester to re-test the GUI software. We provide results of experiments showing the time taken and memory required for GUI analysis, test case and test oracle generation, and test execution. We empirically compare the relative costs of employing different levels of detail in the GUI test oracle. We also show the events and statements covered by the smoke test cases. Copyright {\textcopyright} 2005 John Wiley \& Sons, Ltd.}, keywords = {daily/nightly builds, event-flow graphs, Graphical user interfaces, GUI regression testing, GUI testing, smoke testing, Software quality}, isbn = {1532-0618}, doi = {10.1002/smr.305}, url = {http://onlinelibrary.wiley.com/doi/10.1002/smr.305/abstract}, author = {Memon, Atif M. and Nagarajan,Adithya and Xie,Qing} } @article {14078, title = {Comparative Genomics of Trypanosomatid Parasitic Protozoa}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {404 - 409}, abstract = {A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that{\textemdash}along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions{\textemdash}have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.}, doi = {10.1126/science.1112181}, url = {http://www.sciencemag.org/content/309/5733/404.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Blandin,Ga{\"e}lle and Berriman,Matthew and Crabtree,Jonathan and Aggarwal,Gautam and Caler,Elisabet and Renauld,Hubert and Worthey,Elizabeth A. and Hertz-Fowler,Christiane and Ghedin,Elodie and Peacock,Christopher and Bartholomeu,Daniella C. and Haas,Brian J. and Tran,Anh-Nhi and Wortman,Jennifer R. and Alsmark,U. Cecilia M. and Angiuoli,Samuel and Anupama,Atashi and Badger,Jonathan and Bringaud,Frederic and Cadag,Eithon and Carlton,Jane M. and Cerqueira,Gustavo C. and Creasy,Todd and Delcher,Arthur L. and Djikeng,Appolinaire and Embley,T. Martin and Hauser,Christopher and Ivens,Alasdair C. and Kummerfeld,Sarah K. and Pereira-Leal,Jose B. and Nilsson,Daniel and Peterson,Jeremy and Salzberg,Steven L. and Shallom,Joshua and Silva,Joana C. and Sundaram,Jaideep and Westenberger,Scott and White,Owen and Melville,Sara E. and Donelson,John E. and Andersson,Bj{\"o}rn and Stuart,Kenneth D. and Hall,Neil} } @article {17030, title = {Content Index to Volume 18}, journal = {INTERNATIONAL JOURNAL OF HUMAN{\textendash}COMPUTER INTERACTION}, volume = {18}, year = {2005}, month = {2005///}, pages = {367 - 368}, author = {Kuniavsky,M. and Vaughan,M. and Bederson, Benjamin B. and Shneiderman, Ben and Rau,P.L.P. and from Menus,T. and Lane,D.M. and Napier,H.A. and Peres,S.C. and S{\'a}ndor,A.} } @article {12931, title = {Critical Factors Influencing the Occurrence of Vibrio Cholerae in the Environment of Bangladesh}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {71}, year = {2005}, month = {2005/08/01/}, pages = {4645 - 4654}, abstract = {The occurrence of outbreaks of cholera in Africa in 1970 and in Latin America in 1991, mainly in coastal communities, and the appearance of the new serotype Vibrio cholerae O139 in India and subsequently in Bangladesh have stimulated efforts to understand environmental factors influencing the growth and geographic distribution of epidemic Vibrio cholerae serotypes. Because of the severity of recent epidemics, cholera is now being considered by some infectious disease investigators as a {\textquotedblleft}reemerging{\textquotedblright} disease, prompting new work on the ecology of vibrios. Epidemiological and ecological surveillance for cholera has been under way in four rural, geographically separated locations in Bangladesh for the past 4 years, during which both clinical and environmental samples were collected at biweekly intervals. The clinical epidemiology portion of the research has been published (Sack et al., J. Infect. Dis. 187:96-101, 2003). The results of environmental sampling and analysis of the environmental and clinical data have revealed significant correlations of water temperature, water depth, rainfall, conductivity, and copepod counts with the occurrence of cholera toxin-producing bacteria (presumably V. cholerae). The lag periods between increases or decreases in units of factors, such as temperature and salinity, and occurrence of cholera correlate with biological parameters, e.g., plankton population blooms. The new information on the ecology of V. cholerae is proving useful in developing environmental models for the prediction of cholera epidemics.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.71.8.4645-4654.2005}, url = {http://aem.asm.org/content/71/8/4645}, author = {Huq,Anwar and Sack,R. Bradley and Nizam,Azhar and Longini,Ira M. and Nair,G. Balakrish and Ali,Afsar and Morris,J. Glenn and Khan,M. N. Huda and Siddique,A. Kasem and Yunus,Mohammed and Albert,M. John and Sack,David A. and Rita R Colwell} } @conference {16482, title = {A data model and query language to explore enhanced links and paths in life science sources}, booktitle = {Proceedings of the ACM SIGMOD Workshop on The Web and Databases (WebDB)}, year = {2005}, month = {2005///}, author = {Mihaila,G. and Naumann,F. and Raschid, Louiqa and Vidal,M. E} } @article {17102, title = {Dynamic Queries and Brushing on Choropleth Maps (2001)}, year = {2005}, month = {2005///}, abstract = {Users who must combine demographic, economic or other data in a geographic context are often hampered by the integration of tabular and map representations. Static, paper-based solutions limit the amount of data that can be placed on a single map or table. By providing an effective user interface, we believe that researchers, journalists, teachers, and students can explore complex data sets more rapidly and effectively. This paper presents Dynamaps, a generalized map-based information-visualization tool for dynamic queries and brushing on choropleth maps. Users can use color coding to show a variable on each geographic region, and then filter out areas that do not meet the desired criteria. In addition, a scattergram view and a detailson- demand window support overviews and specific fact finding.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6481}, author = {Dang,Gunjan and North,Chris and Shneiderman, Ben} } @article {17107, title = {Dynamic Query Chloropleth Maps for Information Seeking and Decision Making (2003)}, year = {2005}, month = {2005///}, abstract = {Information retrieval and visualization can be combined in dynamic query systems that allow users unparalleled access to information for decision making. In this paper, we report on the development and evaluation of a dynamic query system (YMap) that displays information on a chloropleth map using double thumb sliders to select ranges of query variables. The YMap prototype is a Java-Applet that supports panning and zooming. Several usability studies were conducted on early prototypes that resulted in the current version. Applications of YMap for decision making tasks are discussed.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6505}, author = {Norman,Kent L and Zhao,Haixia and Shneiderman, Ben and Golub,Evan} } @article {14686, title = {Dynamic software updating}, journal = {ACM Trans. Program. Lang. Syst.}, volume = {27}, year = {2005}, month = {2005/11//}, pages = {1049 - 1096}, abstract = {Many important applications must run continuously and without interruption, and yet also must be changed to fix bugs or upgrade functionality. No prior general-purpose methodology for dynamic updating achieves a practical balance between flexibility, robustness, low overhead, ease of use, and low cost.We present an approach for C-like languages that provides type-safe dynamic updating of native code in an extremely flexible manner---code, data, and types may be updated, at programmer-determined times---and permits the use of automated tools to aid the programmer in the updating process. Our system is based on dynamic patches that contain both the updated code and the code needed to transition from the old version to the new. A novel aspect of our patches is that they consist of verifiable native code (e.g. Proof-Carrying Code or Typed Assembly Language), which is native code accompanied by annotations that allow online verification of the code{\textquoteright}s safety. We discuss how patches are generated mostly automatically, how they are applied using dynamic-linking technology, and how code is compiled to make it updateable.To concretely illustrate our system, we have implemented a dynamically updateable web server, FlashEd. We discuss our experience building and maintaining FlashEd, and generalize to present observations about updateable software development. Performance experiments show that for FlashEd, the overhead due to updating is low: typically less than 1 percent.}, keywords = {dynamic software updating, typed assembly language}, isbn = {0164-0925}, doi = {10.1145/1108970.1108971}, url = {http://doi.acm.org/10.1145/1108970.1108971}, author = {Hicks, Michael W. and Nettles,Scott} } @conference {16877, title = {An efficient nearest neighbor algorithm for P2P settings}, booktitle = {Proceedings of the 2005 national conference on Digital government research}, series = {dg.o {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {21 - 28}, publisher = {Digital Government Society of North America}, organization = {Digital Government Society of North America}, abstract = {New Peer-to-Peer (P2P) applications like P2P job-employee seeker networks and P2P virtual cities, for application domains such as collaborative urban planning and forming virtual communities, are about to emerge. An important component in these applications is spatial data, i.e., data with locational components. Many requests initiated on spatial data involve finding the spatial objects that are nearest to a query location. In this paper, we propose an efficient algorithm that finds the spatial objects that are nearest to a given query location on a P2P network in the order of their minimum distance to the query point. The proposed algorithm makes use of a distributed spatial index that does not rely on the use of a central server. The algorithm is designed to be more efficient by utilizing the parallel nature of the P2P network. A demonstration of the proposed algorithm was implemented as a prototype P2P application that finds events and places of interest in a city.}, keywords = {geographic information systems, nearest neighbor query, peer-to-peer networks, quadtree, spatial data}, url = {http://dl.acm.org/citation.cfm?id=1065226.1065237}, author = {Tanin,Egemen and Nayar,Deepa and Samet, Hanan} } @inbook {19494, title = {Fault-Tolerant Middleware and the Magical 1\%}, booktitle = {Middleware 2005}, series = {Lecture Notes in Computer Science}, year = {2005}, month = {2005/01/01/}, pages = {431 - 441}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Through an extensive experimental analysis of over 900 possible configurations of a fault-tolerant middleware system, we present empirical evidence that the unpredictability inherent in such systems arises from merely 1\% of the remote invocations. The occurrence of very high latencies cannot be regulated through parameters such as the number of clients, the replication style and degree or the request rates. However, by selectively filtering out a {\textquotedblleft}magical 1\%{\textquotedblright} of the raw observations of various metrics, we show that performance, in terms of measured end-to-end latency and throughput, can be bounded, easy to understand and control. This simple statistical technique enables us to guarantee, with some level of confidence, bounds for percentile-based quality of service (QoS) metrics, which dramatically increase our ability to tune and control a middleware system in a predictable manner.}, keywords = {Computer Communication Networks, Information Systems Applications (incl.Internet), Operating systems, Programming Languages, Compilers, Interpreters, Programming Techniques, software engineering}, isbn = {978-3-540-30323-7, 978-3-540-32269-6}, url = {http://link.springer.com/chapter/10.1007/11587552_24}, author = {Tudor Dumitras and Narasimhan, Priya}, editor = {Alonso, Gustavo} } @conference {18875, title = {Game-tree search with combinatorially large belief states}, volume = {19}, year = {2005}, month = {2005///}, pages = {254 - 254}, abstract = {In games such as kriegspiel chess (a chess variantwhere players have no direct knowledge of the op- ponent{\textquoteright}s pieces{\textquoteright} locations) the belief state{\textquoteright}s sizes dwarf those of other partial information games like bridge, scrabble, and poker{\textendash}and there is no easy way to generate states satisfying the given observa- tions. We show that statistical sampling approaches can be developed to do well in such games. We show that it is not necessary for the random sample to consist only of game boards that satisfy each and every one of a player{\textquoteright}s observations. In fact, we win 24\% more often by beginning with such completely consistent boards and gradually switching (as the game progressed) to boards that are merely consistent with the latest observation. This surprising result is explained by noting that as the game progresses, a board that is consistent with the last move becomes more and more likely to be consistent with the entire set of observations, even if we have no idea what sequence of moves might have actually generated this board. }, url = {http://www.ijcai.org/papers/0878.pdf}, author = {Parker,A. and Nau, Dana S. and V.S. Subrahmanian} } @article {14071, title = {The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {16291, title = {The Genome Sequence of Trypanosoma Cruzi, Etiologic Agent of Chagas Disease}, journal = {ScienceScience}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {19073, title = {The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease}, journal = {Science}, volume = {309}, year = {2005}, month = {2005}, author = {El-Sayed, N.M. and Myler,P. J and Bartholomeu,D. C and Nilsson,D. and Aggarwal,G. and Tran,A. N and Ghedin,E. and Worthey,E. A and Delcher,A. L and Blandin,G. and others} } @conference {18882, title = {Going far, logically}, volume = {19}, year = {2005}, month = {2005///}, pages = {615 - 615}, abstract = {There are numerous applications where we need toensure that multiple moving objects are sufficiently far apart. Furthermore, in many moving object do- mains, there is positional indeterminacy {\textemdash} we are not 100\% sure exactly when a given moving object will be at a given location. [Yaman et al., 2004] provided a logic of motion but did not provide algo- rithms to ensure that moving objects are kept suf- ficiently far apart. In this paper, we extend their logic to include a {\textquotedblleft}far{\textquotedblright} predicate. We develop the CheckFar algorithm that checks if any given two objects will always be sufficiently far apart at dur- ing a time interval. We have run a set of experi- ments showing that our CheckFar algorithm scales very well. }, url = {http://www.cs.umd.edu/~nau/papers/yaman2005going.pdf}, author = {Yaman,F. and Nau, Dana S. and V.S. Subrahmanian} } @conference {18872, title = {A hierarchical task-network planner based on symbolic model checking}, year = {2005}, month = {2005///}, pages = {300 - 309}, abstract = {Although several approaches have been developed for planning in nondeterministic domains, solving large planning problems is still quite difficult. In this work, we present a novel algorithm, called YoYo, for planning in nondeterministic domains under the assumption of full observability. This algorithm enables us to combine the power of search-control strategies as in Planning with Hierarchical Task Networks (HTNs) with tech- niques from the Planning via Symbolic Model-Checking (SMC). Our experimental evaluation confirms the po- tentialities of our approach, demonstrating that it com- bines the advantages of these paradigms.}, url = {https://www.aaai.org/Papers/ICAPS/2005/ICAPS05-031.pdf}, author = {Kuter,U. and Nau, Dana S. and Pistore,M. and Traverso,P.} } @article {18908, title = {Inferencing in Support of Active Templates}, year = {2005}, month = {2005/02//}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {The primary accomplishments of this project include the following: (1) HICAP is a general purpose planning architecture to assist military commanders with planning NEOs (Noncombatant Evacuation Operations). HICAP integrates a hierarchical task editor with a planning tool. Military planners select a task to decompose in the task editor and then use the planning tool to interactively refine it into an operational plan. (2) SHOP and SHOP2 are some simple, practical planning tools based on HTN planning. Their practical utility is shown by the mergence of an active set of users, which include government laboratories, industrial R\&D projects, and academic settings. SHOP2 received one of the top four awards in the 2002 International Planning Competition. (3) The Air Force Research Laboratory{\textquoteright}s Causal Analysis Tool (CAT) is a system for creating and analyzing causal models similar to Bayesian networks. We have enhanced CAT by developing an approach to quickly generate plans that have high probabilities of success.}, keywords = {*ARTILLERY AMMUNITION, *HIGH CAPACITY PROJECTILES, AMMUNITION AND EXPLOSIVES, BAYES THEOREM, COALITION, Collaboration, Computer architecture, COMPUTER HARDWARE, Computer networks, HICAP(HIGH CAPACITY ARTILLARY PROJECTILES), MILITARY COMMANDERS, NEO(NONCOMBATANT EVACUATION OPERATIONS), NONCOMBATANT., PE63760E, planning, probability, PROJECTILE TRAJECTORIES, TASK SUPPORT, WUAFRLATEMPO02}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA431023}, author = {Nau, Dana S.} } @article {18910, title = {Information gathering during planning for Web Service composition}, journal = {Web Semantics: Science, Services and Agents on the World Wide Web}, volume = {3}, year = {2005}, month = {2005/10//}, pages = {183 - 205}, abstract = {Hierarchical task network (HTN) based planning techniques have been applied to the problem of composing Web Services, especially when described using the OWL-S service ontologies. Many of the existing Web Services are either exclusively information providing or crucially depend on information-providing services. Thus, many interesting service compositions involve collecting information either during execution or during the composition process itself. In this paper, we focus on the latter issue. In particular, we present ENQUIRER , an HTN-planning algorithm designed for planning domains in which the information about the initial state of the world may not be complete, but it is discoverable through plan-time information-gathering queries. We have shown that ENQUIRER is sound and complete, and derived several mathematical relationships among the amount of available information, the likelihood of the planner finding a plan, and the quality of the plan found. We have performed experimental tests that confirmed our theoretical results and that demonstrated how ENQUIRER can be used for Web Service composition.}, keywords = {HTN planning, Information gathering, Web Service composition}, isbn = {1570-8268}, doi = {10.1016/j.websem.2005.07.001}, url = {http://www.sciencedirect.com/science/article/pii/S1570826805000168}, author = {Kuter,Ugur and Sirin,Evren and Parsia,Bijan and Nau, Dana S. and Hendler,James} } @article {17258, title = {Interactive sonification of choropleth maps}, journal = {IEEE Multimedia}, volume = {12}, year = {2005}, month = {2005/06//April}, pages = {26 - 35}, abstract = {Auditory information is an important channel for the visually impaired. Effective sonification (the use of non-speech audio to convey information) promotes equal working opportunities for people with vision impairments by helping them explore data collections for problem solving and decision making. Interactive sonification systems can make georeferenced data accessible to people with vision impairments. The authors compare methods for using sound to encode georeferenced data patterns and for navigating maps.}, keywords = {audio signal processing, audio user interfaces, Auditory (non-speech) feedback, auditory information, cartography, choropleth maps, data collections, decision making, Evaluation, Feedback, georeferenced data, Guidelines, handicapped aids, Hardware, HUMANS, information resources, interaction style, Interactive sonification, interactive systems, Navigation, nonspeech audio, problem solving, Problem-solving, sound, universal usability, US Government, User interfaces, vision impairments, World Wide Web}, isbn = {1070-986X}, doi = {10.1109/MMUL.2005.28}, author = {Zhao,Haixia and Smith,B. K and Norman,K. and Plaisant, Catherine and Shneiderman, Ben} } @article {16017, title = {Introduction to the special review issue}, journal = {Artificial Intelligence}, volume = {169}, year = {2005}, month = {2005///}, pages = {103 - 103}, author = {Perlis, Don and Norvig,P.} } @inbook {16931, title = {A Knowledge Integration Framework for Information Visualization}, booktitle = {From Integrated Publication and Information Systems to Information and Knowledge EnvironmentsFrom Integrated Publication and Information Systems to Information and Knowledge Environments}, series = {Lecture Notes in Computer Science}, volume = {3379}, year = {2005}, month = {2005///}, pages = {207 - 220}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Users can better understand complex data sets by combining insights from multiple coordinated visual displays that include relevant domain knowledge. When dealing with multidimensional data and clustering results, the most familiar displays and comprehensible are 1- and 2-dimensional projections (histograms, and scatterplots). Other easily understood displays of domain knowledge are tabular and hierarchical information for the same or related data sets. The novel parallel coordinates view [6] powered by a direct-manipulation search, offers strong advantages, but requires some training for most users. We provide a review of related work in the area of information visualization, and introduce new tools and interaction examples on how to incorporate users{\textquoteright} domain knowledge for understanding clustering results. Our examples present hierarchical clustering of gene expression data, coordinated with a parallel coordinates view and with the gene annotation and gene ontology.}, isbn = {978-3-540-24551-3}, url = {http://dx.doi.org/10.1007/978-3-540-31842-2_21}, author = {Seo,Jinwook and Shneiderman, Ben}, editor = {Hemmje,Matthias and Nieder{\'e}e,Claudia and Risse,Thomas} } @article {14918, title = {Lambertian reflectance and linear subspaces}, volume = {:~09/705,507}, year = {2005}, month = {2005/02/08/}, abstract = {A method for choosing an image from a plurality of three-dimensional models which is most similar to an input image is provided. The method includes the steps of: (a) providing a database of the plurality of three-dimensional models; (b) providing an input image; (c) positioning each three-dimensional model relative to the input image; (d) for each three-dimensional model, determining a rendered image that is most similar to the input image by: (d)(i) computing a linear subspace that describes an approximation to the set of all possible rendered images that each three-dimensional model can produce under all possible lighting conditions where each point in the linear subspace represents a possible image; and one of (d)(ii) finding the point on the linear subspace that is closest to the input image or finding a rendered image in a subset of the linear subspace obtained by projecting the set of images that are generated by positive lights onto the linear subspace; (e) computing a...}, url = {http://www.google.com/patents?id=6hEWAAAAEBAJ}, author = {Jacobs, David W. and Basri,Ronen}, editor = {NEC Laboratories America, Inc.} } @conference {18911, title = {Learning approximate preconditions for methods in hierarchical plans}, series = {ICML {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {337 - 344}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A significant challenge in developing planning systems for practical applications is the difficulty of acquiring the domain knowledge needed by such systems. One method for acquiring this knowledge is to learn it from plan traces, but this method typically requires a huge number of plan traces to converge. In this paper, we show that the problem with slow convergence can be circumvented by having the learner generate solution plans even before the planning domain is completely learned. Our empirical results show that these improvements reduce the size of the training set that is needed to find correct answers to a large percentage of planning problems in the test set.}, isbn = {1-59593-180-5}, doi = {10.1145/1102351.1102394}, url = {http://doi.acm.org/10.1145/1102351.1102394}, author = {Ilghami,Okhtay and Mu{\~n}oz-Avila,H{\'e}ctor and Nau, Dana S. and Aha,David W.} } @article {18912, title = {Learning preconditions for planning from plan traces and HTN structure}, journal = {Computational Intelligence}, volume = {21}, year = {2005}, month = {2005///}, pages = {388 - 413}, abstract = {A great challenge in developing planning systems for practical applications is the difficulty of acquiring the domain information needed to guide such systems. This paper describes a way to learn some of that knowledge. More specifically, the following points are discussed. (1) We introduce a theoretical basis for formally defining algorithms that learn preconditions for Hierarchical Task Network (HTN) methods. (2) We describe Candidate Elimination Method Learner (CaMeL), a supervised, eager, and incremental learning process for preconditions of HTN methods. We state and prove theorems about CaMeL{\textquoteright}s soundness, completeness, and convergence properties. (3) We present empirical results about CaMeL{\textquoteright}s convergence under various conditions. Among other things, CaMeL converges the fastest on the preconditions of the HTN methods that are needed the most often. Thus CaMeL{\textquoteright}s output can be useful even before it has fully converged.}, keywords = {candidate elimination, HTN planning, learning, version spaces}, isbn = {1467-8640}, doi = {10.1111/j.1467-8640.2005.00279.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1467-8640.2005.00279.x/abstract}, author = {Ilghami,Okhtay and Nau, Dana S. and Mu{\~n}oz-Avila,H{\'e}ctor and Aha,David W.} } @article {16096, title = {Listening to Maps: User Evaluation of Interactive Sonifications of Geo-Referenced Data}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {In this paper, we summarize the Auditory Information Seeking Principle (AISP) (gist, navigate, filter, and details-ondemand). To improve blind access to geo-referenced statistical data, we developed several interactive sonifications, adhering to the above AISP. Two user studies are presented. In the first user study with nine sighted subjects, a preliminary map design is compared with an enhanced table design. The study shows subjects can recognize geographic data distribution patterns on a real map with 51 geographic regions, in both designs. The map-based design was strongly preferred. The study also shows evidence that AISP conforms to people information seeking strategies. Based on the observations from the first user study, a second user study was conducted with forty-eight sighted subjects comparing four map designs. The effects of using sound to encode vertical geographic positions and two map navigation methods were compared. The result is presented and future work is discussed.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6518}, author = {Zhao,Haixia and Smith,Benjamin K and Norman,Kent L and Plaisant, Catherine and Shneiderman, Ben} } @article {17282, title = {Listening to Maps: User Evaluation of Interactive Sonifications of Geo-Referenced Data (2004)}, journal = {Institute for Systems Research Technical Reports}, year = {2005}, month = {2005///}, abstract = {In this paper, we summarize the Auditory Information Seeking Principle (AISP) (gist, navigate, filter, and details-ondemand). To improve blind access to geo-referenced statistical data, we developed several interactive sonifications, adhering to the above AISP. Two user studies are presented. In the first user study with nine sighted subjects, a preliminary map design is compared with an enhanced table design. The study shows subjects can recognize geographic data distribution patterns on a real map with 51 geographic regions, in both designs. The map-based design was strongly preferred. The study also shows evidence that AISP conforms to people information seeking strategies. Based on the observations from the first user study, a second user study was conducted with forty-eight sighted subjects comparing four map designs. The effects of using sound to encode vertical geographic positions and two map navigation methods were compared. The result is presented and future work is discussed.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6518}, author = {Zhao,Haixia and Smith,Benjamin K and Norman,Kent L and Plaisant, Catherine and Shneiderman, Ben} } @conference {16298, title = {Main effects screening}, booktitle = {Proceedings of the 27th international conference on Software engineering - ICSE {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {293 - 293}, address = {St. Louis, MO, USA}, doi = {10.1145/1062455.1062515}, url = {http://dl.acm.org/citation.cfm?id=1062515}, author = {Yilmaz,Cemal and Krishna,Arvind S. and Memon, Atif M. and Porter, Adam and Schmidt,Douglas C. and Gokhale,Aniruddha and Natarajan,Balachandran} } @conference {15453, title = {Main effects screening: a distributed continuous quality assurance process for monitoring performance degradation in evolving software systems}, booktitle = {Proceedings of the 27th international conference on Software engineering}, series = {ICSE {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {293 - 302}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Developers of highly configurable performance-intensive software systems often use a type of in-house performance-oriented "regression testing" to ensure that their modifications have not adversely affected their software{\textquoteright}s performance across its large configuration space. Unfortunately, time and resource constraints often limit developers to in-house testing of a small number of configurations and unreliable extrapolation from these results to the entire configuration space, which allows many performance bottlenecks and sources of QoS degradation to escape detection until systems are fielded. To improve performance assessment of evolving systems across large configuration spaces, we have developed a distributed continuous quality assurance (DCQA) process called main effects screening that uses in-the-field resources to execute formally designed experiments to help reduce the configuration space, thereby allowing developers to perform more targeted in-house QA. We have evaluated this process via several feasibility studies on several large, widely-used performance-intensive software systems. Our results indicate that main effects screening can detect key sources of performance degradation in large-scale systems with significantly less effort than conventional techniques.}, keywords = {design of experiment theory, distributed continuous quality assurance, performance-oriented regression testing}, isbn = {1-58113-963-2}, doi = {10.1145/1062455.1062515}, url = {http://doi.acm.org/10.1145/1062455.1062515}, author = {Yilmaz,Cemal and Krishna,Arvind S. and Memon, Atif M. and Porter, Adam and Schmidt,Douglas C. and Gokhale,Aniruddha and Natarajan,Balachandran} } @article {19499, title = {MEAD: support for Real-Time Fault-Tolerant CORBA}, journal = {Concurrency and Computation: Practice and Experience}, volume = {17}, year = {2005}, month = {2005///}, pages = {1527 - 1545}, abstract = {The OMG{\textquoteright}s Real-Time CORBA (RT-CORBA) and Fault-Tolerant CORBA (FT-CORBA) specifications make it possible for today{\textquoteright}s CORBA implementations to exhibit either real-time or fault tolerance in isolation. While real-time requires a priori knowledge of the system{\textquoteright}s temporal operation, fault tolerance necessarily deals with faults that occur unexpectedly, and with possibly unpredictable fault recovery times. The MEAD (Middleware for Embedded Adaptive Dependability) system attempts to identify and to reconcile the conflicts between real-time and fault tolerance, in a resource-aware manner, for distributed CORBA applications. MEAD supports transparent yet tunable fault tolerance in real-time, proactive dependability, resource-aware system adaptation to crash, communication and timing faults with bounded fault detection and fault recovery. Copyright {\textcopyright} 2005 John Wiley \& Sons, Ltd.}, keywords = {CORBA, Fault tolerance, non-determinism, predictability, real-time, recovery, trade-offs}, isbn = {1532-0634}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cpe.882/abstract}, author = {Narasimhan, P. and Tudor Dumitras and Paulos, A. M. and Pertet, S. M. and Reverte, C. F. and Slember, J. G. and Srivastava, D.} } @conference {18402, title = {Measuring productivity on high performance computers}, booktitle = {11th IEEE International Symposium on Software Metric}, year = {2005}, month = {2005///}, abstract = {In the high performance computing domain, the speed ofexecution of a program has typically been the primary performance metric. But productivity is also of concern to high performance computing developers. In this paper we will discuss the problems of defining and measuring productivity for these machines and we develop a model of productivity that includes both a performance component and a component that measures the development time of the program. We ran several experiments using students in high performance courses at several universities, and we report on those results with respect to our model of productivity. }, author = {Zelkowitz, Marvin V and Basili, Victor R. and Asgari, S. and Hochstein, L. and Hollingsworth, Jeffrey K and Nakamura, T.} } @conference {12108, title = {A metric space for productivity measurement in software development}, booktitle = {Proceedings of the second international workshop on Software engineering for high performance computing system applications}, series = {SE-HPCS {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {13 - 16}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We define a metric space to measure the contributions of individual programmers to a software development project. It allows us to measure the distance between the contributions of two different programmers as well as the absolute contribution of each individual programmer. Our metric is based on an action function that provides a picture of how one programmer{\textquoteright}s approach differs from another at each instance of time during the project. We apply our metric to data we collected from students taking a course in parallel programming. We display the pictures for two students who showed approximately equal contributions but who followed very different paths through the course.}, isbn = {1-59593-117-1}, doi = {10.1145/1145319.1145324}, url = {http://doi.acm.org/10.1145/1145319.1145324}, author = {Numrich,Robert W. and Hochstein, Lorin and Basili, Victor R.} } @article {12148, title = {Metrics of software architecture changes based on structural distance}, journal = {IEEE METRICS}, year = {2005}, month = {2005///}, pages = {8 - 8}, abstract = {Software architecture is an important form of abstrac-tion, representing the overall system structure and the re- lationship among components. When software is modified from one version to another, its architecture may change. Software modification involving architectural change is of- ten difficult when the change goes beyond the original ar- chitectural design, involving changes to the connectivity of multiple components. Existing research has looked at ar- chitectural change at the level of architecture metrics such as size, complexity, coupling and cohesion, which abstract a particular version of the software in isolation. In this pa- per, we argue that this level of abstraction is often too high to characterize some interesting aspects of the architectural change process, and propose an approach that takes into account the change in connectivity from version to version of individual components. In this approach, two endpoints of a major change are taken as reference points, and inter- mediate connectivity changes are examined relative to the endpoints. We define a distance measure between software structures using a graph kernel function, which is quite powerful as it is applicable to any software structure repre- sentable as a graph. Using this distance measure, we define a metric which models the architecture change as a transi- tion between two endpoints. In addition to theoretical anal- ysis of the approach, we present empirical results obtained by applying the approach to open-source software projects to evaluate its validity and usefulness. }, author = {Nakamura, T. and Basili, Victor R.} } @conference {18887, title = {A motion closed world asumption}, volume = {19}, year = {2005}, month = {2005///}, pages = {621 - 621}, abstract = {Yaman et. al. [Yaman et al., 2004] introduce {\textquotedblleft}gotheories{\textquotedblright} to reason about moving objects. In this paper, we show that this logic often does not allow us to infer that an object is not present at a given place or region, even though common sense would dictate that this is a reasonable inference to make. We define a class of models of go-theories called coherent models. We use this concept to define a motion closed world assumption (MCWA) and de- velop a notion of MCWA-entailment. We show that checking if a go-theory has a coherent model is NP-complete. An in atom checks if a given ob- ject is present in a given region sometime in a given time interval. We provide sound and complete al- gorithms to check if a ground in literal (positive or negative in atom) can be inferred from a go- theory using the MCWA. In our experiments our algorithms answer such queries in less than 1 sec- ond when there are up to 1,000 go-atoms per object. }, url = {http://ijcai.org/papers/1227.pdf}, author = {Yaman,F. and Nau, Dana S. and V.S. Subrahmanian} } @conference {14710, title = {Mutatis mutandis: safe and predictable dynamic software updating}, booktitle = {Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, series = {POPL {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {183 - 194}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Dynamic software updates can be used to fix bugs or add features to a running program without downtime. Essential for some applications and convenient for others, low-level dynamic updating has been used for many years. Perhaps surprisingly, there is little high-level understanding or language support to help programmers write dynamic updates effectively.To bridge this gap, we present Proteus, a core calculus for dynamic software updating in C-like languages that is flexible, safe, and predictable. Proteus supports dynamic updates to functions (even active ones), to named types and to data, allowing on-line evolution to match source-code evolution as we have observed it in practice. We ensure updates are type-safe by checking for a property we call "con-freeness" for updated types t at the point of update. This means that non-updated code will not use t concretely beyond that point (concrete usages are via explicit coercions) and thus t{\textquoteright}s representation can safely change. We show how con-freeness can be enforced dynamically for a particular program state. We additionally define a novel and efficient static updateability analysis to establish con-freeness statically, and can thus automatically infer program points at which all future (well-formed) updates will be type-safe. We have implemented our analysis for C and tested it on several well-known programs.}, keywords = {capability, dynamic software updating, proteus, Type inference, updateability analysis}, isbn = {1-58113-830-X}, doi = {10.1145/1040305.1040321}, url = {http://doi.acm.org/10.1145/1040305.1040321}, author = {Stoyle,Gareth and Hicks, Michael W. and Bierman,Gavin and Sewell,Peter and Neamtiu,Iulian} } @article {12769, title = {Probabilistic temporal logics via the modal mu-calculus}, journal = {Theoretical Computer Science}, volume = {342}, year = {2005}, month = {2005/09/07/}, pages = {316 - 350}, abstract = {This paper presents a mu-calculus-based modal logic for describing properties of reactive probabilistic labeled transition systems (RPLTSs) and develops a model-checking algorithm for determining whether or not states in finite-state RPLTSs satisfy formulas in the logic. The logic is based on the distinction between (probabilistic) {\^a}{\texteuro}{\oe}systems{\^a}{\texteuro} and (nonprobabilistic) {\^a}{\texteuro}{\oe}observations{\^a}{\texteuro}: using the modal mu-calculus, one may specify sets of observations, and the semantics of our logic then enable statements to be made about the measures of such sets at various system states. The logic may be used to encode a variety of probabilistic modal and temporal logics; in addition, the model-checking problem for it may be reduced to the calculation of solutions to systems of non-linear equations. Finally, the logic induces an equivalence on RPLTSs that coincides with accepted notions of probabilistic bisimulation in the literature.}, keywords = {Model-checking, Probabilistic bisimulation, Probabilistic temporal logic, Probabilistic transition systems, reactive systems}, isbn = {0304-3975}, doi = {10.1016/j.tcs.2005.03.048}, url = {http://www.sciencedirect.com/science/article/pii/S0304397505001829}, author = {Cleaveland, Rance and Iyer,S. Purushothaman and Narasimha,Murali} } @article {16285, title = {Serendipitous discovery of Wolbachia genomes in multiple Drosophila species}, journal = {Genome Biology}, volume = {6}, year = {2005}, month = {2005/02/22/}, pages = {R23 - R23}, abstract = {The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism.}, isbn = {1465-6906}, doi = {10.1186/gb-2005-6-3-r23}, url = {http://genomebiology.com/2005/6/3/R23}, author = {Salzberg,Steven L. and Hotopp,Julie CD and Delcher,Arthur L. and Pop, Mihai and Smith,Douglas R. and Eisen,Michael B. and Nelson,William C.} } @article {17362, title = {Snap-Together Visualization: A User Interface for Coordinating Visualizations via Relational Schemata (2000)}, year = {2005}, month = {2005///}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/6470}, author = {North,Chris and Shneiderman, Ben} } @conference {17888, title = {Spatial indexing of distributed multidimensional datasets}, booktitle = {IEEE International Symposium on Cluster Computing and the Grid, 2005. CCGrid 2005}, volume = {2}, year = {2005}, month = {2005/05/09/12}, pages = {743- 750 Vol. 2 - 743- 750 Vol. 2}, publisher = {IEEE}, organization = {IEEE}, abstract = {While declustering methods for distributed multidimensional indexing of large datasets have been researched widely in the past, replication techniques for multidimensional indexes have not been investigated deeply. In general, a centralized index server may become the performance bottleneck in a wide area network rather than the data servers, since the index is likely to be accessed more often than any of the datasets in the servers. In this paper, we present two different multidimensional indexing algorithms for a distributed environment - a centralized global index and a two-level hierarchical index. Our experimental results show that the centralized scheme does not scale well for either insertion or searching the index. In order to improve the scalability of the index server, we have employed a replication protocol for both the centralized and two-level index schemes that allows some inconsistency between replicas without affecting correctness. Our experiments show that the two-level hierarchical index scheme shows better scalability for both building and searching the index than the non-replicated centralized index, but replication can make the centralized index faster than the two-level hierarchical index for searching in some cases.}, keywords = {centralized global index algorithm, centralized index server, Computer science, database indexing, distributed databases, distributed multidimensional dataset, Educational institutions, File servers, Indexing, Large-scale systems, Multidimensional systems, Network servers, replication protocol, replication techniques, scalability, Sensor systems, spatial data structures, spatial indexing, two-level hierarchical index algorithm, wide area networks}, isbn = {0-7803-9074-1}, doi = {10.1109/CCGRID.2005.1558637}, author = {Nam,B. and Sussman, Alan} } @article {16403, title = {Spatial process and data models: Toward integration of agent-based models and GIS}, journal = {Journal of Geographical Systems}, volume = {7}, year = {2005}, month = {2005///}, pages = {25 - 47}, abstract = {The use of object-orientation for both spatial data and spatial process models facilitates their integration, which can allow exploration and explanation of spatial-temporal phenomena. In order to better understand how tight coupling might proceed and to evaluate the possible functional and efficiency gains from such a tight coupling, we identify four key relationships affecting how geographic data (fields and objects) and agent-based process models can interact: identity, causal, temporal and topological. We discuss approaches to implementing tight integration, focusing on a middleware approach that links existing GIS and ABM development platforms, and illustrate the need and approaches with example agent-based models.}, doi = {10.1007/s10109-005-0148-5}, author = {Brown,D.G. and Riolo,R and Robinson,D.T. and North,M. and Rand, William} } @article {14923, title = {Torrance-sparrow off-specular reflection and linear subspaces for object recognition}, volume = {10/230,888}, year = {2005}, month = {2005/05/31/}, abstract = {The Torrance-Sparrow model of off-specular reflection is recast in a significantly simpler and more transparent form in order to render a spherical-harmonic decomposition more feasible. By assuming that a physical surface consists of small, reflecting facets whose surface normals satisfy a normal distribution, the model captures the off-specular enhancement of the reflected intensity distribution often observed at large angles of incidence and reflection, features beyond the reach of the phenomenological broadening models usually employed. In passing we remove a physical inconsistency in the original treatment, restoring reciprocity and correcting the dependence of reflectance on angle near grazing incidence. It is noted that the results predicted by the model are relatively insensitive to values of its one parameter, the width of the distribution of surface normals.}, url = {http://www.google.com/patents?id=LI4VAAAAEBAJ}, author = {Thornber,Karvel K and Jacobs, David W.}, editor = {NEC Laboratories America, Inc.} } @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.} } @conference {18878, title = {Using domain-configurable search control for probabilistic planning}, volume = {20}, year = {2005}, month = {2005///}, pages = {1169 - 1169}, abstract = {We describe how to improve the performance of MDP planning algorithms by modifying them to use the search-control mechanisms of planners such as TLPlan, SHOP2, and TALplanner. In our experiments, modified versions of RTDP, LRTDP, and Value Iteration were ex- ponentially faster than the original algorithms. On the largest problems the original algorithms could solve, the modified ones were about 10,000 times faster. On another set of problems whose state spaces were more than 14,000 times larger than the original algorithms could solve, the modified algorithms took only about 1/3 second.}, url = {http://www.aaai.org/Papers/AAAI/2005/AAAI05-185.pdf}, author = {Kuter,U. and Nau, Dana S.} } @inbook {18924, title = {Web Service Composition with Volatile Information}, booktitle = {The Semantic Web {\textendash} ISWC 2005}, series = {Lecture Notes in Computer Science}, volume = {3729}, year = {2005}, month = {2005///}, pages = {52 - 66}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In many Web service composition problems, information may be needed from Web services during the composition process. Existing research on Web service composition (WSC) procedures has generally assumed that this information will not change. We describe two ways to take such WSC procedures and systematically modify them to deal with volatile information. The black-box approach requires no knowledge of the WSC procedure{\textquoteright}s internals: it places a wrapper around the WSC procedure to deal with volatile information. The gray-box approach requires partial information of those internals, in order to insert coding to perform certain bookkeeping operations. We show theoretically that both approaches work correctly. We present experimental results showing that the WSC procedures produced by the gray-box approach can run much faster than the ones produced by the black-box approach.}, keywords = {Computer science}, isbn = {978-3-540-29754-3}, url = {http://www.springerlink.com/content/y105x8464k54l760/abstract/}, author = {Au,Tsz-Chiu and Kuter,Ugur and Nau, Dana S.}, editor = {Gil,Yolanda and Motta,Enrico and Benjamins,V. and Musen,Mark} } @inbook {15666, title = {Analyzing the number of samples required for an approximate Monte-Carlo LMS line estimator}, booktitle = {Theory and Applications of Recent Robust MethodsTheory and Applications of Recent Robust Methods}, year = {2004}, month = {2004///}, pages = {207 - 219}, publisher = {Birkh{\"a}user}, organization = {Birkh{\"a}user}, isbn = {3764370602, 9783764370602}, author = {Mount, Dave and Netanyahu,N. S and Zuck,E.} } @article {15439, title = {Applying Model-based Distributed Continuous Quality Assurance Processes to Enhance Persistent Software Attributes}, journal = {IEEE Software}, volume = {21}, year = {2004}, month = {2004///}, pages = {32 - 40}, abstract = {Time and resource constraints often force developers of highlyconfigurable quality of service (QoS)-intensive software sys- tems to guarantee their system{\textquoteright}s persistent software attributes (PSAs) (e.g., functional correctness, portability, efficiency, and QoS) on very few platform configurations and to extrapolate from these configurations to the entire configuration space, which allows many sources of degradation to escape detec- tion until systems are fielded. This article illustrates how distributed continuous quality assurance (DCQA) processes help improve the assessment of these PSAs across large QoS- intensive software system configuration spaces. We also il- lustrate how model-based DCQA processes enable developers to run formally-designed screening experiments that isolate the most significant configuration options, such as different workload parameters, operating system, compiler flags, fea- ture sets, and/or run-time optimization controls. Our empir- ical results show that DCQA processes can be used monitor, safeguard, and enforce PSAs at an acceptable level of cost and effort. }, author = {Krishna,A. S and Yilmaz,C. and Memon, Atif M. and Porter, Adam and Schmidt,D. C and Gokhale,A. and Natarajan,B.} } @book {18895, title = {Automated Planning: Theory and Practice}, year = {2004}, month = {2004/05/03/}, publisher = {Elsevier}, organization = {Elsevier}, abstract = {Automated planning technology now plays a significant role in a variety of demanding applications, ranging from controlling space vehicles and robots to playing the game of bridge. These real-world applications create new opportunities for synergy between theory and practice: observing what works well in practice leads to better theories of planning, and better theories lead to better performance of practical applications. Automated Planning mirrors this dialogue by offering a comprehensive, up-to-date resource on both the theory and practice of automated planning. The book goes well beyond classical planning, to include temporal planning, resource scheduling, planning under uncertainty, and modern techniques for plan generation, such as task decomposition, propositional satisfiability, constraint satisfaction, and model checking. The authors combine over 30 years experience in planning research and development to offer an invaluable text to researchers, professionals, and graduate students. *Comprehensively explains paradigms for automated planning. *Provides a thorough understanding of theory and planning practice, and how they relate to each other. *Presents case studies of applications in space, robotics, CAD/CAM, process control, emergency operations, and games.*Provides a thorough understanding of AI planning theory and practice, and how they relate to each other. *Covers all the contemporary topics of planning, as well as important practical applications of planning, such as model checking and game playing. *Presents case studies and applications in planning engineering, space, robotics, CAD/CAM, process control, emergency operations, and games.*Provides lecture notes, examples of programming assignments, pointers to downloadable planning systems and related information online.}, keywords = {Business \& Economics / Management, Computers / Intelligence (AI) \& Semantics, Production planning, Production planning/ Data processing, Technology \& Engineering / Robotics}, isbn = {9781558608566}, author = {Ghallab,Malik and Nau, Dana S. and Traverso,Paolo} } @article {14597, title = {CHARACTERIZATION OF Ath17, A QUANTITATIVE TRAIT LOCUS FOR ATHEROSCLEROSIS SUSCEPTIBILITY BETWEEN C57BL/6J AND 129S1/SvImJ; SINGLE-NUCLEOTIDE POLYMORPHISMS HAVE IMPORTANT IMPLICATIONS ON IDENTIFYING ATHEROSCLEROSIS MODIFIER GENES}, journal = {Cardiovascular Pathology}, volume = {13}, year = {2004}, month = {2004/06//May}, pages = {5 - 6}, abstract = {Although identifying quantitative trait loci (QTL) for atherosclerosis susceptibility in experimental murine models has helped us better understand the pathophysiology of atherosclerosis, identifying the genes underlying these QTL has been a slow and difficult process. We are currently in the process of identifying the gene that underlies Ath17, an atherosclerosis-susceptibility QTL we discovered in a (C57BL/6J{\texttimes}129S1/SvImJ)F2 intercross. Ath17 maps to a 6 cM interval region on chromosome 10 (D10Mit31, LOD score 6.6) and contains 46 annotated and 133 predicted genes. We searched the Celera Discovery System database for single nucleotide polymorphisms (SNPs) between C57BL/6J (B6) and 129S1/SvImJ in the Ath17 region and found defined blocks of high and low diversity and one polymorphic region of over 4 Mb surrounded by nonpolymorphic regions. Four of the genes, including the annotated Desrt, in the polymorphic region contained mis-sense mutations. The Desrt coding region contained four mis-sense mutations: B6 lysine to 129 glutamic acid at aa382, B6 asparagine to 129 serine at aa388, B6 threonine to 129 alanine at aa836, and B6 glycine to 129 serine at aa964. In addition, intron 5 of Desrt contained a SNP which co-localized with a putative transcription factor binding site. Desrt is a DNA binding protein, widely expressed in adult tissues, and likely plays a role in cell proliferation, differentiation, and development, making Dsert a strong candidate gene for Ath17. The murine SNP database dramatically reduced the percentage of the murine genome we had to search to find viable candidate genes for Ath17.}, isbn = {1054-8807}, doi = {10.1016/j.carpath.2004.03.010}, url = {http://www.sciencedirect.com/science/article/pii/S1054880704000377}, author = {Ishimori,Naoki and Walsh,Kenneth and Zheng,Xiangqun and Lu,Fu and Hannenhalli, Sridhar and Nusskern,Deborah and Mural,Richard and Paigen,Beverly} } @article {18016, title = {Circuit architecture for reduced-synchrony on-chip interconnect}, volume = {10/166,008}, year = {2004}, month = {2004/07/27/}, abstract = {The invention relates to an interconnect, and to interconnect architecture, for communicating between processing elements and memory modules in a computer system comprising on-chip parallel computation, in order to reduce the tight synchrony that is required by important components of most present computers.}, url = {http://www.google.com/patents?id=RRUSAAAAEBAJ}, author = {Vishkin, Uzi and Nuzman,Joseph F.}, editor = {University of Maryland, College Park} } @conference {17845, title = {A Comparative Study of Spatial Indexing Techniques for Multidimensional Scientific Datasets}, booktitle = {Scientific and Statistical Database Management, International Conference on}, year = {2004}, month = {2004///}, pages = {171 - 171}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Scientific applications that query into very large multi-dimensional datasets are becoming more common. These datasets are growing in size every day, and are becoming truly enormous, making it infeasible to index individual data elements. We have instead been experimenting with chunking the datasets to index them, grouping data elements into small chunks of a fixed, but dataset-specific, size to take advantage of spatial locality. While spatial indexing structures based on R-trees perform reasonably well for the rectangular bounding boxes of such chunked datasets, other indexing structures based on KDB-trees, such as Hybrid trees, have been shown to perform very well for point data. In this paper, we investigate how all these indexing structures perform for multidimensional scientific datasets, and compare their features and performance with that of SH-trees, an extension of Hybrid trees, for indexing multi-dimensional rectangles. Our experimental results show that the algorithms for building and searching SH-trees outperform those for R-trees, R*-trees, and X-trees for both real application and synthetic datasets and queries. We show that the SH-tree algorithms perform well for both low and high dimensional data, and that they scale well to high dimensions both for building and searching the trees.}, doi = {http://doi.ieeecomputersociety.org/10.1109/SSDM.2004.1311209}, author = {Nam,Beomseok and Sussman, Alan} } @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 {15647, title = {A computational framework for incremental motion}, booktitle = {Proceedings of the twentieth annual symposium on Computational geometry}, series = {SCG {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {200 - 209}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We propose a generic computational framework for maintaining a discrete geometric structure defined by a collection of static and mobile objects. We assume that the mobile objects move incrementally, that is, in discrete time steps. We assume that the structure to be maintained is a function of the current locations of the mobile and static objects (independent of their prior motion). Unlike other models for kinetic computation, we place no restrictions on the motion nor on its predictability.In order to handle unrestricted incremental motion, our framework is based on the coordination of two computational entities. The first is the incremental motion algorithm. It is responsible for maintaining the structure and a set of certificates, or conditions, that prove the structure{\textquoteright}s correctness. The other entity, called the motion processor, is responsible for handling all the low-level aspects of motion, including computing and/or tracking the motion of the mobile objects, answering queries about their current positions and velocities, and validating that the object motions satisfy simple motion estimates, which are generated by the incremental motion algorithm. Computational efficiency is measured in terms of the number of interactions between these two entities.}, keywords = {competitive analysis, incremental motion, kinetic data structures}, isbn = {1-58113-885-7}, doi = {10.1145/997817.997849}, url = {http://doi.acm.org/10.1145/997817.997849}, author = {Mount, Dave and Netanyahu,Nathan S. and Piatko,Christine D. and Silverman,Ruth and Wu,Angela Y.} } @conference {16302, title = {A distributed continuous quality assurance process to manage variability in performance-intensive software}, booktitle = {19th ACM OOPSLA Workshop on Component and Middleware Performance}, year = {2004}, month = {2004///}, author = {Krishna,A. and Yilmaz,C. and Memon, Atif M. and Porter, Adam and Schmidt,D. C and Gokhale,A. and Natarajan,B.} } @article {19004, title = {The Drosophila U1-70K Protein Is Required for Viability, but Its Arginine-Rich Domain Is Dispensable}, journal = {GeneticsGenetics}, volume = {168}, year = {2004}, month = {2004/12/01/}, pages = {2059 - 2065}, abstract = {The conserved spliceosomal U1-70K protein is thought to play a key role in RNA splicing by linking the U1 snRNP particle to regulatory RNA-binding proteins. Although these protein interactions are mediated by repeating units rich in arginines and serines (RS domains) in vitro, tests of this domain{\textquoteright}s importance in intact multicellular organisms have not been carried out. Here we report a comprehensive genetic analysis of U1-70K function in Drosophila. Consistent with the idea that U1-70K is an essential splicing factor, we find that loss of U1-70K function results in lethality during embryogenesis. Surprisingly, and contrary to the current view of U1-70K function, animals carrying a mutant U1-70K protein lacking the arginine-rich domain, which includes two embedded sets of RS dipeptide repeats, have no discernible mutant phenotype. Through double-mutant studies, however, we show that the U1-70K RS domain deletion no longer supports viability when combined with a viable mutation in another U1 snRNP component. Together our studies demonstrate that while the protein interactions mediated by the U1-70K RS domain are not essential for viability, they nevertheless contribute to an essential U1 snRNP function.}, isbn = {0016-6731, 1943-2631}, doi = {10.1534/genetics.104.032532}, url = {http://www.genetics.org/content/168/4/2059}, author = {Salz,Helen K. and Mancebo,Ricardo S. Y. and Nagengast,Alexis A. and Speck,Olga and Psotka,Mitchell and Mount, Stephen M.} } @conference {18871, title = {Forward-chaining planning in nondeterministic domains}, year = {2004}, month = {2004///}, pages = {513 - 518}, abstract = {In this paper, we present a general technique for tak- ing forward-chaining planners for deterministic do- mains (e.g., HSP, TLPlan, TALplanner, and SHOP2) and adapting them to work in nondeterministic do- mains. Our results suggest that our technique pre- serves many of the desirable properties of these plan- ners, such as the ability to use heuristic techniques to achieve highly efficient planning.In our experimental studies on two problem domains, the well-known MBP algorithm took exponential time, confirming prior results by others. A nondeterminized version of SHOP2 took only polynomial time. The polynomial-time figures are confirmed by a complex- ity analysis, and a similar complexity analysis shows that a nondeterminized version of TLPlan would per- form similarly. }, url = {https://www.aaai.org/Papers/AAAI/2004/AAAI04-082.pdf}, author = {Kuter,U. and Nau, Dana S.} } @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 {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.} } @article {18905, title = {HTN planning for Web Service composition using SHOP2}, journal = {Web Semantics: Science, Services and Agents on the World Wide Web}, volume = {1}, year = {2004}, month = {2004/10//}, pages = {377 - 396}, abstract = {Automated composition of Web Services can be achieved by using AI planning techniques. Hierarchical Task Network (HTN) planning is especially well-suited for this task. In this paper, we describe how HTN planning system SHOP2 can be used with OWL-S Web Service descriptions. We provide a sound and complete algorithm to translate OWL-S service descriptions to a SHOP2 domain. We prove the correctness of the algorithm by showing the correspondence to the situation calculus semantics of OWL-S. We implemented a system that plans over sets of OWL-S descriptions using SHOP2 and then executes the resulting plans over the Web. The system is also capable of executing information-providing Web Services during the planning process. We discuss the challenges and difficulties of using planning in the information-rich and human-oriented context of Web Services.}, keywords = {HTN planning, OWL-S, SHOP2, Web Service composition, Web services}, isbn = {1570-8268}, doi = {10.1016/j.websem.2004.06.005}, url = {http://www.sciencedirect.com/science/article/pii/S1570826804000113}, author = {Sirin,Evren and Parsia,Bijan and Wu,Dan and Hendler,James and Nau, Dana S.} } @conference {17806, title = {Implementing stable semantics by linear programming}, booktitle = {Logic Programming and Non-Monotonic Reasoning, Proceedings of the Second International Workshop}, volume = {7}, year = {2004}, month = {2004///}, pages = {23 - 42}, author = {Bell,C. and Nerode,A. and Ng,R. T and V.S. Subrahmanian} } @inbook {18909, title = {Information Gathering During Planning for Web Service Composition}, booktitle = {The Semantic Web {\textendash} ISWC 2004}, series = {Lecture Notes in Computer Science}, volume = {3298}, year = {2004}, month = {2004///}, pages = {335 - 349}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Hierarchical Task-Network (HTN) based planning techniques have been applied to the problem of composing Web Services, especially when described using the OWL - S service ontologies. Many of the existing Web Services are either exclusively information providing or crucially depend on information-providing services. Thus, many interesting service compositions involve collecting information either during execution or during the composition process itself. In this paper, we focus on the latter issue. In particular, we present ENQUIRER , an HTN-planning algorithm designed for planning domains in which the information about the initial state of the world may not be complete, but it is discoverable through plan-time information-gathering queries. We have shown that ENQUIRER is sound and complete, and derived several mathematical relationships among the amount of available information, the likelihood of the planner finding a plan, and the quality of the plan found. We have performed experimental tests that confirmed our theoretical results and that demonstrated how ENQUIRER can be used in Web Service composition.}, keywords = {Computer science}, isbn = {978-3-540-23798-3}, url = {http://www.springerlink.com/content/v829m5080fc0bpng/abstract/}, author = {Kuter,Ugur and Sirin,Evren and Nau, Dana S. and Parsia,Bijan and Hendler,James}, editor = {McIlraith,Sheila and Plexousakis,Dimitris and van Harmelen,Frank} } @conference {16487, title = {Links and paths through life sciences data sources}, booktitle = {Data Integration in the Life Sciences}, year = {2004}, month = {2004///}, pages = {203 - 211}, author = {Lacroix,Z. and Murthy,H. and Naumann,F. and Raschid, Louiqa} } @conference {18881, title = {A logic of motion}, year = {2004}, month = {2004///}, pages = {85 - 94}, abstract = {There are numerous applications such as air traffic manage- ment, cellular phone location tracking, and vehicle protection systems where there is a critical need to reason about moving objects. In this paper, we propose a formal logic of motion (LOM for short). We provide a formal syntax for LOM, as well as a model theory for LOM. In addition, we develop al- gorithms to check consistency of LOM theories, as well as to answer certain kinds of queries posed to LOM theories. We have implemented these algorithms in a prototype LOM sys- tem - we describe experiments showing that such queries can be efficiently executed in practice.}, url = {http://www.aaai.org/Papers/KR/2004/KR04-011.pdf}, author = {Yaman,F. and Nau, Dana S. and V.S. Subrahmanian} } @article {15454, title = {A Model-based Distributed Continuous Quality Assurance Process to Enhance the Quality of Service of Evolving Performance-intensive Software Systems}, journal = {Proceedings of the 2nd ICSE Workshop on Remote Analysis and Measurement of Software Systems (RAMSS), Edinburgh, Scotland, UK}, year = {2004}, month = {2004///}, abstract = {Performance-intensive software, such as that found in high-perfo-rmance computing systems and distributed real-time and embedded systems, increasingly executes on a multitude of platforms and user contexts. To ensure that performance-intensive software meets its quality of service (QoS) requirements, it must often be fine-tuned to specific platforms/contexts by adjusting many (in some cases hun- dreds of) configuration options. Developers who write these types of systems must therefore try to ensure that their additions and mod- ifications work across this large configuration space. In practice, however, time and resource constraints often force developers to assess performance on very few configurations and to extrapolate from these to the entire configuration space, which allows many performance bottlenecks and sources of QoS degradation to escape detection until systems are fielded. To improve the assessment of performance across large config- uration spaces, we present a model-based approach to develop- ing and deploying a new distributed continuous quality assurance (DCQA) process. Our approach builds upon and extends the Skoll environment, which is developing and validating novel software QA processes and tools that leverage the extensive computing resources of worldwide user communities in a distributed, continuous man- ner to significantly and rapidly improve software quality. This pa- per describes how our new DCQA performance assessment process enables developers to run formally-designed screening experiments that isolate the most significant options. After that, exhaustive ex- periments (on the now much smaller configuration space) are con- ducted. We implemented this process using model-based software tools and executed it in the Skoll environment to demonstrate its ef- fectiveness via two experiments on widely used QoS-enabled mid- dleware. Our results show that model-based DCQA processes im- proves developer insight into the effect of system changes on per- formance at an acceptable cost. }, author = {Yilmaz,C. and Krishna,A. S and Memon, Atif M. and Porter, Adam and Schmidt,D. C and Gokhale,A. and Natarajan,B.} } @article {12938, title = {Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh}, journal = {Canadian Journal of Microbiology}, volume = {50}, year = {2004}, month = {2004/10//}, pages = {827 - 834}, abstract = {A total of 1500 environmental strains of Vibrio parahaemolyticus, isolated from the aquatic environment of Bangladesh, were screened for the presence of a major V. parahaemolyticus virulence factor, the thermostable direct haemolysin (tdh) gene, by the colony blot hybridization method using a digoxigenin-labeled tdh gene probe. Of 1500 strains, 5 carried the tdh sequence, which was further confirmed by PCR using primers specific for the tdh gene. Examination by PCR confirmed that the 5 strains were V. parahamolyticus and lacked the thermostable direct haemolysin-related haemolysin (trh) gene, the alternative major virulence gene known to be absent in pandemic strains. All 5 strains gave positive Kanagawa phenomenon reaction with characteristic beta-haemolysis on Wagatsuma agar medium. Southern blot analysis of the HindIII-digested chromosomal DNA demonstrated, in all 5 strains, the presence of 2 tdh genes common to strains positive for Kanagawa phenomenon. However, the 5 strains were found to belong to 3 different serotypes (O3:K29, O4:K37, and O3:K6). The 2 with pandemic serotype O3:K6 gave positive results in group-specific PCR and ORF8 PCR assays, characteristics unique to the pandemic clone. Clonal variations among the 5 isolates were analyzed by comparing RAPD and ribotyping patterns. Results showed different patterns for the 3 serotypes, but the pattern was identical among the O3:K6 strains. This is the first report on the isolation of pandemic O3:K6 strains of V. parahaemolyticus from the aquatic environment of Bangladesh.}, url = {http://umd.library.ingentaconnect.com/content/nrc/cjm/2004/00000050/00000010/art00007}, author = {Islam,M. S. and Tasmin,Rizwana and Khan,Sirajul I. s l a m and Bakht,Habibul B. M. and Mahmood,Zahid H. a y a t and Rahman,M. Z. i a u r and Bhuiyan,Nurul A. m i n and Nishibuchi,Mitsuaki and Nair,G. B. a l a k r i s h and Sack,R. B. r a d l e y and Huq,Anwar and Rita R Colwell and Sack,David A.} } @inbook {18915, title = {Plan Databases: Model and Algebra}, booktitle = {Foundations of Information and Knowledge Systems}, series = {Lecture Notes in Computer Science}, volume = {2942}, year = {2004}, month = {2004///}, pages = {302 - 319}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Despite the fact that thousands of applications manipulate plans, there has been no work to date on managing large databases of plans. In this paper, we first propose a formal model of plan databases. We describe important notions of consistency and coherence for such databases. We then propose a set of operators similar to the relational algebra to query such databases of plans.}, keywords = {Computer science}, isbn = {978-3-540-20965-2}, url = {http://www.springerlink.com/content/yqhlqtu4te18q2e1/abstract/}, author = {Yaman,Fusun and Adali,Sibel and Nau, Dana S. and Sapino,Maria and Subrahmanian,V.}, editor = {Seipel,Dietmar and Turull-Torres,Jos{\'e}} } @article {15498, title = {Preserving distributed systems critical properties: a model-driven approach}, journal = {Software, IEEE}, volume = {21}, year = {2004}, month = {2004///}, pages = {32 - 40}, abstract = {The need for creating predictability in distributed systems is most often specified in terms of quality-of-service (QoS) requirements, which help define the acceptable levels of dependability with which capabilities such as processing capacity, data throughput, or service availability reach users. For longer-term properties such as scalability, maintainability, adaptability, and system security, we can similarly use persistent software attributes (PSAs) to specify how and to what degree such properties must remain intact as a network expands and evolves over time. The Skoll distributed continuous software quality assurance process helps to identify viable system and software configurations for meeting stringent QOS and PSA requirements by coordinating the use of distributed computing resources. The authors tested their process using the large, rapidly evolving ACE+TAO middleware suite.}, keywords = {configuration management, formal verification, Middleware, middleware suite, model-driven approach, persistent software attributes, QoS requirements, Quality assurance, quality of service, quality-of-service, Skoll distributed computing resources, software configuration, Software maintenance, Software quality, software quality assurance process, system dependability}, isbn = {0740-7459}, doi = {10.1109/MS.2004.50}, author = {Yilmaz,C. and Memon, Atif M. and Porter, Adam and Krishna,A. S and Schmidt,D. C and Gokhale,A. and Natarajan,B.} } @conference {16493, title = {Querying Web-Accessible Life Science Sources: Which paths to choose?}, booktitle = {Proceedings of VLDB Workshop on Information Integration on the Web (IIWeb-2004)}, year = {2004}, month = {2004///}, pages = {83 - 83}, author = {Bleiholder,J. and Naumann,F. and Raschid, Louiqa and Vidal,M. E} } @article {13020, title = {Section-level relationships of North American {\i}t Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions}, journal = {BMC Evol Biol}, volume = {4}, year = {2004}, month = {2004/06//}, pages = {15 - 15}, abstract = {BACKGROUND: The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (=Gerardia), and between Agalinis and closely related genera within Orobanchaceae. RESULTS: Maximum likelihood analysis of sequences data from rbcL, ndhF, and matK gene regions (total aligned length 7323 bp) yielded a phylogenetic tree with high bootstrap values for most branches. Likelihood ratio tests showed that all but a few branch lengths were significantly greater than zero, and an additional likelihood ratio test rejected the molecular clock hypothesis. Comparisons of substitution rates between gene regions based on linear models of pairwise distance estimates between taxa show both ndhF and matK evolve more rapidly than rbcL, although the there is substantial rate heterogeneity within gene regions due in part to rate differences among codon positions. CONCLUSIONS: Phylogenetic analysis supports the monophyly of Agalinis, including species formerly in Tomanthera, and this group is sister to a group formed by the genera Aureolaria, Brachystigma, Dasistoma, and Seymeria. Many of the previously described sections within Agalinis are polyphyletic, although many of the subsections appear to form natural groups. The analysis reveals a single evolutionary event leading to a reduction in chromosome number from n = 14 to n = 13 based on the sister group relationship of section Erectae and section Purpureae subsection Pedunculares. Our results establish the evolutionary distinctiveness of A. tenella from the more widespread and common A. obtusifolia. However, further data are required to clearly resolve the relationship between A. acuta and A. tenella.}, doi = {10.1186/1471-2148-4-15}, author = {Neel,M. C and Cummings, Michael P.} } @conference {16885, title = {A serverless 3D world}, booktitle = {Proceedings of the 12th annual ACM international workshop on Geographic information systems}, series = {GIS {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {157 - 165}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Online multi-participant virtual-world systems have attracted significant interest from the Internet community but are hindered by their inability to efficiently support interactivity for a large number of participants. Current solutions divide a large virtual-world into a few mutually exclusive zones, with each zone controlled by a different server, and/or limit the number of participants per server or per virtual-world. Peer-to-Peer (P2P) systems are known to provide excellent scalability in a networked environment (one peer is introduced to the system by each participant), however current P2P applications can only provide file sharing and other forms of relatively simple data communications. In this paper, we present a generic 3D virtual-world application that runs on a P2P network with no central administration or server. Two issues are addressed by this paper to enable such a spatial application on a P2P network. First, we demonstrate how to index and query a 3D space on a dynamic distributed network. Second, we show how to build such a complex application from the ground level of a P2P routing algorithm. Our work leads to new directions for the development of online virtual-worlds that we believe can be used for many government, industry, and public domain applications.}, keywords = {distributed hash tables, peer-to-peer systems, spatial data, virtual-worlds}, isbn = {1-58113-979-9}, doi = {10.1145/1032222.1032246}, url = {http://doi.acm.org/10.1145/1032222.1032246}, author = {Tanin,Egemen and Harwood,Aaron and Samet, Hanan and Nutanong,Sarana and Truong,Minh Tri} } @conference {15468, title = {Skoll: distributed continuous quality assurance}, booktitle = {Software Engineering, 2004. ICSE 2004. Proceedings. 26th International Conference on}, year = {2004}, month = {2004/05//}, pages = {459 - 468}, abstract = {Quality assurance (QA) tasks, such as testing, profiling, and performance evaluation, have historically been done in-house on developer-generated workloads and regression suites. Since this approach is inadequate for many systems, tools and processes are being developed to improve software quality by increasing user participation in the QA process. A limitation of these approaches is that they focus on isolated mechanisms, not on the coordination and control policies and tools needed to make the global QA process efficient, effective, and scalable. To address these issues, we have initiated the Skoll project, which is developing and validating novel software QA processes and tools that leverage the extensive computing resources of worldwide user communities in a distributed, continuous manner to significantly and rapidly improve software quality. This paper provides several contributions to the study of distributed continuous QA. First, it illustrates the structure and functionality of a generic around-the-world, around-the-clock QA process and describes several sophisticated tools that support this process. Second, it describes several QA scenarios built using these tools and process. Finally, it presents a feasibility study applying these scenarios to a 1MLOC+ software package called ACE+TAO. While much work remains to be done, the study suggests that the Skoll process and tools effectively manage and control distributed, continuous QA processes. Using Skoll we rapidly identified problems that had taken the ACE+TAO developers substantially longer to find and several of which had previously not been found. Moreover, automatic analysis of QA task results often provided developers information that quickly led them to the root cause of the problems.}, keywords = {1MLOC+ software package, ACE+TAO, around-the-clock QA process, around-the-world QA process, distributed continuous QA, distributed continuous quality assurance, distributed programming, program verification, Quality assurance, Skoll, software performance evaluation, software profiling, Software quality, Software testing}, doi = {10.1109/ICSE.2004.1317468}, author = {Memon, Atif M. and Porter, Adam and Yilmaz,C. and Nagarajan,A. and Schmidt,D. and Natarajan,B.} } @conference {19046, title = {The sybil attack in sensor networks: analysis \& defenses}, series = {IPSN {\textquoteright}04}, year = {2004}, month = {2004}, pages = {259 - 268}, publisher = {ACM}, organization = {ACM}, abstract = {Security is important for many sensor network applications. A particularly harmful attack against sensor and ad hoc networks is known as the Sybil attack [6], where a node illegitimately claims multiple identities. This paper systematically analyzes the threat posed by the Sybil attack to wireless sensor networks. We demonstrate that the attack can be exceedingly detrimental to many important functions of the sensor network such as routing, resource allocation, misbehavior detection, etc. We establish a classification of different types of the Sybil attack, which enables us to better understand the threats posed by each type, and better design countermeasures against each type. We then propose several novel techniques to defend against the Sybil attack, and analyze their effectiveness quantitatively.}, keywords = {Security, sensor networks, sybil attack}, isbn = {1-58113-846-6}, url = {http://doi.acm.org/10.1145/984622.984660}, author = {Newsome, James and Elaine Shi and Song, Dawn and Perrig, Adrian} } @conference {17807, title = {Utilizing volatile external information during planning}, booktitle = {Proceedings of the European Conference on Artificial Intelligence (ECAI)}, year = {2004}, month = {2004///}, pages = {647 - 651}, author = {Au,T. C and Nau, Dana S. and V.S. Subrahmanian} } @article {12942, title = {Variation of toxigenic Vibrio cholerae O1 in the aquatic environment of Bangladesh and its correlation with the clinical strains}, journal = {Microbiology and immunology}, volume = {48}, year = {2004}, month = {2004///}, pages = {773 - 777}, author = {Islam,M. S. and Talukder,K. A. and Khan,N. H. and Mahmud,Z. H. and Rahman,M. Z. and Nair,G. B. and Siddique,A. K. M. and Yunus,M. and Sack,D. A. and Sack,R. B. and Rita R Colwell} } @article {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 {18812, title = {Algorithms for selecting cutters in multi-part milling problems}, journal = {Computer-Aided Design}, volume = {35}, year = {2003}, month = {2003/08//}, pages = {825 - 839}, abstract = {This paper describes geometric algorithms for automatically selecting an optimal sequence of cutters for machining a set of 2.5-D parts. In milling operations, cutter size affects the machining time significantly. Meanwhile, if the batch size is small, it is also important to shorten the time spent on loading tools into the tool magazine and establishing z-length compensation values. Therefore, in small-batch manufacturing, if we can select a set of milling tools that will produce good machining time on more than one type of parts, then several unnecessary machine-tool reconfiguration operations can be eliminated. In selecting milling cutters we consider both the tool loading time and the machining time and generate solutions that allow us to minimize the total machining time. In this paper we first present algorithms for finding the area that can be cut by a given cutter. Then we describe a graph search formulation for the tool selection problem. Finally, the optimal sequence of cutters is selected by using Dijkstra{\textquoteright}s shortest path planning algorithm.}, keywords = {2.5-D Milling, cutter selection, Geometric Algorithms}, isbn = {0010-4485}, doi = {10.1016/S0010-4485(02)00110-0}, url = {http://www.sciencedirect.com/science/article/pii/S0010448502001100}, author = {Yao,Zhiyang and Gupta, Satyandra K. and Nau, Dana S.} } @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} } @article {16996, title = {Bringing Treasures to the Surface: Previews and Overviews in a Prototype for the Library of Congress National Digital Library}, journal = {The craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {388 - 388}, author = {Marchionini,A.S. and Nation,D. and Karasik,S. and Cronnell,T. and Shneiderman, Ben and Spotfire,V.D.M.U. and Bederson, Benjamin B. and Data,T.S. and Hochheiser,H. and Shneiderman, Ben and others} } @conference {13359, title = {Cache-and-query for wide area sensor databases}, booktitle = {Proceedings of the 2003 ACM SIGMOD international conference on Management of data}, series = {SIGMOD {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {503 - 514}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Webcams, microphones, pressure gauges and other sensors provide exciting new opportunities for querying and monitoring the physical world. In this paper we focus on querying wide area sensor databases, containing (XML) data derived from sensors spread over tens to thousands of miles. We present the first scalable system for executing XPATH queries on such databases. The system maintains the logical view of the data as a single XML document, while physically the data is fragmented across any number of host nodes. For scalability, sensor data is stored close to the sensors, but can be cached elsewhere as dictated by the queries. Our design enables self starting distributed queries that jump directly to the lowest common ancestor of the query result, dramatically reducing query response times. We present a novel query-evaluate gather technique (using XSLT) for detecting (1) which data in a local database fragment is part of the query result, and (2) how to gather the missing parts. We define partitioning and cache invariants that ensure that even partial matches on cached data are exploited and that correct answers are returned, despite our dynamic query-driven caching. Experimental results demonstrate that our techniques dramatically increase query throughputs and decrease query response times in wide area sensor databases.}, isbn = {1-58113-634-X}, doi = {10.1145/872757.872818}, url = {http://doi.acm.org/10.1145/872757.872818}, author = {Deshpande, Amol and Nath,Suman and Gibbons,Phillip B. and Seshan,Srinivasan} } @article {12951, title = {Characterization of a Vibrio cholerae phage isolated from the coastal water of Peru}, journal = {Environmental Microbiology}, volume = {5}, year = {2003}, month = {2003/04/25/}, pages = {350 - 354}, abstract = {A Vibrio cholerae bacteriophage, family Myoviridae, was isolated from seawater collected from the coastal water of Lima, Peru. Genome size was estimated to be 29~kbp. The temperate phage was specific to V. cholerae and infected 12/13 V. cholerae O1 strains and half of the four non-O1/non-O139 strains tested in this study. Vibrio cholerae O139 strains were resistant to infection and highest infection rates were obtained in low nutrient media amended with NaCl or prepared using seawater as diluent.}, isbn = {1462-2920}, doi = {10.1046/j.1462-2920.2003.00411.x}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1462-2920.2003.00411.x/abstract?userIsAuthenticated=false\&deniedAccessCustomisedMessage=}, author = {Talledo,Miguel and Rivera,Irma N. G. and Lipp,Erin K. and Neale,Angela and Karaolis,David and Huq,Anwar and Rita R Colwell} } @article {15854, title = {Comparing user-assisted and automatic query translation}, journal = {Advances in cross-language information retrieval}, year = {2003}, month = {2003///}, pages = {400 - 415}, author = {He,D. and Wang,J. and Oard, Douglas and Nossal,M.} } @conference {15479, title = {DART: a framework for regression testing "nightly/daily builds" of GUI applications}, booktitle = {Software Maintenance, 2003. ICSM 2003. Proceedings. International Conference on}, year = {2003}, month = {2003/09//}, pages = {410 - 419}, abstract = {"Nightly/daily building and smoke testing" have become widespread since they often reveal bugs early in the software development process. During these builds, software is compiled, linked, and (re)tested with the goal of validating its basic functionality. Although successful for conventional software, smoke tests are difficult to develop and automatically rerun for software that has a graphical user interface (GUI). In this paper, we describe a framework called DART (daily automated regression tester) that addresses the needs of frequent and automated re-testing of GUI software. The key to our success is automation: DART automates everything from structural GUI analysis; test case generation; test oracle creation; to code instrumentation; test execution; coverage evaluation; regeneration of test cases; and their re-execution. Together with the operating system{\textquoteright}s task scheduler, DART can execute frequently with little input from the developer/tester to retest the GUI software. We provide results of experiments showing the time taken and memory required for GUI analysis, test case and test oracle generation, and test execution. We also empirically compare the relative costs of employing different levels of detail in the GUI test cases.}, keywords = {automated retesting, automatic test software, coverage evaluation, daily automated regression tester, DART, frequent retesting, graphical user interface, Graphical user interfaces, GUI software, instrumentation coding, program testing, regression testing, Software development management, Software development process, Software maintenance, Software quality, structural GUI analysis, Test Case Generation, test cases regeneration, Test execution, test oracle creation}, doi = {10.1109/ICSM.2003.1235451}, author = {Memon, Atif M. and Banerjee,I. and Hashmi,N. and Nagarajan,A.} } @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 {17844, title = {Driving scientific applications by data in distributed environments}, journal = {Computational Science{\textemdash}ICCS 2003}, year = {2003}, month = {2003///}, pages = {713 - 713}, author = {Saltz, J. and Catalyurek,U. and Kurc, T. and Gray,M. and Hastings,S. and Langella,S. and Narayanan,S. and Martino,R. and Bryant,S. and Peszynska,M. and others} } @article {17108, title = {Dynamic query choropleth maps for information seeking and decision making}, journal = {Proc. Human-Computer Interaction International}, year = {2003}, month = {2003///}, abstract = {Information retrieval and visualization can be combined in dynamic query systems that allow users unparalleled access to information for decision making. In this paper, we report on the development and evaluation of a dynamic query system (YMap) that displays information on a chloropleth map using double thumb sliders to select ranges of query variables. The YMap prototype is a Java-Applet that supports panning and zooming. Several usability studies were conducted on early prototypes that resulted in the current version. Applications of YMap for decision making tasks are discussed.}, author = {Norman,K. and Zhao,H. and Shneiderman, Ben and Golub,E.} } @article {12992, title = {Effectiveness of conservation targets in capturing genetic diversity}, journal = {Conserv Biol}, volume = {17}, year = {2003}, month = {2003/02//}, pages = {219 - 229}, abstract = {Any conservation actions that preserve some populations and not others will have genetic consequences. We used empirical data from four rare plant taxa to assess these consequences in terms of how well allele numbers ( all alleles and alleles occurring at a frequency openface>0.05 in any population ) and expected heterozygosity are represented when different numbers of populations are conserved. We determined sampling distributions for these three measures of genetic diversity using Monte Carlo methods. We assessed the proportion of alleles included in the number of populations considered adequate for conservation, needed to capture all alleles, and needed to meet an accepted standard of genetic-diversity conservation of having a 90-95\% probability of including all common alleles. We also assessed the number of populations necessary to obtain values of heterozygosity within +/-10\% of the value obtained from all populations. Numbers of alleles were strongly affected by the number of populations sampled. Heterozygosity was only slightly less sensitive to numbers of populations than were alleles. On average, currently advocated conservation intensities represented 67-83\% of all alleles and 85-93\% of common alleles. The smallest number of populations to include all alleles ranged from 6 to 17 ( 42-57\% ), but <0.2\% of 1000 samples of these numbers of populations included them all. It was necessary to conserve 16-29 ( 53-93\% ) of the sampled populations to meet the standard for common alleles. Between 20\% and 64\% of populations were needed to reliably represent species-level heterozygosity. Thus, higher percentages of populations are needed than are currently considered adequate to conserve genetic diversity if populations are selected without genetic data.}, author = {Neel,M. C and Cummings, Michael P.} } @conference {12200, title = {Electronic voting system usability issues}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2003}, month = {2003///}, pages = {145 - 152}, author = {Bederson, Benjamin B. and Lee,B. and Sherman,R.M. and Herrnson,P.S. and Niemi,R.G.} } @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 {15594, title = {A Fast Implementation of the ISOCLUS Algorithm}, journal = {IEEE 2003 International Geoscience and Remote Sensing Symposium}, year = {2003}, month = {2003///}, abstract = {Unsupervised clustering is a fundamental building block in numerous image processing applications. One of the most popular and widely used clustering schemes for remote sensing applications is the ISOCLUS algorithm, which is based on the ISODATA method. The algorithm is given a set of n data points in d-dimensional space, an integer k indicating the initial number of clusters, and a number of additional parameters. The general goal is to compute the coordinates of a set of cluster centers in d-space, such that those centers minimize the mean squared distance from each data point to its nearest center. This clustering algorithm is similar to another well-known clustering method, called k-means. One significant feature of ISOCLUS over k-means is that the actual number of clusters reported might be fewer or more than the number supplied as part of the input. The algorithm uses different heuristics to determine whether to merge lor split clusters. As ISOCLUS can run very slowly, particularly on large data sets, there has been a growing .interest in the remote sensing community in computing it efficiently. We have developed a faster implementation of the ISOCLUS algorithm. Our improvement is based on a recent acceleration to the k-means algorithm of Kanungo, et al. They showed that, by using a kd-tree data structure for storing the data, it is possible to reduce the running time of k-means. We have adapted this method for the ISOCLUS algorithm, and we show that it is possible to achieve essentially the same results as ISOCLUS on large data sets, but with significantly lower running times. This adaptation involves computing a number of cluster statistics that are needed for ISOCLUS but not for k-means. Both the k-means and ISOCLUS algorithms are based on iterative schemes, in which nearest neighbors are calculated until some convergence criterion is satisfied. Each iteration requires that the nearest center for each data point be computed. Naively, this requires O(kn) time, where k denotes the current number of centers. Traditional techniques for accelerating nearest neighbor searching involve storing the k centers in a data structure. However, because of the iterative nature of the algorithm, this data structure would need to be rebuilt with each new iteration. Our approach is to store the data points in a kd-tree data structure. The assignment of points to nearest neighbors is carried out by a filtering process, which successively eliminates centers that can not possibly be the nearest neighbor for a given region of space. This algorithm is significantly faster, because large groups of data points can be assigned to their nearest center in a single operation. Preliminary results on a number of real Landsat datasets show that our revised ISOCLUS-like scheme runs about twice as fast.}, keywords = {algorithms, Cluster Analysis, Data structures, HEURISTIC METHODS, IMAGE PROCESSING, INTEGERS, LANDSAT SATELLITES, MEAN SQUARE VALUES, Remote sensing}, url = {http://ntrs.nasa.gov/search.jsp?R=20030053175}, author = {Memarsadeghi,Nargess and Mount, Dave and Netanyahu,Nathan S. and LeMoigne,Jacqueline} } @inbook {12741, title = {Gait Analysis for Human Identification}, booktitle = {Audio- and Video-Based Biometric Person AuthenticationAudio- and Video-Based Biometric Person Authentication}, series = {Lecture Notes in Computer Science}, volume = {2688}, year = {2003}, month = {2003///}, pages = {1058 - 1058}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Human gait is an attractive modality for recognizing people at a distance. In this paper we adopt an appearance-based approach to the problem of gait recognition. The width of the outer contour of the binarized silhouette of a walking person is chosen as the basic image feature. Different gait features are extracted from the width vector such as the dowsampled, smoothed width vectors, the velocity profile etc. and sequences of such temporally ordered feature vectors are used for representing a person{\textquoteright}s gait. We use the dynamic time-warping (DTW) approach for matching so that non-linear time normalization may be used to deal with the naturally-occuring changes in walking speed. The performance of the proposed method is tested using different gait databases.}, isbn = {978-3-540-40302-9}, url = {http://dx.doi.org/10.1007/3-540-44887-X_82}, author = {Kale, A. and Cuntoor, N. and Yegnanarayana,B. and Rajagopalan, AN and Chellapa, Rama}, editor = {Kittler,Josef and Nixon,Mark} } @article {18892, title = {A General Approach to Synthesize Problem-Specific Planners}, year = {2003}, month = {2003/10/27/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {In this paper, we describe a way to improve the performance of hand-tailorable planners by compiling each domain description into a separate domain-specific planner. We discuss why and when this approach can be useful, and we present experimental results showing that our approach produces significant increases in the speed of planning.}, keywords = {*PLANNING, *SOFTWARE ENGINEERING, Artificial intelligence, COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER PROGRAMS, Logic, problem solving}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA455023}, author = {Ilghami,Okhtay and Nau, Dana S.} } @article {13000, title = {Genetic consequences of ecological reserve design guidelines: An empirical investigation}, journal = {Conserv Genet}, volume = {4}, year = {2003}, month = {2003///}, pages = {427 - 439}, abstract = {We assessed the genetic diversity consequences of applying ecological reserve design guidelines to four federally-listed globally-rare plant species. Consequences were measured using two metrics: proportion of all alleles and of common alleles included in reserves. Common alleles were defined as those alleles having a frequency of greater than or equal to0.05 in at least one population. Four conservation professionals applied ecological reserve guidelines to choose specific populations of each species for inclusion in reserves of size 1 to N - 1, where N is the total number of populations of each species. Information regarding genetic diversity was not used in selecting populations. The resulting reserve designs were compared to random designs, and the agreement among experts was assessed using Kendall{\textquoteright}s coefficient of concordance. Application of ecological reserve design guidelines proved mostly ineffective in capturing more genetic diversity than is captured selecting populations randomly. Meeting established targets for genetic diversity, such as one advocated by the Center for Plant Conservation, required larger numbers of populations than are suggested to be sufficient. Relative performance of expert designs differed among species and was dependent on whether the proportion of all alleles or of common alleles was used as a measure of diversity. Furthermore there was no significant concordance among experts in order in which populations were incorporated into reserves as experts differed in priority they placed on individual guidelines.}, keywords = {albens;, Astragulus, Bernardino, conservation, conservation;, design;, diversity;, Erigeron, Eriogonum, genetic, genetics;, goodmaniana;, Mountains, ovalifolium, Oxytheca, parishii, parishii;, plant, reserve, San, var., vineum;}, author = {Neel,M. C and Cummings, Michael P.} } @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 {15448, title = {GUI ripping: Reverse engineering of graphical user interfaces for testing}, journal = {Proceedings of the 10th working conference on reverse engineering (WCRE{\textquoteright}03)}, volume = {1095}, year = {2003}, month = {2003///}, pages = {17 - 00}, abstract = {Graphical user interfaces (GUIs) are important parts oftoday{\textquoteright}s software and their correct execution is required to ensure the correctness of the overall software. A popular technique to detect defects in GUIs is to test them by exe- cuting test cases and checking the execution results. Test cases may either be created manually or generated auto- matically from a model of the GUI. While manual testing is unacceptably slow for many applications, our experience with GUI testing has shown that creating a model that can be used for automated test case generation is difficult. We describe a new approach to reverse engineer a model represented as structures called a GUI forest, event-flow graphs and an integration tree directly from the executable GUI. We describe {\textquotedblleft}GUI Ripping{\textquotedblright}, a dynamic process in which the software{\textquoteright}s GUI is automatically {\textquotedblleft}traversed{\textquotedblright} by opening all its windows and extracting all their widgets (GUI objects), properties, and values. The extracted infor- mation is then verified by the test designer and used to auto- matically generate test cases. We present algorithms for the ripping process and describe their implementation in a tool suite that operates on Java and Microsoft Windows{\textquoteright} GUIs. We present results of case studies which show that our approach requires very little human intervention and is es- pecially useful for regression testing of software that is mod- ified frequently. We have successfully used the {\textquotedblleft}GUI Rip- per{\textquotedblright} in several large experiments and have made it avail- able as a downloadable tool. }, author = {Memon, Atif M. and Banerjee,I. and Nagarajan,A.} } @article {18907, title = {IMPACTing SHOP: Putting an AI Planner Into a Multi-Agent Environment}, journal = {Annals of Mathematics and Artificial Intelligence}, volume = {37}, year = {2003}, month = {2003///}, pages = {381 - 407}, abstract = {In this paper we describe a formalism for integrating the SHOP HTN planning system with the IMPACT multi-agent environment. We define the A-SHOP algorithm, an agentized adaptation of the SHOP planning algorithm that takes advantage of IMPACT{\textquoteright}s capabilities for interacting with external agents, performing mixed symbolic/numeric computations, and making queries to distributed, heterogeneous information sources (such as arbitrary legacy and/or specialized data structures or external databases). We show that A-SHOP is both sound and complete if certain conditions are met.}, keywords = {Computer science}, isbn = {1012-2443}, doi = {10.1023/A:1021560510377}, url = {http://www.springerlink.com/content/g4r0mn835846p65w/abstract/}, author = {Dix,J{\"u}rgen and Mu{\~n}oz-Avila,H{\'e}ctor and Nau, Dana S. and Zhang,Lingling} } @conference {17878, title = {Improving access to multi-dimensional self-describing scientific datasets}, booktitle = {3rd IEEE/ACM International Symposium on Cluster Computing and the Grid, 2003. Proceedings. CCGrid 2003}, year = {2003}, month = {2003/05/12/15}, pages = {172 - 179}, publisher = {IEEE}, organization = {IEEE}, abstract = {Applications that query into very large multidimensional datasets are becoming more common. Many self-describing scientific data file formats have also emerged, which have structural metadata to help navigate the multi-dimensional arrays that are stored in the files. The files may also contain application-specific semantic metadata. In this paper, we discuss efficient methods for performing searches for subsets of multi-dimensional data objects, using semantic information to build multidimensional indexes, and group data items into properly sized chunks to maximize disk I/O bandwidth. This work is the first step in the design and implementation of a generic indexing library that will work with various high-dimension scientific data file formats containing semantic information about the stored data. To validate the approach, we have implemented indexing structures for NASA remote sensing data stored in the HDF format with a specific schema (HDF-EOS), and show the performance improvements that are gained from indexing the datasets, compared to using the existing HDF library for accessing the data.}, keywords = {Application software, application-specific semantic metadata, Bandwidth, Computer science, database indexing, disk I/O bandwidth, distributed databases, Educational institutions, Indexing, indexing structures, Libraries, meta data, Middleware, multidimensional arrays, multidimensional datasets, Multidimensional systems, NASA, NASA remote sensing data, Navigation, query formulation, self-describing scientific data file formats, structural metadata, very large databases}, isbn = {0-7695-1919-9}, doi = {10.1109/CCGRID.2003.1199366}, author = {Nam,B. and Sussman, Alan} } @article {13376, title = {IRIS: Internet-scale Resource-Intensive Sensor Services}, journal = {Intel Research, UC Berkeley, Carnegie Mellon University}, year = {2003}, month = {2003///}, abstract = {The proliferation and affordability of smart sensors such aswebcams, microphones etc., has created opportunities for exciting new classes of distributed services. A key stum- bling block to mining these rich information sources is the lack of a common, scalable networked infrastructure for col- lecting, filtering, and combining the video feeds, extracting the useful information, and enabling distributed queries. In this demo, we demonstrate the design and an early prototype of such an infrastructure, called IRIS (Internet- scale Resource-Intensive Sensor services). IRIS is a poten- tially global network of smart sensor nodes, with webcams or other sensors, and organizing nodes that provide the means to query recent and historical sensor-based data. IRIS ex- ploits the fact that high-volume sensor feeds are typically attached to devices with significant computing power and storage, and running a standard operating system. Aggres- sive filtering, smart query routing, and semantic caching are used to dramatically reduce network bandwidth utilization and improve query response times, as we will demonstrate. The service that we demonstrate here is that of a park- ing space finder. This service utilizes webcams that monitor parking spaces to answer queries such as the availability of parking spaces near a user{\textquoteright}s destination. }, author = {Deshpande, Amol and Nath,S. and Gibbons,P.B. and Seshan,S.} } @conference {13378, title = {IrisNet: an architecture for internet-scale sensing services}, booktitle = {Proceedings of the 29th international conference on Very large data bases - Volume 29}, series = {VLDB {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {1137 - 1140}, publisher = {VLDB Endowment}, organization = {VLDB Endowment}, abstract = {We demonstrate the design and an early prototype of IrisNet (Internet-scale Resource-Intensive Sensor Network services), a common, scalable networked infrastructure for deploying wide area sensing services. IrisNet is a potentially global network of smart sensing nodes, with webcams or other monitoring devices, and organizing nodes that provide the means to query recent and historical sensor-based data. IrisNet exploits the fact that high-volume sensor feeds are typically attached to devices with significant computing power and storage, and running a standard operating system. It uses aggressive filtering, smart query routing, and semantic caching to dramatically reduce network bandwidth utilization and improve query response times, as we demonstrate. Our demo will present two services built on Iris-Net, from two very different application domains. The first one, a parking space finder, utilizes webcams that monitor parking spaces to answer queries such as the availability of parking spaces near a user{\textquoteright}s destination. The second one, a distributed infrastructure monitor, uses measurement tools installed in individual nodes of a large distributed infrastructure to answer queries such as average network bandwidth usage of a set of nodes.}, isbn = {0-12-722442-4}, url = {http://dl.acm.org/citation.cfm?id=1315451.1315568}, author = {Nath,Suman and Deshpande, Amol and Ke,Yan and Gibbons,Phillip B. and Karp,Brad and Seshan,Srinivasan} } @article {12392, title = {Logic foundry: rapid prototyping for FPGA-based DSP systems}, journal = {EURASIP J. Appl. Signal Process.}, volume = {2003}, year = {2003}, month = {2003/01//}, pages = {565 - 579}, abstract = {We introduce the Logic Foundry, a system for the rapid creation and integration of FPGA-based digital signal processing systems. Recognizing that some of the greatest challenges in creating FPGA-based systems occur in the integration of the various components, we have proposed a system that targets the following four areas of integration: design flow integration, component integration, platform integration, and software integration. Using the Logic Foundry, a system can be easily specified, and then automatically constructed and integrated with system level software.}, keywords = {CAD tools, Design methodology, DSP, FPGA, integration, rapid prototyping}, isbn = {1110-8657}, doi = {10.1155/S1110865703301039}, url = {http://dx.doi.org/10.1155/S1110865703301039}, author = {Spivey,Gary and Bhattacharyya, Shuvra S. and Nakajima,Kazuo} } @article {15847, title = {Making miracles: Interactive translingual search for cebuano and hindi}, journal = {ACM Transactions on Asian Language Information Processing (TALIP)}, volume = {2}, year = {2003}, month = {2003///}, pages = {219 - 244}, author = {He,D. and Oard, Douglas and Wang,J. and Luo,J. and Demner-Fushman,D. and Darwish,K. and Resnik, Philip and Khudanpur,S. and Nossal,M. and Subotin,M. and others} } @article {13386, title = {MobiCom poster: mining a world of smart sensors}, journal = {SIGMOBILE Mob. Comput. Commun. Rev.}, volume = {7}, year = {2003}, month = {2003/01//}, pages = {34 - 36}, isbn = {1559-1662}, doi = {10.1145/881978.881987}, url = {http://doi.acm.org/10.1145/881978.881987}, author = {Nath,Suman and Deshpande, Amol and Gibbons,Phillip B. and Seshan,Srinivasan} } @conference {13246, title = {Modelling pedestrian shapes for outlier detection: a neural net based approach}, booktitle = {Intelligent Vehicles Symposium, 2003. Proceedings. IEEE}, year = {2003}, month = {2003/06//}, pages = {428 - 433}, abstract = {In this paper we present an example-based approach to learn a given class of complex shapes, and recognize instances of that shape with outliers. The system consists of a two-layer custom-designed neural network. We apply this approach to the recognition of pedestrians carrying objects from a single camera. The system is able to capture and model an ample range of pedestrian shapes at varying poses and camera orientations, and achieves a 90\% correct recognition rate.}, keywords = {(artificial, complex, Computer, computing;, custom, design;, detection;, engineering, intelligence);, layer, learning, method;, modelling;, net;, nets;, neural, object, outlier, pedestrian, pedestrians, rate;, recognition, recognition;, SHAPE, shapes;, traffic, two, vision;}, doi = {10.1109/IVS.2003.1212949}, author = {Nanda,H. and Benabdelkedar,C. and Davis, Larry S.} } @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 {13010, title = {Phylogenetic analysis reveals five independent transfers of the chloroplast gene {\i}t rbcL to the mitochondrial genome in angiosperms}, journal = {Curr Genet}, volume = {43}, year = {2003}, month = {2003/05//}, pages = {131 - 138}, abstract = {We used the chloroplast gene rbcL as a model to study the frequency and relative timing of transfer of chloroplast sequences to the mitochondrial genome. Southern blot survey of 20 mitochondrial DNAs confirmed three previously reported groups of plants containing rbcL in their mitochondrion, while PCR studies identified a new mitochondrial rbcL. Published and newly determined mitochondrial and chloroplast rbcL sequences were used to reconstruct rbcL phylogeny. The results imply five or six separate interorganellar transfers of rbcL among the angiosperms examined, and hundreds of successful transfers across all flowering plants. By taxonomic criteria, the crucifer transfer is the most ancient, two separate transfers within the grass family are of intermediate ancestry, and the morning-glory transfer is most recent. All five mitochondrial copies of rbcL examined exhibit insertion and/or deletion events that disrupt the reading frame (three are grossly truncated); and all are elevated in the proportion of nonsynonymous substitutions, providing clear evidence that these sequences are pseudogenes.}, doi = {10.1007/s00294-003-0378-3}, author = {Cummings, Michael P. and Nugent,J. M and Olmstead,R. G and Palmer,J. D} } @inbook {18918, title = {Planning in Answer Set Programming Using Ordered Task Decomposition}, booktitle = {KI 2003: Advances in Artificial Intelligence}, series = {Lecture Notes in Computer Science}, volume = {2821}, year = {2003}, month = {2003///}, pages = {490 - 504}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper we introduce a formalism for solving Hierarchical Task Network ( HTN ) Planning using Answer Set Programming ( ASP ). We consider the formulation of HTN planning as described in the SHOP planning system and define a systematic translation method from SHOP {\textquoteright}s representation of the planning problem into logic programs with negation. We show that our translation is sound and complete : answer sets of the logic program obtained by our translation correspond exactly to the solutions of the planning problem. We compare our method to (1) similar approaches based on non- HTN planning and (2) SHOP , a dedicated planning system. We show that our approach outperforms non- HTN methods and that its performance is better with ASP systems that allow for nonground programs than with ASP systems that require ground programs.}, keywords = {Computer science}, isbn = {978-3-540-20059-8}, url = {http://www.springerlink.com/content/ekt1kye92lh12lpj/abstract/}, author = {Dix,J{\"u}rgen and Kuter,Ugur and Nau, Dana S.}, editor = {G{\"u}nter,Andreas and Kruse,Rudolf and Neumann,Bernd} } @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 {12953, title = {Reduction of Cholera in Bangladeshi Villages by Simple Filtration}, journal = {Proceedings of the National Academy of SciencesPNAS}, volume = {100}, year = {2003}, month = {2003/02/04/}, pages = {1051 - 1055}, abstract = {Based on results of ecological studies demonstrating that Vibrio cholerae, the etiological agent of epidemic cholera, is commensal to zooplankton, notably copepods, a simple filtration procedure was developed whereby zooplankton, most phytoplankton, and particulates >20 μm were removed from water before use. Effective deployment of this filtration procedure, from September 1999 through July 2002 in 65 villages of rural Bangladesh, of which the total population for the entire study comprised ≈133,000 individuals, yielded a 48\% reduction in cholera (P < 0.005) compared with the control.}, isbn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0237386100}, url = {http://www.pnas.org/content/100/3/1051}, author = {Rita R Colwell and Huq,Anwar and M. Sirajul Islam and K. M. A. Aziz and Yunus,M. and N. Huda Khan and A. Mahmud and Sack,R. Bradley and Nair,G. B. and J. Chakraborty and Sack,David A. and E. Russek-Cohen} } @article {15434, title = {Refactoring using event-based profiling}, journal = {First International Workshop on REFactoring: Achievements, Challenges, Effects (REFACE)}, year = {2003}, month = {2003///}, abstract = {Refactoring is a disciplined process of restructuring soft-ware code in order to improve it, e.g., to make it more reusable, reliable and maintainable. The source of infor- mation that guides the refactoring process may be the soft- ware{\textquoteright}s user profiles. An increasingly important class of soft- ware is event-based software. Event-based software take an event as an input, change their state, and perhaps output an event. They provide new opportunities for refactoring. For example, reorganizing the objects related to an event and restructuring the event handlers based on the behavior of the software. These opportunities require that we collect user profiles at the level of events rather than the code and model the software in such a way that allows refactoring of event handlers. We present new techniques to collect event- level profiles and organize event handlers. We describe our techniques on one class of event-based software {\textendash} Graphi- cal User Interfaces (GUIs). We demonstrate the practicality and usefulness of our techniques on a large software system. }, author = {Nagarajan,A. and Memon, Atif M.} } @inbook {12739, title = {Robust Face Recognition in the Presence of Clutter}, booktitle = {Audio- and Video-Based Biometric Person AuthenticationAudio- and Video-Based Biometric Person Authentication}, series = {Lecture Notes in Computer Science}, volume = {2688}, year = {2003}, month = {2003///}, pages = {1062 - 1062}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We propose a new method within the framework of principal component analysis to robustly recognize faces in the presence of clutter. The traditional eigenface recognition method performs poorly when confronted with the more general task of recognizing faces appearing against a background. It misses faces completely or throws up many false alarms. We argue in favor of learning the distribution of background patterns and show how this can be done for a given test image. An eigenbackground space is constructed and this space in conjunction with the eigenface space is used to impart robustness in the presence of background. A suitable classifier is derived to distinguish non-face patterns from faces. When tested on real images, the performance of the proposed method is found to be quite good.}, isbn = {978-3-540-40302-9}, url = {http://dx.doi.org/10.1007/3-540-44887-X_1}, author = {Rajagopalan, AN and Chellapa, Rama and Koterba,Nathan}, editor = {Kittler,Josef and Nixon,Mark} } @inbook {16132, title = {Seeing the World Through Image Libraries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {47 - 47}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {North,C. and Shneiderman, Ben and Plaisant, Catherine and Kang,H. and Bederson, Benjamin B.} } @article {18995, title = {Sex-lethal splicing autoregulation in vivo: interactions between SEX-LETHAL, the U1 snRNP and U2AF underlie male exon skipping}, journal = {DevelopmentDevelopment}, volume = {130}, year = {2003}, month = {2003/02/01/}, pages = {463 - 471}, abstract = {Alternative splicing of the Sex-lethal pre-mRNA has long served as a model example of a regulated splicing event, yet the mechanism by which the female-specific SEX-LETHAL RNA-binding protein prevents inclusion of the translation-terminating male exon is not understood. Thus far, the only general splicing factor for which there is in vivo evidence for a regulatory role in the pathway leading to male-exon skipping is sans-fille (snf), a protein component of the spliceosomal U1 and U2 snRNPs. Its role, however, has remained enigmatic because of questions about whether SNF acts as part of an intact snRNP or a free protein. We provide evidence that SEX-LETHAL interacts with SANS-FILLE in the context of the U1 snRNP, through the characterization of a point mutation that interferes with both assembly into the U1 snRNP and complex formation with SEX-LETHAL. Moreover, we find that SEX-LETHAL associates with other integral U1 snRNP components, and we provide genetic evidence to support the biological relevance of these physical interactions. Similar genetic and biochemical approaches also link SEX-LETHAL with the heterodimeric splicing factor, U2AF. These studies point specifically to a mechanism by which SEX-LETHAL represses splicing by interacting with these key splicing factors at both ends of the regulated male exon. Moreover, because U2AF and the U1 snRNP are only associated transiently with the pre-mRNA during the course of spliceosome assembly, our studies are difficult to reconcile with the current model that proposes that the SEX-LETHAL blocks splicing at the second catalytic step, and instead argue that the SEX-LETHAL protein acts after splice site recognition, but before catalysis begins.}, keywords = {Drosophila, SNF, Splicing regulation, SXL, U1 snRNP, U2AF}, isbn = {0950-1991, 1477-9129}, doi = {10.1242/dev.00274}, url = {http://dev.biologists.org/content/130/3/463}, author = {Nagengast,Alexis A. and Stitzinger,Shane M. and Tseng,Chin-Hsiu and Mount, Stephen M. and Salz,Helen K.} } @article {18870, title = {SHOP2: An HTN planning system}, journal = {J. Artif. Intell. Res. (JAIR)}, volume = {20}, year = {2003}, month = {2003///}, pages = {379 - 404}, abstract = {The SHOP2 planning system received one of the awards for distinguished performance in the 2002 International Planning Competition. This paper describes the features of SHOP2 which enabled it to excel in the competition, especially those aspects of SHOP2 that deal with temporal and metric planning domains.}, url = {https://www.aaai.org/Papers/JAIR/Vol20/JAIR-2013.pdf}, author = {Nau, Dana S. and Au,T. C and Ilghami,O. and Kuter,U. and Murdock,J. W. and Wu,D. and Yaman,F.} } @article {18022, title = {Towards a first vertical prototyping of an extremely fine-grained parallel programming approach}, journal = {Theory of Computing Systems}, volume = {36}, year = {2003}, month = {2003///}, pages = {521 - 552}, abstract = {Explicit multithreading (XMT) is a parallel programming approach for exploiting on-chip parallelism. XMT introduces a computational framework with (1) a simple programming style that relies on fine-grained PRAM-style algorithms; (2) hardware support for low-overhead parallel threads, scalable load balancing, and efficient synchronization. The missing link between the algorithmic-programming level and the architecture level is provided by the first prototype XMT compiler. This paper also takes this new opportunity to evaluate the overall effectiveness of the interaction between the programming model and the hardware, and enhance its performance where needed, incorporating new optimizations into the XMT compiler. We present a wide range of applications, which written in XMT obtain significant speedups relative to the best serial programs. We show that XMT is especially useful for more advanced applications with dynamic, irregular access patterns, where for regular computations we demonstrate performance gains that scale up to much higher levels than have been demonstrated before for on-chip systems.}, author = {Naishlos,D. and Nuzman,J. and Tseng,C. W and Vishkin, Uzi} } @conference {14753, title = {User-specified adaptive scheduling in a streaming media network}, booktitle = {2003 IEEE Conference on Open Architectures and Network Programming}, year = {2003}, month = {2003/04/04/5}, pages = {87 - 96}, publisher = {IEEE}, organization = {IEEE}, abstract = {In disaster and combat situations, mobile cameras and other sensors transmit real-time data, used by many operators or analysis tools. Unfortunately, in the face of limited, unreliable resources, and varying demands, not all users may be able to get the fidelity they require. This paper describes MediaNet, a distributed stream processing system designed with the above scenarios in mind. Unlike past approaches, MediaNet{\textquoteright}s users can intuitively specify how the system should adapt based on their individual needs. MediaNet uses both local and online global resource scheduling to improve user performance and network utilization, and adapts without requiring underlying support for resource reservations. Performance experiments show that our scheduling algorithm is reasonably fast, and that user performance and network utilization are both significantly improved.}, keywords = {Adaptive scheduling, CAMERAS, Computer networks, Computer science, distributed stream processing system, Educational institutions, global resource scheduling, Intelligent networks, MediaNet, Mobile computing, network utilization, Process design, Processor scheduling, quality of service, Streaming media, streaming media network, user performance, user-specified adaptive scheduling}, isbn = {0-7803-7764-8}, doi = {10.1109/OPNARC.2003.1196376}, author = {Hicks, Michael W. and Nagarajan,A. and van Renesse,R.} } @conference {15428, title = {What test oracle should I use for effective GUI testing?}, booktitle = {Automated Software Engineering, 2003. Proceedings. 18th IEEE International Conference on}, year = {2003}, month = {2003/10//}, pages = {164 - 173}, abstract = {Test designers widely believe that the overall effectiveness and cost of software testing depends largely on the type and number of test cases executed on the software. In this paper we show that the test oracle used during testing also contributes significantly to test effectiveness and cost. A test oracle is a mechanism that determines whether software executed correctly for a test case. We define a test oracle to contain two essential parts: oracle information that represents expected output; and an oracle procedure that compares the oracle information with the actual output. By varying the level of detail of oracle information and changing the oracle procedure, a test designer can create different types of test oracles. We design 11 types of test oracles and empirically compare them on four software systems. We seed faults in software to create 100 faulty versions, execute 600 test cases on each version, for all 11 types of oracles. In all, we report results of 660,000 test runs on software. We show (1) the time and space requirements of the oracles, (2) that faults are detected early in the testing process when using detailed oracle information and complex oracle procedures, although at a higher cost per test case, and (3) that employing expensive oracles results in detecting a large number of faults using relatively smaller number of test cases.}, keywords = {empirical studies, graphical user interface, Graphical user interfaces, GUI testing, oracle information, oracle procedure, oracle space requirement, oracle time requirements, program testing, software engineering, Software testing, test cost, test effectiveness, test oracle}, doi = {10.1109/ASE.2003.1240304}, author = {Memon, Atif M. and Banerjee,I. and Nagarajan,A.} } @inbook {16131, title = {The World{\textquoteright}s Information in Digital Libraries}, booktitle = {The craft of information visualization: readings and reflectionsThe craft of information visualization: readings and reflections}, year = {2003}, month = {2003///}, pages = {149 - 149}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, isbn = {978-1-55860-915-0}, author = {Plaisant, Catherine and Marchimini,G. and Bruns,T. and Komlodi,A. and Campbell,L. and Rose,A. and Ding,G.M. and Beale Jr,J. and Nolet,V. and Shneiderman, Ben and others} } @conference {16002, title = {ALLI: An Information Integration System Based on Active Logic Framework}, booktitle = {Proceedings of the Third International Conference on Management Information Systems, Greece}, year = {2002}, month = {2002///}, pages = {339 - 348}, author = {Barfourosh,A. A. and Nezhad,H. R.M and Anderson,M. and Perlis, Don} } @conference {18873, title = {CaMeL: Learning method preconditions for HTN planning}, year = {2002}, month = {2002///}, pages = {131 - 14}, abstract = {A great challenge in using any planning system to solve real-world problems is the difficulty of acquiring the do- main knowledge that the system will need. We present a way to address part of this problem, in the context of Hierarchical Task Network (HTN) planning, by having the planning system incrementally learn conditions for HTN methods under expert supervision. We present a general formal framework for learning HTN methods, and a supervised learning algorithm, named CaMeL, based on this formalism. We present theoretical results about CaMeL{\textquoteright}s soundness, completeness, and conver- gence properties. We also report experimental results about its speed of convergence under different condi- tions. The experimental results suggest that CaMeL has the potential to be useful in real-world applications.}, url = {https://www.aaai.org/Papers/AIPS/2002/AIPS02-014.pdf}, author = {Ilghami,O. and Nau, Dana S. and Munoz-Avila,H. and Aha,D. W.} } @conference {17009, title = {CHI@20: fighting our way from marginality to power}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {688 - 691}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The Special Interest Group on Computer Human Interaction (SIGCHI) has had a successful history of 20 years of growth in its numbers and influence. To help guide the continued evolution of the academic discipline and professional community, we invite several senior members to offer their visions for what the field of CHI actually accomplished over the past several decades, and what do we still need to accomplish? What do we need to do differently/ better/smarter? What haven{\textquoteright}t we tried because the technology, the money or the will wasn{\textquoteright}t there in the past, but perhaps is now.The CHI field is more than just technology. We understand that our work can have a profound effect on individuals, families, neighborhoods, corporations, and countries. We know that we can influence education, commerce, healthcare, and government. How can we contribute to bridging the digital divides in developed and developing countries? What agendas can we offer for the academic, research, industrial, and civic spheres for the next 20 years? How can we be more ambitious? How can we truly serve human needs.}, keywords = {education, future vision, Human-computer interaction, practice, professional, THEORY, usability engineering}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506548}, url = {http://doi.acm.org/10.1145/506443.506548}, author = {Shneiderman, Ben and Card,Stuart and Norman,Donald A. and Tremaine,Marilyn and Waldrop,M. Mitchell} } @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 {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} } @inbook {18914, title = {On the Complexity of Plan Adaptation by Derivational Analogy in a Universal Classical Planning Framework}, booktitle = {Advances in Case-Based Reasoning}, series = {Lecture Notes in Computer Science}, volume = {2416}, year = {2002}, month = {2002///}, pages = {199 - 206}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In this paper we present an algorithm called DerUCP, which can be regarded as a general model for plan adaptation using Derivational Analogy. Using DerUCP, we show that previous results on the complexity of plan adaptation do not apply to Derivational Analogy. We also show that Derivational Analogy can potentially produce exponential reductions in the size of the search space generated by a planning system.}, keywords = {Computer science}, isbn = {978-3-540-44109-0}, url = {http://www.springerlink.com/content/db2mr13j90mfrcaw/abstract/}, author = {Au,Tsz-Chiu and Mu{\~n}oz-Avila,H{\'e}ctor and Nau, Dana S.}, editor = {Craw,Susan and Preece,Alun} } @conference {12372, title = {A component architecture for FPGA-based, DSP system design}, booktitle = {Application-Specific Systems, Architectures and Processors, 2002. Proceedings. The IEEE International Conference on}, year = {2002}, month = {2002///}, pages = {41 - 51}, author = {Spivey,G. and Bhattacharyya, Shuvra S. and Nakajima,K.} } @article {15613, title = {An efficient k-means clustering algorithm: analysis and implementation}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {24}, year = {2002}, month = {2002/07//}, pages = {881 - 892}, abstract = {In k-means clustering, we are given a set of n data points in d-dimensional space Rd and an integer k and the problem is to determine a set of k points in Rd, called centers, so as to minimize the mean squared distance from each data point to its nearest center. A popular heuristic for k-means clustering is Lloyd{\textquoteright}s (1982) algorithm. We present a simple and efficient implementation of Lloyd{\textquoteright}s k-means clustering algorithm, which we call the filtering algorithm. This algorithm is easy to implement, requiring a kd-tree as the only major data structure. We establish the practical efficiency of the filtering algorithm in two ways. First, we present a data-sensitive analysis of the algorithm{\textquoteright}s running time, which shows that the algorithm runs faster as the separation between clusters increases. Second, we present a number of empirical studies both on synthetically generated data and on real data sets from applications in color quantization, data compression, and image segmentation}, keywords = {algorithm;color, algorithm;image, algorithm;kd-tree;mean, analysis;filtering, clustering, clustering;, compression;data, distance;covariance, Lloyd, matrices;filtering, quantization;data, segmentation;k-means, squared, structure;data-sensitive, theory;pattern}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2002.1017616}, author = {Kanungo,T. and Mount, Dave and Netanyahu,N. S and Piatko,C. D and Silverman,R. and Wu,A. Y} } @inbook {14692, title = {Evolution in Action: Using Active Networking to Evolve Network Support for Mobility}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {2546}, year = {2002}, month = {2002///}, pages = {146 - 161}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A key early objective of Active Networking (AN) was to support on-the-fly network evolution. Although AN has been used relatively extensively to build application-customized protocols and even whole networking systems, demonstrations of evolution have been limited. This paper examines three AN mechanisms and how they enable evolution: active packets and plug-in extensions, well-known to the AN community, and update extensions, which are novel to AN. We devote our presentation to a series of demonstrations of how each type of evolution can be applied to the problem of adding support for mobility to a network. This represents the most large-scale demonstration of AN evolution to date. These demonstrations show what previous AN research has not: that AN technology can, in fact, support very significant changes to the network, even while the network is operational.}, isbn = {978-3-540-00223-9}, url = {http://dx.doi.org/10.1007/3-540-36199-5_12}, author = {Seong-Kyu,Song and Shannon,Stephen and Hicks, Michael W. and Nettles,Scott}, editor = {Sterbenz,James and Takada,Osamu and Tschudin,Christian and Plattner,Bernhard} } @article {17146, title = {Expandable indexes vs. sequential menus for searching hierarchies on the World Wide Web}, journal = {Behaviour \& Information Technology}, volume = {21}, year = {2002}, month = {2002///}, pages = {201 - 207}, abstract = {An experiment is reported that compared expandable indexes providing full menu context with sequential menus providing only partial context. Menu depth was varied using hierarchies of two, three and four levels deep in an asymmetric structure of 457 root level items. Menus were presented on the World Wide Web within a browser. Participants searched for specific targets. Results suggest that reducing the depth of hierarchies improves performance in terms of speed and search efficiency. Surprisingly, expandable indexes resulted in poorer performance with deeper hierarchies than did sequential menus.An experiment is reported that compared expandable indexes providing full menu context with sequential menus providing only partial context. Menu depth was varied using hierarchies of two, three and four levels deep in an asymmetric structure of 457 root level items. Menus were presented on the World Wide Web within a browser. Participants searched for specific targets. Results suggest that reducing the depth of hierarchies improves performance in terms of speed and search efficiency. Surprisingly, expandable indexes resulted in poorer performance with deeper hierarchies than did sequential menus. }, isbn = {0144-929X}, doi = {10.1080/0144929021000009045}, url = {http://www.tandfonline.com/doi/abs/10.1080/0144929021000009045}, author = {Zaphiris,Panayiotis and Shneiderman, Ben and Norman,Kent L} } @conference {14695, title = {Experiences with capsule-based active networking}, booktitle = {DARPA Active NEtworks Conference and Exposition, 2002. Proceedings}, year = {2002}, month = {2002///}, pages = {16 - 24}, publisher = {IEEE}, organization = {IEEE}, abstract = {Active networking adds programmability to the elements of the network, most aggressively by using programmable packets, or capsules. ANTS [22, 21] and PLANet [10, 8] are the most mature examples of capsule-based systems, both having been publicly available for several years. This paper presents our experience with these systems and the lessons they hold for the future of capsule-based active networking. The paper focuses on four key issues: flexibility, performance, security, and usability. We consider how ANTS and PLANet address these issues, noting that despite substantial surface differences, both systems identify similar key problems and use closely related solutions. Based on our experience with these systems we conclude that capsule-based systems can achieve useful levels of flexibility, performance, and usability. Many aspects of security can also be adequately addressed, but some important problems related to denial of service remain as open problems}, keywords = {active networking, ANTS, application-specific routing, capsule architecture, capsule-based systems, computer crime, Computer network management, Computer networks, Computer science, Contracts, Electronic switching systems, INFORMATION SCIENCE, Internet, internetworking, network management, PLANet, Planets, programmability, programmable packets, Programming, Security, Standards development, telecommunication network routing, usability}, isbn = {0-7695-1564-9}, doi = {10.1109/DANCE.2002.1003481}, author = {Hicks, Michael W. and Moore,J. T and Wetherall,D. and Nettles,S.} } @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.} } @conference {17178, title = {Getting real about speech: overdue or overhyped?}, booktitle = {CHI {\textquoteright}02 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {708 - 709}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Speech has recently made headway towards becoming a more mainstream interface modality. For example, there is an increasing number of call center applications, especially in the airline and banking industries. However, speech still has many properties that cause its use to be problematic, such as its inappropriateness in both very quiet and very noisy environments, and the tendency of speech to increase cognitive load. Concerns about such problems are valid; however, they do not explain why the use of speech is so controversial in the HCI community. This panel would like to address the issues underlying the controversy around speech, by discussing the current state of the art, the reasons it is so difficult to build a good speech interface, and how HCI research can contribute to the development of speech interfaces.}, keywords = {cognitive load, social responses, speech interfaces}, isbn = {1-58113-454-1}, doi = {10.1145/506443.506557}, url = {http://doi.acm.org/10.1145/506443.506557}, author = {James,Frankie and Lai,Jennifer and Suhm,Bernhard and Balentine,Bruce and Makhoul,John and Nass,Clifford and Shneiderman, Ben} } @article {18906, title = {HTN Planning in Answer Set Programming}, volume = {UMIACS-TR-2002-18}, year = {2002}, month = {2002/05/22/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In this paper we introduce a formalism for solving Hierarchical Task NEtwork(HTN) Planning using Answer Set Programming (ASP). The ASP paradigm evolved out of the stable semantics for logic programs in recent years and is strongly related to nonmonotonic logics. We consider the formulation of HTM planning as described in the SHOP planning system and define a systematic translation method from SHOP{\textquoteright}s representation of the planning problems into logic programs with negation. We show that our translation is sound and complete: answer sets of the logic programs obtained by our translation correspond exactly to the solutions of the planning problems. Our approach does not rly on a particular system for computing answer sets. It can therefore serve as a means to evaluate ASP systems by using well-established benchmarks from the planning community. We tested our method on various such benchmarks and used smodels and DLV for computing answer sets. We compared our method to (1) similar approaches based on non-HTN planning and (2) SHOP, a dedicated planning system. We show that our approach outperforms non-HTN methods and that its performance is closer to that of SHOP, when we are using ASP systems which allow for nonground programs. (Also UMIACS-TR-2002-18) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1182}, author = {Dix,Jurgen and Kuter,Ugur and Nau, Dana S.} } @article {15758, title = {Image Restoration through Subimages and Confidence Images}, journal = {Electronic Transactions on Numerical Analysis}, volume = {13}, year = {2002}, month = {2002///}, pages = {22 - 37}, url = {http://etna.mcs.kent.edu/vol.13.2002/pp22-37.dir/pp22-37.pdfhttp://etna.mcs.kent.edu/vol.13.2002/pp22-37.dir/pp22-37.pdf}, author = {Nagy,James G. and O{\textquoteright}Leary, Dianne P.} } @article {16907, title = {Integration of local and global shape analysis for logo classification}, journal = {Pattern Recognition Letters}, volume = {23}, year = {2002}, month = {2002/10//}, pages = {1449 - 1457}, abstract = {A comparison is made of global and local methods for the shape analysis of logos in an image database. The qualities of the methods are judged by using the shape signatures to define a similarity metric on the logos. As representatives for the two classes of methods, we use the negative shape method which is based on local shape information and a wavelet-based method which makes use of global information. We apply both methods to images with different kinds of degradations and examine how a particular degradation highlights the strengths and shortcomings of each method. Finally, we use these results to develop a new adaptive weighting scheme which is based on the relative performances of the two methods. This scheme gives rise to a new method that is much more robust with respect to all degradations examined and works by automatically predicting if the negative shape or wavelet method is performing better.}, keywords = {Image databases, Logos, shape recognition, shape representation, Symbol recognition}, isbn = {0167-8655}, doi = {10.1016/S0167-8655(02)00105-8}, url = {http://www.sciencedirect.com/science/article/pii/S0167865502001058}, author = {Neumann, Jan and Samet, Hanan and Soffer,Aya} } @article {13377, title = {Irisnet: An architecture for compute-intensive wide-area sensor network services}, journal = {Intel Corporation, Pittsburgh IRPTR-02}, volume = {10}, year = {2002}, month = {2002///}, abstract = {Previous work on sensor networks has targeted adhoc wireless networks of closely-colocated, resource- constrained scalar sensor motes. Such work has over- looked richer sensor types such as webcams and mi- crophones, which are typically attached to Internet- connected machines with significant computing power and storage. In this paper, we describe IrisNet (Internet- scale Resource-Intensive Sensor Network services), an architecture for wide-area sensor networks based on these more capable sensing nodes. IrisNet provides a common, scalable software infrastructure that enables the flexible creation of sensor-based Internet services. It dramatically reduces network bandwidth utilization through the use of senselets, binary code fragments that perform intensive data filtering at the sensing nodes, leveraging the available processing power and mem- ory. IrisNet employs a two-tier hierarchy of sensing nodes and query processing nodes. Key features of IrisNet include flexible data partitioning, efficient and protected sharing of sensor nodes, low-latency queries, partial match caching, query-specified freshness toler- ances, and monitoring and logging support. This pa- per reports on experiments with a working IrisNet pro- totype running a parking space finder service, demon- strating the effectiveness of IrisNet{\textquoteright}s features in achiev- ing scalability and reducing query response times. }, author = {Nath,S. and Deshpande, Amol and Ke,Y. and Gibbons,P. and Karp,B. and Seshan,S.} } @conference {15624, title = {A local search approximation algorithm for k-means clustering}, booktitle = {Proceedings of the eighteenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {10 - 18}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {In k-means clustering we are given a set of n data points in d-dimensional space Rd and an integer k, and the problem is to determine a set of k points in {\'O}C;d, called centers, to minimize the mean squared distance from each data point to its nearest center. No exact polynomial-time algorithms are known for this problem. Although asymptotically efficient approximation algorithms exist, these algorithms are not practical due to the extremely high constant factors involved. There are many heuristics that are used in practice, but we know of no bounds on their performance.We consider the question of whether there exists a simple and practical approximation algorithm for k-means clustering. We present a local improvement heuristic based on swapping centers in and out. We prove that this yields a (9+\&egr;)-approximation algorithm. We show that the approximation factor is almost tight, by giving an example for which the algorithm achieves an approximation factor of (9-\&egr;). To establish the practical value of the heuristic, we present an empirical study that shows that, when combined with Lloyd{\textquoteright}s algorithm, this heuristic performs quite well in practice.}, keywords = {Approximation algorithms, clustering, computational geometry, k-means, local search}, isbn = {1-58113-504-1}, doi = {10.1145/513400.513402}, url = {http://doi.acm.org/10.1145/513400.513402}, author = {Kanungo,Tapas and Mount, Dave and Netanyahu,Nathan S. and Piatko,Christine D. and Silverman,Ruth and Wu,Angela Y.} } @article {18913, title = {M-Translog-2: A Planning Domain Designed for AIPS-2002}, volume = {UMIACS-TR-2002-82}, year = {2002}, month = {2002/10/03/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This document describes UM-Translog-2, which is an extended version of theUM Translog planning domain. The extensions include some numerical-computation features to make the domain a more realistic model of transportation-logistics problems. We are proposing UM- Translog-2 as a candidate domain for AIPS-2002 planning competition. (Also UMIACS-TR-2002-82) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/1228}, author = {Wu,Dan and Nau, Dana S.} } @conference {18917, title = {Planning in a multi-agent environment: theory and practice}, series = {AAMAS {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {944 - 945}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We give the theoretical foundations and empirical evaluation of a planning agent, shop, performing HTN planning in a multi-agent environment. shop is based on A-SHOP, an agentized 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 optimizations 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 in a significant way.}, keywords = {agent architectures, agent selection and planning, formalisms and logics}, isbn = {1-58113-480-0}, doi = {10.1145/544862.544960}, url = {http://doi.acm.org/10.1145/544862.544960}, author = {Dix,J{\"u}rgen and Mu{\~n}oz-Avila,H{\'e}ctor and Nau, Dana S. and Zhang,Lingling} } @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 {11914, title = {A Probabilistic Clustering-Based Indoor Location Determination System}, journal = {Technical Reports from UMIACS, UMIACS-TR-2002-30}, year = {2002}, month = {2002/04/04/}, abstract = {We present an indoor location determination system based on signalstrength probability distributions for tackling the noisy wireless channel and clustering to reduce computation requirements. We provide two implementation techniques, namely, Joint Clustering and Incremental Triangulation and describe their tradeoffs in terms of location determination accuracy and computation requirement. Both techniques have been incorporated in two implemented context-aware systems: User Positioning System and the Rover System, both running on Compaq iPAQ Pocket PC{\textquoteright}s with Familiar distribution of Linux for PDA{\textquoteright}s. The results obtained show that both techniques give the user location with over 90\% accuracy to within 7 feet with very low computation requirements, hence enabling a set of context-aware applications. Also UMIACS-TR-2002-30 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1192}, author = {Youssef,Moustafa A and Agrawala, Ashok K. and A. Udaya Shankar and Noh,Sam H} } @inbook {12755, title = {Probabilistic Human Recognition from Video}, booktitle = {Computer Vision {\textemdash} ECCV 2002Computer Vision {\textemdash} ECCV 2002}, series = {Lecture Notes in Computer Science}, volume = {2352}, year = {2002}, month = {2002///}, pages = {173 - 183}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper presents a method for incorporating temporal information in a video sequence for the task of human recognition. A time series state space model, parameterized by a tracking state vector and a recognizing identity variable , is proposed to simultaneously characterize the kinematics and identity. Two sequential importance sampling (SIS) methods, a brute-force version and an efficient version, are developed to provide numerical solutions to the model. The joint distribution of both state vector and identity variable is estimated at each time instant and then propagated to the next time instant. Marginalization over the state vector yields a robust estimate of the posterior distribution of the identity variable. Due to the propagation of identity and kinematics, a degeneracy in posterior probability of the identity variable is achieved to give improved recognition. This evolving behavior is characterized using changes in entropy . The effectiveness of this approach is illustrated using experimental results on low resolution face data and upper body data.}, isbn = {978-3-540-43746-8}, url = {http://dx.doi.org/10.1007/3-540-47977-5_45}, author = {Zhou,Shaohua and Chellapa, Rama}, editor = {Heyden,Anders and Sparr,Gunnar and Nielsen,Mads and Johansen,Peter} } @article {11913, title = {Rover: scalable location-aware computing}, journal = {Computer}, volume = {35}, year = {2002}, month = {2002/10//}, pages = {46 - 53}, abstract = {All the components necessary for realizing location-aware computing are available in the marketplace today. What has hindered the widespread deployment of location-based systems is the lack of an integration architecture that scales with user populations. The authors have completed the initial implementation of Rover, a system designed to achieve this sort of integration and to automatically tailor information and services to a mobile user{\textquoteright}s location. Their studies have validated Rover{\textquoteright}s underlying software architecture, which achieves system scalability through high-resolution, application-specific resource scheduling at the servers and network. The authors believe that this technology will greatly enhance the user experience in many places, including museums, amusement and theme parks, shopping malls, game fields, offices, and business centers. They designed the system specifically to scale to large user populations and expect its benefits to increase with them.}, keywords = {amusement, application-specific, architecture;, automation;, business, business;, computing;, data, entertainment;, handheld, humanities;, integration, LAN;, location-aware, malls;, mobile, museums;, office, parks;, processing;, resource, Rover;, scalability;, scalable, scheduling;, shopping, software, system, theme, units;, user;, wireless}, isbn = {0018-9162}, doi = {10.1109/MC.2002.1039517}, author = {Banerjee,S. and Agarwal,S. and Kamel,K. and Kochut, A. and Kommareddy,C. and Nadeem,T. and Thakkar,P. and Trinh,Bao and Youssef,A. and Youssef, M. and Larsen,R.L. and Udaya Shankar,A. and Agrawala, Ashok K.} } @article {12032, title = {Spatio-temporal stereo using multi-resolution subdivision surfaces}, journal = {International Journal of Computer Vision}, volume = {47}, year = {2002}, month = {2002///}, pages = {181 - 193}, author = {Neumann, J. and Aloimonos, J.} } @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 {15303, title = {Web question answering: is more always better?}, booktitle = {Proceedings of the 25th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {291 - 298}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a question answering system that is designed to capitalize on the tremendous amount of data that is now available online. Most question answering systems use a wide variety of linguistic resources. We focus instead on the redundancy available in large corpora as an important resource. We use this redundancy to simplify the query rewrites that we need to use, and to support answer mining from returned snippets. Our system performs quite well given the simplicity of the techniques being utilized. Experimental results show that question answering accuracy can be greatly improved by analyzing more and more matching passages. Simple passage ranking and n-gram extraction techniques work well in our system making it efficient to use with many backend retrieval engines.}, isbn = {1-58113-561-0}, doi = {10.1145/564376.564428}, url = {http://doi.acm.org/10.1145/564376.564428}, author = {Dumais,Susan and Banko,Michele and Brill,Eric and Jimmy Lin and Ng,Andrew} } @article {16720, title = {Word-level Alignment for Multilingual Resource Acquisition}, year = {2002}, month = {2002/04//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We present a simple, one-pass word alignment algorithm for parallel text. Our algorithm utilizes synchronous parsing and takes advantage of existing syntactic annotations. In our experiments the performance of this model is comparable to more complicated iterative methods. We discuss the challenges and potential benefits of using the model to train syntactic parsers for new languages.}, keywords = {*LEARNING MACHINES, *MULTILINGUAL RESOURCES, *WORDS(LANGUAGE), ACQUISITION, algorithms, ALIGNMENT, BENEFITS, ITERATIONS, LANGUAGE, linguistics}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458782}, author = {Lopez,Adam and Nossal,Michael and Hwa,Rebecca and Resnik, Philip} } @conference {15646, title = {Algorithms for facility location problems with outliers}, booktitle = {Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {642 - 651}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, abstract = {Facility location problems are traditionally investigated with the assumption that all the clients are to be provided service. A significant shortcoming of this formulation is that a few very distant clients, called outliers, can exert a disproportionately strong influence over the final solution. In this paper we explore a generalization of various facility location problems (K-center, K-median, uncapacitated facility location etc) to the case when only a specified fraction of the customers are to be served. What makes the problems harder is that we have to also select the subset that should get service. We provide generalizations of various approximation algorithms to deal with this added constraint.}, isbn = {0-89871-490-7}, url = {http://dl.acm.org/citation.cfm?id=365411.365555}, author = {Charikar,Moses and Khuller, Samir and Mount, Dave and Narasimhan,Giri} } @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.} } @article {15596, title = {Approximating large convolutions in digital images}, journal = {Image Processing, IEEE Transactions on}, volume = {10}, year = {2001}, month = {2001/12//}, pages = {1826 - 1835}, abstract = {Computing discrete two-dimensional (2-D) convolutions is an important problem in image processing. In mathematical morphology, an important variant is that of computing binary convolutions, where the kernel of the convolution is a 0-1 valued function. This operation can be quite costly, especially when large kernels are involved. We present an algorithm for computing convolutions of this form, where the kernel of the binary convolution is derived from a convex polygon. Because the kernel is a geometric object, we allow the algorithm some flexibility in how it elects to digitize the convex kernel at each placement, as long as the digitization satisfies certain reasonable requirements. We say that such a convolution is valid. Given this flexibility we show that it is possible to compute binary convolutions more efficiently than would normally be possible for large kernels. Our main result is an algorithm which, given an m times;n image and a k-sided convex polygonal kernel K, computes a valid convolution in O(kmn) time. Unlike standard algorithms for computing correlations and convolutions, the running time is independent of the area or perimeter of K, and our techniques do not rely on computing fast Fourier transforms. Our algorithm is based on a novel use of Bresenham{\textquoteright}s (1965) line-drawing algorithm and prefix-sums to update the convolution incrementally as the kernel is moved from one position to another across the image}, keywords = {2D, algorithm;binary, approximation;mathematical, convolution, convolution;binary, convolutions;Bresenham{\textquoteright}s, convolutions;convex, convolutions;geometric, images;discrete, kernel;convex, kernel;digital, line-drawing, morphology;, morphology;approximation, object;image, polygonal, processing;large, processing;mathematical, theory;convolution;image, two-dimensional}, isbn = {1057-7149}, doi = {10.1109/83.974567}, author = {Mount, Dave and Kanungo,T. and Netanyahu,N. S and Piatko,C. and Silverman,R. and Wu,A. Y} } @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} } @inbook {14667, title = {Compiling PLAN to SNAP}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {2207}, year = {2001}, month = {2001///}, pages = {134 - 151}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {PLAN (Packet Language for Active Networks) [ 3 ] is a highly flexible and usable active packet language, whereas SNAP (Safe and Nimble Active Packets) [ 12 ] offers significant resource usage safety and achieves much higher performance compared to PLAN, but at the cost of flexibility and usability. Ideally, we would like to combine the good properties of PLAN with those of SNAP. We have achieved this end by developing a compiler that translates PLANi nto SNAP. The compiler allows us to achieve the flexibility and usability of PLAN, but with the safety and efficiency of SNAP. In this paper, we describe both languages, highlighting the features that require special compilation techniques. We then present the details of our compiler and experimental results to evaluate our compiler with respect to code size.}, isbn = {978-3-540-42678-3}, url = {http://dx.doi.org/10.1007/3-540-45451-9_9}, author = {Hicks, Michael W. and Moore,Jonathan and Nettles,Scott}, editor = {Marshall,Ian and Nettles,Scott and Wakamiya,Naoki} } @conference {17025, title = {Component-based, user-constructed, multiple-view visualization}, booktitle = {CHI {\textquoteright}01 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {201 - 202}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {A major hindrance to the usage of information visualization in common tasks is that typically a new visualization interface must be custom programmed to suit each task. This video demonstrates a system and user interface that attempts to solve this problem by enabling end users to construct their own multiple-view visualization interfaces that are appropriate for their tasks and data. Users accomplish this by snapping together component visualizations and specifying tight couplings between them. Then they can use their newly constructed visualization interfaces to perform their tasks.}, keywords = {Information Visualization, multiple views, software components, Specification, tight coupling, user interface}, isbn = {1-58113-340-5}, doi = {10.1145/634067.634188}, url = {http://doi.acm.org/10.1145/634067.634188}, author = {North,Chris and Shneiderman, Ben} } @conference {17101, title = {Dynamic queries and brushing on choropleth maps}, booktitle = {Fifth International Conference on Information Visualisation, 2001. Proceedings}, year = {2001}, month = {2001///}, pages = {757 - 764}, publisher = {IEEE}, organization = {IEEE}, abstract = {Users who must combine demographic, economic or other data in a geographic context are often hampered by the integration of tabular and map representations. Static, paper-based solutions limit the amount of data that can be placed on a single map or table. By providing an effective user interface, we believe that researchers, journalists, teachers, and students can explore complex data sets more rapidly and effectively. This paper presents Dynamaps, a generalized map-based information visualization tool for dynamic queries and brushing on choropleth maps. Users can use color coding to show a variable on each geographic region, and then filter out areas that do not meet the desired criteria. In addition, a scatterplot view and a details-on-demand window support overviews and specific fact-finding}, keywords = {brushing, business, cartography, choropleth maps, color coding, colour graphics, complex data sets, Computational Intelligence Society, Computer science, data visualisation, Data visualization, demographic data, Demography, Dynamaps, dynamic queries, economic data, Educational institutions, geographic information system, geographic information systems, Joining processes, map representations, map-based information visualization, Query processing, Scattering, scatterplot view, tabular representations, user interface, User interfaces, World Wide Web}, isbn = {0-7695-1195-3}, doi = {10.1109/IV.2001.942141}, author = {Dang,G. and North,C. and Shneiderman, Ben} } @conference {14685, title = {Dynamic software updating}, booktitle = {Proceedings of the ACM SIGPLAN 2001 conference on Programming language design and implementation}, series = {PLDI {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {13 - 23}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Many important applications must run continuously and without interruption, yet must be changed to fix bugs or upgrade functionality. No prior general-purpose methodology for dynamic updating achieves a practical balance between flexibility, robustness, low overhead, and ease of use.We present a new approach for C-like languages that provides type-safe dynamic updating of native code in an extremely flexible manner (code, data, and types may be updated, at programmer-determined times) and permits the use of automated tools to aid the programmer in the updating process. Our system is based on dynamic patches that both contain the updated code and the code needed to transition from the old version to the new. A novel aspect of our patches is that they consist of verifiable native code (e.g. Proof-Carrying Code [17] or Typed Assembly Language [16]), which is native code accompanied by annotations that allow on-line verification of the code{\textquoteright}s safety. We discuss how patches are generated mostly automatically, how they are applied using dynamic-linking technology, and how code is compiled to make it updateable. To concretely illustrate our system, we have implemented a dynamically-updateable web server, FlashEd. We discuss our experience building and maintaining FlashEd. Performance experiments show that for FlashEd, the overhead due to updating is typically less than 1\%. }, isbn = {1-58113-414-2}, doi = {10.1145/378795.378798}, url = {http://doi.acm.org/10.1145/378795.378798}, author = {Hicks, Michael W. and Moore,Jonathan T. and Nettles,Scott} } @article {15567, title = {Efficient randomized algorithms for robust estimation of circular arcs and aligned ellipses}, journal = {Computational Geometry}, volume = {19}, year = {2001}, month = {2001/06//}, pages = {1 - 33}, abstract = {Fitting two-dimensional conic sections (e.g., circular and elliptical arcs) to a finite collection of points in the plane is an important problem in statistical estimation and has significant industrial applications. Recently there has been a great deal of interest in robust estimators, because of their lack of sensitivity to outlying data points. The basic measure of the robustness of an estimator is its breakdown point, that is, the fraction (up to 50\%) of outlying data points that can corrupt the estimator. In this paper we introduce nonlinear Theil{\textendash}Sen and repeated median (RM) variants for estimating the center and radius of a circular arc, and for estimating the center and horizontal and vertical radii of an axis-aligned ellipse. The circular arc estimators have breakdown points of ≈~21\% and 50\%, respectively, and the ellipse estimators have breakdown points of ≈ 16\% and 50\%, respectively. We present randomized algorithms for these estimators, whose expected running times are O(n2logn) for the circular case and O(n3logn) for the elliptical case. All algorithms use O(n) space in the worst case.}, keywords = {Aligned ellipse fitting, Arrangements, Circular arc fitting, computational geometry, randomized algorithms, Range searching, RM estimator, robust estimation, Theil{\textendash}Sen estimator}, isbn = {0925-7721}, doi = {10.1016/S0925-7721(01)00009-8}, url = {http://www.sciencedirect.com/science/article/pii/S0925772101000098}, author = {Mount, Dave and Netanyahu,Nathan S.} } @article {18027, title = {Evaluating the XMT parallel programming model}, journal = {High-Level Parallel Programming Models and Supportive Environments}, year = {2001}, month = {2001///}, pages = {95 - 108}, abstract = {Explicit-multithreading (XMT) is a parallel programming model designed for exploiting on-chip parallelism. Its features include a simple thread execution model and an efficient prefix-sum instruction for synchronizing shared data accesses. By taking advantage of low-overhead parallel threads and high on-chip memory bandwidth, the XMT model tries to reduce the burden on programmers by obviating the need for explicit task assignment and thread coarsening. This paper presents features of the XMT programming model, and evaluates their utility through experiments on a prototype XMT compiler and architecture simulator. We find the lack of explicit task assignment has slight effects on performance for the XMT architecture. Despite low thread overhead, thread coarsening is still necessary to some extent, but can usually be automatically applied by the XMT compiler. The prefix-sum instruction provides more scalable synchronization than traditional locks, and the simple run-untilcompletion thread execution model (no busy-waits) does not impair performance. Finally, the combination of features in XMT can encourage simpler parallel algorithms that may be more efficient than more traditional complex approaches.}, author = {Naishlos,D. and Nuzman,J. and Tseng,C. W and Vishkin, Uzi} } @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 {18802, title = {A geometric algorithm for selecting optimal set of cutters for multi-part milling}, series = {SMA {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {130 - 139}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {For the manufacture of milled parts, it is well known that the size of the cutter significantly affects the machining time. However, for small-batch manufacturing, the time spent on loading tools into the tool magazine and establishing z-length compensation values is just as important. If we can select a set of milling tools that will produce good machining time on more than one type of parts, then several unnecessary machine-tool reconfiguration operations can be eliminated. This paper describes a geometric algorithm for finding an optimal set of cutters for machining a set of 2{\textonehalf}D parts. In selecting milling cutters we consider both the tool loading time and the machining time and generate solutions that allow us to minimize the total machining time. Our problem formulation addresses the general problem of how to cover a target region to be milled with a cylindrical cutter without intersecting with the obstruction region; this definition allows us to handle both open and closed edges in the target region. Our algorithm improves upon previous work in the tool selection area in following ways: (1) in selecting cutters, it accounts for the tool loading time, and (2) it can simultaneously consider multiple different parts and select the optimal set of cutters to minimize the total manufacturing time.}, keywords = {computer-aided process planning, milling cutter selection}, isbn = {1-58113-366-9}, doi = {10.1145/376957.376973}, url = {http://doi.acm.org/10.1145/376957.376973}, author = {Yao,Zhiyang and Gupta, Satyandra K. and Nau, Dana S.} } @conference {13064, title = {Integrated information management: an interactive, extensible architecture for information retrieval}, booktitle = {Proceedings of the first international conference on Human language technology research}, series = {HLT {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {1 - 6}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Most current IR research is focused on specific technologies, such as filtering, classification, entity extraction, question answering, etc. There is relatively little research on merging multiple technologies into sophisticated applications, due in part to the high cost of integrating independently-developed text processing modules.}, doi = {10.3115/1072133.1072191}, url = {http://dx.doi.org/10.3115/1072133.1072191}, author = {Nyberg,Eric and Daum{\'e}, Hal} } @conference {18481, title = {Multimodal tracking for smart videoconferencing}, booktitle = {Second International Conference on Multimedia and Expo, Tokyo, Japan}, year = {2001}, month = {2001///}, author = {Zotkin,Dmitry N and Duraiswami, Ramani and Nanda,H. and Davis, Larry S.} } @conference {14725, title = {Practical programmable packets}, booktitle = {IEEE INFOCOM 2001. Twentieth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {1}, year = {2001}, month = {2001///}, pages = {41-50 vol.1 - 41-50 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present SNAP (safe and nimble active packets), a new scheme for programmable (or active) packets centered around a new low-level packet language. Unlike previous active packet approaches, SNAP is practical: namely, adding significant flexibility over IP without compromising safety and security or efficiency. In this paper we show how to compile from the well-known active picket language PLAN to SNAP, showing that SNAP retains PLAN{\textquoteright}s flexibility; give proof sketches of its novel approach to resource control; and present experimental data showing SNAP attains performance very close to that of a software IP router}, keywords = {active picket language, Application software, complier, Contracts, Data security, efficiency, Explosives, INFORMATION SCIENCE, Internet, IP, IP networks, low-level packet language, packet switching, performance, PLAN, practical programmable packets, program compilers, Protection, resource control, Resource management, safe and nimble active packets, Safety, Security, SNAP, software IP router, Software performance, telecommunication security, Transport protocols}, isbn = {0-7803-7016-3}, doi = {10.1109/INFCOM.2001.916685}, author = {Moore,J. T and Hicks, Michael W. and Nettles,S.} } @conference {15592, title = {Robust matching of wavelet features for sub-pixel registration of Landsat data}, booktitle = {Geoscience and Remote Sensing Symposium, 2001. IGARSS {\textquoteright}01. IEEE 2001 International}, volume = {2}, year = {2001}, month = {2001///}, pages = {706 -708 vol.2 - 706 -708 vol.2}, abstract = {For many Earth and space science applications, automatic geo-registration at sub-pixel accuracy has become a necessity. In this work, we are focusing on building an operational system, which will provide a sub-pixel accuracy registration of Landsat-5 and Landsat-7 data. The input to our registration method consists of scenes that have been geometrically and radiometrically corrected. Such preprocessed scenes are then geo-registered relative to a database of Landsat chips. The method assumes a transformation composed of a rotation and a translation, and utilizes rotation- and translation-invariant wavelets to extract image features that are matched using statistically robust feature matching and a partial Hausdorff distance metric. The registration process is described and results on four Landsat input scenes of the Washington, D.C., area are presented}, keywords = {Feature extraction, geo-registration, geophysical measurement technique, geophysical signal processing, geophysical techniques, Hausdorff distance metric, image registration, infrared, IR, land surface, Landsat, Landsat-5, Landsat-7, multispectral remote sensing, robust feature matching, robust matching, sub pixel registration, subpixel accuracy, terrain mapping, visible, wavelet feature, wavelet method, Wavelet transforms}, doi = {10.1109/IGARSS.2001.976609}, author = {Le Moigne,J. and Netanyahu,N. S and Masek,J. G and Mount, Dave and Goward, S.N.} } @inbook {14659, title = {Active Networking Means Evolution (or Enhanced Extensibility Required)}, booktitle = {Active NetworksActive Networks}, series = {Lecture Notes in Computer Science}, volume = {1942}, year = {2000}, month = {2000///}, pages = {16 - 32}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A primary goal of active networking is to increase the pace of network evolution. Evolution is typically achieved via extensibility; that is, typical active network implementations provide an interface to extend network nodes withdyna mically loaded code. Most implementations employ plug-in extensibility , a technique for loading code characterized by a concrete, pre-defined abstraction of future change. While flexible and convenient, we argue that plug-in extensibility alone is not sufficient for true network evolution. Instead, we propose dynamic software updating , a technique that reduces the a priori assumptions of plug-in extensibility, improving flexibility and eliminating the need to pre-plan extensions. However, this additional flexibility creates issues involving validity and security. We discuss these issues, and describe the state-of-the-art in systems that support dynamic software updating, thus framing the problem for researchers developing next-generation active networks.}, isbn = {978-3-540-41179-6}, url = {http://dx.doi.org/10.1007/3-540-40057-5_2}, author = {Hicks, Michael W. and Nettles,Scott}, editor = {Yasuda,Hiroshi} } @conference {15639, title = {The analysis of a simple k-means clustering algorithm}, booktitle = {Proceedings of the sixteenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {100 - 109}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {1-58113-224-7}, doi = {10.1145/336154.336189}, url = {http://doi.acm.org/10.1145/336154.336189}, author = {Kanungo,Tapas and Mount, Dave and Netanyahu,Nathan S. and Piatko,Christine and Silverman,Ruth and Wu,Angela Y.} } @article {14899, title = {Breakout Session Report: Principles and Methods}, journal = {Perceptual Organization for Artificial Vision Systems}, year = {2000}, month = {2000///}, pages = {17 - 28}, abstract = {This report will present a summary of views presented during a discussion at the 1999 Workshop on Perceptual Organization in Computer Vision. Our goal is to present diverse views, informally expressed on principles and algorithms of perceptual organization. Naturally, such a discussion must be somewhat limited both by the time available and by the specific set of researchers who could be present. Still, we hope to describe some interesting ideas expressed and to note the number of areas of apparent consensus among a fairly broad group. In particular, we will describe views on the state of the art in perceptual grouping, and what seem to be key open questions and promising directions for addressing them.}, doi = {10.1007/978-1-4615-4413-5_2}, author = {Jacobs, David W. and Malik,J. and Nevatia, R.} } @article {15568, title = {Chromatic nearest neighbor searching: A query sensitive approach}, journal = {Computational Geometry}, volume = {17}, year = {2000}, month = {2000/12//}, pages = {97 - 119}, abstract = {The nearest neighbor problem is that of preprocessing a set P of n data points in Rd so that, given any query point q, the closest point in P to q can be determined efficiently. In the chromatic nearest neighbor problem, each point of P is assigned a color, and the problem is to determine the color of the nearest point to the query point. More generally, given k⩾1, the problem is to determine the color occurring most frequently among the k nearest neighbors. The chromatic version of the nearest neighbor problem is used in many applications in pattern recognition and learning. In this paper we present a simple algorithm for solving the chromatic k nearest neighbor problem. We provide a query sensitive analysis, which shows that if the color classes form spatially well separated clusters (as often happens in practice), then queries can be answered quite efficiently. We also allow the user to specify an error bound ε⩾0, and consider the same problem in the context of approximate nearest neighbor searching. We present empirical evidence that for well clustered data sets, this approach leads to significant improvements in efficiency.}, keywords = {BBD trees, Branch-and-bound search, Chromatic nearest neighbors, Classification algorithms, Multidimensional searching, pattern recognition, Query sensitive analysis}, isbn = {0925-7721}, doi = {10.1016/S0925-7721(00)00021-3}, url = {http://www.sciencedirect.com/science/article/pii/S0925772100000213}, author = {Mount, Dave and Netanyahu,Nathan S. and Silverman,Ruth and Wu,Angela Y.} } @conference {13912, title = {Designing storytelling technologies to encouraging collaboration between young children}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems}, year = {2000}, month = {2000///}, pages = {556 - 563}, author = {Benford,S. and Bederson, Benjamin B. and \AAkesson,K. P and Bayon,V. and Druin, Allison and Hansson,P. and Hourcade,J. P and Ingram,R. and Neale,H. and O{\textquoteright}Malley,C. and others} } @conference {18031, title = {Evaluating multi-threading in the prototype XMT environment}, booktitle = {Proc. 4th Workshop on Multi-Threaded Execution, Architecture and Compliation (MTEAC2000)}, year = {2000}, month = {2000///}, abstract = {XMT is a multi-threaded programming model designed toexploit explicit specification of parallel threads. Its main features are a simple thread execution model and an efficient prefix-sum instruction for synchronizing shared data accesses. This paper presents and evaluates the performance of multi- threading in the XMT programming environment. A prototype XMT compiler converts parallel regions into procedure calls, which are then executed efficiently in XMT hardware. An architecture simulator similar to SimpleScalar is used to evaluate the performance of the XMT system for twelve benchmark codes. Results show the XMT architecture generally succeeds in providing low-overhead parallel threads and uniform access times on-chip. However, compiler optimizations to cluster (coarsen) threads are still needed for very fine-grained threads. }, author = {Naishlos,D. and Nuzman,J. and Tseng,C. W and Vishkin, Uzi} } @conference {18769, title = {Finding the maximal cutter for 2-D milling operations}, year = {2000}, month = {2000///}, pages = {10 - 13}, abstract = {In this paper, we describe a new geometricalgorithm to determine the biggest feasible cutter size for 2-D milling operations to be performed using a single cutter. In particular: {\textbullet} We give a general definition of the problem as the task of covering a target region without interfering with an obstruction region. This definition encompasses the task of milling a general 2-D profile that includes both open and closed edges. {\textbullet} We discuss three alternative definitions of what it means for a cutter to be feasible, and explain which of these definitions is most appropriate for the above problem. {\textbullet} We present a geometric algorithm for finding the maximal cutter for 2-D milling operations, and we give an outline of a proof that our algorithm is correct. }, url = {http://www.cs.umd.edu/~nau/papers/yao2000finding.pdf}, author = {Yao,Z. and Gupta,S.K. and Nau, Dana S.} } @article {18800, title = {A Geometric Algorithm for Finding the Largest Milling Cutter}, volume = {ISR; TR 2000-40}, year = {2000}, month = {2000///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {In this paper, we describe a new geometric algorithm to determine the largest feasible cutter size for2-D milling operations to be performed using a single cutter. In particular:

1. We give a general definition of the problem as the task of covering a target region without interfering with anobstruction region. This definition encompasses the task of milling a general 2-D profile that includes bothopen and closed edges.

2. We discuss three alternative definitions of what it means for a cutter to be feasible, and explain which of thesedefinitions is most appropriate for the above problem.

3. We present a geometric algorithm for finding the maximal cutter for 2-D milling operations, and we show thatour algorithm is correct.}, keywords = {algorithms, computational geometry, computer aided manufacturing CAM, cutter selection, Manufacturing, Next-Generation Product Realization Systems, path planning}, url = {http://drum.lib.umd.edu//handle/1903/6137}, author = {Yao,Zhiyang and Gupta, Satyandra K. and Nau, Dana S.} } @conference {18770, title = {A geometric algorithm for finding the maximal cutter for 2-D milling operations}, year = {2000}, month = {2000///}, pages = {26 - 28}, abstract = {In this paper, we present a geometric algorithm of finding the maximal cutter for 2-Dmilling operations. Our algorithm works not only for the common closed pocket problem, but also for the general 2-D milling problems with open edges. We define the general 2-D milling process in terms of a {\textquotedblleft}target region{\textquotedblright} to be machined and an {\textquotedblleft}obstruction region{\textquotedblright} that should not intersect with the cutter during machining. Our algorithm finds the largest cutter that can cover the target region without interfering with the obstruction region. Finding the biggest cutter is expected to help in the selection of the right sets of tools and the right type of cutter trajectories, and thereby ensure high production rate and meet the required quality level. }, url = {http://www.cs.umd.edu/~nau/papers/yao2000geometric.pdf}, author = {Yao,Z. and Gupta,S.K. and Nau, Dana S.} } @article {18801, title = {A Geometric Algorithm for Multi-Part Milling Cutter Selection}, volume = {ISR; TR 2000-42}, year = {2000}, month = {2000///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {Mass customization results in smaller batch sizes in manufacturing that require large numbers of setup and tool changes. The traditional process planning that generates plans for one part at a time is no longer applicable.

In this paper, we propose the idea of process planning for small batch manufacturing, i.e., we simultaneously consider multiple parts and exploit opportunities for sharing manufacturing resources such that the process plan will be optimized over the entire set of parts. In particular, we discuss a geometric algorithm for multiple part cutter selection in 2-1/2D milling operations.

We define the 2-1/2D milling operations as covering the target region without intersecting with the obstruction region. This definition allows us to handle the open edge problem. Based on this definition, we first discuss the lower and upper bond of cutter sizes that are feasible for given parts. Then we introduce the geometric algorithm to find the coverable area for a given cutter. Following that, we discuss the approach of considering cutter loading time and changing time in multiple cutter selection for multiple parts. We represent the cutter selection problem as shortest path problem and use Dijkstra{\textquoteright}s algorithm to solve it. By using this algorithm, a set of cutters is selected to achieve the optimum machining cost for multiple parts.

Our research illustrates the multiple parts process planning approach that is suitable for small batch manufacturing. At the same time, the algorithm given in this paper clarifies the 2-1/2D milling problem and can also help in cutter path planning problem.}, keywords = {algorithms, computer aided manufacturing CAM, cutter selection, Manufacturing, multi-part process planning, Next-Generation Product Realization Systems, OPTIMIZATION}, url = {http://drum.lib.umd.edu//handle/1903/6139}, author = {Yao,Zhiyang and Gupta, Satyandra K. and Nau, Dana S.} } @conference {15591, title = {Geo-registration of Landsat data by robust matching of wavelet features}, booktitle = {Geoscience and Remote Sensing Symposium, 2000. Proceedings. IGARSS 2000. IEEE 2000 International}, volume = {4}, year = {2000}, month = {2000///}, pages = {1610 -1612 vol.4 - 1610 -1612 vol.4}, abstract = {The goal of our project is to build an operational system, which will provide a sub-pixel accuracy registration of Landsat-5 and Landsat-7 data. Integrated within an automated mass processing/analysis system for Landsat data (REALM), the input to our registration method consists of scenes that have been geometrically and radiometrically corrected, as well as pre-processed for the detection of clouds and cloud shadows. Such pre-processed scenes are then geo-registered relative to a database of Landsat chips. This paper describes our registration process, including the use of a database of landmark chips, a feature extraction performed by an overcomplete wavelet representation, and feature matching using statistically robust techniques. Knowing the approximate longitudes and latitudes of the four corners of the scene, a subset of chips which represent landmarks included in the scene are extracted from the database. For each of these selected landmark chips, a corresponding window is extracted from the scene, and each chip-window pair is registered using our robust wavelet feature matching. First results and future directions are presented in the paper}, keywords = {atmospheric techniques, automated mass processing/analysis system, chip-window pair, cloud shadows, Clouds, Feature extraction, feature matching, geo-registration, geometrically corrected scene, geophysical signal processing, Image matching, image registration, landmark chips, Landsat chips, Landsat data, Landsat-5 data, Landsat-7 data, overcomplete wavelet representation, pre-processed scenes, radiometrically corrected scene, REALM, Remote sensing, robust matching, robust wavelet feature matching, scenes, statistically robust techniques, sub-pixel accuracy registration, wavelet features, Wavelet transforms, window}, doi = {10.1109/IGARSS.2000.857287}, author = {Le Moigne,J. and Netanyahu,N. S and Masek,J. G and Mount, Dave and Goward,S. and Honzak,M.} } @article {15233, title = {The Loading Time Scheduling Problem}, journal = {Journal of Algorithms}, volume = {36}, year = {2000}, month = {2000/07//}, pages = {1 - 33}, abstract = {In this paper we study precedence constrained scheduling problems, where the tasks can only be executed on a specified subset of the set of machines. Each machine has a loading time that is incurred only for the first task that is scheduled on the machine in a particular run. This basic scheduling problem arises in the context of machining on numerically controlled machines and query optimization in databases and in other artificial intelligence applications. We give the first nontrivial approximation algorithm for this problem. We also prove nontrivial lower bounds on best possible approximation ratios for these problems. These improve on the nonapproximability results that are implied by the nonapproximability results for the shortest common supersequence problem. We use the same algorithm technique to obtain approximation algorithms for a problem arising in the context of code generation for parallel machines and for the weighted shortest common supersequence problem.}, isbn = {0196-6774}, doi = {10.1006/jagm.2000.1076}, url = {http://www.sciencedirect.com/science/article/pii/S0196677400910769}, author = {Bhatia,Randeep and Khuller, Samir and Naor,Joseph (Seffi)} } @conference {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.} } @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.} } @conference {17640, title = {Optimal design of signaling networks for Internet telephony}, booktitle = {IEEE INFOCOM 2000. Nineteenth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {2}, year = {2000}, month = {2000///}, pages = {707-716 vol.2 - 707-716 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present an approach for efficient design of a signaling network for a network of software switches supporting Internet telephony. While one may take an integer programming approach to solve this problem, it quickly becomes intractable even for modest-sized networks. Instead, our topology design uses random graphs that we show to be nearly optimal in cost, highly connected, and computationally efficient even for large networks. We then formulate a quadratic assignment problem (QAP) to map the abstract topology into the physical network to achieve optimal load balancing for given demand forecasts, which we solve using randomized heuristics. Numerical results on several example networks illustrate the performance and computational efficiency of our method. A graphical design tool has been developed based on our algorithms}, keywords = {bandwidth allocation, Computational efficiency, Computer networks, Cost function, Demand forecasting, demand forecasts, graph theory, graphical design tool, Internet telephony, Linear programming, Load forecasting, Load management, Network topology, optimal design, optimal load balancing, optimisation, performance, quadratic assignment problem, random graphs, randomised algorithms, randomized heuristics, Signal design, signaling networks, Switches, telecommunication signalling, topology design}, isbn = {0-7803-5880-5}, doi = {10.1109/INFCOM.2000.832245}, author = {Srinivasan, Aravind and Ramakrishnan,K. G and Kumaran,K. and Aravamudan,M. and Naqvi,S.} } @article {15607, title = {Quantile approximation for robust statistical estimation and k-enclosing problems}, journal = {International Journal of Computational Geometry and Applications}, volume = {10}, year = {2000}, month = {2000///}, pages = {593 - 608}, abstract = {Given a set P of n points in Rd, a fundamental problem in computational geometryis concerned with finding the smallest shape of some type that encloses all the points of P. Well-known instances of this problem include finding the smallest enclosing box, minimum volume ball, and minimum volume annulus. In this paper we consider the following variant: Given a set of n points in Rd, find the smallest shape in question that contains at least k points or a certain quantile of the data. This type of problem is known as a k-enclosing problem. We present a simple algorithmic framework for computing quantile approximations for the minimum strip, ellipsoid, and annulus containing a given quantile of the points. The algorithms run in O(n log n) time. }, author = {Mount, Dave and Netanyahu,N. S and Piatko,C. D and Silverman,R. and Wu,A. Y} } @article {14652, title = {A Review of Current Routing Protocols for Ad Hoc}, journal = {IEEE Personal Communications}, volume = {29}, year = {2000}, month = {2000///}, pages = {156 - 71}, author = {Royer,E.M. and Toh,C.K. and Hicks, Michael W. and Kakkar,P. and Moore,J. T and Hicks, Michael W. and Moore,J. T and Alexander,D. S and Gunter,C. A and Nettles,S. and others} } @article {18863, title = {Selecting Flat End Mills for 2-1/2D Milling Operations}, volume = {ISR; TR 2000-41}, year = {2000}, month = {2000///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The size of milling cutter significantly affects the machining time. Therefore, in order to perform milling operations efficiently, we need to select a set of milling cutters with optimal sizes. It is difficult for human process planners to select the optimal or near optimal set of milling cutters due to complex geometric interactions among tools size, part shapes, and tool trajectories.

In this paper, we give a geometric algorithm to find the optimal cutters for 2-1/2D milling operations. We define the 2-1/2D milling operations as covering the target region without intersecting with the obstruction region. This definition allows us to handle the open edge problem. Based on this definition, we introduced the offsetting and inverse-offsetting algorithm to find the coverable area for a given cutter. Following that, we represent the cutter selection problem as shortest path problem and discuss the lower and upper bond of cutter sizes that are feasible for given parts. The Dijkstra{\textquoteright}s algorithm is used to solve the problem and thus a set of cutters is selected in order to achieve the optimum machining cost.

We believe the selection of optimum cutter combination can not only save manufacturing time but also help automatic process planning.}, keywords = {algorithms, computer aided manufacturing CAM, cutter selection, Manufacturing, Next-Generation Product Realization Systems}, url = {http://drum.lib.umd.edu//handle/1903/6138}, author = {Yao,Zhiyang and Gupta, Satyandra K. and Nau, Dana S.} } @conference {17361, title = {Snap-together visualization: a user interface for coordinating visualizations via relational schemata}, booktitle = {Proceedings of the working conference on Advanced visual interfaces}, series = {AVI {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {128 - 135}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Multiple coordinated visualizations enable users to rapidly explore complex information. However, users often need unforeseen combinations of coordinated visualizations that are appropriate for their data. Snap-Together Visualization enables data users to rapidly and dynamically mix and match visualizations and coordinations to construct custom exploration interfaces without programming. Snap{\textquoteright}s conceptual model is based on the relational database model. Users load relations into visualizations then coordinate them based on the relational joins between them. Users can create different types of coordinations such as: brushing, drill down, overview and detail view, and synchronized scrolling. Visualization developers can make their independent visualizations snap-able with a simple API.Evaluation of Snap revealed benefits, cognitive issues, and usability concerns. Data savvy users were very capable and thrilled to rapidly construct powerful coordinated visualizations. A snapped overview and detail-view coordination improved user performance by 30-80\%, depending on task. }, keywords = {Coordination, Information Visualization, multiple views, relational database, tight coupling, user interface, user study}, isbn = {1-58113-252-2}, doi = {10.1145/345513.345282}, url = {http://doi.acm.org/10.1145/345513.345282}, author = {North,Chris and Shneiderman, Ben} } @article {17363, title = {Snap-together visualization: can users construct and operate coordinated visualizations?}, journal = {International Journal of Human-Computer Studies}, volume = {53}, year = {2000}, month = {2000/11//}, pages = {715 - 739}, abstract = {Multiple coordinated visualizations enable users to rapidly explore complex information. However, users often need unforeseen combinations of coordinated visualizations. Snap-together visualization (Snap) enables users to rapidly and dynamically construct coordinated{\textendash}visualization interfaces, customized for their data, without programming. Users U001load data into desired visualizations, then construct coordinations between them for brushing and linking, overview and detail view, drill down, etc. Snap formalizes a conceptual model of visualization coordination based on the relational data model. Visualization developers can easily Snap-enable their independent visualizations using a simple API.Empirical evaluation reveals benefits, cognitive issues and usability concerns with coordination concepts and Snap. Two user studies explore coordination construction and operation. Data-savvy users successfully, enthusiastically and rapidly constructed powerful coordinated{\textendash}visualization interfaces of their own. Operating an overview-and-detail coordination reliably improved user performance by 30{\textendash}80\% over detail-only and uncoordinated interfaces for most tasks. }, isbn = {1071-5819}, doi = {10.1006/ijhc.2000.0418}, url = {http://www.sciencedirect.com/science/article/pii/S107158190090418X}, author = {North,Chris and Shneiderman, Ben} } @article {17365, title = {Snap-together visualization: Evaluating coordination usage and construction}, journal = {Int{\textquoteright}l Journal of Human-Computer Studies special issue on Empirical Studies of Information Visualization}, volume = {53}, year = {2000}, month = {2000///}, pages = {715 - 739}, abstract = {Multiple coordinated visualizations enable users to rapidly explore complex information. However, users often need unforeseen combinations of coordinated visualizations. Snap-Together Visualization is a conceptual model, based on the relational model, and system to enable users to quickly coordinate otherwise-independent visualization tools. Users construct customized browsing environments with coordinations for selecting, navigating, and loading data, without programming.Evaluation revealed benefits, cognitive issues, and usability concerns with coordination concepts and the Snap system. Two user studies explore the value of coordination usage and the learnability of coordination construction. The overview and detail-view coordination improved user performance by 30-80\%, depending on task. Data savvy users were very capable and thrilled to rapidly construct powerful coordinated visualizations. }, author = {North,C. and Shneiderman, Ben} } @article {15351, title = {Toward the large-eddy simulation over a hypersonic elliptical cross-section cone}, journal = {AIAA Paper No. 00-2311}, year = {2000}, month = {2000///}, author = {Martin, M.P and Weirs,G. and Candler,G. V and Piomelli,U. and Johnson,H. and Nompelis,I.} } @article {15228, title = {The budgeted maximum coverage problem}, journal = {Information Processing Letters}, volume = {70}, year = {1999}, month = {1999///}, pages = {39 - 45}, author = {Khuller, Samir and Moss,A. and Naor,J. S} } @article {14665, title = {Chunks in PLAN: Language support for programs as packets}, journal = {PROCEEDINGS OF THE ANNUAL ALLERTON CONFERENCE ON COMMUNICATION CONTROL AND COMPUTING}, volume = {37}, year = {1999}, month = {1999///}, pages = {PROCEEDINGS OF THE ANNUAL ALLERTON CONFERENCE ON COMMUNICATION CONTROL AND COMPUTING - PROCEEDINGS OF THE ANNUAL ALLERTON CONFER}, author = {Moore,J. T and Hicks, Michael W. and Nettles,S.} } @conference {15640, title = {Computing nearest neighbors for moving points and applications to clustering}, booktitle = {Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {931 - 932}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, isbn = {0-89871-434-6}, url = {http://dl.acm.org/citation.cfm?id=314500.315095}, author = {Kanungo,Tapas and Mount, Dave and Netanyahu,Nathan S. and Piatko,Christine and Silverman,Ruth and Wu,Angela Y.} } @article {15614, title = {Efficient algorithms for robust feature matching}, journal = {Pattern Recognition}, volume = {32}, year = {1999}, month = {1999///}, pages = {17 - 38}, abstract = {One of the basic building blocks in any point-based registration scheme involves matching feature points that areextracted from a sensed image to their counterparts in a reference image. This leads to the fundamental problem of point matching: Given two sets of points, find the (affine) transformation that transforms one point set so that its distance from the other point set is minimized. Because of measurement errors and the presence of outlying data points, it is important that the distance measure between the two point sets be robust to these effects. We measure distances using the partial Hausdorff distance. Point matching can be a computationally intensive task, and a number of theoretical and applied approaches have been proposed for solving this problem. In this paper, we present two algorithmic approaches to the point matching problem, in an attempt to reduce its computational complexity, while still providing a guarantee of the quality of the final match. Our first method is an approximation algorithm, which is loosely based on a branch-and- bound approach due to Huttenlocher and Rucklidge, (Technical Report 1321, Dept. of Computer Science, Cornell University, Ithaca, 1992; Proc. IEEE Conf. on Computer vision and Pattern Recognition, New York, 1993, pp. 705{\textemdash}706). We show that by varying the approximation error bounds, it is possible to achieve a tradeoff between the quality of the match and the running time of the algorithm. Our second method involves a Monte Carlo method for accelerating the search process used in the first algorithm. This algorithm operates within the framework of a branch-and-bound procedure, but employs point-to-point alignments to accelerate the search. We show that this combination retains many of the strengths of branch-and-bound search, but provides significantly faster search times by exploiting alignments. With high probability, this method succeeds in finding an approximately optimal match. We demonstrate the algorithms{\textquoteright} performances on both synthetically generated data points and actual satellite images. }, author = {Mount, Dave and Netanyahu,N. S and Le Moigne,J.} } @conference {16972, title = {An international SIGCHI research agenda}, booktitle = {CHI {\textquoteright}99 extended abstracts on Human factors in computing systems}, series = {CHI EA {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {171 - 171}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The goal of this workshop is to articulate an HCI research agenda statement, along with plans for continued refinement with the greater CHI community and plans for disseminating the information beyond the CHI community. There are been several similar prior efforts, including:{\textbullet} 1998 Universal Access program [2]{\textbullet} European community report, "Building the European Information Society for Us All" [1];{\textbullet} CHI 97 workshop [5] and paper [6], "HCI Research and Practice Agenda based on Human Needs {\textellipsis}";{\textbullet} CHI 96 Workshop, "CHI Ten-Year View{\textellipsis}" [3];{\textbullet} 1995 US National Science Foundation report, "New Directions in Human-Computer Interaction {\textellipsis}" [9];{\textbullet} 1995 report from the US National Research Council [7];{\textbullet} 1991 report, "{\textellipsis}HCI{\textellipsis} Serving Human Needs" [4]}, keywords = {agenda, human-computer, interaction, research}, isbn = {1-58113-158-5}, doi = {10.1145/632716.632821}, url = {http://doi.acm.org/10.1145/632716.632821}, author = {Scholtz,Jean C. and Muller,Michael and Novick,David and Olsen,Jr.,Dan R. and Shneiderman, Ben and Wharton,Cathleen} } @article {14917, title = {Linear fitting with missing data: applications to structure-from-motion and to characterizing intensity images}, year = {1999}, month = {1999/12/28/}, abstract = {A method for generating a complete scene structure from a video sequence that provides incomplete data. The method has a first step of building a first matrix consisting of point locations from a motion sequence by acquiring a sequence of images of a fixed scene using a moving camera; identifying and tracking point features through the sequence; and using the coordinates of the features to build the first matrix with some missing elements where some features are not present in some images. In a second step an approximate solution is built by selecting triples of columns from the first matrix; forming their nullspaces into a second matrix; and taking the three smallest components of the second matrix. In a third step, an iterative algorithm is applied to the three smallest components to build a third matrix and to improve the estimate. Lastly, in a fourth step the third matrix is decomposed to determine the complete scene structure. Another aspect of the present invention are...}, url = {http://www.google.com/patents?id=7LkYAAAAEBAJ}, author = {Jacobs, David W.}, editor = {NEC Research Institute, Inc.} } @inbook {14712, title = {Network Programming Using PLAN}, booktitle = {Internet Programming LanguagesInternet Programming Languages}, series = {Lecture Notes in Computer Science}, volume = {1686}, year = {1999}, month = {1999///}, pages = {127 - 143}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present here a methodology for programming active networks in the environment defined by our new language PLAN (Packet Language for Active Networks). This environment presumes a two-level architecture consisting of: 1. active packets carrying PLAN code; and 2. downloadable, node-resident services written in more general-purpose languages. We present several examples which illustrate how these two features can be combined to implement various network functions.}, isbn = {978-3-540-66673-8}, url = {http://dx.doi.org/10.1007/3-540-47959-7_7}, author = {Hicks, Michael W. and Kakkar,Pankaj and Moore,Jonathan and Gunter,Carl and Nettles,Scott}, editor = {Bal,Henri and Belkhouche,Boumediene and Cardelli,Luca} } @article {14722, title = {PLAN: A programming language for active networks}, journal = {ACM SIGPLAN NOTICES}, volume = {34}, year = {1999}, month = {1999///}, pages = {86 - 93}, abstract = {PLAN (Programming Language for Active Networks) is anew language for programs that are carried in the packets of a programmable network. PLAN programs replace the packet headers (which can be viewed as {\textquoteleft}dumb{\textquoteright} programs) used in current networks. As a header replacement, PLAN programs must be lightweight and of limited functionality. These limitations are mitigated by allowing PLAN code to call service routines written in other, more powerful lan- guages. These service routines may also be loaded into the routers dynamically. This two-level architecture, in which PLAN serves as a scripting or {\textquoteleft}glue{\textquoteright} language for more gen- eral services, is the primary contribution of the paper. PLAN is a strict functional language providing a limited set of primitives and datatypes. PLAN de nes primitives for remotely executing PLAN programs on other nodes, and these primitives are used to provide basic data transport in the network. Because remote execution makes debugging di cult, PLAN provides strong static guarantees to the pro- grammer, such as type safety. A more novel property aimed at protecting network availability is a guarantee that PLAN programs use a bounded amount of space and time on active routers and bandwidth in the network. }, author = {Hicks, Michael W. and Kakkar,P. and Moore,J. T and Gunter,C. A and Nettles,S.} } @conference {14723, title = {PLANet: an active internetwork}, booktitle = {IEEE INFOCOM {\textquoteright}99. Eighteenth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings}, volume = {3}, year = {1999}, month = {1999/03/21/25}, pages = {1124-1133 vol.3 - 1124-1133 vol.3}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present PLANet: an active network architecture and implementation. In addition to a standard suite of Internet-like services, PLANet has two key programmability features: (1) all packets contain programs; and (2) router functionality may be extended dynamically. Packet programs are written in our special purpose programming language PLAN, the Packet Language for Active Networks, while dynamic router extensions are written in OCaml, a dialect of ML. Currently, PLANet routers run as byte-code-interpreted Linux user-space applications, and support Ethernet and IP as link layers. PLANet achieves respectable performance on standard networking operations: on 300 MHz Pentium-II{\textquoteright}s attached to 100 Mbps Ethernet, PLANet can route 48 Mbps and switch over 5000 packets per second. We demonstrate the utility of PLANet{\textquoteright}s activeness by showing experimentally how it can nontrivially improve application and aggregate network performance in congested conditions}, keywords = {100 Mbit/s, 300 MHz, 48 Mbit/s, active internetwork, active network architecture, active network implementation, byte-code-interpreted applications, Computer architecture, Computer languages, Computer networks, congested conditions, dynamic programming, dynamic router extensions, Ethernet, Ethernet networks, INFORMATION SCIENCE, Internet, Internet-like services, internetworking, IP, IP networks, link layers, Linux user-space applications, Local area networks, ML dialect, Network performance, networking operations, OCaml, Packet Language for Active Networks, packet programs, packet switching, Pentium-II, performance, performance evaluation, PLAN, PLANet, Planets, programmability features, programming languages, router functionality, special purpose programming language, Switches, telecommunication network routing, Transport protocols, Web and internet services}, isbn = {0-7803-5417-6}, doi = {10.1109/INFCOM.1999.751668}, author = {Hicks, Michael W. and Moore,J. T and Alexander,D. S and Gunter,C. A and Nettles,S. M} } @conference {16167, title = {Refining query previews techniques for data with multivalued attributes: the case of NASA EOSDIS}, booktitle = {Research and Technology Advances in Digital Libraries, 1999. ADL {\textquoteright}99. Proceedings. IEEE Forum on}, year = {1999}, month = {1999///}, pages = {50 - 59}, abstract = {Query Previews allow users to rapidly gain an understanding of the content and scope of a digital data collection. These previews present overviews of abstracted metadata, enabling users to rapidly and dynamically avoid undesired data. We present our recent work on developing query previews for a variety of NASA EOSDIS situations. We focus on approaches that successfully address the challenge of multi-valued attribute data. Memory requirements and processing time associated with running these new solutions remain independent of the number of records in the dataset. We describe two techniques and their respective prototypes used to preview NASA Earth science data}, keywords = {attribute, attributes;processing, collection;memory, computing;meta, data, data;abstracted, data;digital, data;multivalued, data;query, Earth, EOSDIS;NASA, libraries;geophysics, metadata;dataset;digital, NASA, previews, processing;, requirements;multi-valued, Science, techniques;undesired, time;query}, doi = {10.1109/ADL.1999.777690}, author = {Plaisant, Catherine and Venkatraman,M. and Ngamkajorwiwat,K. and Barth,R. and Harberts,B. and Feng,Wenlan} } @article {17364, title = {Snap-Together Visualization: Coordinating Multiple Views to Explore Information}, journal = {Technical Reports from UMIACS}, year = {1999}, month = {1999/06/08/}, abstract = {Information visualizations with multiple coordinated views enable users torapidly explore complex data and discover relationships. However, it is usually difficult for users to find or create the coordinated visualizations they need. Snap-Together Visualization allows users to coordinate multiple views that are customized to their needs. Users query their relational database and load results into desired visualizations. Then they specify coordinations between visualizations for selecting, navigating, or re-querying. Developers can make independent visualization tools {\textquoteright}snap-able{\textquoteright} by including a few hooks. Also cross-referenced as UMIACS-TR-99-28 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/1010}, author = {North,Chris and Shneiderman, Ben} } @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} } @article {18033, title = {Trade-offs between communication throughput and parallel time}, journal = {Journal of Complexity}, volume = {15}, year = {1999}, month = {1999///}, pages = {148 - 166}, author = {Mansour,Y. and Nisan,N. and Vishkin, Uzi} } @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 {15651, title = {Approximating large convolutions in digital images}, journal = {PROCEEDINGS-SPIE THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING}, year = {1998}, month = {1998///}, pages = {216 - 227}, abstract = {Computing discrete two-dimensional convolutions is an important problem in image processing. In mathematicalmorphology, an important variant is that of computing binary convolutions, where the kernel of the convolution is a 0{1 valued function. This operation can be quite costly, especially when large kernels are involved. In this paper, we present an algorithm for computing convolutions of this form, where the kernel of the binary convolution is derived from a convex polygon. Because the kernel is a geometric object, we allow the algorithm some exibility in how it elects to digitize the convex kernel at each placement, as long as the digitization satis es certain reasonable requirements. We say that such a convolution is valid. Given this exibility we show that it is possible to compute binary convolutions more e ciently than would normally be possible for large kernels. Our main result is an algorithm, which given an m n image and a k-sided convex polygonal kernel, computes a valid convolution in time O(kmn) time. Unlike standard algorithms for computing correlations and convolutions, the running time is independent of the area or perimeter of K, and our techniques do not rely on computing fast Fourier transforms. Our algorithm is based on a novel use of Bresenham{\textquoteright}s line-drawing algorithm and pre x-sums to update the convolution e ciently as the kernel is moved from one position to another across the image. }, author = {Kanungo,T. and Mount, Dave and Netanyahu,N. S and Piatko,C. and Silverman,R. and Wu,A. Y} } @article {16979, title = {Assessing users{\textquoteright} subjective satisfaction with the Information System for Youth Services (ISYS)}, journal = {Institute for Systems Research Technical Reports}, year = {1998}, month = {1998/10/15/}, abstract = {In this investigation, the Questionnaire for User Interaction Satisfaction(QUIS 5.5), a tool for assessing users{\textquoteright} subjective satisfaction with specific aspects of the human/computer interface was used to assess the strengths and weaknesses of the Info rmation System for Youth Services (ISYS). ISYS is used by over 600 employees of the Maryland State Department of Juvenile Services (DJS) as a tracking device for juvenile offenders. Ratings and comments were collected from 254 DJS employees who use ISYS. The overall mean rating across all questions was 5.1 on a one to nine scale. The ten highest and lowest rated questions were identified. The QUIS allowed us to isolate subgroups which were compared with mean ratings from four measures of specific interfac e factors. The comments obtained from users provided suggestions, complaints and endorsements of the system. Also cross-referenced as CAR-TR-768 }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/431}, author = {Slaughter,Laura and Norman,Kent L and Shneiderman, Ben} } @article {15720, title = {BFGS with Update Skipping and Varying Memory}, journal = {SIAM Journal on Optimization}, volume = {8}, year = {1998}, month = {1998///}, pages = {1060 - 1083}, abstract = {We give conditions under which limited-memory quasi-Newton methods with exact line searches will terminate in n steps when minimizing n-dimensional quadratic functions. We show that although all Broyden family methods terminate in n steps in their full-memory versions, only BFGS does so with limited-memory. Additionally, we show that full-memory Broyden family methods with exact line searches terminate in at most n + p steps when p matrix updates are skipped. We introduce new limited-memory BFGS variants and test them on nonquadratic minimization problems.}, keywords = {bfgs, Broyden family, limited-memory, minimization, quasi-Newton, update skipping}, doi = {10.1137/S1052623496306450}, url = {http://link.aip.org/link/?SJE/8/1060/1}, author = {Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P. and Nazareth,Larry} } @conference {17094, title = {Distance learning: is it the end of education as most of us know it?}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {86 - 87}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {distance learning, education, Internet, Web}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286542}, url = {http://doi.acm.org/10.1145/286498.286542}, author = {Laurillard,Diana and Preece,Jenny and Shneiderman, Ben and Neal,Lisa and W{\ae}rn,Yvonne} } @article {15551, title = {Efficient randomized algorithms for the repeated median line estimator}, journal = {Algorithmica}, volume = {20}, year = {1998}, month = {1998///}, pages = {136 - 150}, abstract = {The problem of fitting a straight line to a finite collection of points in the plane is an important problem in statistical estimation. Recently there has been a great deal of interest is robust estimators, because of their lack of sensitivity to outlying data points. The basic measure of the robustness of an estimator is its breakdown point, that is, the fraction (up to 50\%) of outlying data points that can corrupt the estimator. One problem with robust estimators is that achieving high breakdown points (near 50\%) has proved to be computationally demanding. In this paper we present the best known theoretical algorithm and a practical subquadratic algorithm for computing a 50\% breakdown point line estimator, the Siegel or repeated median line estimator. We first present an O(n\log n) randomized expected-time algorithm, where n is the number of given points. This algorithm relies, however, on sophisticated data structures. We also present a very simple O(n log 2 n) randomized algorithm for this problem, which uses no complex data structures. We provide empirical evidence that, for many realistic input distributions, the running time of this second algorithm is actually O(n log n) expected time.}, doi = {10.1007/PL00009190}, author = {Matou{\v s}ek,J. and Mount, Dave and Netanyahu,N. S} } @article {17130, title = {Emergent patterns of teaching/learning in electronic classrooms}, journal = {Educational Technology Research and Development}, volume = {46}, year = {1998}, month = {1998///}, pages = {23 - 42}, abstract = {Novel patterns of teaching/learning have emerged from faculty and students who use our three teaching/learning theaters at the University of Maryland, College Park. These fully-equipped electronic classrooms have been used by 74 faculty in 264 semester-long courses since the fall of 1991 with largely enthusiastic reception by both faculty and students. The designers of the teaching/learning theaters sought to provide a technologically rich environment and a support staff so that faculty could concentrate on changing the traditional lecture from its unidirectional information flow to a more collaborative activity. As faculty have evolved their personal styles in using the electronic classrooms, novel patterns of teaching/learning have emerged. In addition to enhanced lectures, we identified three common patterns: (a) active individual learning, (b) small-group collaborative learning, and (c) entire-class collaborative learning.}, isbn = {1042-1629}, url = {http://dx.doi.org/10.1007/BF02299671}, author = {Shneiderman, Ben and Borkowski,Ellen and Alavi,Maryam and Norman,Kent} } @conference {18036, title = {Explicit Multi-Threading (XMT) bridging models for instruction parallelism (extended abstract)}, booktitle = {Proceedings of the tenth annual ACM symposium on Parallel algorithms and architectures}, year = {1998}, month = {1998///}, pages = {140 - 151}, author = {Vishkin, Uzi and Dascal,S. and Berkovich,E. and Nuzman,J.} } @article {18832, title = {Feature Recognition for Interactive Applications: Exploiting Distributed Resources}, volume = {UMIACS-TR-94-126.1}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {The availability of low-cost computational power is a drivingforce behind the growing sophistication of CAD software. Tools designed to reduce time-consuming build-test-redesign iterations are essential for increasing engineering quality and productivity. However, automation of the design process poses many difficult computational problems. As more downstream engineering activities are being considered during the design phase, guaranteeing reasonable response times within design systems becomes problematic. Design is an interactive process and speed is a critical factor in systems that enable designers to explore and experiment with alternative ideas during the design phase. Achieving interactivity requires an increasingly sophisticated allocation of computational resources in order to perform realistic design analyses and generate feedback in real time. This paper presents our initial efforts to develop techniques to apply distributed algorithms to the problem of recognizing machining features from solid models. Existing work on recognition of features has focused exclusively on serial computer architectures. Our objective is to show that distributed algorithms can be employed on realistic parts with large numbers of features and many geometric and topological entities to obtain significant improvements in computation time using existing hardware and software tools. Migrating solid modeling applications toward a distributed computing framework enables interconnection of many of the autonomous and geographically diverse software tools used in the modern manufacturing enterprise. (Also cross-referenced as UMIACS-TR-94-126.1) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/675}, author = {Regli,William C. and Gupta, Satyandra K. and Nau, Dana S.} } @article {18849, title = {IMACS: a case study in real-world planning}, journal = {Intelligent Systems and their Applications, IEEE}, volume = {13}, year = {1998}, month = {1998/06//may}, pages = {49 - 60}, abstract = {This article discusses the complexities of real-world planning and how to create planning systems to address them. IMACS (Interactive Manufacturability Analysis and Critiquing System), an automated designer{\textquoteright}s aid, evaluates machined parts and suggests design modifications to improve their manufacturability, offering advantages over the planning techniques used in classical planning systems}, keywords = {automated designer{\textquoteright}s aid, CAD/CAM, case study, computer aided analysis, computer aided production planning, design modifications, IMACS, intelligent design assistants, Interactive Manufacturability Analysis and Critiquing System, interactive systems, machined parts evaluation, machining, manufacturability, planning (artificial intelligence), planning systems}, isbn = {1094-7167}, doi = {10.1109/5254.683210}, author = {Gupta,S.K. and Nau, Dana S. and Regli,W. C.} } @conference {15635, title = {Improved algorithms for robust point pattern matching and applications to image registration}, booktitle = {Proceedings of the fourteenth annual symposium on Computational geometry}, series = {SCG {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {155 - 164}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-973-4}, doi = {10.1145/276884.276902}, url = {http://doi.acm.org/10.1145/276884.276902}, author = {Mount, Dave and Netanyahu,Nathan S. and LeMoigne,Jacqueline} } @article {18147, title = {Looking to Parallel Algorithms for ILP and Decentralization}, volume = {CS-TR-3921}, year = {1998}, month = {1998/10/15/}, institution = {Department of Computer Science, University of Maryland, College Park}, abstract = {We introduce explicit multi-threading (XMT), a decentralized architecturethat exploits fine-grained SPMD-style programming; a SPMD program can translate directly to MIPS assembly language using three additional instruction primitives. The motivation for XMT is: (i) to define an inherently decentralizable architecture, taking into account that the performance of future integrated circuits will be dominated by wire costs, (ii) to increase available instruction-level parallelism (ILP) by leveraging expertise in the world of parallel algorithms, and (iii) to reduce hardware complexity by alleviating the need to detect ILP at run-time: if parallel algorithms can give us an overabundance of work to do in the form of thread-level parallelism, one can extract instruction-level parallelism with greatly simplified dependence-checking. We show that implementations of such an architecture tend towards decentralization and that, when global communication is necessary, overall performance is relatively insensitive to large on-chip delays. We compare the performance of the design to more traditional parallel architectures and to a high-performance superscalar implementation, but the intent is merely to illustrate the performance behavior of the organization and to stimulate debate on the viability of introducing SPMD to the single-chip processor domain. We cannot offer at this stage hard comparisons with well-researched models of execution. When programming for the SPMD model, the total number of operations that the processor has to perform is often slightly higher. To counter this, we have observed that the length of the critical path through the dynamic execution graph is smaller than in the serial domain, and the amount of ILP is correspondingly larger. Fine-grained SPMD programming connects with a broad knowledge base in parallel algorithms and scales down to provide good performance relative to high-performance superscalar designs even with small input sizes and small numbers of functional units. Keywords: Fine-grained SPMD, parallel algorithms. spawn-join, prefix-sum, instruction-level parallelism, decentralized architecture. (Also cross-referenced as UMIACS-TR- 98-40) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/496}, author = {Berkovich,Efraim and Jacob,Bruce and Nuzman,Joseph and Vishkin, Uzi} } @article {15611, title = {An optimal algorithm for approximate nearest neighbor searching fixed dimensions}, journal = {Journal of the ACM (JACM)}, volume = {45}, year = {1998}, month = {1998/11//}, pages = {891 - 923}, abstract = {Consider a set of S of n data points in real d-dimensional space, Rd, where distances are measured using any Minkowski metric. In nearest neighbor searching, we preprocess S into a data structure, so that given any query point q ∈ Rd, is the closest point of S to q can be reported quickly. Given any positive real \&egr;, data point p is a (1 +\&egr;)-approximate nearest neighbor of q if its distance from q is within a factor of (1 + \&egr;) of the distance to the true nearest neighbor. We show that it is possible to preprocess a set of n points in Rd in O(dn log n) time and O(dn) space, so that given a query point q ∈ Rd, and \&egr; > 0, a (1 + \&egr;)-approximate nearest neighbor of q can be computed in O(cd, \&egr; log n) time, where cd,\&egr;<=d 1 + 6d/e;d is a factor depending only on dimension and \&egr;. In general, we show that given an integer k >= 1, (1 + \&egr;)-approximations to the k nearest neighbors of q can be computed in additional O(kd log n) time.}, keywords = {Approximation algorithms, Box-decomposition trees, closet-point queries, nearest neighbor searching, post-office problem, priority search}, isbn = {0004-5411}, doi = {10.1145/293347.293348}, url = {http://doi.acm.org/10.1145/293347.293348}, author = {Arya,Sunil and Mount, Dave and Netanyahu,Nathan S. and Silverman,Ruth and Wu,Angela Y.} } @article {14721, title = {PLAN: a packet language for active networks}, journal = {SIGPLAN Not.}, volume = {34}, year = {1998}, month = {1998/09//}, pages = {86 - 93}, abstract = {PLAN (Packet Language for Active Networks) is a new language for programs that form the packets of a programmable network. These programs replace the packet headers (which can be viewed as very rudimentary programs) used in current networks. As such, PLAN programs are lightweight and of restricted functionality. These limitations are mitigated by allowing PLAN code to call node-resident service routines written in other, more powerful languages. This two-level architecture, in which PLAN serves as a scripting or {\textquoteright}glue{\textquoteright} language for more general services, is the primary contribution of this paper. We have successfully applied the PLAN programming environment to implement an IP-free internetwork.PLAN is based on the simply typed lambda calculus and provides a restricted set of primitives and datatypes. PLAN defines a special construct called a chunk used to describe the remote execution of PLAN programs on other nodes. Primitive operations on chunks are used to provide basic data transport in the network and to support layering of protocols. Remote execution can make debugging difficult, so PLAN provides strong static guarantees to the programmer, such as type safety. A more novel property aimed at protecting network availability is a guarantee that PLAN programs use a bounded amount of network resources.}, isbn = {0362-1340}, doi = {10.1145/291251.289431}, url = {http://doi.acm.org/10.1145/291251.289431}, author = {Hicks, Michael W. and Kakkar,Pankaj and Moore,Jonathan T. and Gunter,Carl A. and Nettles,Scott} } @article {14742, title = {The PLAN system for building Active Networks}, journal = {University of Pennsylvania (February 27, 1998)}, year = {1998}, month = {1998///}, author = {Hicks, Michael W. and Kakkar,P. and Moore,J. T and Gunter,C. A and Alexander,D. S and Nettles,S.} } @article {15800, title = {Restoring Images Degraded by Spatially Variant Blur}, journal = {SIAM Journal on Scientific Computing}, volume = {19}, year = {1998}, month = {1998///}, pages = {1063 - 1082}, abstract = {Restoration of images that have been blurred by the effects of a Gaussian blurring function is an ill-posed but well-studied problem. Any blur that is spatially invariant can be expressed as a convolution kernel in an integral equation. Fast and effective algorithms then exist for determining the original image by preconditioned iterative methods. If the blurring function is spatially variant, however, then the problem is more difficult. In this work we develop fast algorithms for forming the convolution and for recovering the original image when the convolution functions are spatially variant but have a small domain of support. This assumption leads to a discrete problem involving a banded matrix. We devise an effective preconditioner and prove that the preconditioned matrix differs from the identity by a matrix of small rank plus a matrix of small norm. Numerical examples are given, related to the Hubble Space Telescope (HST) Wide-Field/Planetary Camera. The algorithms that we develop are applicable to other ill-posed integral equations as well.}, keywords = {convolution, discrete ill-posed problems, first-kind integral equations, image restoration, regularization, spatially variant point spread function}, doi = {10.1137/S106482759528507X}, url = {http://link.aip.org/link/?SCE/19/1063/1}, author = {Nagy,James G. and O{\textquoteright}Leary, Dianne P.} } @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} } @conference {14656, title = {A study of large object spaces}, booktitle = {Proceedings of the 1st international symposium on Memory management}, series = {ISMM {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {138 - 145}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper examines the design space for copying garbage collectors (GCs) in which "large objects" are managed in a separate, non-copy-collected space. We focus on two main issues:1. how to set the policy for classifying objects as "large"2. how to manage the large object spaceWe explore these issues experimentally using the Oscar GC testbed. In particular, we vary the threshold size of large objects and also whether the objects may contain pointers. Furthermore, we compare the performance of treadmill collection to that of mark-and-sweep collection for managing the large object space.We find that for some heaps there is a minimum cutoff size below which adding objects to the large object space does not result in a performance improvement, while for others no such cutoff exists. In general, including pointer-containing objects in the large object space seems beneficial. Finally, the exact method used to collect the large object space does not significantly influence overall performance.}, isbn = {1-58113-114-3}, doi = {10.1145/286860.286875}, url = {http://doi.acm.org/10.1145/286860.286875}, author = {Hicks, Michael W. and Hornof,Luke and Moore,Jonathan T. and Nettles,Scott M.} } @article {12079, title = {The SwitchWare active network architecture}, journal = {IEEE Network}, volume = {12}, year = {1998}, month = {1998/06//May}, pages = {29 - 36}, abstract = {Active networks must balance the flexibility of a programmable network infrastructure against the safety and security requirements inherent in sharing that infrastructure. Furthermore, this balance must be achieved while maintaining the usability of the network. The SwitchWare active network architecture is a novel approach to achieving this balance using three layers: active packets, which contain mobile programs that replace traditional packets; active extensions, which provide services on the network elements and can be dynamically loaded; and a secure active router infrastructure, which forms a high-integrity base on which the security of the other layers depends. In addition to integrity checking and cryptography-based authentication, security in our architecture depends heavily on verification techniques from programming languages, such as strong type checking}, keywords = {active extensions, active packets, Authentication, Computer languages, Computer networks, cryptography, cryptography-based authentication, high-integrity base, integrity checking, IP networks, LAN interconnection, mobile programs, network operating systems, packet switching, programmable network infrastructure, programming languages, Protocols, Safety, safety requirements, scalability, secure active router infrastructure, Security, security requirements, services, strong type checking, Switches, SwitchWare active network architecture, telecommunication network routing, Tin, usability, verification techniques}, isbn = {0890-8044}, doi = {10.1109/65.690959}, author = {Alexander,D. S and Arbaugh, William A. and Hicks, Michael W. and Kakkar,P. and Keromytis,A. D and Moore,J. T and Gunter,C. A and Nettles,S. M and Smith,J. M} } @article {14745, title = {The switchware active network implementation}, journal = {The ML Workshop, International Conference on Functional Programming (ICFP)}, year = {1998}, month = {1998///}, author = {Alexander,D. S and Hicks, Michael W. and Kakkar,P. and Keromytis,A. D and Shaw,M. and Moore,J. T and Gunter,C. A and Jim,T. and Nettles,S. M and Smith,J. M} } @conference {14468, title = {Utility elicitation as a classification problem}, booktitle = {Proceedings of the Fourteenth conference on Uncertainty in artificial intelligence}, series = {UAI{\textquoteright}98}, year = {1998}, month = {1998///}, pages = {79 - 88}, publisher = {Morgan Kaufmann Publishers Inc.}, organization = {Morgan Kaufmann Publishers Inc.}, address = {San Francisco, CA, USA}, abstract = {We investigate the application of classification techniques to utility elicitation. In a decision problem, two sets of parameters must generally be elicited: the probabilities and the utilities. While the prior and conditional probabilities in the model do not change from user to user, the utility models do. Thus it is necessary to elicit a utility model separately for each new user. Elicitation is long and tedious, particularly if the outcome space is large and not decomposable. There are two common approaches to utility function elicitation. The first is to base the determination of the user{\textquoteright}s utility function solely on elicitation of qualitative preferences. The second makes assumptions about the form and decomposability of the utility function. Here we take a different approach: we attempt to identify the new user{\textquoteright}s utility function based on classification relative to a database of previously collected utility functions. We do this by identifying clusters of utility functions that minimize an appropriate distance measure. Having identified the clusters, we develop a classification scheme that requires many fewer and simpler assessments than full utility elicitation and is more robust than utility elicitation based solely on preferences. We have tested our algorithm on a small database of utility functions in a prenatal diagnosis domain and the results are quite promising.}, isbn = {1-55860-555-X}, url = {http://dl.acm.org/citation.cfm?id=2074094.2074104}, author = {Chajewska,Urszula and Getoor, Lise and Norman,Joseph and Shahar,Yuval} } @article {16192, title = {Viewing personal history records: A comparison of tabular format and graphical presentation using LifeLines}, journal = {Behaviour \& Information Technology}, volume = {17}, year = {1998}, month = {1998///}, pages = {249 - 262}, abstract = {Thirty-six participants used a static version of either LifeLines, a graphical interface, or a tabular representation to answer questions about a database of temporal personal history information. Results suggest that overall the LifeLines representation led to much faster response times, primarily for questions which involved interval comparisons and making intercategorical connections. A {\textquoteright}first impression{\textquoteright} test showed that LifeLines can reduce some of the biases of the tabular record summary. A post-experimental memory test led to significantly (p< 0.004) higher recall for LifeLines. Finally, simple interaction techniques are proposed to compensate for the problems of the static LifeLines display{\textquoteright}s ability to deal with precise dates, attribute coding and overlaps.Thirty-six participants used a static version of either LifeLines, a graphical interface, or a tabular representation to answer questions about a database of temporal personal history information. Results suggest that overall the LifeLines representation led to much faster response times, primarily for questions which involved interval comparisons and making intercategorical connections. A {\textquoteright}first impression{\textquoteright} test showed that LifeLines can reduce some of the biases of the tabular record summary. A post-experimental memory test led to significantly (p< 0.004) higher recall for LifeLines. Finally, simple interaction techniques are proposed to compensate for the problems of the static LifeLines display{\textquoteright}s ability to deal with precise dates, attribute coding and overlaps. }, isbn = {0144-929X}, doi = {10.1080/014492998119328}, url = {http://www.tandfonline.com/doi/abs/10.1080/014492998119328}, author = {Alonso,Diane Lindwarm and Rose,Anne and Plaisant, Catherine and Norman,Kent L} } @conference {17269, title = {Is the Web really different from everything else?}, booktitle = {CHI 98 conference summary on Human factors in computing systems}, series = {CHI {\textquoteright}98}, year = {1998}, month = {1998///}, pages = {92 - 93}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {design, user experience, World Wide Web}, isbn = {1-58113-028-7}, doi = {10.1145/286498.286545}, url = {http://doi.acm.org/10.1145/286498.286545}, author = {Shneiderman, Ben and Nielsen,Jakob and Butler,Scott and Levi,Michael and Conrad,Frederick} } @inbook {14277, title = {What is computed by structure from motion algorithms?}, booktitle = {Computer Vision {\textemdash} ECCV{\textquoteright}98}, series = {Lecture Notes in Computer Science}, volume = {1406}, year = {1998}, month = {1998///}, pages = {359 - 375}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {In the literature we find two classes of algorithms which, on the basis of two views of a scene, recover the rigid transformation between the views and subsequently the structure of the scene. The first class contains techniques which require knowledge of the correspondence or the motion field between the images and are based on the epipolar constraint. The second class contains so-called direct algorithms which require knowledge about the value of the flow in one direction only and are based on the positive depth constraint. Algorithms in the first class achieve the solution by minimizing a function representing deviation from the epipolar constraint while direct algorithms find the 3D motion that, when used to estimate depth, produces a minimum number of negative depth values. This paper presents a stability analysis of both classes of algorithms. The formulation is such that it allows comparison of the robustness of algorithms in the two classes as well as within each class. Specifically, a general statistical model is employed to express the functions which measure the deviation from the epipolar constraint and the number of negative depth values, and these functions are studied with regard to their topographic structure, specifically as regards the errors in the 3D motion parameters at the places representing the minima of the functions. The analysis shows that for algorithms in both classes which estimate all motion parameters simultaneously, the obtained solution has an error such that the projections of the translational and rotational errors on the image plane are perpendicular to each other. Furthermore, the estimated projection of the translation on the image lies on a line through the origin and the projection of the real translation.}, isbn = {978-3-540-64569-6}, url = {http://dx.doi.org/10.1007/BFb0055678}, author = {Ferm{\"u}ller, Cornelia and Aloimonos, J.}, editor = {Burkhardt,Hans and Neumann,Bernd} } @article {18817, title = {Automated manufacturability analysis: A survey}, journal = {Research in Engineering Design}, volume = {9}, year = {1997}, month = {1997///}, pages = {168 - 190}, abstract = {In the market-place of the 21st century, there is no place for traditional {\textquoteleft}over-the-wall{\textquoteright} communications between design and manufacturing. In order to {\textquoteleft}design it right the very first time{\textquoteright}, designers must ensure that their products are both functional and easy to manufacture. Software tools have had some successes in reducing the barriers between design and manufacturing. Manufacturability analysis systems are emerging as one such tool {\textemdash} enabling identification of potential manufacturing problems during the design phase and providing suggestions to designers on how to eliminate them.}, keywords = {engineering}, isbn = {0934-9839}, doi = {10.1007/BF01596601}, url = {http://www.springerlink.com/content/p8p5516251023777/abstract/}, author = {Gupta, Satyandra K. and Regli,William C. and Das,Diganta and Nau, Dana S.} } @conference {15693, title = {Challenges in sending large radiology images over military communications channels}, booktitle = {Proceedings of SPIE}, volume = {3035}, year = {1997}, month = {1997///}, pages = {230 - 230}, author = {Cleary,K.R. and Levine,B.A. and Norton,G.S. and Mundur,P.V.} } @conference {16461, title = {The distributed information search component (disco) and the world wide web}, booktitle = {Proc. of ACM SIGMOD Conf. on Management of Data}, year = {1997}, month = {1997///}, author = {Naacke,H. and Kapitskaia,O. and Tomasic,A. and Bonnet,P. and Raschid, Louiqa and Amouroux,R.} } @conference {15598, title = {Efficient algorithms for robust feature matching}, booktitle = {Image Registration Workshop Proceedings}, year = {1997}, month = {1997///}, publisher = {NASA}, organization = {NASA}, abstract = {One of the basic building blocks in any point-based registration scheme involves matching feature points that are extracted from the sensed image to their counterparts in the reference image. This leads to the fundamental problem of point matching: given two sets of points, find the affine transformation that transforms one point set so that its distance from the other point set is minimized. Because of measurement errors and the presence of outlying data points, it is important that the distance measure between two point sets be robust to these effects. We measure distances using the generalized Hausdorff distance. Point matching can be a computationally intensive task, and there have been a number of algorithms and approaches proposed for solving this problem both theoretical and applied. We present two approaches to the point matching problem, in an attempt to reduce the computational complexity of the problem, while still providing guarantees on the quality of the final match. Our first method is an approximation algorithm, which is loosely based on a branch-and-bound approach due to Huttenlocher and Rucklidge. We show that by varying the approximation error bounds, it is possible to achieve a tradeoff between the quality of the match and the running time of the algorithm. Our second method involves a Monte Carlo method for accelerating the search process used in the first algorithm. With high probability this method succeeds in finding an approximately optimal match. We establish the efficiency of our approaches empirically.}, author = {Mount, Dave and Netanyahu,N. S and Le Moigne,J.} } @article {15753, title = {Fast iterative image restoration with a spatially varying PSF}, journal = {Proceedings of SPIE}, volume = {3162}, year = {1997}, month = {1997/10/24/}, pages = {388 - 399}, abstract = {We describe how to efficiently apply a spatially-variant blurring operator using linear interpolation of measured point spread functions. Numerical experiments illustrate that substantially better resolution can be obtained at very little additional cost compared to piecewise constant interpolation.}, isbn = {0277786X}, doi = {doi:10.1117/12.279513}, url = {http://spiedigitallibrary.org/proceedings/resource/2/psisdg/3162/1/388_1?isAuthorized=no}, author = {Nagy,James G. and O{\textquoteright}Leary, Dianne P.} } @article {15952, title = {How to (plan to) meet a deadline between now and then}, journal = {Journal of Logic and Computation}, volume = {7}, year = {1997}, month = {1997///}, pages = {109 - 109}, author = {Nirkhe,M. and Kraus,S. and Miller,M. and Perlis, Don} } @conference {14813, title = {MDL: a language and compiler for dynamic program instrumentation}, booktitle = {, 1997 International Conference on Parallel Architectures and Compilation Techniques., 1997. Proceedings}, year = {1997}, month = {1997/11/10/14}, pages = {201 - 212}, publisher = {IEEE}, organization = {IEEE}, abstract = {We use a form of dynamic code generation, called dynamic instrumentation, to collect data about the execution of an application program. Dynamic instrumentation allows us to instrument running programs to collect performance and other types of information. The instrumentation code is generated incrementally and can be inserted and removed at any time. Our instrumentation currently runs on the SPARC, PA-RISC, Power 2, Alpha, and x86 architectures. Specification of what data to collect are written in a specialized language called the Metric Description Language, that is part of the Paradyn Parallel Performance Tools. This language allows platform independent descriptions of how to collect performance data. It also provides a concise way to specify, how to constrain performance data to particular resources such as modules, procedures, nodes, files, or message channels (or combinations of these resources). We also describe the details of how we weave instrumentation into a running program}, keywords = {Alpha architecture, application program, application program interfaces, Application software, compiler generators, Computer science, dynamic code generation, Dynamic compiler, dynamic program instrumentation, Educational institutions, files, instrumentation code, Instruments, MDL, measurement, message channels, Message passing, Metric Description Language, modules, nodes, Operating systems, optimising compilers, PA-RISC, Paradyn Parallel Performance Tools, Parallel architectures, parallel programming, performance data, platform independent descriptions, Power 2 architecture, Power generation, procedures, program debugging, Program processors, running programs, Runtime, software metrics, SPARC, Specification languages, x86 architecture}, isbn = {0-8186-8090-3}, doi = {10.1109/PACT.1997.644016}, author = {Hollingsworth, Jeffrey K and Niam, O. and Miller, B. P and Zhichen Xu and Goncalves,M. J.R and Ling Zheng} } @article {14741, title = {The measured cost of copying garbage collection mechanisms}, journal = {SIGPLAN Not.}, volume = {32}, year = {1997}, month = {1997/08//}, pages = {292 - 305}, abstract = {We examine the costs and benefits of a variety of copying garbage collection (GC) mechanisms across multiple architectures and programming languages. Our study covers both low-level object representation and copying issues as well as the mechanisms needed to support more advanced techniques such as generational collection, large object spaces, and type segregated areas.Our experiments are made possible by a novel performance analysis tool, Oscar. Oscar allows us to capture snapshots of programming language heaps that may then be used to replay garbage collections. The replay program is self-contained and written in C, which makes it easy to port to other architectures and to analyze with standard performance analysis tools. Furthermore, it is possible to study additional programming languages simply by instrumenting existing implementations to capture heap snapshots.In general, we found that careful implementation of GC mechanisms can have a significant benefit. For a simple collector, we measured improvements of as much as 95\%. We then found that while the addition of advanced features can have a sizeable overhead (up to 15\%), the net benefit is quite positive, resulting in additional gains of up to 42\%. We also found that results varied depending upon the platform and language. Machine characteristics such as cache arrangements, instruction set (RISC/CISC), and register pool were important. For different languages, average object size seemed to be most important.The results of our experiments demonstrate the usefulness of a tool like Oscar for studying GC performance. Without much overhead, we can easily identify areas where programming language implementors could collaborate with GC implementors to improve GC performance.}, isbn = {0362-1340}, doi = {10.1145/258949.258976}, url = {http://doi.acm.org/10.1145/258949.258976}, author = {Hicks, Michael W. and Moore,Jonathan T. and Nettles,Scott M.} } @article {14106, title = {A note on conjugate gradient convergence}, journal = {Numerische Mathematik}, volume = {76}, year = {1997}, month = {1997///}, pages = {209 - 230}, author = {Naiman, A. E and Babu{\v s}ka, I. M and Elman, Howard} } @conference {15625, title = {A practical approximation algorithm for the LMS line estimator}, booktitle = {Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms}, series = {SODA {\textquoteright}97}, year = {1997}, month = {1997///}, pages = {473 - 482}, publisher = {Society for Industrial and Applied Mathematics}, organization = {Society for Industrial and Applied Mathematics}, address = {Philadelphia, PA, USA}, keywords = {Approximation algorithms, least median-of-squares regression, line arrangements, line fitting, randomized algorithms, robust estimation}, isbn = {0-89871-390-0}, url = {http://dl.acm.org/citation.cfm?id=314161.314349}, author = {Mount, Dave and Netanyahu,Nathan S. and Romanik,Kathleen and Silverman,Ruth and Wu,Angela Y.} } @article {16948, title = {A Taxonomy of Multiple Window Coordination}, journal = {Institute for Systems Research Technical Reports}, year = {1997}, month = {1997///}, abstract = {In current windowing environments, individual windows are treated independently, making it difficult for users to coordinate information across multiple windows. While coordinated multi- window strategies are increasingly used in visualization and web user interfaces, designs are inflexible and haphazard. The space of such linked-window strategies is not well understood and largely unexplored. This paper presents a taxonomy of coordinations, identifies important components, and reviews example interfaces. This 2x3 taxonomy provides guidelines for designers of applications, user interface toolkits, and window managers. We hope to encourage construction of generalized, end- user programmable, robust, multiple-window coordination capabilities.}, keywords = {Human-Computer Interaction,}, url = {http://drum.lib.umd.edu/handle/1903/5892}, author = {North,Chris and Shneiderman, Ben} } @article {18868, title = {Towards multiprocessor feature recognition}, journal = {Computer-Aided Design}, volume = {29}, year = {1997}, month = {1997/01//}, pages = {37 - 51}, abstract = {The availability of low-cost computational power is enabling the development of increasingly sophisticated cad software. Automation of design and manufacturing activities poses many difficult computational problems{\textemdash}significant among them is how to develop interactive systems that enable designers to explore and experiment with alternative ideas. As more downstream manufacturing activities are considered during the design phase, computational costs become problematic. Creating working software-based solutions requires a sophisticated allocation of computational resources in order to perform realistic design analyses and generate feedback. This paper presents our initial efforts to employ multiprocessor algorithms to recognize machining features from solid models of parts with large numbers of features and many geometric and topological entities. Our goal is to outline how improvements in computation time can be obtained by migrating existing software tools to multiprocessor architectures. An implementation of our approach is discussed.}, keywords = {Distributed computing, feature recognition, feature-based modelling, multiprocessor solid modelling}, isbn = {0010-4485}, doi = {10.1016/S0010-4485(96)00047-4}, url = {http://www.sciencedirect.com/science/article/pii/S0010448596000474}, author = {Regli,William C. and Gupta, Satyandra K. and Nau, Dana S.} } @article {16198, title = {Visual Information Seeking in Digital Image Libraries: The Visible Human Explorer}, journal = {Information in Images}, year = {1997}, month = {1997///}, abstract = {This chapter presents the Visible Human Explorer user interface, developed at theHuman-Computer Interaction Lab of the University of Maryland at College Park, for remotely accessing the National Library of Medicine{\textquoteright}s Visible Human digital image library. With the interface, users can visualize the library, browse contents, locate data of interest, and retrieve and zoom on desired image details. The interface presents a pair of tightly coupled views of library data: an overview of the overall search space, and a preview of high-resolution images available for retrieval. To explore, the user sweeps the views through the search space and receives smooth, rapid, visual feedback of contents. Desired details are automatically downloaded over the internet from the library. The interface software is completely functional (runs on Sun Workstations) and freely available for public use, at: http://www.nlm.nih.gov/. We also present several human-computer interaction design principles used to create the Visible Human Explorer interface, describe how these were applied to the design, and discuss issues in employing these techniques in user interfaces for other information collections. These principles are direct manipulation, visual information seeking, query previews, and multiple tightly coupled views. We illustrate these concepts with a plethora of pictures of user interface screens. Please also check the included CD-ROM for additional illustration media. }, author = {North,C. and Shneiderman, Ben and Plaisant, Catherine} } @article {15580, title = {Accounting for boundary effects in nearest-neighbor searching}, journal = {Discrete \& Computational Geometry}, volume = {16}, year = {1996}, month = {1996///}, pages = {155 - 176}, abstract = {Given n data points ind-dimensional space, nearest-neighbor searching involves determining the nearest of these data points to a given query point. Most averagecase analyses of nearest-neighbor searching algorithms are made under the simplifying assumption thatd is fixed and thatn is so large relative tod thatboundary effects can be ignored. This means that for any query point the statistical distribution of the data points surrounding it is independent of the location of the query point. However, in many applications of nearest-neighbor searching (such as data compression by vector quantization) this assumption is not met, since the number of data pointsn grows roughly as 2 d .Largely for this reason, the actual performances of many nearest-neighbor algorithms tend to be much better than their theoretical analyses would suggest. We present evidence of why this is the case. We provide an accurate analysis of the number of cells visited in nearest-neighbor searching by the bucketing andk-d tree algorithms. We assumem dpoints uniformly distributed in dimensiond, wherem is a fixed integer >=2. Further, we assume that distances are measured in theL $\infty$ metric. Our analysis is tight in the limit asd approaches infinity. Empirical evidence is presented showing that the analysis applies even in low dimensions.}, doi = {10.1007/BF02716805}, author = {Arya,S. and Mount, Dave and Narayan,O.} } @conference {12802, title = {An algebraic theory of process efficiency}, booktitle = {, Eleventh Annual IEEE Symposium on Logic in Computer Science, 1996. LICS {\textquoteright}96. Proceedings}, year = {1996}, month = {1996/07/27/30}, pages = {63 - 72}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper presents a testing-based semantic theory for reasoning about the efficiency of concurrent systems as measured in terms of the amount of their internal activity. The semantic preorders are given an algebraic characterization, and their optimality is established by means of a full abstractness result. They are also shown to subsume existing bisimulation-based efficiency preorders. An example is provided to illustrate the utility of this approach}, keywords = {algebraic characterization, algebraic specification, algebraic theory, bisimulation-based efficiency preorders, Calculus, calculus of communicating systems, Carbon capture and storage, Computer science, concurrent systems, formal logic, formal specification, full abstractness result, internal activity, optimality, process efficiency, reasoning, semantic preorders, System testing, testing-based semantic theory}, isbn = {0-8186-7463-6}, doi = {10.1109/LICS.1996.561304}, author = {Natarajan,V. and Cleaveland, Rance} } @inbook {15735, title = {Conjugate Gradients and Related KMP Algorithms: The Beginnings}, booktitle = {Linear and Nonlinear Conjugate Gradient-Related MethodsLinear and Nonlinear Conjugate Gradient-Related Methods}, year = {1996}, month = {1996///}, pages = {1 - 8}, publisher = {SIAM}, organization = {SIAM}, address = {Philadelphia}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Adams,Loyce and Nazareth,J. L.} } @article {18839, title = {Generating redesign suggestions to reduce setup cost: a step towards automated redesign}, journal = {Computer-Aided Design}, volume = {28}, year = {1996}, month = {1996/10//}, pages = {763 - 782}, abstract = {All mechanical designs pass through a series of formal and informal redesign steps, involving the analysis of functionality, manufacturability, cost and other life-cycle factors. The speed and efficacy of these steps has a major influence on the lead time of the product from conceptualization to launching. In this paper we propose a methodology for automatically generating redesign suggestions for reducing setup costs for machined parts.Given an interpretation of the design as a collection of machinable features, our approach is to generate alternate machining features by making geometric changes to the original features, and add them to the feature set of the original part to create an extended feature set. The designer may provide restrictions on the design indicating the type and extent of modifications allowed on certain faces and volumes, in which case all redesign suggestions generated by our approach honour those restrictions. By taking combinations of features from the extended feature set generated above, we can generate modified versions of the original design that still satisfy the designer{\textquoteright}s intent. By considering precedence constraints, we can estimate the setup time that will be required for each design. Any modified design whose setup time is less than that of the original design can be presented to the designer as a possible way to modify the original design. }, isbn = {0010-4485}, doi = {10.1016/0010-4485(95)00034-8}, url = {http://www.sciencedirect.com/science/article/pii/0010448595000348}, author = {Das,Diganta and Gupta, Satyandra K. and Nau, Dana S.} } @inbook {13005, title = {Inferring phylogenies from DNA sequence data: The effects of sampling}, booktitle = {New Uses for New PhylogeniesNew Uses for New Phylogenies}, year = {1996}, month = {1996///}, pages = {103 - 115}, publisher = {Oxford University Press}, organization = {Oxford University Press}, author = {Otto,S. P and Cummings, Michael P. and Wakeley,J.}, editor = {Harvey,PH and Leigh Brown,AJ and Maynard Smith,J and Nee,S} } @article {12785, title = {Modeling and verifying distributed systems using priorities: A case study}, journal = {Software - Concepts and Tools}, volume = {17}, year = {1996}, month = {1996///}, pages = {50 - 62}, author = {Cleaveland, Rance and Natarajan,V. and Sims,S. and Luettgen,G.} } @conference {12818, title = {Predictability of real-time systems: a process-algebraic approach}, booktitle = {Real-Time Systems Symposium, IEEE International}, year = {1996}, month = {1996///}, pages = {82 - 82}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {This paper presents a testing-based semantic preorder that relates real-time systems given in the process description language TPL on the basis of the predictability of their timing behavior. This predictability is measured in terms of the amount of variability present in processes{\textquoteright} "activity-completion times". The semantic preorder is shown to coincide with an already existing, well-investigated implementation relation for TPL-the must-preorder. The optimality of our relation is also established by means of a full abstraction result. An example is provided to illustrate the utility of this work.}, keywords = {process algebra; real time systems predictability; process algebra; testing-based semantic preorder; process description language; tpl; timing behavior; variability; activity-completion times; semantic preorder; must-preorder; optimality}, doi = {http://doi.ieeecomputersociety.org/10.1109/REAL.1996.563703}, author = {Natarajan,V. and Cleaveland, Rance} } @article {12824, title = {Priorities for modeling and verifying distributed systems}, journal = {Tools and Algorithms for the Construction and Analysis of Systems}, year = {1996}, month = {1996///}, pages = {278 - 297}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Natarajan,V. and Sims,S.} } @article {12804, title = {A process algebra with distributed priorities}, journal = {CONCUR{\textquoteright}96: Concurrency Theory}, year = {1996}, month = {1996///}, pages = {34 - 49}, author = {Cleaveland, Rance and L\{\"u}ttgen,G. and Natarajan,V.} } @conference {16204, title = {User controlled overviews of an image library: a case study of the visible human}, booktitle = {Proceedings of the first ACM international conference on Digital libraries}, series = {DL {\textquoteright}96}, year = {1996}, month = {1996///}, pages = {74 - 82}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, keywords = {Browsing, digital library, image database, information exploration, Information retrieval, Internet, medical image, remote access, user interface, Visualization, World-wide web}, isbn = {0-89791-830-4}, doi = {10.1145/226931.226946}, url = {http://doi.acm.org/10.1145/226931.226946}, author = {North,Chris and Shneiderman, Ben and Plaisant, Catherine} } @article {18818, title = {Automated Manufacturability Analysis: A Survey}, volume = {ISR; TR 1995-14}, year = {1995}, month = {1995///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {In the marketplace of the 21st century, there is no place for traditional {\textquoteleft}{\textquoteleft}over-the-wall{\textquoteright}{\textquoteright} communications between design and manufacturing. In order to {\textquoteleft}{\textquoteleft}design it right the very first time,{\textquoteright}{\textquoteright} designers must ensure that their products are both functional and easy to manufacture. Software tools have had some successes in reducing the barriers between design and manufacturing. Manufacturability analysis systems are emerging as one such tool---enabling identification of potential manufacturing problems during the design phase and providing suggestions to designers on how to eliminate them.

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

}, keywords = {manufacturability, Manufacturing, Solid modeling, Systems Integration Methodology}, url = {http://drum.lib.umd.edu//handle/1903/5609}, author = {Das,Diganta and Gupta, Satyandra K. and Regli,W. C. and Nau, Dana S.} } @article {18824, title = {Current Trends and Future Challenges in Automated Manufacturability Analysis}, volume = {ISR; TR 1995-16}, year = {1995}, month = {1995///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {In the marketplace of the 21st century, there is no place for traditional communications between design and manufacturing. In order to {\textquoteleft}{\textquoteleft}design it right the first time,{\textquoteright}{\textquoteright} designers must ensure that their products are both functional and easy to manufacture. Software tools have had some successes in reducing the barriers between design and manufacturing. Manufacturability analysis systems are emerging as one such tool---enabling identification of potential manufacturing problems during the design phase and providing suggestions to designers on how to eliminate them.

In this paper, we survey of current state of the art in automated manufacturability analysis. We describe the two dominant approaches to automated manufacturability analysis and overview representative systems based on their application domain. Finally, we attempt to expose some of the existing research challenges and future directions.}, keywords = {computer integrated manufacturing, manufacturability, Manufacturing, Solid modeling, Systems Integration Methodology}, url = {http://drum.lib.umd.edu//handle/1903/5611}, author = {Gupta, Satyandra K. and Das,Diganta and Regli,W. C. and Nau, Dana S.} } @article {12809, title = {Divergence and fair testing}, journal = {Automata, Languages and Programming}, year = {1995}, month = {1995///}, pages = {648 - 659}, author = {Natarajan,V. and Cleaveland, Rance} } @article {18745, title = {Estimation of setup time for machined parts: accounting for work-holding constraints using a vise}, journal = {COMPUTERS IN ENGINEERING}, year = {1995}, month = {1995///}, pages = {619 - 632}, abstract = {For machined parts, setup time is a major component ofthe total time required to manufacture a machined part from a stock. If the number of setups and hence setup time can be reduced, this will not only decrease the manufacturing time, but will also ensure better machining accuracy, require fewer work-holding devices and increase machine usage time. To achieve any improvement in setup time, rst we need to estimate the setup time accurately. In this paper we pro- pose a methodology to estimate the setup time for machin- ing prismatic parts in a three axis vertical machining center. We concurrently consider three major factors for estimating the number of setups, namely|the precedence constraints among machining operations, the feasibility of work holding using vise clamping, and the availability of datum faces for locating the workpiece on the machine table during machin- ing on a 3 axis vertical machining center. }, url = {http://www.cs.umd.edu/~nau/papers/das1995estimation.pdf}, author = {Das,D. and Gupta,S.K. and Nau, Dana S.} } @article {18831, title = {Extracting alternative machining features: An algorithmic approach}, journal = {Research in Engineering Design}, volume = {7}, year = {1995}, month = {1995///}, pages = {173 - 192}, abstract = {Automated recognition of features from CAD models has been attempted for a wide range of application domains. In this article we address the problem of representing and recognizing a complete class of features in alternative interpretation for a given design.}, keywords = {engineering}, isbn = {0934-9839}, doi = {10.1007/BF01638098}, url = {http://www.springerlink.com/content/t271m7t670m36484/abstract/}, author = {Regli,William C. and Gupta, Satyandra K. and Nau, Dana S.} } @conference {18750, title = {Interactive feature recognition using multi-processor methods}, year = {1995}, month = {1995///}, author = {Regli,W. C. and Gupta,S.K. and Nau, Dana S.} } @conference {18858, title = {Manufacturing feature instances: which ones to recognize?}, series = {SMA {\textquoteright}95}, year = {1995}, month = {1995///}, pages = {141 - 152}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-672-7}, doi = {10.1145/218013.218052}, url = {http://doi.acm.org/10.1145/218013.218052}, author = {Gupta, Satyandra K. and Regli,William C. and Nau, Dana S.} } @article {16607, title = {A modified cellular automata model of nucleotide interactions and non-enzymatic transcription of DNA}, journal = {inbs}, year = {1995}, month = {1995///}, pages = {136 - 136}, author = {Hilke,J. and Reggia, James A. and Navarro-Gonzalez,R. and Lohn,J.} } @article {14816, title = {The Paradyn parallel performance measurement tool}, journal = {Computer}, volume = {28}, year = {1995}, month = {1995/11//}, pages = {37 - 46}, abstract = {Paradyn is a tool for measuring the performance of large-scale parallel programs. Our goal in designing a new performance tool was to provide detailed, flexible performance information without incurring the space (and time) overhead typically associated with trace-based tools. Paradyn achieves this goal by dynamically instrumenting the application and automatically controlling this instrumentation in search of performance problems. Dynamic instrumentation lets us defer insertion until the moment it is needed (and remove it when it is no longer needed); Paradyn{\textquoteright}s Performance Consultant decides when and where to insert instrumentation}, keywords = {Aerodynamics, Automatic control, automatic instrumentation control, Debugging, dynamic instrumentation, flexible performance information, high level languages, insertion, Instruments, large-scale parallel program, Large-scale systems, measurement, Paradyn parallel performance measurement tool, Parallel machines, parallel programming, Performance Consultant, Programming profession, scalability, software performance evaluation, software tools}, isbn = {0018-9162}, doi = {10.1109/2.471178}, author = {Miller, B. P and Callaghan, M. D and Cargille, J. M and Hollingsworth, Jeffrey K and Irvin, R. B and Karavanic, K. L and Kunchithapadam, K. and Newhall, T.} } @conference {17660, title = {Splitters and near-optimal derandomization}, booktitle = {, 36th Annual Symposium on Foundations of Computer Science, 1995. Proceedings}, year = {1995}, month = {1995/10/23/25}, pages = {182 - 191}, publisher = {IEEE}, organization = {IEEE}, abstract = {We present a fairly general method for finding deterministic constructions obeying what we call k-restrictions; this yields structures of size not much larger than the probabilistic bound. The structures constructed by our method include (n,k)-universal sets (a collection of binary vectors of length n such that for any subset of size k of the indices, all 2k configurations appear) and families of perfect hash functions. The near-optimal constructions of these objects imply the very efficient derandomization of algorithms in learning, of fixed-subgraph finding algorithms, and of near optimal ΣIIΣ threshold formulae. In addition, they derandomize the reduction showing the hardness of approximation of set cover. They also yield deterministic constructions for a local-coloring protocol, and for exhaustive testing of circuits}, keywords = {Boosting, Circuit testing, computational complexity, computational linguistics, Computer science, Contracts, derandomization, deterministic constructions, Educational institutions, Engineering profession, exhaustive testing, fairly general method, fixed-subgraph finding algorithms, hardness of approximation, Information systems, k-restrictions, learning, local-coloring protocol, MATHEMATICS, near-optimal constructions, near-optimal derandomization, Parallel algorithms, probabilistic bound, probability, Protocols, randomised algorithms, Set cover, splitters}, isbn = {0-8186-7183-1}, doi = {10.1109/SFCS.1995.492475}, author = {Naor,M. and Schulman,L. J and Srinivasan, Aravind} } @article {18866, title = {Systematic approach to analysing the manufacturability of machined parts}, journal = {Computer-Aided Design}, volume = {27}, year = {1995}, month = {1995/05//}, pages = {323 - 342}, abstract = {The ability to quickly introduce new quality products is a decisive factor in capturing market share. Because of pressing demands to reduce leadtimes, analysing the manufacturability of the proposed design has become an important step in the design stage. The paper presents an approach to analysing the manufacturability of machined parts.Evaluating the manufacturability of a proposed design involves determining whether or not it is manufacturable with a given set of manufacturing operations, and, if it is, finding the associated manufacturing efficiency. Since there can be several different ways to manufacture a proposed design, this requires that different ways to manufacture it be considered, in order to determine which one best meets the design and manufacturing objectives. The first step in the approach is to identify all the machining operations which can potentially be used to create the given design. Using these operations, different operation plans are generated for machining the part. Each time a new operation plan is generated, the user examines whether it can produce the desired shape and tolerances, and calculates its manufacturability rating. If no operation plan can be found that is capable of producing the design, then the given design is considered unmachinable; otherwise, the manufacturability rating for the design is the rating of the best operation plan. The authors expect that, by providing feedback about possible problems with the design, the work described in the paper will help in speeding up the evaluation of new product designs so that it can be decided how or whether to manufacture them. Such a capability will be useful in responding quickly to changing demands and opportunities in the marketplace. }, keywords = {computer-aided manufacturability analysis, design for manufacturability, feature-based models}, isbn = {0010-4485}, doi = {10.1016/0010-4485(95)96797-P}, url = {http://www.sciencedirect.com/science/article/pii/001044859596797P}, author = {Gupta, Satyandra K. and Nau, Dana S.} } @article {15985, title = {Thinking takes time: a modal active-logic for reasoning in time}, journal = {Proc. of BISFAI-95}, year = {1995}, month = {1995///}, author = {Nirkhe,M. and Kraus,S. and Perlis, Don} } @article {17512, title = {Windows of opportunity in electronic classrooms}, journal = {Communications of the ACM}, volume = {38}, year = {1995}, month = {1995/11//}, pages = {19 - 24}, abstract = {Paradigm-shifting landmark buildings are cherished by their occupants and remembered because they reshape our expectations of schools, homes, or offices. Classic examples include Thomas Jefferson{\textquoteright}s communal design of the {\textquotedblleft}academical village{\textquotedblright} at the University of Virginia where faculty and students lived close to classrooms, Frank Lloyd Wright{\textquoteright}s organic harmony with nature in Fallingwater (in western Pennsylvania) where the waterfall sounds and leafy surroundings offered a stress-reducing getaway for an urban executive, or Kevin Roche{\textquoteright}s open glass-walled Ford Foundation (in New York City) that promoted new team-oriented management strategies.}, isbn = {0001-0782}, doi = {10.1145/219717.219725}, url = {http://doi.acm.org/10.1145/219717.219725}, author = {Shneiderman, Ben and Alavi,Maryann and Norman,Kent and Borkowski,Ellen Yu} } @article {18813, title = {An Application of Distributed Solid Modeling: Feature Recognition}, volume = {ISR; TR 1994-82}, year = {1994}, month = {1994///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The availability of low-cost computational power is a driving force behind the growing sophistication of CAD software. Tools designed to reduce time-consuming build-test-redesign iterations are essential for increasing engineering quality and productivity. However, automation of the design process poses many difficult computational problems. As more downstream engineering activities are being considered during the design phase, guaranteeing reasonable response times within design systems becomes problematic. Design is an interactive process and speed is a critical factor in systems that enable designers to explore and experiment with alternative ideas during the design phase. Achieving interactivity requires an increasingly sophisticated allocation of computational resources in order to perform realistic design analyses and generate feedback in real time.

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

This has been implemented on a network of SUN workstations using the ACIS solid modeler and the NIH C++ class library; inter-processor communication is handled with TCP/IP- based network communication tools.}, keywords = {Distributed computing, feature recognition, feature- based modeling, multiprocessor solid modeling, Systems Integration Methodology}, url = {http://drum.lib.umd.edu//handle/1903/5552}, author = {Regli,W. C. and Gupta, Satyandra K. and Nau, Dana S.} } @article {18821, title = {Building MRSEV models for CAM applications}, journal = {Advances in Engineering Software}, volume = {20}, year = {1994}, month = {1994///}, pages = {121 - 139}, abstract = {In integrating CAD and CAM applications, one major problem is how to interpret CAD information in a manner that makes sense for CAM. The goal is to develop a general approach that can be used with a variety of CAD and CAM applications for the manufacture of machined parts.In particular, a methodology is presented for taking a CAD model, extracting alternative interpretations of the model as collections of MRSEVs (material removal shape element volumes, a STEP-based library of machining features), and evaluating these interpretations to determine which one is optimal. The evaluation criteria may be defined by the user, in order to select the best interpretation for the particular application at hand. }, keywords = {CAD/CAM integration, design critiquing, feature recognition}, isbn = {0965-9978}, doi = {10.1016/0965-9978(94)90054-X}, url = {http://www.sciencedirect.com/science/article/pii/096599789490054X}, author = {Gupta, Satyandra K. and Kramer,Thomas R. and Nau, Dana S. and Regli,William C. and Zhang,Guangming} } @article {15992, title = {Calibrating, Counting, Grounding, Grouping}, volume = {FS-94-03}, year = {1994}, month = {1994///}, institution = {Association for the Advancement of Artificial Intelligence}, author = {Elgot-drapkin,J. and Gordon,D. and Kraus,S. and Miller,M. and Nirkhe,M. and Perlis, Don} } @article {15576, title = {Computationally Efficient Algorithms for High-Dimensional Robust Estimators}, journal = {CVGIP: Graphical Models and Image Processing}, volume = {56}, year = {1994}, month = {1994/07//}, pages = {289 - 303}, abstract = {Given a set of n distinct points in d-dimensional space that are hypothesized to lie on a hyperplane, robust statistical estimators have been recently proposed for the parameters of the model that best fits these points. This paper presents efficient algorithms for computing median-based robust estimators (e.g., the Theil-Sen and repeated median (RM) estimators) in high-dimensional space. We briefly review basic computational geometry techniques that were used to achieve efficient algorithms in the 2-D case. Then generalization of these techniques to higher dimensions is introduced. Geometric observations are followed by a presentation of O(nd - 1 log n) expected time algorithms for the d-dimensional Theil-Sen and RM estimators. Both algorithms are space optimal; i.e., they require O(n) storage, for fixed d. Finally, an extension of the methodology to nonlinear domain(s) is demonstrated.}, isbn = {1049-9652}, doi = {10.1006/cgip.1994.1026}, url = {http://www.sciencedirect.com/science/article/pii/S1049965284710261}, author = {Mount, Dave and Netanyahu,N. S} } @conference {18746, title = {Design for manufacture in multi-enterprise partnerships: current status and future directions}, year = {1994}, month = {1994///}, pages = {117 - 125}, abstract = {To pursue market and technology opportunities effectively, US commercial and defense industries will be relying increasingly on multi-enterprise partnerships. Horizontal partnering combines the strengths of multiple firms in product design, manufacture, after sales support and customer service, in order to launch superior products in the global market. To support effective partnering, new approaches will be needed for integrating the activities of design, planning, and production. It is important to address both the fundamental modeling of design, process planning, and production planning in ways that account for the capabilities of potential manufacturing partners, and the development of optimization procedures to address the underlying decision problems. This paper elaborates on these issues and discusses approaches for addressing them.}, url = {http://www.csa.com/partners/viewrecord.php?requester=gs\&collection=TRD\&recid=0160471CI}, author = {Nau, Dana S. and Ball,M. O and Gupta,S.K. and Minis,I. E. and Zhang, G.} } @article {16595, title = {An extended cellular space method for simulating autocatalytic oligonucleotides}, journal = {Computers \& chemistry}, volume = {18}, year = {1994}, month = {1994///}, pages = {33 - 43}, author = {Chou,H. H. and Reggia, James A. and Navarro-Gonzalez,R. and Wu,J.} } @article {18833, title = {Feature Recognition for Manufacturability Analysis}, volume = {ISR; TR 1994-10}, year = {1994}, month = {1994///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {While automated recognition of features has been attempted for a wide range of applications, no single existing approach possesses the functionality required to perform manufacturability analysis. In this paper, we present a methodology for taking a CAD model and extracting a set of machinable features suitable for generating all alternative interpretations of the model as collections of MRSEVs (Material Removal Shape Element Volumes, a STEP-based library of machining, features). This set of MRSEVs is to be employed for manufacturability analysis. The algorithm handles a variety of features including those describing holes, pockets, slots, and chamfering and filleting operations. In addition, it considers elementary accessibility constraints for these features and is provably complete over a, significant class of machinable parts the features describe. Further, the approach has low-order polynomial-time worst-case complexity.}, keywords = {algorithms, Automation, COMPUTER AIDED DESIGN, computer aided manufacturing, computer integrated manufacturing, Feature extraction, manufacturability, Manufacturing, Solid modeling, Systems Integration}, url = {http://drum.lib.umd.edu//handle/1903/5490}, author = {Regli,W. C. and Gupta, Satyandra K. and Nau, Dana S.} } @article {15211, title = {Flow in planar graphs with vertex capacities}, journal = {Algorithmica}, volume = {11}, year = {1994}, month = {1994///}, pages = {200 - 225}, abstract = {Max-flow in planar graphs has always been studied with the assumption that there are capacities only on the edges. Here we consider a more general version of the problem when the vertices as well as edges have capacity constraints. In the context of general graphs considering only edge capacities is not restrictive, since the vertex-capacity problem can be reduced to the edge-capacity problem. However, in the case of planar graphs this reduction does not maintainplanarity and cannot be used. We study different versions of the planar flow problem (all of which have been extensively investigated in the context of edge capacities).}, doi = {10.1007/BF01240733}, author = {Khuller, Samir and Naor,J.} } @article {18853, title = {Integrating DFM with CAD through Design Critiquing}, journal = {Concurrent EngineeringConcurrent Engineering}, volume = {2}, year = {1994}, month = {1994/06/01/}, pages = {85 - 95}, abstract = {The increasing focus on design for manufacturability (DFM) in research in concurrent engineering and engineering design is expanding the scope of traditional design activities in order to identify and eliminate manufacturing problems during the design stage. Manufacturing a product generally involves many different kinds of manufacturing activities, each having different characteristics. A design that is good for one kind of activity may not be good for another; for example, a design that is easy to assemble may not be easy to machine. One obstacle to DFM is the difficulty involved in building a single system that can handle the various manufacturing domains relevant to a design.}, keywords = {design critiquing, design for manufacturability, feature-based modeling, manufacturability analysis, multi-agent coordination.}, isbn = {1063-293X, 1531-2003}, doi = {10.1177/1063293X9400200202}, url = {http://cer.sagepub.com/content/2/2/85}, author = {Gupta, Satyandra K. and Regli,William C. and Nau, Dana S.} } @article {16649, title = {A modified cellular automata model of nucleotide interactions and DNA replication}, year = {1994}, month = {1994///}, institution = {University of Maryland at College Park}, address = {College Park, MD, USA}, author = {Hilke,James and Lohn,Jason and Reggia, James A. and Navarro,Rafael} } @conference {18054, title = {Trade-offs between communication throughput and parallel time}, booktitle = {Proceedings of the twenty-sixth annual ACM symposium on Theory of computing}, year = {1994}, month = {1994///}, pages = {372 - 381}, author = {Mansour,Y. and Nisan,N. and Vishkin, Uzi} } @article {18822, title = {Concurrent evaluation of machinability during product design}, journal = {Computer}, volume = {26}, year = {1993}, month = {1993/01//}, pages = {61 - 63}, abstract = {An approach to evaluating the machinability of a part during the design stage, which performs systematic generation and evaluation of machining alternatives, is discussed. The results of the analysis provide feedback to the designer about problems that might arise with the machining and information to the manufacturing engineer about which machining processes and process parameters are most desirable.<>}, keywords = {concurrent engineering, concurrent evaluation, machinability, machining, manufacturing engineer, product design}, isbn = {0018-9162}, doi = {10.1109/2.179158}, author = {Gupta,S.K. and Nau, Dana S. and Zhang, G.} } @article {18743, title = {Development of machining alternatives, based on MRSEVs}, journal = {Computers in Engineering}, year = {1993}, month = {1993///}, pages = {47 - 47}, abstract = {One missing link between CAD and CAM is the lack ofa systematic methodology for generating and evaluating al- ternative ways to manufacture a proposed design. To ad- dress this problem, we are developing a systematic approach for generating and evaluating alternative ways to manufac- ture machined parts, in order to provide information to the designer about the manufacturability of the proposed de- sign, and information to the process engineer about how best to machine the part. This paper describes our overall approach, and how MRSEVs (Material Removal Shape El- ement Volumes, a STEP library of machining features) can be used to support it. }, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.37.6348\&rep=rep1\&type=pdf}, author = {Nau, Dana S. and Gupta,S.K. and Kramer,T. R. and Regli,W. C. and Zhang, G.} } @conference {15631, title = {Efficient algorithms for robust circular arc estimators}, booktitle = {Proceedings of the Fifth Canadian Conference on Computational Geometry, Waterloo, Ontario, Canada}, year = {1993}, month = {1993///}, author = {Mount, Dave and Netanyahu,N. S} } @article {18830, title = {Estimation of Achievable Tolerances}, volume = {ISR; TR 1993-44}, year = {1993}, month = {1993///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {This report presents a new and systematic approach to assist decision-making in selecting machining operation plans. We present a methodology to estimate achievable tolerances of operations plan. Given an operation plan, we use variety of empirical and mathematical models to evaluate process capabilities of various machining operations and compute achievable tolerances using tolerance charting techniques.}, keywords = {Automation, computer aided manufacturing, Manufacturing, Manufacturing Systems}, url = {http://drum.lib.umd.edu//handle/1903/5389}, author = {Gupta, Satyandra K. and Nau, Dana S. and Zhang,G. M.} } @article {18744, title = {Evaluating product machinability for concurrent engineering}, journal = {Concurrent Engineering: Contemporary Issues and Modern Design Tools}, year = {1993}, month = {1993///}, pages = {264 - 279}, url = {http://books.google.com/books?hl=en\&lr=\&id=S5rjzPSsM5EC\&oi=fnd\&pg=PA264\&dq=Satyandra+Gupta\&ots=Ldu80IZ66F\&sig=xZN6yo6NsLi2y3CZskweXchossg}, author = {Nau, Dana S. and Zhang, G. and Gupta,S.K. and Karinthi,R. R.} } @conference {18841, title = {Generation of alternative feature-based models and precedence orderings for machining applications}, series = {SMA {\textquoteright}93}, year = {1993}, month = {1993///}, pages = {465 - 466}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-584-4}, doi = {10.1145/164360.164520}, url = {http://doi.acm.org/10.1145/164360.164520}, author = {Gupta, Satyandra K. and Nau, Dana S.} } @article {18854, title = {Interpreting Product Designs for Manufacturability Evaluation}, volume = {ISR; TR 1993-45}, year = {1993}, month = {1993///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The ability to quickly introduce new quality products is a decisive factor in capturing market share. Because of pressing demands to reduce lead time, analyzing the manufacturability of the proposed design has become an important step in the design stage. In this paper we present an approach for evaluating the manufacturability of machined parts.

Evaluating manufacturability involves finding a way to manufacture the proposed design, and estimating the associated production cost and quality. However, there often can be several different ways to manufacture a proposed design - so to evaluate the manufacturability of the proposed design, we need to consider different ways to manufacture it, and determine which one best meets the manufacturing objectives.

In this paper we describe a methodology for systematically generating and evaluating alternative operation plans. As a first step, we identify all machining operations which can potentially be used to create the given design. Using these operations, we generate different operation plans for machining the part. Each time we generate a new operation plan, we assign it a manufacturability rating. The manufacturability rating for the design is the rating of the best operation plan.

We anticipate that by providing feedback about possible problems with the design, this work will be useful in providing a way to speed up the evaluation of new product designs in order to decide how or whether to manufacture them.}, keywords = {Automation, computer aided manufacturing, manufacturability, Manufacturing Systems}, url = {http://drum.lib.umd.edu//handle/1903/5390}, author = {Gupta, Satyandra K. and Nau, Dana S. and Zhang,G. M.} } @article {15209, title = {The lattice structure of flow in planar graphs}, journal = {SIAM Journal on Discrete Mathematics}, volume = {6}, year = {1993}, month = {1993///}, pages = {477 - 477}, author = {Khuller, Samir and Naor,J. S and Klein,P.} } @conference {11926, title = {Multiple Resource Allocation for Multiprocessor Distributed Real-Time Systems}, booktitle = {In Workshop on Parallel and Distributed Real-Time Systems (PDRTS), IEEE IPPS{\textquoteright}93}, year = {1993}, month = {1993///}, abstract = {this report are those of the author(s) and should not be interpreted as representing the official policies, either expressed or implied, of the Defense Advanced Research Projects Agency, ONR, the U.S. Government or Honeywell. Computer facilities were provided in part by NSF grant CCR-8811954. Workshop on Parallel and Dist Real-Time Syst, IEEE IPPS{\textquoteright}93 April 1993 in the queue and tries to schedule it. If the task is successfully scheduled, it is removed from the queue and executed. Otherwise, the task is unlocked so that other processors may examine it in the same fashion. This scheme is convenient for a shared memory architecture, but becomes too expensive and cumbersome when such facility is not available in hardware (for example, in distributed systems). The goal of this paper is twofold: first, to study the problem of allocating multiple resources to a single task; and second, to provide a heuristic allocation policy for selecting a resource among multiple instances of identical resources. We consider a distributed system in which each site is a uniform memory access (UMA) multiprocessor, but the scheme is easily extensible to non-UMA models. For the first problem, a three-tiered resource allocation scheme is proposed. A hierarchy of the resources is defined to reduce the probability of allocation failure as the allocation progresses. To reduce the complexity of multiple resource allocation, we group the resources into schedulable sets of resources. Since the objective in real-time systems is to meet deadlines, this approach is acceptable so long as it meets a justifiable minimum level of resource utilization. It is shown that our approach allows modularity, flexibility, and potential concurrency in scheduling. Another contribution of this paper is in explicitly ide...}, author = {Mosse,Daniel and Noh,Sam H and Trinh,Bao and Agrawala, Ashok K.} } @article {16366, title = {A partial evaluator for the Maruti hard real-time system}, journal = {Real-Time Systems}, volume = {5}, year = {1993}, month = {1993///}, pages = {13 - 30}, author = {Nirkhe,V. and Pugh, William} } @conference {16020, title = {Situated reasoning within tight deadlines and realistic space and computation bounds}, booktitle = {Proc. Common Sense}, volume = {93}, year = {1993}, month = {1993///}, author = {Nirkhe,M. and Kraus,S. and Perlis, Don} } @article {18809, title = {A Systematic Approach for Analyzing the Manufacturability of Machined Parts}, volume = {ISR; TR 1993-76}, year = {1993}, month = {1993///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {The ability to quickly introduce new quality products is a decisive factor in capturing market share. Because of pressing demands to reduce lead time, analyzing the manufacturability of the proposed design has become an important step in the design stage. This paper presents an approach for analyzing the manufacturability of machined parts.

Evaluating the manufacturability of a proposed design involves determining whether or not it is manufacturable with a given set of manufacturing operations - and if so, then finding the associated manufacturing efficiency. Since there can be several different ways to manufacture a proposed design, this requires us to consider different ways to manufacture it, in order to determine which one best meets the design and manufacturing objectives.

The first step in our approach is to identify all machining operations which can potentially be used to create the given design. Using these operations, we generate different operation plans for machining the part. Each time we generate a new operation plan, we examine whether it can produce the desired shape and tolerances, and calculate its manufacturability rating. If no operation plan can be found that is capable of producing the design, then the given design is considered unmachinable; otherwise, the manufacturability rating for the design is the rating of the best operation plan.

We anticipate that by providing feedback about possible problems with the design, this work will help in speeding up the evaluation of new product designs in order to decide how or whether to manufacture them. Such a capability will be useful in responding quickly to changing demands and opportunities in the marketplace.}, keywords = {Automation, computer aided manufacturing, Feature extraction, manufacturability, Systems Integration}, url = {http://drum.lib.umd.edu//handle/1903/5420}, author = {Gupta, Satyandra K. and Nau, Dana S.} } @conference {18779, title = {Using MRSEVs to develop machining alternatives}, year = {1993}, month = {1993///}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.47.4870\&rep=rep1\&type=pdf}, author = {Nau, Dana S. and Gupta,S.K. and Kramer,T. R. and Regli,W. C. and Zhang, G.} } @conference {15977, title = {Vacuum-logic}, booktitle = {Proceedings of AAAI 1993 Fall Symposium Series: Instantiating Real-World Agents}, year = {1993}, month = {1993///}, pages = {51 - 54}, author = {Elgot-drapkin,J. and Kraus,S. and Miller,M. and Nirkhe,M. and Perlis, Don} } @article {18836, title = {General of Machining Alternatives for Machinability Evaluation}, volume = {ISR; TR 1992-106}, year = {1992}, month = {1992///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {This paper presents a new methodology for evaluating the machinability of a machined part during the design stage of the product development cycle, so that problems related to machining can be recognized and corrected while the product is being designed. Our basic approach is to perform a systematic evaluation of machining alternatives throughout each step in the design stage. This involves three basic steps: (1) generate alternative interpretations of the design as different collections of machinable features, (2) generate the various possible sequences of machining operations capable of producing each interpretation, and (3) evaluate each operation sequence, to determine the relevant information on achievable quality and associated costs. The information provided by this analysis can be used not only to give feedback to the designer about problems that might arise with the machining, but also to provide information to the manufacturing engineer about alternative ways in which the part might be machined.}, keywords = {Automation, computer aided manufacturing, manufacturability, Manufacturing Systems}, url = {http://hdl.handle.net/1903/5287}, author = {Gupta, Satyandra K. and Nau, Dana S. and Zhang,G. M.} } @article {18840, title = {Generation and Evaluation of Alternative Operation}, volume = {ISR; TR 1992-20}, year = {1992}, month = {1992///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {This paper presents a new and systematic approach to assist decision-making in selecting machining operation sequences. The approach is to produce alternative interpretations of design as different collections of machinable features, use these interpretations to generate alternative machining operation sequences, and evaluate the cost and achievable machining accuracy of each operations sequence. Given the operation sequences and their evaluations, it is then possible to calculate the performance measures of interest, and use these performance measures to select, from among the various alternatives, one or more of them that can best balance the need for a quality product against the need for efficient machining.}, keywords = {Automation, computer aided manufacturing, computer integrated manufacturing, Feature extraction, flexible manufacturing, Manufacturing, Manufacturing Systems, Solid modeling}, url = {http://drum.lib.umd.edu//handle/1903/5203}, author = {Nau, Dana S. and Zhang,G. M. and Gupta, Satyandra K.} } @article {18842, title = {Generation of Machining Alternatives for Machinability Evaluation}, volume = {ISR; TR 1992-106}, year = {1992}, month = {1992///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {This paper presents a new methodology for evaluating the machinability of a machined part during the design stage of the product development cycle, so that problems related to machining can be recognized and corrected while the product is being designed. Our basic approach is to perform a systematic evaluation of machining alternatives throughout each step in the design stage. This involves three basic steps: (1) generate alternative interpretations of the design as different collections of machinable features, (2) generate the various possible sequences of machining operations capable of producing each interpretation, and (3) evaluate each operation sequence, to determine the relevant information on achievable quality and associated costs. The information provided by this analysis can be used not only to give feedback to the designer about problems that might arise with the machining, but also to provide information to the manufacturing engineer about alternative ways in which the part might be machined.}, keywords = {Automation, computer aided manufacturing, manufacturability, Manufacturing Systems}, url = {http://drum.lib.umd.edu//handle/1903/5287}, author = {Gupta, Satyandra K. and Nau, Dana S. and Zhang,G. M.} } @article {16727, title = {Incrementally maintained network{\textrightarrow}relational database mapping}, journal = {Software: Practice and Experience}, volume = {22}, year = {1992}, month = {1992/12/01/}, pages = {1099 - 1131}, abstract = {An incrementally maintained mapping from a network to a relational database is presented. This mapping may be established either to support the efficient retrieval of data from a network database through a relational interface, or as the first step in a gradual conversion of data and applications from a network to a relational database system. After the mapping has been established, the only data mapped from the network to the relational database are the increments resulting from updates on the network database. The mapping is therefore an efficient alternative to mappings that repeatedly map the results of retrievals through the relational interface from the network database to the relational database. This is in particular the case when the two databases reside on different hosts. Applications on the network database may, under certain restrictions, gradually be moved to the relational database, while the mapping incrementally maintains the relational database for the applications that remain on the network database.}, keywords = {Database conversion, Database gateway, Database mapping, Incremental database mapping}, isbn = {1097-024X}, doi = {10.1002/spe.4380221205}, url = {http://onlinelibrary.wiley.com/doi/10.1002/spe.4380221205/abstract}, author = {Mark,Leo and Roussopoulos, Nick and Newsome,Tina and Laohapipattana,Piriya} } @conference {16383, title = {Partial evaluation of high-level imperative programming languages with applications in hard real-time systems}, booktitle = {Proceedings of the 19th ACM SIGPLAN-SIGACT symposium on Principles of programming languages}, year = {1992}, month = {1992///}, pages = {269 - 280}, author = {Nirkhe,V. and Pugh, William} } @article {15604, title = {A randomized algorithm for slope selection}, journal = {International Journal of Computational Geometry and Applications}, volume = {2}, year = {1992}, month = {1992///}, pages = {1 - 27}, author = {Dillencourt,M. B and Mount, Dave and Netanyahu,N. S} } @conference {17935, title = {Real-time procedural textures}, booktitle = {Proceedings of the 1992 symposium on Interactive 3D graphics}, series = {I3D {\textquoteright}92}, year = {1992}, month = {1992///}, pages = {95 - 100}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, isbn = {0-89791-467-8}, doi = {10.1145/147156.147171}, url = {http://doi.acm.org/10.1145/147156.147171}, author = {Rhoades,John and Turk,Greg and Bell,Andrew and State,Andrei and Neumann,Ulrich and Varshney, Amitabh} } @article {17971, title = {Six Generations of Building Walkthrough: Final Technical Report to the National Science Foundation}, year = {1992}, month = {1992///}, institution = {University of North Carolina at Chapel Hill}, address = {Chapel Hill, NC, USA}, author = {Brooks,Frederick P. and Airey,John and Alspaugh,John and Bell,Andrew and Brown,Randolph and Hill,Curtis and Nimscheck,Uwe and Rheingans,Penny and Rohlf,John and Smith,Dana and Turner,Douglass and Varshney, Amitabh and Wang,Yulan and Weber,Hans and Yuan,Xialin} } @conference {15979, title = {Deadline-coupled real-time planning}, booktitle = {Innovative approaches to planning, scheduling and control: proceedings of a Workshop [on Innovative Approaches to Planning, Scheduling, and Control], held at San Diego, California, November 5-8, 1991}, year = {1991}, month = {1991///}, pages = {100 - 100}, author = {Kraus,S. and Nirkhe,M. and Perlis, Don} } @article {15950, title = {Fully deadline-coupled planning: One step at a time}, journal = {Methodologies for Intelligent Systems}, year = {1991}, month = {1991///}, pages = {589 - 599}, author = {Nirkhe,M. and Kraus,S. and Perlis, Don} } @article {18083, title = {[31] Fast alignment of DNA and protein sequences}, journal = {Methods in Enzymology}, volume = {183}, year = {1990}, month = {1990///}, pages = {487 - 502}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @article {16805, title = {Efficient compilation of large rule bases using logical access paths}, journal = {Information Systems}, volume = {15}, year = {1990}, month = {1990///}, pages = {73 - 84}, abstract = {This paper presents an efficient way to compile and store large deductive databases. Deductive rules are modeled through logical access paths and then integrated into a global structure, the Rule-base Access Path Schema (RAP Schema). The RAP Schema stores information on the interrelationships that exist among the computations required for rule executions. Ground data as well as data derived through some rule executions and cached for later reuse are also modeled in the RAP Schema. Some of the advantages of using this rule base organization scheme include the automatic detection of shared computations, the inclusion of cached results of rule executions and query results in the knowledge base. The details of the compilation and query processing phases are the focus of the paper.}, isbn = {0306-4379}, doi = {16/0306-4379(90)90017-J}, url = {http://www.sciencedirect.com/science/article/pii/030643799090017J}, author = {Sellis,Timos K. and Roussopoulos, Nick and Ng,Raymond T.} } @article {17139, title = {EVALUATING HYPERMEDIA SYSTEMS}, journal = {Human factors in computing systems: CHI{\textquoteright}90 Conference proceedings, April 1-5, Seattle}, year = {1990}, month = {1990///}, pages = {387 - 387}, author = {Ehrlich,K. and Microsytems,S. and Marchionini,G. and Nielsen,J. and Shneiderman, Ben} } @article {18084, title = {Fast alignment of DNA and protein sequences}, journal = {Methods in enzymology}, volume = {183}, year = {1990}, month = {1990///}, pages = {487 - 502}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @article {16236, title = {The American Voice and Robotics" Guardian" System: A Case Study in User Interface Usability Evaluation}, year = {1988}, month = {1988///}, institution = {University of Maryland}, abstract = {American Voice and Robotics (AVR), in conjunction with the Maryland Industrial Partnerships(MIPS) program, contracted the Human-Computer Interaction Laboratory (HCIL) to evaluate the user interface of AVR{\textquoteright}s "Guardian"home automation system. Among their goals for the system were:Ease of use and learning of the system (intuitiveness), Aesthetic appeal, Unintimidating, Impressive, High Functionality, Fast and accurate input of useraction, Clear feedback, Forgiving to errors, and Fun to use. Researchers found that users were initially impressed with the system, but that they were not fully satisfied with it. Specific initial recommendations, theoretical and methodological concerns, procedures, results, and direction of future research will be discussed. }, author = {Wallace,D.F. and Norman,K. L and Plaisant, Catherine} } @article {18091, title = {Locating alignments with k differences for nucleotide and amino acid sequences}, journal = {Computer applications in the biosciences: CABIOS}, volume = {4}, year = {1988}, month = {1988///}, pages = {19 - 19}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @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} } @conference {11962, title = {Using flow field divergence for obstacle avoidance in visual navigation}, booktitle = {Science Applications International Corp, Proceedings: Image Understanding Workshop,}, volume = {2}, year = {1988}, month = {1988///}, author = {Nelson, R. and Aloimonos, J.} } @article {18101, title = {An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences*}, journal = {Journal of theoretical biology}, volume = {126}, year = {1987}, month = {1987///}, pages = {483 - 490}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @article {16965, title = {An evaluation of jump-ahead techniques in menu selection}, journal = {Behaviour \& Information Technology}, volume = {6}, year = {1987}, month = {1987///}, pages = {97 - 108}, abstract = {Menu selection systems provide a means of selecting operations and retrieving information which requires little training and reduces the need for memorizing complex command sequences. However, a major disadvantage of many menu selection systems is that experienced users cannot traverse the menu tree significantly faster than novices. A common solution to this problem is to provide the menu selection system with a jump-ahead capability.The purpose of this research was to evaluate two jump-ahead methods (type-ahead and direct-access). In the type-ahead method the user anticipates a selection on each of several successive menus and enters as many selections at one time as desired. In the direct-access method, each menu frame is assigned a unique name which the user must enter to locate it. Thirty-two students were given training on an information retrieval system for college course information and were required to learn the two jump-ahead methods in a counterbalanced design. The direct-access method resulted in fewer traversals to learn the system, lower error rates, and reduced learning time. The subjective impressions, obtained from post-experiment questionnaires and oral comments, indicated that the direct-access jump-ahead method was also preferred in a frequently used menu selection system. }, isbn = {0144-929X}, doi = {10.1080/01449298708901820}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449298708901820}, author = {Laverson,Alan and Norman,Kent and Shneiderman, Ben} } @article {17384, title = {Subjective user evaluation of CF PASCAL programming tools}, journal = {Department of Computer Science and Human-Computer Interaction Laboratory Working Paper}, year = {1987}, month = {1987///}, abstract = {This study investigated subjective evaluations of two programming environments: 1) SUPPORT, an interactive programming environment with a syntax directed editor on a personal computer and 2) a batch run environment on a large mainframe computer. Participants were students in a 15 week introductory computer science course. In Part 1, one group of 128 first used SUPPORT, while another group of 85 programmed on a mainframe environment. After 6 weeks they were given an evaluative questionnaire and then switched programming environments. In Part 2, 68 used SUPPORT and 60 used the mainframe. At the twelfth week of the course, they were given two questionnaires, one evaluating the environment they had used in the last 6 weeks and one comparing both enviro nments. A measure of programming performance (exam and programming project grades) was also collected. SUPPORT was predicted to reduce the burden of remembering syntactic details resulting in better performance and higher subjective evaluations. Unexpectedly, the SUPPORT users did not earn statistically significantly higher grades. Furthermore, participants expressed a preference for the mainframe over SUPPORT. Specific items on the questionnaires were used to diagnose the strengths and weaknesses of each environment. Designers of syntax directed editors should focus on reducing the syntactic burden not only in programming , but also in the user interface of these tools.}, author = {Chin,JP and Norman,K. L and Shneiderman, Ben} } @article {17015, title = {Cognitive layouts of windows and multiple screens for user interfaces}, journal = {International Journal of Man-Machine Studies}, volume = {25}, year = {1986}, month = {1986/08//}, pages = {229 - 248}, abstract = {In order to make computers easier to use and more versatile many system designers are exploring the use of multiple windows on a single screen and multiple coordinated screens in a single work station displaying linked or related information. The designers of such systems attempt to take into account the characteristics of the human user and the structure of the tasks to be performed. Central to this design issue is the way in which the user views and cognitively processes information presented in the windows or in multiple screens. This paper develops a theory of the {\textquotedblleft}cognitive layout{\textquotedblright} of information presented in multiple windows or screens. It is assumed that users adopt a cognitive representation or layout of the type of information to be presented and the relationships among the windows or screens and the information they contain. A number of cognitive layouts are derived from theories in cognitive psychology and are discussed in terms of the intent of the software driving the system and congruence with the cognitive processing of the information. It is hypothesized that the particular layout adopted by a user will drastically affect the user{\textquoteright}s understanding and expectation of events at the human-computer interface and could either greatly facilitate or frustrate the interaction. Ways of ensuring the former and avoiding the latter are discussed in terms of implementations on existing multiple-window and multiple-screen systems.}, isbn = {0020-7373}, doi = {10.1016/S0020-7373(86)80077-3}, url = {http://www.sciencedirect.com/science/article/pii/S0020737386800773}, author = {Norman,Kent L and Weldon,Linda J. and Shneiderman, Ben} } @article {16628, title = {A comparative analysis of methods for expert systems}, journal = {International journal of man-machine studies}, volume = {24}, year = {1986}, month = {1986///}, pages = {475 - 499}, author = {Ramsey,C. L and Reggia, James A. and Nau, Dana S. and Ferrentino,A.} } @article {18107, title = {An efficient string matching algorithm with k differences for nudeotide and amino acid sequences}, journal = {Nucleic acids research}, volume = {14}, year = {1986}, month = {1986///}, pages = {31 - 31}, author = {Landau,G. M and Vishkin, Uzi and Nussinov,R.} } @conference {16598, title = {Relationships between deductive and abductive inference in knowledge-based diagnostic problem solving}, booktitle = {Expert Database Systems: Proceedings of the First International Workshop. New York: Benjamin Cummings}, year = {1986}, month = {1986///}, author = {Nau, Dana S. and Reggia, James A.} } @article {16580, title = {Answer justification in abductive expert systems for diagnostic problem solving}, journal = {IEEE Transactions on Biomedical Engineering}, year = {1985}, month = {1985///}, author = {Reggia, James A. and Perricone,B. and Nau, Dana S. and Peng,Y.} } @article {16624, title = {Answer Justification in Diagnostic Expert Systems-Part II: Supporting Plausible Justifications}, journal = {Biomedical Engineering, IEEE Transactions on}, year = {1985}, month = {1985///}, pages = {268 - 272}, author = {Reggia, James A. and Perricone,B. T. and Nau, Dana S. and Peng,Y.} } @book {17017, title = {Cognitive Representations of Windows and Multiple Screen Layouts of Computer Interfaces}, year = {1985}, month = {1985///}, publisher = {University of Maryland}, organization = {University of Maryland}, author = {Norman,K. L and Weldon,L.J. and Shneiderman, Ben} } @article {16636, title = {A formal model of abductive inference}, journal = {Information Sciences}, volume = {37}, year = {1985}, month = {1985///}, pages = {227 - 285}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. and Peng,Y.} } @article {16612, title = {A formal model of diagnostic inference, II. Algorithmic solution and application}, journal = {Information Sciences}, volume = {37}, year = {1985}, month = {1985///}, pages = {257 - 285}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. Y and Peng,Y.} } @article {17273, title = {Learning a menu selection tree: training methods compared}, journal = {Behaviour \& Information Technology}, volume = {4}, year = {1985}, month = {1985///}, pages = {81 - 91}, abstract = {Abstract Abstract. Menu selection systems sometimes present learning problems for novice users. This comparison of four training methods for novice users found that the global tree diagram of the menu system was superior to command sequence and frame presentation methods, and somewhat better than trial and error. Methods were evaluated on the basis of (1) number of target nodes found, (2) mean number of selections to a target node, (3) recall of the menu structure, and (4) subjective rating of ease of learning.Abstract Abstract. Menu selection systems sometimes present learning problems for novice users. This comparison of four training methods for novice users found that the global tree diagram of the menu system was superior to command sequence and frame presentation methods, and somewhat better than trial and error. Methods were evaluated on the basis of (1) number of target nodes found, (2) mean number of selections to a target node, (3) recall of the menu structure, and (4) subjective rating of ease of learning. }, isbn = {0144-929X}, doi = {10.1080/01449298508901790}, url = {http://www.tandfonline.com/doi/abs/10.1080/01449298508901790}, author = {Parton,Diana and Huffman,Keith and Pridgen,Patty and Norman,Kent and Shneiderman, Ben} } @article {17320, title = {Performance on content-free menus as a function of study method}, journal = {Tech Report HCIL-85-03}, year = {1985}, month = {1985///}, author = {Schwartz,J.P. and Norman,K. L and Shneiderman, Ben} } @book {16535, title = {A theoretical foundation for abductive expert systems}, year = {1985}, month = {1985///}, publisher = {North-Holland, New York}, organization = {North-Holland, New York}, author = {Reggia, James A. and Nau, Dana S. and Peng,Y. and Perricone,B.} } @conference {16519, title = {An abductive non-monotonic logic}, booktitle = {Workshop on Nonmonotonic Reasoning}, year = {1984}, month = {1984///}, author = {Reggia, James A. and Nau, Dana S.} } @article {17294, title = {Memory For Menus: Effects of Study Mode}, journal = {University of Maryland Computer Science Technical Report Series, CS-TR-1412}, year = {1984}, month = {1984///}, abstract = {Menu selection systems require a certain amount of training in order for users to remember how to access target functions. In this experiment users studied four different types of documentation before searching for target words in a content-free menu containing no meaningful relationships among terms. Documentation was presented to subjects in one of four modes of study. In the Command Mode subjects studied sequences of choices to arrive at a desired target. In the Menu Frame Mode subjects studied individual frames in the menu system. In the Global Tree Mode subjects studied a diagram of the menu tree. Finally, in the Trial and Error Mode subjects studied the menu system by actually selecting alternatives. Although the Global Tree and Command Sequence Groups found the most target words during the test phase, the four groups did not differ significantly. On the other hand, differences in the ability to recall menu terms were significant with the command Sequence and Menu Frame Groups recalling the most terms. Furthermore, results indicated that the type of training fundamentally affected the type of information used in order to find targets. Subjects in the Command Sequence and Menu Frame Groups tended to rely on recall of menu terms. Furthermore, all groups relied heavily on memory of the menu tree except for the Command Squence Group. Results of this study are related to practical considerations for the design of menu selection systems.}, author = {Norman,K. L and Schwartz,J.P. and Shneiderman, Ben} } @article {16616, title = {Diagnostic expert systems based on a set covering model}, journal = {International Journal of Man-Machine Studies}, volume = {19}, year = {1983}, month = {1983///}, pages = {437 - 460}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. Y} } @article {17141, title = {Evaluating multiple coordinated windows for programming workstations}, journal = {NASA. Goddard Space Flight Center Proc. of the Eighth Ann. Software Eng. Workshop 11 p(SEE N 84-23137 13-61)}, year = {1983}, month = {1983///}, abstract = {Programmers might benefit from larger screens with multiple windows or multiple screens, especially if convenient coordination among screens are arranged. Uses for multiple coordinated displays in a programmers workstation are explored. Initial efforts focus on the potential applications, a command language for coordinating the displays, and the psychological basis for effective utilization so as to avoid information overload. Subsequent efforts will be devoted to implementing the concepts and performing controlled psychologically oriented experiments to validate the hypotheses.}, author = {Shneiderman, Ben and GRANTHAM,C. and Norman,K. and ROGERS,J. and Roussopoulos, Nick} } @article {15772, title = {Multi-resolution relaxation}, journal = {Pattern Recognition}, volume = {16}, year = {1983}, month = {1983///}, pages = {223 - 230}, abstract = {Several types of iterative methods can be used to segment the pixels in an image into light and dark regions; these include {\textquotedblleft}relaxation{\textquotedblright} methods of probability adjustment and steepest-descent methods of cost function minimization. Conventionally, these methods operate on the image at a single resolution. This paper investigates the possibility of using these approaches at two (or more) resolutions in order to reduce their computational cost{\textemdash}e.g. first obtain an approximate solution by iterating at low resolution, then refine the solution using a few iterations at high resolution.}, keywords = {Multigrid methods, Pyramids, Relaxation, segmentation}, isbn = {0031-3203}, doi = {10.1016/0031-3203(83)90026-2}, url = {http://www.sciencedirect.com/science/article/pii/0031320383900262}, author = {Narayanan,K. A. and O{\textquoteright}Leary, Dianne P. and Rosenfeld,Azriel} } @conference {16605, title = {A New Inference Method for Frame-based Expert System}, booktitle = {Proceedings of the National Conference on Artificial Intelligence}, year = {1983}, month = {1983///}, pages = {333 - 337}, author = {Reggia, James A. and Nau, Dana S. and Wang,P. Y} } @article {17328, title = {Program indentation and comprehensibility}, journal = {Communications of the ACM}, volume = {26}, year = {1983}, month = {1983/11//}, pages = {861 - 867}, keywords = {indentation, program format, program readability}, isbn = {0001-0782}, doi = {10.1145/182.358437}, url = {http://doi.acm.org/10.1145/182.358437}, author = {Miara,Richard J. and Musselman,Joyce A. and Navarro,Juan A. and Shneiderman, Ben} } @article {16547, title = {S., Wang. PY, Diagnostic Expert Systems Based on a Set Covering Model}, journal = {International Journal on Man-Machine studies}, volume = {19}, year = {1983}, month = {1983///}, pages = {437{\textendash}46O - 437{\textendash}46O}, author = {Reggia, James A. and Nau, Dana S.} } @article {15759, title = {Image Smoothing and Segmentation by Cost Minimization}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {SMC-12}, year = {1982}, month = {1982///}, pages = {91 - 96}, author = {Narayanan,K. A. and O{\textquoteright}Leary, Dianne P. and Rosenfeld,Azriel} } @article {15714, title = {An Optimization Approach to Edge Reinforcement}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {SMC-12}, year = {1982}, month = {1982///}, pages = {551 - 553}, abstract = {The present investigation is concerned with an optimization approach to edge reinforcement which does not involve probabilistic concepts. A cost function is defined, based on the local pattern of edge responses, which is low for sharp, strong edges, and a steepest descent method is used to adjust the edge magnitudes so as to reduce the value of this cost function. The edge reinforcement results obtained in this way appear to be better than those obtained by relaxation methods, whether based on conditional probability or on optimization. The results of an application of the considered procedure to a portion of a Landsat scene are shown, taking into account the input image, the results of 10 iterations of the steepest descent procedure, results produced by means of the relaxation process reported by Schachter et al. (1977), and results obtained with the aid of the optimization relaxation process considered by Faugeras and Berthod (1979).}, author = {Narayanan,K. A. and O{\textquoteright}Leary, Dianne P. and Rosenfeld,Azriel} } @article {17171, title = {Flowchart techniques for structured programming}, journal = {ACM SIGPLAN Notices}, volume = {8}, year = {1973}, month = {1973/08//}, pages = {12 - 26}, abstract = {With the advent of structured programming and GOTO-less programming a method is needed to model computation in simply ordered structures, each representing a complete thought possibly defined in terms of other thoughts as yet undefined. A model is needed which prevents unrestricted transfers of control and has a control structure closer to languages amenable to structured programming. We present an attempt at such a model.}, isbn = {0362-1340}, doi = {10.1145/953349.953350}, url = {http://doi.acm.org/10.1145/953349.953350}, author = {Nassi,I. and Shneiderman, Ben} }