@article {20299, title = {Occurrence of Vibrio cholerae in water reservoirs of Burkina Faso}, journal = {Research in Microbiology}, volume = {169}, year = {2018}, month = {Jan-01-2018}, pages = {1 - 10}, abstract = {Africa is currently an important region in which cholera epidemics occur. Little is known about the presence of Vibrio cholerae in freshwater bodies in Africa. There are ca. 1700 lakes and reservoirs in Burkina Faso, most of which have been built within recent decades to secure water resources. The purpose of this study was to investigate the presence of V. cholerae in the water of reservoirs, using the most-probable-number polymerase chain reaction. Results showed that V. cholerae could be detected in water samples collected from 14 of 39 sampled reservoirs. The concentrations varied from 0 MPN/l to more than 1100 MPN/l. Fifty strains of V. cholerae isolated on CHROMagar{\texttrademark} vibrio were identified as V. cholerae non-O1/non-O139, none of which carried the ctxA gene. A significant positive correlation was found between the presence of V. cholerae in the reservoirs and both alkaline pH and phytoplankton biomass. V. cholerae was present in significantly higher numbers in reservoirs of urban areas than in rural areas. Since V. cholerae non-O1/non-O139 has been shown to be a causative agent of endemic diarrheal outbreaks, their presence in Burkina Faso reservoirs suggests they may play a role in gastroenteritis in that country.}, issn = {09232508}, doi = {10.1016/j.resmic.2017.08.004}, url = {https://www.sciencedirect.com/science/article/pii/S092325081730147X?via\%3Dihub}, author = {Kabor{\'e}, Saidou and Cecchi, Philippe and Mosser, Thomas and Toubiana, Myl{\`e}ne and Traor{\'e}, Oumar and Ouattara, Aboubakar S. and Traor{\'e}, Alfred S. and Barro, Nicolas and Rita R Colwell and Monfort, Patrick} } @article {20308, title = {Comprehensive benchmarking and ensemble approaches for metagenomic classifiers}, journal = {Genome Biology}, year = {2017}, month = {Jan-12-2017}, doi = {10.1186/s13059-017-1299-7}, url = {http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1299-7}, author = {McIntyre, Alexa B. R. and Ounit, Rachid and Afshinnekoo, Ebrahim and Prill, Robert J. and H{\'e}naff, Elizabeth and Alexander, Noah and Minot, Samuel S. and Danko, David and Foox, Jonathan and Ahsanuddin, Sofia and Tighe, Scott and Hasan, Nur A. and Subramanian, Poorani and Moffat, Kelly and Levy, Shawn and Lonardi, Stefano and Greenfield, Nick and Rita R Colwell and Rosen, Gail L. and Mason, Christopher E.} } @conference {20065, title = {3D Cellular Morphotyping of Scaffold Niches}, booktitle = {2016 32nd Southern Biomedical Engineering Conference (SBEC)}, year = {2016}, publisher = {IEEE}, organization = {IEEE}, author = {Florczyk, Stephen J and Simon, Mylene and Juba, Derek and Pine, P Scott and Sarkar, Sumona and Chen, Desu and Baker, Paula J and Bodhak, Subhadip and Cardone, Antonio and Brady, Mary and others} } @article {20325, title = {Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak}, journal = {BMC Microbiology}, year = {2016}, month = {Jan-12-2016}, doi = {10.1186/s12866-016-0894-1}, url = {http://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0894-1}, author = {Ottesen, Andrea and Ramachandran, Padmini and Reed, Elizabeth and White, James R. and Hasan, Nur and Subramanian, Poorani and Ryan, Gina and Jarvis, Karen and Grim, Christopher and Daquiqan, Ninalynn and Hanes, Darcy and Allard, Marc and Rita R Colwell and Brown, Eric and Chen, Yi} } @article {20062, title = {Survey statistics of automated segmentations applied to optical imaging of mammalian cells}, journal = {BMC bioinformatics}, volume = {16}, year = {2015}, pages = {1}, author = {Bajcsy, Peter and Cardone, Antonio and Chalfoun, Joe and Halter, Michael and Juba, Derek and Kociolek, Marcin and Majurski, Michael and Peskin, Adele and Simon, Carl and Simon, Mylene and others} } @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 {19654, title = {BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection}, journal = {Proceedings of the National Academy of Sciences}, volume = {109}, year = {2012}, month = {2012/06/12/}, pages = {9575 - 9580}, abstract = {Cell proteins can restrict the replication of viruses. Here, we identify the cellular BclAF1 protein as a human cytomegalovirus restriction factor and describe two independent mechanisms the virus uses to decrease its steady-state levels. Immediately following infection, the viral pp71 and UL35 proteins, which are delivered to cells within virions, direct the proteasomal degradation of BclAF1. Although BclAF1 reaccumulates through the middle stages of infection, it is subsequently down-regulated at late times by miR-UL112-1, a virus-encoded microRNA. In the absence of BclAF1 neutralization, viral gene expression and replication are inhibited. These data identify two temporally and mechanistically distinct functions used by human cytomegalovirus to down-regulate a cellular antiviral protein.}, keywords = {innate immunity, intrinsic immunity, miRNA, Proteasome, UL82}, isbn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/content/109/24/9575}, author = {Lee, Song Hee and Kalejta, Robert F. and Kerry, Julie and Semmes, Oliver John and O{\textquoteright}Connor, Christine M. and Zia Khan and Garcia, Benjamin A. and Shenk, Thomas and Murphy, Eain} } @conference {19218, title = {The design and evaluation of prototype eco-feedback displays for fixture-level water usage data}, year = {2012}, month = {2012}, pages = {2367 - 2376}, publisher = {ACM}, organization = {ACM}, isbn = {145031015X}, author = {Jon Froehlich and Findlater,L. and Ostergren, M. and Ramanathan, S. and Peterson,J. and Wragg, I. and Larson,E. and Fu, F. and Bai, M. and Patel,S.} } @article {19612, title = {Efficient Verification of Web-content Searching Through Authenticated Web Crawlers}, journal = {Proc. VLDB Endow.}, volume = {5}, year = {2012}, month = {2012/06//}, pages = {920 - 931}, abstract = {We consider the problem of verifying the correctness and completeness of the result of a keyword search. We introduce the concept of an authenticated web crawler and present its design and prototype implementation. An authenticated web crawler is a trusted program that computes a specially-crafted signature over the web contents it visits. This signature enables (i) the verification of common Internet queries on web pages, such as conjunctive keyword searches---this guarantees that the output of a conjunctive keyword search is correct and complete; (ii) the verification of the content returned by such Internet queries---this guarantees that web data is authentic and has not been maliciously altered since the computation of the signature by the crawler. In our solution, the search engine returns a cryptographic proof of the query result. Both the proof size and the verification time are proportional only to the sizes of the query description and the query result, but do not depend on the number or sizes of the web pages over which the search is performed. As we experimentally demonstrate, the prototype implementation of our system provides a low communication overhead between the search engine and the user, and fast verification of the returned results by the user.}, isbn = {2150-8097}, url = {http://dl.acm.org/citation.cfm?id=2336664.2336666}, author = {Goodrich, Michael T. and Charalampos Papamanthou and Nguyen, Duy and Tamassia, Roberto and Lopes, Cristina Videira and Ohrimenko, Olga and Triandopoulos, Nikos} } @conference {Ture:2012:ECT:2382029.2382088, title = {Encouraging consistent translation choices}, booktitle = {Proceedings of the 2012 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies}, series = {NAACL HLT {\textquoteright}12}, year = {2012}, pages = {417{\textendash}426}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, isbn = {978-1-937284-20-6}, url = {http://dl.acm.org/citation.cfm?id=2382029.2382088}, author = {Ture, Ferhan and Oard, Douglas and Resnik, Philip} } @article {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 {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 {19132, title = {Structure, function and diversity of the healthy human microbiome}, journal = {Nature}, volume = {486}, year = {2012}, month = {2012}, pages = {207 - 214}, abstract = {Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat{\textquoteright}s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81{\textendash}99\% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.}, author = {Huttenhower, C. and Gevers, D. and Knight,R. and Abubucker, S. and Badger, J.H. and Chinwalla, A.T. and Creasy, H.H. and Earl, A.M. and Fitzgerald, M.G. and Fulton, R.S. and others} } @article {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 {13069, title = {AVSS 2011 demo session: A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Advanced Video and Signal-Based Surveillance (AVSS), 2011 8th IEEE International Conference on}, year = {2011}, month = {2011/09/30/2}, pages = {527 - 528}, abstract = {We introduce to the surveillance community the VIRAT Video Dataset[1], which is a new large-scale surveillance video dataset designed to assess the performance of event recognition algorithms in realistic scenes1.}, doi = {10.1109/AVSS.2011.6027400}, author = {Oh,Sangmin and Hoogs,Anthony and Perera,Amitha and Cuntoor,Naresh and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,Saurajit and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,Eran and Wang,Xiaoyang and Ji,Qiang and Reddy,Kishore and Shah,Mubarak and Vondrick,Carl and Pirsiavash,Hamed and Ramanan,Deva and Yuen,Jenny and Torralba,Antonio and Song,Bi and Fong,Anesco and Roy-Chowdhury,Amit and Desai,Mita} } @conference {12398, title = {Believe Me{\textemdash}We Can Do This! Annotating Persuasive Acts in Blog Text}, booktitle = {Workshops at the Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, author = {Anand,P. and King,J. and Jordan Boyd-Graber and Wagner,E. and Martell,C. and Oard, Douglas and Resnik, Philip} } @conference {13067, title = {Birdlets: Subordinate categorization using volumetric primitives and pose-normalized appearance}, booktitle = {Computer Vision (ICCV), 2011 IEEE International Conference on}, year = {2011}, month = {2011/11//}, pages = {161 - 168}, abstract = {Subordinate-level categorization typically rests on establishing salient distinctions between part-level characteristics of objects, in contrast to basic-level categorization, where the presence or absence of parts is determinative. We develop an approach for subordinate categorization in vision, focusing on an avian domain due to the fine-grained structure of the category taxonomy for this domain. We explore a pose-normalized appearance model based on a volumetric poselet scheme. The variation in shape and appearance properties of these parts across a taxonomy provides the cues needed for subordinate categorization. Training pose detectors requires a relatively large amount of training data per category when done from scratch; using a subordinate-level approach, we exploit a pose classifier trained at the basic-level, and extract part appearance and shape information to build subordinate-level models. Our model associates the underlying image pattern parameters used for detection with corresponding volumetric part location, scale and orientation parameters. These parameters implicitly define a mapping from the image pixels into a pose-normalized appearance space, removing view and pose dependencies, facilitating fine-grained categorization from relatively few training examples.}, keywords = {appearance, Birdlets;category, categorization;subordinate-level, detection;pose, detectors;pose-normalized, distinctions;shape, estimation;, extraction;pose, extraction;subordinate-level, information, model;salient, models;volumetric, pixels;part, poselet, primitives;computer, resolution;information, retrieval;object, scheme;volumetric, taxonomy;computer, vision;image}, doi = {10.1109/ICCV.2011.6126238}, author = {Farrell,R. and Oza,O. and Zhang,Ning and Morariu,V.I. and Darrell,T. and Davis, Larry S.} } @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.} } @article {18558, title = {Countering Botnets: Anomaly-Based Detection, Comprehensive Analysis, and Efficient Mitigation}, year = {2011}, month = {2011/05//}, institution = {GEORGIA TECH RESEARCH CORP ATLANTA}, abstract = {We cover five general areas: (1) botnet detection, (2) botnet analysis, (3) botnet mitigation, (4) add-on tasks to the original contract, including the Conficker Working Group Lessons Learned, Layer-8 Exploration of Botnet Organization, and DREN research, and (5) commercialization in this paper. We have successfully developed new botnet detection and analysis capabilities in this project. These algorithms have been evaluated using real-world data, and have been put into actual, deployed systems. The most significant technical developments include a new dynamic reputation systems for DNS domains, a scalable anomaly detection system for botnet detection in very large network, and a transparent malware analysis system. In addition, on several occasions we have used our botnet data and analysis to help law enforcement agencies arrest botmasters. We also have had great success transitioning technologies to commercial products that are now used by government agencies, ISPs, and major corporations.}, keywords = {*ELECTRONIC SECURITY, *INFORMATION SECURITY, *INTERNET, *INTRUSION DETECTION(COMPUTERS), algorithms, BGP ROUTE INJECTION, BGP(BORDER GATEWAY PROTOCOLS), BOTNET DETECTION, BOTNET TRACEBACK AND ATTRIBUTION, BOTNETS(MALWARE), CLIENT SERVER SYSTEMS, COMMUNICATIONS PROTOCOLS, COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER SYSTEMS MANAGEMENT AND STANDARDS, CYBER ATTACKS, CYBER SECURITY, CYBERNETICS, CYBERTERRORISM, CYBERWARFARE, DATA PROCESSING SECURITY, DNS BASED MONITORING, DNS BASED REDIRECTION, DNS(DOMAIN NAME SYSTEMS), INFORMATION SCIENCE, INTERNET BROWSERS, ISP(INTERNET SERVICE PROVIDERS), MALWARE, MALWARE ANALYSIS, Online Systems, WUAFRLDHS1BOTN}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA543919}, author = {Lee,Wenke and Dagon,David and Giffin,Jon and Feamster, Nick and Ollman,Gunter and Westby,Jody and Wesson,Rick and Vixie,Paul} } @conference {13532, title = {Cross Language Entity Linking}, booktitle = {IJCNLP: International Joint Conference on Natural Language Processing}, year = {2011}, month = {2011///}, abstract = {There has been substantial recent interest in aligning mentions of named entities in unstructured texts to knowledge base descriptors, a task commonly called entity linking. This technology is crucial for applications in knowledge discovery and text data mining. This paper presents experiments in the new problem of cross language entity linking, where documents and named entities are in a different language than that used for the content of the reference knowledge base. We have created a new test collection to evaluate cross-language entity linking performance in twenty-one languages. We present experiments that examine issues such as: the importance of transliteration; the utility of cross-language information retrieval; and, the potential benefit of multilingual named entity recognition. Our best model achieves performance which is 94\% of a strong monolingual baseline.}, author = {McNamee,Paul and Mayfield,James and Lawrie,Dawn and Oard, Douglas and David Doermann} } @conference {13533, title = {Cross-Language Entity Linking in Maryland during a Hurricane}, booktitle = {TAC}, year = {2011}, month = {2011///}, abstract = {Our team from the JHUHLTCOE and the University of Maryland submitted runs for all three variants of the TACKBP entity linking task. For the monolingual tasks, we essentially mirrored our HLTCOETAC-KBP 2010 submission, making only modest changes to accommodate differences in 2011, namely the requirement to cluster NIL responses, and the change in evaluation measure. However, our work on the cross-lingual task was significantly more involved, requiring development of robust, multiphased transliteration software, use of techniques in cross-language information retrieval, and reliance on a Chinese-to- English statistical machine translation system. In this paper we describe our work for the 2011 evaluation and the results we obtained.}, author = {McNamee,Paul and Mayfield,James and Oard, Douglas and David Doermann and Xu,Tan and Wu,Ke} } @article {15741, title = {Designing Optimal Spectral Filters for Inverse Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {33}, year = {2011}, month = {2011///}, doi = {DOI: 10.1137/100809787}, author = {Chung,Julianne M. and Chung,Matthias and O{\textquoteright}Leary, Dianne P.} } @article {15751, title = {Euclidean distance matrix completion problems}, journal = {Optimization Methods and Software}, year = {2011}, month = {2011///}, pages = {1 - 23}, abstract = {A Euclidean distance matrix (EDM) is one in which the (i, j) entry specifies the squared distance between particle i and particle j. Given a partially specified symmetric matrix A with zero diagonal, the Euclidean distance matrix completion problem (EDMCP) is to determine the unspecified entries to make A an EDM. We survey three different approaches to solving the EDMCP. We advocate expressing the EDMCP as a non-convex optimization problem using the particle positions as variables and solving using a modified Newton or quasi-Newton method. To avoid local minima, we develop a randomized initialization technique that involves a nonlinear version of the classical multidimensional scaling, and a dimensionality relaxation scheme with optional weighting. Our experiments show that the method easily solves the artificial problems introduced by Mor{\'e} and Wu. It also solves the 12 much more difficult protein fragment problems introduced by Hendrickson, and the six larger protein problems introduced by Grooms, Lewis and Trosset.A Euclidean distance matrix (EDM) is one in which the (i, j) entry specifies the squared distance between particle i and particle j. Given a partially specified symmetric matrix A with zero diagonal, the Euclidean distance matrix completion problem (EDMCP) is to determine the unspecified entries to make A an EDM. We survey three different approaches to solving the EDMCP. We advocate expressing the EDMCP as a non-convex optimization problem using the particle positions as variables and solving using a modified Newton or quasi-Newton method. To avoid local minima, we develop a randomized initialization technique that involves a nonlinear version of the classical multidimensional scaling, and a dimensionality relaxation scheme with optional weighting. Our experiments show that the method easily solves the artificial problems introduced by Mor{\'e} and Wu. It also solves the 12 much more difficult protein fragment problems introduced by Hendrickson, and the six larger protein problems introduced by Grooms, Lewis and Trosset. }, isbn = {1055-6788}, doi = {10.1080/10556788.2011.643888}, url = {http://www.tandfonline.com/doi/abs/10.1080/10556788.2011.643888}, author = {Fang,Haw-ren and O{\textquoteright}Leary, Dianne P.} } @article {15752, title = {Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes}, journal = {Proteins: Structure, Function, and Bioinformatics}, volume = {79}, year = {2011}, month = {2011/07/01/}, pages = {2268 - 2281}, abstract = {We present and evaluate a rigid-body, deterministic, molecular docking method, called ELMDOCK, that relies solely on the three-dimensional structure of the individual components and the overall rotational diffusion tensor of the complex, obtained from nuclear spin-relaxation measurements. We also introduce a docking method, called ELMPATIDOCK, derived from ELMDOCK and based on the new concept of combining the shape-related restraints from rotational diffusion with those from residual dipolar couplings, along with ambiguous contact/interface-related restraints obtained from chemical shift perturbations. ELMDOCK and ELMPATIDOCK use two novel approximations of the molecular rotational diffusion tensor that allow computationally efficient docking. We show that these approximations are accurate enough to properly dock the two components of a complex without the need to recompute the diffusion tensor at each iteration step. We analyze the accuracy, robustness, and efficiency of these methods using synthetic relaxation data for a large variety of protein-protein complexes. We also test our method on three protein systems for which the structure of the complex and experimental relaxation data are available, and analyze the effect of flexible unstructured tails on the outcome of docking. Additionally, we describe a method for integrating the new approximation methods into the existing docking approaches that use the rotational diffusion tensor as a restraint. The results show that the proposed docking method is robust against experimental errors in the relaxation data or structural rearrangements upon complex formation and is computationally more efficient than current methods. The developed approximations are accurate enough to be used in structure refinement protocols. Proteins 2011; {\textcopyright} 2011 Wiley-Liss, Inc.}, keywords = {diffusion-guided molecular assembly, ellipsoid model, ELM, PATI, protein complexes, residual dipolar couplings, rigid-body docking}, isbn = {1097-0134}, doi = {10.1002/prot.23053}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.23053/full}, author = {Berlin,Konstantin and O{\textquoteright}Leary, Dianne P. and Fushman, David} } @article {15762, title = {Implicitly-weighted total least squares}, journal = {Linear Algebra and its Applications}, volume = {435}, year = {2011}, month = {2011/08/01/}, pages = {560 - 577}, abstract = {In a total least squares (TLS) problem, we estimate an optimal set of model parameters X , so that ( A - Δ A ) X = B - Δ B , where A is the model matrix, B is the observed data, and Δ A and Δ B are corresponding corrections. When B is a single vector, Rao (1997) and Paige and Strako{\v s} (2002) suggested formulating standard least squares problems, for which Δ A = 0 , and data least squares problems, for which Δ B = 0 , as weighted and scaled TLS problems. In this work we define an implicitly-weighted TLS formulation (ITLS) that reparameterizes these formulations to make computation easier. We derive asymptotic properties of the estimates as the number of rows in the problem approaches infinity, handling the rank-deficient case as well. We discuss the role of the ratio between the variances of errors in A and B in choosing an appropriate parameter in ITLS. We also propose methods for computing the family of solutions efficiently and for choosing the appropriate solution if the ratio of variances is unknown. We provide experimental results on the usefulness of the ITLS family of solutions.}, keywords = {Data least squares, Errors in variables, least squares, Linear regression, total least squares, Variance estimation}, isbn = {0024-3795}, doi = {10.1016/j.laa.2010.06.020}, url = {http://www.sciencedirect.com/science/article/pii/S0024379510003162}, author = {Park,Sungwoo and O{\textquoteright}Leary,Dianne P.} } @article {13003, title = {Increased gene sampling provides stronger support for higher-level groups within gracillariid leaf mining moths and relatives (Lepidoptera: Gracillariidae)}, journal = {BMC Evol Biol}, volume = {11:182}, year = {2011}, month = {2011///}, author = {Kawahara,A. Y and Ohshima,I and Kawakita,A and Regier,J. C and Mitter,C and Cummings, Michael P. and Davis,DR and Wagner,DL and De Prinis,J and Lopez-Vaamonde,C} } @conference {13074, title = {A large-scale benchmark dataset for event recognition in surveillance video}, booktitle = {Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on}, year = {2011}, month = {2011/06//}, pages = {3153 - 3160}, abstract = {We introduce a new large-scale video dataset designed to assess the performance of diverse visual event recognition algorithms with a focus on continuous visual event recognition (CVER) in outdoor areas with wide coverage. Previous datasets for action recognition are unrealistic for real-world surveillance because they consist of short clips showing one action by one individual [15, 8]. Datasets have been developed for movies [11] and sports [12], but, these actions and scene conditions do not apply effectively to surveillance videos. Our dataset consists of many outdoor scenes with actions occurring naturally by non-actors in continuously captured videos of the real world. The dataset includes large numbers of instances for 23 event types distributed throughout 29 hours of video. This data is accompanied by detailed annotations which include both moving object tracks and event examples, which will provide solid basis for large-scale evaluation. Additionally, we propose different types of evaluation modes for visual recognition tasks and evaluation metrics along with our preliminary experimental results. We believe that this dataset will stimulate diverse aspects of computer vision research and help us to advance the CVER tasks in the years ahead.}, keywords = {algorithm;evaluation, CVER, databases;, databases;video, dataset;moving, event, metrics;large-scale, object, recognition, recognition;diverse, recognition;video, scenes;surveillance, surveillance;visual, tasks;computer, tracks;outdoor, video, video;computer, vision;continuous, vision;image, visual}, doi = {10.1109/CVPR.2011.5995586}, author = {Oh,Sangmin and Hoogs, A. and Perera,A. and Cuntoor, N. and Chen,Chia-Chih and Lee,Jong Taek and Mukherjee,S. and Aggarwal, JK and Lee,Hyungtae and Davis, Larry S. and Swears,E. and Wang,Xioyang and Ji,Qiang and Reddy,K. and Shah,M. and Vondrick,C. and Pirsiavash,H. and Ramanan,D. and Yuen,J. and Torralba,A. and Song,Bi and Fong,A. and Roy-Chowdhury, A. and Desai,M.} } @inbook {13822, title = {Machine Translation Evaluation and Optimization}, booktitle = {Handbook of Natural Language Processing and Machine TranslationHandbook of Natural Language Processing and Machine Translation}, year = {2011}, month = {2011///}, pages = {745 - 843}, publisher = {Springer New York}, organization = {Springer New York}, abstract = {The evaluation of machine translation (MT) systems is a vital field of research, both for determining the effectiveness of existing MT systems and for optimizing the performance of MT systems. This part describes a range of different evaluation approaches used in the GALE community and introduces evaluation protocols and methodologies used in the program. We discuss the development and use of automatic, human, task-based and semi-automatic (human-in-the-loop) methods of evaluating machine translation, focusing on the use of a human-mediated translation error rate HTER as the evaluation standard used in GALE. We discuss the workflow associated with the use of this measure, including post editing, quality control, and scoring. We document the evaluation tasks, data, protocols, and results of recent GALE MT Evaluations. In addition, we present a range of different approaches for optimizing MT systems on the basis of different measures. We outline the requirements and specific problems when using different optimization approaches and describe how the characteristics of different MT metrics affect the optimization. Finally, we describe novel recent and ongoing work on the development of fully automatic MT evaluation metrics that have the potential to substantially improve the effectiveness of evaluation and optimization of MT systems.}, isbn = {978-1-4419-7713-7}, url = {http://dx.doi.org/10.1007/978-1-4419-7713-7_5}, author = {Dorr, Bonnie J and Olive,Joseph and McCary,John and Christianson,Caitlin}, editor = {Olive,Joseph and Christianson,Caitlin and McCary,John} } @conference {13595, title = {Maryland at FIRE 2011: Retrieval of OCRed Bengali}, booktitle = {FIRE}, year = {2011}, month = {2011///}, abstract = {In this year{\textquoteright}s Forum for Information Retrieval Evaluation (FIRE), the University of Maryland participated in the Retrieval of Indic Script OCRed Text (RISOT) task to experiment with the retrieval of Bengali script OCR{\textquoteright}d documents. The experiments focused on evaluating a retrieval strategy motivated by recent work on Cross-Language Information Retrieval (CLIR), but which makes use of OCR error modeling rather than parallel text alignment. The approach obtains a probability distribution over substitutions for the actual query terms that possibly correspond to terms in the document representation. The results reported indicate that this is a promising way of using OCR error modeling to improve CLIR.}, author = {Garain,Utpal and David Doermann and Oard,Douglas D.} } @article {13944, title = {Method and System for Dereverberation of Signals Propagating in ...}, volume = {13/047,311}, year = {2011}, month = {2011/03//}, abstract = {The dereverberation of signals in reverberating environments is carried out via acquiring the representation (image) of spatial distribution of the signals in space of interest and automatic identification of reflections of the source signal in the reverberative space. The technique relies on identification of prominent features at the image, as well as corresponding directions of propagation of signals manifested by the prominent features at the image, and computation of similarity metric between signals corresponding to the prominent features in the image. The time delays between the correlated signals (i.e., source signal and related reflections) are found and the signals are added coherently. Multiple beamformers operate on the source signal and corresponding reflections, enabling one to improve the signal-to-noise ratio in multi-path environments.}, url = {http://www.google.com/patents?id=gBHuAQAAEBAJ}, author = {O{\textquoteright}donovan,Adam and Duraiswami, Ramani and Zotkin,Dmitry N}, editor = {University of Maryland} } @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} } @article {15774, title = {Nouveau-ROUGE: A Novelty Metric for Update Summarization}, journal = {Computational Linguistics}, volume = {37}, year = {2011}, month = {2011///}, pages = {1 - 8}, abstract = {An update summary should provide a fluent summarization of new information on a time-evolving topic, assuming that the reader has already reviewed older documents or summaries. In 2007 and 2008, an annual summarization evaluation included an update summarization task. Several participating systems produced update summaries indistinguishable from human-generated summaries when measured using ROUGE. However, no machine system performed near human-level performance in manual evaluations such as pyramid and overall responsiveness scoring.}, isbn = {0891-2017}, doi = {10.1162/coli_a_00033}, url = {http://dx.doi.org/10.1162/coli_a_00033}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @conference {14994, title = {NSF/IEEE-TCPP curriculum initiative on parallel and distributed computing: core topics for undergraduates}, booktitle = {Proceedings of the 42nd ACM technical symposium on Computer science education}, year = {2011}, month = {2011///}, pages = {617 - 618}, author = {Prasad,S. K. and Chtchelkanova,A. and Das,S. and Dehne,F. and Gouda,M. and Gupta,A. and JaJa, Joseph F. and Kant,K. and La Salle,A. and LeBlanc,R. and others} } @conference {13617, title = {Overview of the FIRE 2011 RISOTTask}, booktitle = {FIRE}, year = {2011}, month = {2011///}, abstract = {RISOT was a pilot task in FIRE 2011 which focused on the retrieval of automatically recognized text from machine printed sources. The collection used for search was a subset of the FIRE 2008 and 2010 Bengali test collections that contained 92 topics and 62,825 documents. Two teams participated, submitting a total of 11 monolingual runs.}, author = {Garain,Utpal and Paik,Jiaul and Pal,Tamaltaru and Majumder,Prasenjit and David Doermann and Oard, Douglas} } @conference {13467, title = {Selective transfer between learning tasks using task-based boosting}, booktitle = {Twenty-Fifth AAAI Conference on Artificial Intelligence}, year = {2011}, month = {2011///}, author = {Eaton,E. and desJardins, Marie and others} } @conference {13412, title = {A trust model for supply chain management}, booktitle = {The 10th International Conference on Autonomous Agents and Multiagent Systems-Volume 3}, year = {2011}, month = {2011///}, pages = {1375 - 1376}, author = {Haghpanah,Y. and desJardins, Marie and others} } @article {17462, title = {Usability and Accessibility in Consumer Health Informatics: Current Trends and Future Challenges}, journal = {American Journal of Preventive Medicine}, volume = {40}, year = {2011}, month = {2011/05//}, pages = {S187-S197 - S187-S197}, abstract = {It is a truism that, for innovative eHealth systems to have true value and impact, they must first and foremost be usable and accessible by clinicians, consumers, and other stakeholders. In this paper, current trends and future challenges in the usability and accessibility of consumer health informatics will be described. Consumer expectations of their healthcare providers and healthcare records in this new era of consumer-directed care will be explored, and innovative visualizations, assistive technologies, and other ways that healthcare information is currently being provided and/or shared will be described. Challenges for ensuring the usability of current and future systems will also be discussed. An innovative model for conducting systematic, timely, user-centered research on consumer-facing websites at the National Cancer Institute (NCI) and the ongoing efforts at the National Institute of Standards and Technology (NIST) to promote health information technology (HIT) usability standards and evaluation criteria will also be presented.}, isbn = {0749-3797}, doi = {10.1016/j.amepre.2011.01.009}, url = {http://www.sciencedirect.com/science/article/pii/S0749379711000869}, author = {Goldberg,Larry and Lide,Bettijoyce and Lowry,Svetlana and Massett,Holly A. and O{\textquoteright}Connell,Trisha and Preece,Jennifer and Quesenbery,Whitney and Shneiderman, Ben} } @conference {13476, title = {Using Agent-Based Simulation to Determine an Optimal Lane-Changing Strategy on a Multi-Lane Highway}, booktitle = {2011 AAAI Fall Symposium Series}, year = {2011}, month = {2011///}, author = {Tuzo,J. and Seymour,J. and desJardins, Marie and others} } @conference {19464, title = {Why is My Internet Slow?: Making Network Speeds Visible}, booktitle = {SIGCHI {\textquoteright}11}, series = {CHI {\textquoteright}11}, year = {2011}, month = {2011///}, pages = {1889 - 1898}, publisher = {ACM}, organization = {ACM}, abstract = {With widespread broadband adoption, more households report experiencing sub-optimal speeds. Not only are slow speeds frustrating, they may indicate consumers are not receiving the services they are paying for from their internet service providers. Yet, determining the speed and source of slow-downs is difficult because few tools exist for broadband management. We report on results of a field trial with 10 households using a visual network probe designed to address these problems. We describe the results of the study and provide design implications for future tools. More importantly, we argue that tools like this can educate and empower consumers by making broadband speeds and sources of slow-downs more visible.}, keywords = {broadband speed, broadband tools, home networks}, isbn = {978-1-4503-0228-9}, url = {http://doi.acm.org/10.1145/1978942.1979217}, author = {Marshini Chetty and Haslem, David and Baird, Andrew and Ofoha, Ugochi and Sumner, Bethany and Grinter, Rebecca} } @article {15832, title = {Windowed Spectral Regularization of Inverse Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {33}, year = {2011}, month = {2011///}, doi = {DOI: 10.1137/100809787}, author = {Chung,Julianne M. and Easley,Glenn R and O{\textquoteright}Leary, Dianne P.} } @article {15707, title = {Adaptive Constraint Reduction for Convex Quadratic Programming}, journal = {Computational Optimization and Applications}, year = {2010}, month = {2010/03//}, abstract = {We propose an adaptive, constraint-reduced, primal-dual interior-point algorithm for convex quadratic programming with many more inequality constraints than variables. We reduce the computational effort by assembling, instead of the exact normal-equation matrix, an approximate matrix from a well chosen index set which includes indices of constraints that seem to be most critical. Starting with a large portion of the constraints, our proposed scheme excludes more unnecessary constraints at later iterations. We provide proofs for the global convergence and the quadratic local convergence rate of an affine-scaling variant. Numerical experiments on random problems, on a data-fitting problem, and on a problem in array pattern synthesis show the effectiveness of the constraint reduction in decreasing the time per iteration without significantly affecting the number of iterations. We note that a similar constraint-reduction approach can be applied to algorithms of Mehrotra{\textquoteright}s predictor-corrector type, although no convergence theory is supplied.}, doi = {DOI:10.1007/s10589-010-9324-8}, author = {Jung,Jin Hyuk and O{\textquoteright}Leary, Dianne P. and Tits,Andre{\textquoteright} L.} } @conference {13422, title = {An animated multivariate visualization for physiological and clinical data in the ICU}, booktitle = {Proceedings of the 1st ACM International Health Informatics Symposium}, series = {IHI {\textquoteright}10}, year = {2010}, month = {2010///}, pages = {771 - 779}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Current visualizations of electronic medical data in the Intensive Care Unit (ICU) consist of stacked univariate plots of variables over time and a tabular display of the current numeric values for the corresponding variables and occasionally an alarm limit. The value of information is dependent upon knowledge of historic values to determine a change in state. With the ability to acquire more historic information, providers need more sophisticated visualization tools to assist them in analyzing the data in a multivariate fashion over time. We present a multivariate time series visualization that is interactive and animated, and has proven to be as effective as current methods in the ICU for predicting an episode of acute hypotension in terms of accuracy, confidence, and efficiency with only 30-60 minutes of training.}, keywords = {computational physiology, Information Visualization, multivariate, time series}, isbn = {978-1-4503-0030-8}, doi = {10.1145/1882992.1883109}, url = {http://doi.acm.org/10.1145/1882992.1883109}, author = {Ord{\'o}{\~n}ez,Patricia and desJardins, Marie and Lombardi,Michael and Lehmann,Christoph U. and Fackler,Jim} } @conference {15849, title = {Assessor error in stratified evaluation}, booktitle = {Proceedings of the 19th ACM international conference on Information and knowledge management}, year = {2010}, month = {2010///}, pages = {539 - 548}, author = {Webber,W. and Oard, Douglas and Scholer,F. and Hedin,B.} } @article {13962, title = {Audio visual scene analysis using spherical arrays and cameras.}, journal = {The Journal of the Acoustical Society of America}, volume = {127}, year = {2010}, month = {2010///}, pages = {1979 - 1979}, abstract = {While audition and vision are used together by living beings to make sense of the world, the observation of the world using machines in applications such as surveillance and robotics has proceeded largely separately. We describe the use of spherical microphone arrays as {\textquotedblleft}audio cameras{\textquotedblright} and spherical array of video cameras as a tool to perform multi-modal scene analysis that attempts to answer questions such as {\textquotedblleft}Who?,{\textquotedblright}, {\textquotedblleft}What?,{\textquotedblright} {\textquotedblleft}Where?,{\textquotedblright} and {\textquotedblleft}Why?.{\textquotedblright} Signal processing algorithms to identify the number of people and their identities and to isolate and dereverberate their speech using multi-modal processing will be described. The use of graphics processor based signal processing allows for real-time implementation of these algorithms. [Work supported by ONR.]}, doi = {10.1121/1.3385079}, url = {http://link.aip.org/link/?JAS/127/1979/3}, author = {O{\textquoteright}donovan,Adam and Duraiswami, Ramani and Zotkin,Dmitry N and Gumerov, Nail A.} } @conference {13953, title = {Automatic matched filter recovery via the audio camera}, booktitle = {Acoustics Speech and Signal Processing (ICASSP), 2010 IEEE International Conference on}, year = {2010}, month = {2010/03//}, pages = {2826 - 2829}, abstract = {The sound reaching the acoustic sensor in a realistic environment contains not only the part arriving directly from the sound source but also a number of environmental reflections. The effect of those on the sound is equivalent to a convolution with the room impulse response and can be undone via deconvolution - a technique known as matched filter processing. However, the filter is usually pre-computed in advance using known room geometry and source/receiver positions, and any deviations from those cause the performance to degrade significantly. In this work, an algorithm is proposed to compute the matched filter automatically using an audio camera - a microphone array based system that provides real-time audio images (essentially plots of steered response power in various directions) of environment. Acoustic sources, as well as their significant reflections, are revealed as peaks in the audio image. The reflections are associated with sound source(s) using an acoustic similarity metric, and an approximate matched filter is computed to align the reflections in time with the direct arrival. Preliminary experimental evaluation of the method is performed. It is shown that in case of two sources the reflections are identified correctly, the time delays recovered agree well with those computed from geometric constraints, and that the output SNR improves when the reflections are added coherently to the signal obtained by beamforming directly at the source.}, keywords = {acoustic, array;real-time, arrays;transient, audio, camera;automatic, constraints;microphone, filter, filters;microphone, images;room, impulse, Matched, positions;acoustic, processing;cameras;matched, radiators;array, recovery;beamforming;geometric, response;, response;sound, sensor;acoustic, signal, source;source/receiver, sources;audio}, doi = {10.1109/ICASSP.2010.5496187}, author = {O{\textquoteright}Donovan,A.E. and Duraiswami, Ramani and Zotkin,Dmitry N} } @article {13963, title = {Computation of the head-related transfer function via the fast multipole accelerated boundary element method and its spherical harmonic representation}, journal = {The Journal of the Acoustical Society of America}, volume = {127}, year = {2010}, month = {2010///}, pages = {370 - 386}, abstract = {The head-related transfer function (HRTF) is computed using the fast multipole accelerated boundary element method. For efficiency, the HRTF is computed using the reciprocity principle by placing a source at the ear and computing its field. Analysis is presented to modify the boundary value problem accordingly. To compute the HRTF corresponding to different ranges via a single computation, a compact and accurate representation of the HRTF, termed the spherical spectrum, is developed. Computations are reduced to a two stage process, the computation of the spherical spectrum and a subsequent evaluation of the HRTF. This representation allows easy interpolation and range extrapolation of HRTFs. HRTF computations are performed for the range of audible frequencies up to 20 kHz for several models including a sphere, human head models [the Neumann KU-100 ({\textquotedblleft}Fritz{\textquotedblright}) and the Knowles KEMAR ({\textquotedblleft}Kemar{\textquotedblright}) manikins], and head-and-torso model (the Kemar manikin). Comparisons between the different cases are provided. Comparisons with the computational data of other authors and available experimental data are conducted and show satisfactory agreement for the frequencies for which reliable experimental data are available. Results show that, given a good mesh, it is feasible to compute the HRTF over the full audible range on a regular personal computer.}, keywords = {auditory evoked potentials, bioacoustics, boundary-elements methods, Ear, Harmonic analysis}, doi = {10.1121/1.3257598}, url = {http://link.aip.org/link/?JAS/127/370/1}, author = {Gumerov, Nail A. and O{\textquoteright}Donovan,Adam E. and Duraiswami, Ramani and Zotkin,Dmitry N} } @article {15882, title = {Evaluation of information retrieval for E-discovery}, journal = {Artificial Intelligence and Law}, volume = {18}, year = {2010}, month = {2010/08/10/}, pages = {347 - 386}, isbn = {0924-8463, 1572-8382}, doi = {10.1007/s10506-010-9093-9}, url = {http://www.springerlink.com/content/m700w2k26n264u01/}, author = {Oard, Douglas and Baron,Jason R. and Hedin,Bruce and Lewis,David D. and Tomlinson,Stephen} } @conference {15874, title = {Exploring the Relationships among ICTs: A Scalable Computational Approach Using KL Divergence and Hierarchical Clustering}, booktitle = {Hawaii International Conference on System Sciences}, year = {2010}, month = {2010///}, pages = {1 - 10}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Different information and communication technologies (ICTs) are related in complex ways and, accordingly, their diffusion trajectories are related, too. How can the relationships among multiple ICTs be described and analyzed in a scalable way? In this study, we offer a scalable methodology, based on computational analysis of discourse, to examine the relationships among ICTs. Specifically, we employed Kullback-Leibler (KL) divergence to compare the semantic similarity of forty-seven ICTs discussed in the trade magazine InformationWeek over a decade. Using hierarchical clustering, we have found that the similarity of the technologies can be mapped in a hierarchy and similar technologies demonstrated similar discourses. The results establish the validity of our approach and demonstrate its scalability and richness. This analytical approach not only enables diffusion researchers to undertake multi-innovation, multi-source, and multi-period studies, but also helps practitioners effectively adopt and efficiently use new ICTs in their organizations.}, isbn = {978-0-7695-3869-3}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2010.203}, author = {Tsui,Chia-jung and Wang,Ping and Fleischmann,Kenneth R. and Oard, Douglas and Sayeed,Asad B.} } @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 {15883, title = {Investigating multi-label classification for human values}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {47}, year = {2010}, month = {2010///}, pages = {1 - 4}, author = {Ishita,E. and Oard, Douglas and Fleischmann,K.R. and Cheng,A.S. and Templeton,T.C.} } @article {16050, title = {Making sense of archived e-mail: Exploring the Enron collection with NetLens}, journal = {Journal of the American Society for Information Science and Technology}, volume = {61}, year = {2010}, month = {2010/04/01/}, pages = {723 - 744}, abstract = {Informal communications media pose new challenges for information-systems design, but the nature of informal interaction offers new opportunities as well. This paper describes NetLens-E-mail, a system designed to support exploration of the content-actor network in large e-mail collections. Unique features of NetLens-E-mail include close coupling of orientation, specification, restriction, and expansion, and introduction and incorporation of a novel capability for iterative projection between content and actor networks within the same collection. Scenarios are presented to illustrate the intended employment of NetLens-E-mail, and design walkthroughs with two domain experts provide an initial basis for assessment of the suitability of the design by scholars and analysts.}, isbn = {1532-2890}, doi = {10.1002/asi.21275}, url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.21275/full}, author = {Kang,Hyunmo and Plaisant, Catherine and Elsayed,Tamer and Oard, Douglas} } @conference {16025, title = {The Metacognitive Loop: An Architecture for Building Robust Intelligent Systems}, booktitle = {2010 AAAI Fall Symposium Series}, year = {2010}, month = {2010/03/11/}, abstract = {The Metacognitive Loop: An Architecture for Building Robust Intelligent Systems}, keywords = {commonsense, ontologies, robust intelligent systems}, url = {http://www.aaai.org/ocs/index.php/FSS/FSS10/paper/view/2161}, author = {Shahri,Hamid Haidarian and Dinalankara,Wikum and Fults,Scott and Wilson,Shomir and Perlis, Don and Schmill,Matt and Oates,Tim and Josyula,Darsana and Anderson,Michael} } @inbook {15770, title = {Modelling Type 1a Supernova Light Curves}, booktitle = {Exponential Data Fitting and Its ApplicationsExponential Data Fitting and Its Applications}, year = {2010}, month = {2010///}, pages = {169 - 186}, publisher = {Bentham Science Publishers Ltd.}, organization = {Bentham Science Publishers Ltd.}, url = {http://www.bentham.org/ebooks/9781608050482/http://www.bentham.org/ebooks/9781608050482/}, author = {Rust,Bert W. and O{\textquoteright}Leary, Dianne P. and Mullen,Katharine M.}, editor = {Pereyra,V. and Scherer,G.} } @inbook {19604, title = {Optimal Authenticated Data Structures with Multilinear Forms}, booktitle = {Pairing-Based Cryptography - Pairing 2010}, series = {Lecture Notes in Computer Science}, year = {2010}, month = {2010/01/01/}, pages = {246 - 264}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, abstract = {Cloud computing and cloud storage are becoming increasingly prevalent. In this paradigm, clients outsource their data and computations to third-party service providers. Data integrity in the cloud therefore becomes an important factor for the functionality of these web services.Authenticated data structures, implemented with various cryptographic primitives, have been widely studied as a means of providing efficient solutions to data integrity problems (e.g., Merkle trees). In this paper, we introduce a new authenticated dictionary data structure that employs multilinear forms, a cryptographic primitive proposed by Silverberg and Boneh in 2003 [10], the construction of which, however, remains an open problem to date. Our authenticated dictionary is optimal, that is, it does not add any extra asymptotic cost to the plain dictionary data structure, yielding proofs of constant size, i.e., asymptotically equal to the size of the answer, while maintaining other relevant complexities logarithmic. Instead, solutions based on cryptographic hashing (e.g., Merkle trees) require proofs of logarithmic size [40]. Because multilinear forms are not known to exist yet, our result can be viewed from a different angle: if one could prove that optimal authenticated dictionaries cannot exist in the computational model, irrespectively of cryptographic primitives, then our solution would imply that cryptographically interesting multilinear form generators cannot exist as well (i.e., it can be viewed as a reduction). Thus, we provide an alternative avenue towards proving the nonexistence of multilinear form generators in the context of general lower bounds for authenticated data structures [40] and for memory checking [18], a model similar to the authenticated data structures model.}, keywords = {Algorithm Analysis and Problem Complexity, authenticated dictionary, Coding and Information Theory, Computer Communication Networks, Data Encryption, Discrete Mathematics in Computer Science, multilinear forms, Systems and Data Security}, isbn = {978-3-642-17454-4, 978-3-642-17455-1}, url = {http://link.springer.com/chapter/10.1007/978-3-642-17455-1_16}, author = {Charalampos Papamanthou and Tamassia, Roberto and Triandopoulos, Nikos}, editor = {Joye, Marc and Miyaji, Atsuko and Otsuka, Akira} } @article {15788, title = {Portfolio Selection Using Tikhonov Filtering to Estimate the Covariance Matrix}, journal = {SIAM Journal on Financial Mathematics}, volume = {1}, year = {2010}, month = {2010///}, pages = {932 - 961}, abstract = {Markowitz{\textquoteright}s portfolio selection problem chooses weights for stocks in a portfolio based on an estimated covariance matrix of stock returns. Our study proposes reducing noise in the estimation by using a Tikhonov filter function. In addition, we prevent rank deficiency of the estimated covariance matrix and propose a method for effectively choosing the Tikhonov parameter, which determines the filtering intensity. We put previous estimators into a common framework and compare their filtering functions for eigenvalues of the correlation matrix. We demonstrate the effectiveness of our estimator using stock return data from 1958 through 2007.}, keywords = {covariance matrix estimate, Markowitz portfolio selection, ridge regression, Tikhonov regularization}, doi = {10.1137/090749372}, url = {http://link.aip.org/link/?SJF/1/932/1}, author = {Park,Sungwoo and O{\textquoteright}Leary, Dianne P.} } @conference {12486, title = {Pose estimation in heavy clutter using a multi-flash camera}, booktitle = {Robotics and Automation (ICRA), 2010 IEEE International Conference on}, year = {2010}, month = {2010/05//}, pages = {2028 - 2035}, abstract = {We propose a novel solution to object detection, localization and pose estimation with applications in robot vision. The proposed method is especially applicable when the objects of interest may not be richly textured and are immersed in heavy clutter. We show that a multi-flash camera (MFC) provides accurate separation of depth edges and texture edges in such scenes. Then, we reformulate the problem, as one of finding matches between the depth edges obtained in one or more MFC images to the rendered depth edges that are computed offline using 3D CAD model of the objects. In order to facilitate accurate matching of these binary depth edge maps, we introduce a novel cost function that respects both the position and the local orientation of each edge pixel. This cost function is significantly superior to traditional Chamfer cost and leads to accurate matching even in heavily cluttered scenes where traditional methods are unreliable. We present a sub-linear time algorithm to compute the cost function using techniques from 3D distance transforms and integral images. Finally, we also propose a multi-view based pose-refinement algorithm to improve the estimated pose. We implemented the algorithm on an industrial robot arm and obtained location and angular estimation accuracy of the order of 1 mm and 2 $\#$x00B0; respectively for a variety of parts with minimal texture.}, keywords = {3D, algorithm;object, based, camera;multiview, depth, detection;object, detection;pose, distance, edge, edges;cameras;image, edges;integral, estimation;binary, estimation;multiflash, estimation;robot, function;depth, images;location, localization;pose, maps, matching;cost, matching;image, pose-refinement, texture;object, transforms;angular, vision;texture, vision;transforms;}, doi = {10.1109/ROBOT.2010.5509897}, author = {Ming-Yu Liu and Tuzel, O. and Veeraraghavan,A. and Chellapa, Rama and Agrawal,A. and Okuda, H.} } @article {13087, title = {SPECIAL SECTION ON SHAPE ANALYSIS AND ITS APPLICATIONS IN IMAGE UNDERSTANDING}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {32}, year = {2010}, month = {2010///}, pages = {0162 - 8828}, author = {Srivastava, A. and Damon,J.N. and Dryden,I.L. and Jermyn,I.H. and Das,S. and Vaswani, N. and Huckemann,S. and Hotz,T. and Munk,A. and Lin,Z. and others} } @article {15811, title = {Structural Assembly of Molecular Complexes Based on Residual Dipolar Couplings}, journal = {J. Am. Chem. Soc.}, volume = {132}, year = {2010}, month = {2010///}, pages = {8961 - 8972}, abstract = {We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein?protein complex by utilizing the RDCs? sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein?protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein?protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes.We present and evaluate a rigid-body molecular docking method, called PATIDOCK, that relies solely on the three-dimensional structure of the individual components and the experimentally derived residual dipolar couplings (RDCs) for the complex. We show that, given an accurate ab initio predictor of the alignment tensor from a protein structure, it is possible to accurately assemble a protein?protein complex by utilizing the RDCs? sensitivity to molecular shape to guide the docking. The proposed docking method is robust against experimental errors in the RDCs and computationally efficient. We analyze the accuracy and efficiency of this method using experimental or synthetic RDC data for several proteins, as well as synthetic data for a large variety of protein?protein complexes. We also test our method on two protein systems for which the structure of the complex and steric-alignment data are available (Lys48-linked diubiquitin and a complex of ubiquitin and a ubiquitin-associated domain) and analyze the effect of flexible unstructured tails on the outcome of docking. The results demonstrate that it is fundamentally possible to assemble a protein?protein complex solely on the basis of experimental RDC data and the prediction of the alignment tensor from 3D structures. Thus, despite the purely angular nature of RDCs, they can be converted into intermolecular distance/translational constraints. Additionally, we show a method for combining RDCs with other experimental data, such as ambiguous constraints from interface mapping, to further improve structure characterization of protein complexes. }, isbn = {0002-7863}, doi = {10.1021/ja100447p}, url = {http://dx.doi.org/10.1021/ja100447p}, author = {Berlin,Konstantin and O{\textquoteright}Leary,Dianne P. and Fushman, David} } @article {18284, title = {System and Method for Confidentiality-Preserving Rank-Ordered Search}, volume = {12/608,724}, year = {2010}, month = {2010/06/10/}, abstract = {A confidentiality preserving system and method for performing a rank-ordered search and retrieval of contents of a data collection. The system includes at least one computer system including a search and retrieval algorithm using term frequency and/or similar features for rank-ordering selective contents of the data collection, and enabling secure retrieval of the selective contents based on the rank-order. The search and retrieval algorithm includes a baseline algorithm, a partially server oriented algorithm, and/or a fully server oriented algorithm. The partially and/or fully server oriented algorithms use homomorphic and/or order preserving encryption for enabling search capability from a user other than an owner of the contents of the data collection. The confidentiality preserving method includes using term frequency for rank-ordering selective contents of the data collection, and retrieving the selective contents based on the rank-order.}, url = {http://www.google.com/patents?id=kInVAAAAEBAJ}, author = {Swaminathan,Ashwin and Mao,Yinian and Su,Guan-Ming and Gou,Hongmei and Varna,Avinash L. and He,Shan and M. Wu and Oard, Douglas} } @conference {13475, title = {Using a Trust Model in Decision Making for Supply Chain Management}, booktitle = {Workshops at the Twenty-Fourth AAAI Conference on Artificial Intelligence}, year = {2010}, month = {2010///}, author = {Haghpanah,Y. and desJardins, Marie and others} } @conference {15862, title = {Values of Stakeholders in the Net Neutrality Debate: Applying Content Analysis to Telecommunications Policy}, booktitle = {Hawaii International Conference on System Sciences}, year = {2010}, month = {2010///}, pages = {1 - 10}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {Net neutrality is an important telecommunications policy debate. This debate is closely tied to technological innovation, economic development, and information access. Values help shape stakeholders{\textquoteright} positions on this debate. This paper examines the role of values in shaping the Net neutrality debate through a content analysis of public hearings on Net neutrality. The paper presents a quantitative analysis that reveals the top values implicated in the Net neutrality debate and statistically significant differences among individuals on opposite sides of the Net neutrality debate. A qualitative analysis reveals insights into the connection between specific values and positions on the Net neutrality debate. The paper concludes that values, technology, and policy are interconnected, and that it is useful to understand the values of the various stakeholders within policy debates.}, isbn = {978-0-7695-3869-3}, doi = {http://doi.ieeecomputersociety.org/10.1109/HICSS.2010.434}, author = {Cheng,An-Shou and Fleischmann,Kenneth R. and Wang,Ping and Ishita,Emi and Oard, Douglas} } @conference {15855, title = {Arabic Cross-Document Coreference Resolution}, booktitle = {Proceedings of the ACL-IJCNLP 2009 Conference Short Papers$}$}, year = {2009}, month = {2009///}, pages = {357 - 360}, author = {Sayeed,A. and Elsayed,T. and Garera,N. and Alexander,D. and Xu,T. and Oard, Douglas and Yarowsky,D. and Piatko,C.} } @article {15876, title = {Automatic classification of human values: Applying computational thinking to information ethics}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {46}, year = {2009}, month = {2009///}, pages = {1 - 4}, author = {Fleischmann,K.R. and Oard, Douglas and Cheng,A.S. and Wang,P. and Ishita,E.} } @inbook {15726, title = {CLASSY 2009: Summarization and Metrics}, booktitle = {TAC 2009 Workshop ProceedingsTAC 2009 Workshop Proceedings}, year = {2009}, month = {2009/11/16/17}, publisher = {NIST}, organization = {NIST}, url = {http://www.nist.gov/tac/publications/2009/participant.papers/CLASSY.proceedings.pdfhttp://www.nist.gov/tac/publications/2009/participant.papers/CLASSY.proceedings.pdf}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @article {13968, title = {Computation of the head-related transfer function via the boundary element method and representation via the spherical harmonic spectrum}, journal = {Technical Reports from UMIACS UMIACS-TR-2009-06}, year = {2009}, month = {2009/05/15/}, abstract = {The head-related transfer function (HRTF) is computed using the fast multipole accelerated boundary element method. For efficiency, the HRTF is computed using the reciprocity principle, by placing a source at the ear and computing its field. Analysis is presented to modify the boundary value problem accordingly. To compute the HRTF corresponding to different ranges via a single computation, a compact and accurate representation of the HRTF, termed the spherical spectrum, is developed. Computations are reduced to a two stage process, the computation of the spherical spectrum and a subsequent evaluation of the HRTF. This representation allows easy interpolation and range extrapolation of HRTFs.HRTF computations are performed for the range of audible frequencies up to 20 kHz for several models including a sphere, human head models (for the {\textquotedblleft}Fritz{\textquotedblright} and {\textquotedblleft}Kemar{\textquotedblright}), and head and torso model (the Kemar manikin). Comparisons between the different cases and analysis of limiting cases is provided. Comparisons with the computational data of other authors and available experimental data are conducted and show satisfactory agreement for the frequencies for which reliable experimental data is available. Our results show that, given a good mesh it is feasible to compute the HRTF over the full audible range on a regular personal computer. }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/9085}, author = {Gumerov, Nail A. and O{\textquoteright}donovan,Adam and Duraiswami, Ramani and Zotkin,Dmitry N} } @conference {15845, title = {Context-based message expansion for disentanglement of interleaved text conversations}, booktitle = {Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics}, year = {2009}, month = {2009///}, pages = {200 - 208}, author = {Wang,L. and Oard, Douglas} } @conference {15891, title = {Cross-document coreference resolution: A key technology for learning by reading}, booktitle = {AAAI Spring Symposium on Learning by Reading and Learning to Read}, year = {2009}, month = {2009///}, author = {Mayfield,J. and Alexander,D. and Dorr, Bonnie J and Eisner,J. and Elsayed,T. and Finin,T. and Fink,C. and Freedman,M. and Garera,N. and McNamee,P. and others} } @article {15127, title = {Efficient and secure authenticated key exchange using weak passwords}, journal = {Journal of the ACM (JACM)}, volume = {57}, year = {2009}, month = {2009/11//}, pages = {3:1{\textendash}3:39 - 3:1{\textendash}3:39}, abstract = {Mutual authentication and authenticated key exchange are fundamental techniques for enabling secure communication over public, insecure networks. It is well known how to design secure protocols for achieving these goals when parties share high-entropy cryptographic keys in advance of the authentication stage. Unfortunately, it is much more common for users to share weak, low-entropy passwords which furthermore may be chosen from a known space of possibilities (say, a dictionary of English words). In this case, the problem becomes much more difficult as one must ensure that protocols are immune to off-line dictionary attacks in which an adversary exhaustively enumerates all possible passwords in an attempt to determine the correct one. We propose a 3-round protocol for password-only authenticated key exchange, and provide a rigorous proof of security for our protocol based on the decisional Diffie-Hellman assumption. The protocol assumes only public parameters{\textemdash}specifically, a {\textquotedblleft}common reference string{\textquotedblright}{\textemdash}which can be {\textquotedblleft}hard-coded{\textquotedblright} into an implementation of the protocol; in particular, and in contrast to some previous work, our protocol does not require either party to pre-share a public key. The protocol is also remarkably efficient, requiring computation only (roughly) 4 times greater than {\textquotedblleft}classical{\textquotedblright} Diffie-Hellman key exchange that provides no authentication at all. Ours is the first protocol for password-only authentication that is both practical and provably-secure using standard cryptographic assumptions.}, keywords = {Authentication, cryptography, passwords}, isbn = {0004-5411}, doi = {10.1145/1613676.1613679}, url = {http://doi.acm.org/10.1145/1613676.1613679}, author = {Katz, Jonathan and Ostrovsky,Rafail and Yung,Moti} } @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 {13973, title = {Imaging room acoustics with the audio camera.}, journal = {The Journal of the Acoustical Society of America}, volume = {125}, year = {2009}, month = {2009///}, pages = {2544 - 2544}, abstract = {Using a spherical microphone array and real time signal processing using a graphical processing unit (GPU), an audio camera has been developed. This device provides images of the intensity of the sound field arriving at a point from a specified direction to the spherical array. Real-time performance is achieved via use of GPUs. The intensity can be displayed integrated over the whole frequency band of the array, or in false color, with different frequency bands mapped to different color bands. The resulting audio camera may be combined with video cameras to achieve multimodal scene capture and analysis. A theory of registration of audio camera images with video camera images is developed, and joint analysis of audio and video images performed. An interesting application of the audio camera is the imaging of concert hall acoustics. The individual reflections that constitute the impulse response measured at a particular seat may be imaged, and their spatial origin determined. Other applications of the audio camera to people tracking, noise suppression, and camera pointing are also presented. [Work partially supported by NVIDIA and the VA.]}, url = {http://link.aip.org/link/?JAS/125/2544/2}, author = {O{\textquoteright}donovan,Adam and Duraiswami, Ramani and Gumerov, Nail A. and Zotkin,Dmitry N} } @article {15763, title = {Improvement and analysis of computational methods for prediction of residual dipolar couplings}, journal = {Journal of Magnetic Resonance}, volume = {201}, year = {2009}, month = {2009/11//}, pages = {25 - 33}, abstract = {We describe a new, computationally efficient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a molecule. This method is applicable to bicelles, PEG/hexanol, and other alignment media that can be modeled by steric restrictions introduced by a planar barrier. This method is used to further explore and compare various representations of protein shape by an equivalent ellipsoid. We also examine the accuracy of the alignment tensor and residual dipolar couplings (RDC) prediction using various ab initio methods. We separately quantify the inaccuracy in RDC prediction caused by the inaccuracy in the orientation and in the magnitude of the alignment tensor, concluding that orientation accuracy is much more important in accurate prediction of RDCs.}, keywords = {Ab initio prediction, Alignment tensor, PALES, Residual dipolar coupling}, isbn = {1090-7807}, doi = {10.1016/j.jmr.2009.07.028}, url = {http://www.sciencedirect.com/science/article/pii/S1090780709002304}, author = {Berlin,Konstantin and O{\textquoteright}Leary,Dianne P. and Fushman, David} } @conference {15863, title = {Improving search effectiveness in the legal e-discovery process using relevance feedback}, booktitle = {Proceedings of the global E-Discovery/E-Disclosure workshop on electronically stored information in discovery at the 12th international conference on artificial intelligence and law (ICAIL09 DESI Workshop). DESI Press, Barcelona}, year = {2009}, month = {2009///}, author = {Zhao,F.C. and Oard, Douglas and Baron,J.R.} } @article {15768, title = {Locality bounds on hamiltonians for stabilizer codes}, journal = {Quantum Info. Comput.}, volume = {9}, year = {2009}, month = {2009/05//}, pages = {487 - 499}, abstract = {In this paper, we study the complexity of Hamiltonians whose groundstate is a stabilizer code. Weintroduce various notions of k-locality of a stabilizer code, inherited from the associated stabilizergroup. A choice of generators leads to a Hamiltonian with the code in its groundspace. We establishbounds on the locality of any other Hamiltonian whose groundspace contains such a code, whetheror not its Pauli tensor summands commute. Our results provide insight into the cost of creating anenergy gap for passive error correction and for adiabatic quantum computing. The results simplify inthe cases of XZ-split codes such as Calderbank-Shor-Steane stabilizer codes and topologically-orderedstabilizer codes arising from surface cellulations.}, isbn = {1533-7146}, url = {http://dl.acm.org/citation.cfm?id=2011791.2011800}, author = {Bullock,Stephen S. and O{\textquoteright}Leary, Dianne P.} } @conference {15896, title = {Matching person names through name transformation}, booktitle = {Proceedings of the 18th ACM conference on Information and knowledge management}, series = {CIKM {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {1875 - 1878}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Matching person names plays an important role in many applications, including bibliographic databases and indexing systems. Name variations and spelling errors make exact string matching problematic; therefore, it is useful to develop methodologies that can handle variant forms for the same named entity. In this paper, a novel person name matching model is presented. Common name variations in the English speaking world are formalized, and the concept of name transformation paths is introduced; name similarity is measured after the best transformation path has been selected. Supervised techniques are used to learn a similarity function and a decision rule. Experiments with three datasets show the method to be effective.}, keywords = {name matching, string distance metrics, string similarity}, isbn = {978-1-60558-512-3}, doi = {10.1145/1645953.1646253}, url = {http://doi.acm.org/10.1145/1645953.1646253}, author = {Gong,Jun and Wang,Lidan and Oard, Douglas} } @article {15321, title = {Pairwise Document Similarity in Large Collections with MapReduce}, journal = {Relation}, volume = {10}, year = {2009}, month = {2009///}, pages = {8372 - 8372}, author = {Elsayed,T. and Jimmy Lin and Oard, Douglas} } @article {15704, title = {A Polynomial-Time Interior-Point Method for Conic Optimization, with Inexact Barrier Evaluations}, journal = {SIAM Journal on Optimization}, volume = {20}, year = {2009}, month = {2009///}, pages = {548 - 571}, doi = {DOI: 10.1137/080722825}, author = {Schurr,Simon P. and O{\textquoteright}Leary, Dianne P. and Tits,Andre{\textquoteright} L.} } @article {15792, title = {Quadratic fermionic interactions yield Hamiltonians with large ground-state energy gaps}, journal = {Physical Review APhys. Rev. A}, volume = {79}, year = {2009}, month = {2009/03/24/}, pages = {032331 - 032331}, abstract = {Polynomially large ground-state energy gaps are rare in many-body quantum systems, but useful in quantum information and an interesting feature of the one-dimensional quantum Ising model. We show analytically that the gap is generically polynomially large not just for the quantum Ising model, but for one-, two-, and three-dimensional interaction lattices and Hamiltonians with certain random interactions. We extend the analysis to Hamiltonian evolutions and we use the Jordan-Wigner transformation and a related transformation for spin-3/2 particles to show that our results can be restated using spin operators in a surprisingly simple manner. These results also yield a new perspective on the one-dimensional cluster state.}, doi = {10.1103/PhysRevA.79.032331}, url = {http://link.aps.org/doi/10.1103/PhysRevA.79.032331}, author = {O{\textquoteright}Hara,Michael J. and O{\textquoteright}Leary,Dianne P.} } @conference {15856, title = {Replication and automation of expert judgments: Information engineering in legal e-discovery}, booktitle = {IEEE International Conference on Systems, Man and Cybernetics, 2009. SMC 2009}, year = {2009}, month = {2009/10/11/14}, pages = {102 - 107}, publisher = {IEEE}, organization = {IEEE}, abstract = {The retrieval of digital evidence responsive to discovery requests in civil litigation, known in the United States as {\~A}‚{\^A}{\textquestiondown}e-discovery,{\~A}‚{\^A}{\textquestiondown} presents several important and understudied conditions and challenges. Among the most important of these are (i) that the definition of responsiveness that governs the search effort can be learned and made explicit through effective interaction with the responding party, (ii) that the governing definition of responsiveness is generally complex, deriving both from considerations of subject-matter relevance and from considerations of litigation strategy, and (iii) that the result of the search effort is a set (rather than a ranked list) of documents, and sometimes a quite large set, that is turned over to the requesting party and that the responding party certifies to be an accurate and complete response to the request. This paper describes the design of an {\~A}‚{\^A}{\textquestiondown}interactive task{\~A}‚{\^A}{\textquestiondown} for the text retrieval conference{\textquoteright}s legal track that had the evaluation of the effectiveness of e-discovery applications at the {\~A}‚{\^A}{\textquestiondown}responsive review{\~A}‚{\^A}{\textquestiondown} task as its goal. Notable features of the 2008 interactive task were high-fidelity human-system task modeling, authority control for the definition of {\~A}‚{\^A}{\textquestiondown}responsiveness,{\~A}‚{\^A}{\textquestiondown} and relatively deep sampling for estimation of type 1 and type 2 errors (expressed as {\~A}‚{\^A}{\textquestiondown}precision{\~A}‚{\^A}{\textquestiondown} and {\~A}‚{\^A}{\textquestiondown}recall{\~A}‚{\^A}{\textquestiondown}). The paper presents a critical assessment of the strengths and weaknesses of the evaluation design from the perspectives of reliability, reusability, and cost-benefit tradeoffs.}, keywords = {authorisation, authority control, Automation, civil litigation, CYBERNETICS, Delay, digital evidence retrieval, discovery request, Educational institutions, expert judgment automation, Human computer interaction, Human-machine cooperation and systems, human-system task modeling, information engineering, Information retrieval, interactive task, Law, law administration, legal e-discovery, Legal factors, PROBES, Production, Protocols, search effort, Search methods, text analysis, text retrieval conference legal track, United States, USA Councils, User modeling}, isbn = {978-1-4244-2793-2}, doi = {10.1109/ICSMC.2009.5346118}, author = {Hedin,B. and Oard, Douglas} } @article {13114, title = {Scene it or not? incremental multiple kernel learning for object detection}, journal = {Proceedings of the International Conference on Computer Vision}, year = {2009}, month = {2009///}, author = {Kembhavi,A. and Siddiquie,B. and Miezianko,R. and McCloskey,S. and Davis, Larry S. and Schwartz, W.R. and Harwood,D. and Gupta,A. and Farrell,R. and Luo,Y. and others} } @book {19349, title = {Scientific Computing with Case Studies}, year = {2009}, month = {2009}, publisher = {SIAM}, organization = {SIAM}, abstract = {This book is a practical guide to the numerical solution of linear and nonlinear equations, differential equations, optimization problems, and eigenvalue problems. It treats standard problems and introduces important variants such as sparse systems, differential-algebraic equations, constrained optimization, Monte Carlo simulations, and parametric studies. Stability and error analysis are emphasized, and the Matlab algorithms are grounded in sound principles of software design and understanding of machine arithmetic and memory management. Nineteen case studies provide experience in mathematical modeling and algorithm design, motivated by problems in physics, engineering, epidemiology, chemistry, and biology. The topics included go well beyond the standard first-course syllabus, introducing important problems such as differential-algebraic equations and conic optimization problems, and important solution techniques such as continuation methods. The case studies cover a wide variety of fascinating applications, from modeling the spread of an epidemic to determining truss configurations.}, isbn = {9780898717723}, author = {O{\textquoteright}Leary, Dianne P.} } @conference {15895, title = {Selecting hierarchical clustering cut points for web person-name disambiguation}, booktitle = {Proceedings of the 32nd international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}09}, year = {2009}, month = {2009///}, pages = {778 - 779}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Hierarchical clustering is often used to cluster person-names referring to the same entities. Since the correct number of clusters for a given person-name is not known a priori, some way of deciding where to cut the resulting dendrogram to balance risks of over- or under-clustering is needed. This paper reports on experiments in which outcome-specific and result-set measures are used to learn a global similarity threshold. Results on the Web People Search (WePS)-2 task indicate that approximately 85\% of the optimal F1 measure can be achieved on held-out data.}, keywords = {clustering, person-name disambiguation}, isbn = {978-1-60558-483-6}, doi = {10.1145/1571941.1572124}, url = {http://doi.acm.org/10.1145/1571941.1572124}, author = {Gong,Jun and Oard, Douglas} } @article {13856, title = {Semantically informed machine translation (SIMT)}, journal = {SCALE summer workshop final report, Human Language Technology Center Of Excellence}, year = {2009}, month = {2009///}, author = {Baker,K. and Bethard,S. and Bloodgood,M. and Brown,R. and Callison-Burch,C. and Coppersmith,G. and Dorr, Bonnie J and Filardo,W. and Giles,K. and Irvine,A. and others} } @conference {14322, title = {Sensing and predicting the pulse of the city through shared bicycling}, booktitle = {International Joint Conference on Artificial Intelligence}, year = {2009}, month = {2009///}, pages = {1420 - 1426}, author = {Jon Froehlich and Neumann, J. and Oliver,N.} } @article {15843, title = {Understanding IT Innovations Through Computational Analysis of Discourse}, journal = {ICIS 2009 Proceedings}, year = {2009}, month = {2009/01/01/}, url = {http://aisel.aisnet.org/icis2009/102}, author = {Tsui,Chia-jung and Wang,Ping and Fleischmann,Kenneth and Oard, Douglas and Sayeed,Asad} } @article {15838, title = {Access to recorded interviews}, journal = {Journal on Computing and Cultural Heritage}, volume = {1}, year = {2008}, month = {2008/06/01/}, pages = {1 - 27}, isbn = {15564673}, doi = {10.1145/1367080.1367083}, url = {http://dl.acm.org/citation.cfm?id=1367083}, author = {Jong,Franciska De and Oard, Douglas and Heeren,Willemijn and Ordelman,Roeland} } @conference {14323, title = {Activity sensing in the wild: a field trial of ubifit garden}, booktitle = {Proceeding of the twenty-sixth annual SIGCHI conference on Human factors in computing systems}, year = {2008}, month = {2008///}, pages = {1797 - 1806}, author = {Consolvo,S. and McDonald,D.W. and Toscos,T. and Chen,M.Y. and Jon Froehlich and Harrison,B. and Klasnja,P. and LaMarca,A. and LeGrand,L. and Libby,R. and others} } @article {15708, title = {Adaptive Constraint Reduction for Training Support Vector Machines}, journal = {Electronic Transactions on Numerical Analysis}, volume = {31}, year = {2008}, month = {2008///}, pages = {156 - 177}, url = {http://etna.mcs.kent.edu/vol.31.2008/pp156-177.dir/pp156-177.pdfhttp://etna.mcs.kent.edu/vol.31.2008/pp156-177.dir/pp156-177.pdf}, author = {Jung,Jin Hyuk and O{\textquoteright}Leary, Dianne P. and Tits,Andre{\textquoteright} L.} } @article {15815, title = {The Adiabatic Theorem in the Presence of Noise}, journal = {Physical Review A}, volume = {77}, year = {2008}, month = {2008///}, pages = {042319, 20 pages - 042319, 20 pages}, doi = {DOI: 10.1103/PhysRevA.77.042319}, url = {http://link.aps.org/abstract/PRA/v77/e042319http://link.aps.org/abstract/PRA/v77/e042319}, author = {O{\textquoteright}Hara,Michael J. and O{\textquoteright}Leary, Dianne P.} } @article {15835, title = {Advances in multilingual and multimodal information retrieval}, journal = {Lecture Notes in Computer Science}, volume = {5152}, year = {2008}, month = {2008///}, author = {Peters,C. and Jijkoun,V. and Mandl,T. and M{\"u}ller,H. and Oard, Douglas and Pe{\~n}as,A. and Santos,D.} } @article {15857, title = {Advancing social science research by applying computational linguistics}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {45}, year = {2008}, month = {2008///}, pages = {1 - 12}, author = {Cheng,A.S. and Fleischmann,K.R. and Wang,P. and Oard, Douglas} } @inbook {15716, title = {Arabic/English Multi-document Summarization with CLASSYThe Past and the Future}, booktitle = {Computational Linguistics and Intelligent Text Processing, Lecture Notes in Computer Science Volume 4919Computational Linguistics and Intelligent Text Processing, Lecture Notes in Computer Science Volume 4919}, year = {2008}, month = {2008///}, pages = {568 - 581}, publisher = {Springer Berlin}, organization = {Springer Berlin}, url = {http://dx.doi.org/10.1007/978-3-540-78135-6_49http://dx.doi.org/10.1007/978-3-540-78135-6_49}, author = {Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P. and Conroy,John M.} } @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.} } @conference {15867, title = {Combining Speech Retrieval Results with Generalized Additive Models}, booktitle = {ACL{\textquoteright}08: Proceedings of the 2008 Conference of the Association for Computational Linguistics}, year = {2008}, month = {2008///}, author = {Olsson,J.S. and Oard, Douglas} } @article {18961, title = {The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)}, journal = {Nature}, volume = {452}, year = {2008}, month = {2008///}, pages = {991 - 996}, abstract = {Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3 draft genome sequence of {\textquoteright}SunUp{\textquoteright} papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica{\textquoteright}s distinguishing morpho-physiological, medicinal and nutritional properties.}, isbn = {0028-0836}, doi = {10.1038/nature06856}, url = {http://www.nature.com/nature/journal/v452/n7190/full/nature06856.html}, author = {Ming,R. and Hou,S. and Feng,Y. and Yu,Q. and Dionne-Laporte,A. and Saw,J.H. and Senin,P. and Wang,W. and Ly,B.V. and Lewis,K.L.T. and others} } @article {16066, title = {Evaluating Visual Analytics at the 2007 VAST Symposium Contest}, journal = {Computer Graphics and Applications, IEEE}, volume = {28}, year = {2008}, month = {2008/04//march}, pages = {12 - 21}, abstract = {In this article, we report on the contest{\textquoteright}s data set and tasks, the judging criteria, the winning tools, and the overall lessons learned in the competition. We believe that by organizing these contests, we{\textquoteright}re creating useful resources for researchers and are beginning to understand how to better evaluate VA tools. Competitions encourage the community to work on difficult problems, improve their tools, and develop baselines for others to build or improve upon. We continue to evolve a collection of data sets, scenarios, and evaluation methodologies that reflect the richness of the many VA tasks and applications.}, keywords = {2007, analytics, analytics;data, and, Contest;Visual, Science, Symposium, Technology;data, VAST, visualisation;, visualization;visual}, isbn = {0272-1716}, doi = {10.1109/MCG.2008.27}, author = {Plaisant, Catherine and Grinstein,G. and Scholtz,J. and Whiting,M. and O{\textquoteright}Connell,T. and Laskowski,S. and Chien,L. and Tat,A. and Wright,W. and Gorg,C. and Zhicheng Liu and Parekh,N. and Singhal,K. and Stasko,J.} } @article {15866, title = {Extending sense-making models with ideas from cognition and learning theories}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {45}, year = {2008}, month = {2008///}, pages = {23 - 23}, author = {Zhang,P. and Soergel,D. and Klavans,J. L and Oard, Douglas} } @conference {12106, title = {A Framework for Software Engineering Experimental Replications}, booktitle = {Engineering of Complex Computer Systems, 2008. ICECCS 2008. 13th IEEE International Conference on}, year = {2008}, month = {2008/04/31/3}, pages = {203 - 212}, abstract = {Experimental replications are very important to the advancement of empirical software engineering. Replications are one of the key mechanisms to confirm previous experimental findings. They are also used to transfer experimental knowledge, to train people, and to expand a base of experimental evidence. Unfortunately, experimental replications are difficult endeavors. It is not easy to transfer experimental know-how and experimental findings. Based on our experience, this paper discusses this problem and proposes a Framework for Improving the Replication of Experiments (FIRE). The FIRE addresses knowledge sharing issues both at the intra-group (internal replications) and inter-group (external replications) levels. It encourages coordination of replications in order to facilitate knowledge transfer for lower cost, higher quality replications and more generalizable results.}, keywords = {engineering, engineering;, evidence;experimental, experimental, Experiments;experimental, for, Framework, Improving, knowledge, of, replication, replication;software, sharing;software, the, transfer;knowledge}, doi = {10.1109/ICECCS.2008.38}, author = {Mendonca,M.G. and Maldonado,J.C. and de Oliveira,M.C.F. and Carver, J. and Fabbri,C.P.F. and Shull, F. and Travassos,G.H. and Hohn,E.N. and Basili, Victor R.} } @conference {18477, title = {Imaging concert hall acoustics using visual and audio cameras}, booktitle = {IEEE International Conference on Acoustics, Speech and Signal Processing, 2008. ICASSP 2008}, year = {2008}, month = {2008///}, pages = {5284 - 5287}, publisher = {IEEE}, organization = {IEEE}, abstract = {Using a developed real time audio camera, that uses the output of a spherical microphone array beamformer steered in all directions to create central projection to create acoustic intensity images, we present a technique to measure the acoustics of rooms and halls. A panoramic mosaiced visual image of the space is also create. Since both the visual and the audio camera images are central projection, registration of the acquired audio and video images can be performed using standard computer vision techniques. We describe the technique, and apply it to the examine the relation between acoustical features and architectural details of the Dekelbaum concert hall at the Clarice Smith Performing Arts Center in College Park, MD.}, keywords = {Acoustic imaging, acoustic intensity images, acoustic measurement, Acoustic measurements, Acoustic scattering, acoustic signal processing, acoustical camera, acoustical scene analysis, acquired audio registration, audio cameras, audio signal processing, CAMERAS, central projection, Computer vision, Educational institutions, HUMANS, image registration, Image segmentation, imaging concert hall acoustics, Layout, microphone arrays, panoramic mosaiced visual image, Raman scattering, reverberation, room acoustics, spherical microphone array beamformer, spherical microphone arrays, video image registration, visual cameras}, isbn = {978-1-4244-1483-3}, doi = {10.1109/ICASSP.2008.4518852}, author = {O{\textquoteright}Donovan,A. and Duraiswami, Ramani and Zotkin,Dmitry N} } @article {15761, title = {Implementing an Interior Point Method for Linear Programs on a CPU-GPU System}, journal = {Electronic Transactions on Numerical Analysis}, volume = {28}, year = {2008}, month = {2008///}, pages = {174 - 189}, url = {http://etna.mcs.kent.edu/vol.28.2007-2008/pp174-189.dir/pp174-189.pdfhttp://etna.mcs.kent.edu/vol.28.2007-2008/pp174-189.dir/pp174-189.pdf}, author = {Jung,Jin Hyuk and O{\textquoteright}Leary, Dianne P.} } @article {19197, title = {Measuring the pulse of the city through shared bicycle programs}, journal = {Proc. of UrbanSense08}, year = {2008}, month = {2008}, author = {Jon Froehlich and Neumann, J. and Oliver,N.} } @article {16338, title = {Pooled ANOVA}, journal = {Computational Statistics \& Data Analysis}, volume = {52}, year = {2008}, month = {2008/08/15/}, pages = {5215 - 5228}, abstract = {We introduce Pooled ANOVA, a greedy algorithm to sequentially select the rare important factors from a large set of factors. Problems such as computer simulations and software performance tuning involve a large number of factors, few of which have an important effect on the outcome or performance measure. We pool multiple factors together, and test the pool for significance. If the pool has a significant effect we retain the factors for deconfounding. If not, we either declare that none of the factors are important, or retain them for follow-up decoding, depending on our assumptions and stage of testing. The sparser important factors are, the bigger the savings. Pooled ANOVA requires fewer assumptions than other, similar methods (e.g.~sequential bifurcation), such as not requiring all important effects to have the same sign. We demonstrate savings of 25\%-35\% when compared to a conventional ANOVA, and also the ability to work in a setting where Sequential Bifurcation fails.}, isbn = {0167-9473}, doi = {16/j.csda.2008.04.024}, url = {http://www.sciencedirect.com/science/article/pii/S0167947308002168}, author = {Last,Michael and Luta,Gheorghe and Orso,Alex and Porter, Adam and Young,Stan} } @article {15799, title = {Residual periodograms for choosing regularization parameters for ill-posed problems}, journal = {Inverse Problems}, volume = {24}, year = {2008}, month = {2008/06/01/}, pages = {034005 - 034005}, abstract = {Consider an ill-posed problem transformed if necessary so that the errors in the data are independent identically normally distributed with mean zero and variance 1. We survey regularization and parameter selection from a linear algebra and statistics viewpoint and compare the statistical distributions of regularized estimates of the solution and the residual. We discuss methods for choosing a regularization parameter in order to assure that the residual for the model is statistically plausible. Ideally, as proposed by Rust (1998 Tech. Rep. NISTIR 6131, 2000 Comput. Sci. Stat. 32 333{\textendash}47 ), the results of candidate parameter choices should be evaluated by plotting the resulting residual along with its periodogram and its cumulative periodogram, but sometimes an automated choice is needed. We evaluate a method for choosing the regularization parameter that makes the residuals as close as possible to white noise, using a diagnostic test based on the periodogram. We compare this method with standard techniques such as the discrepancy principle, the L-curve and generalized cross validation, showing that it performs better on two new test problems as well as a variety of standard problems.}, isbn = {0266-5611, 1361-6420}, doi = {10.1088/0266-5611/24/3/034005}, url = {http://iopscience.iop.org/0266-5611/24/3/034005}, author = {Rust,Bert W. and O{\textquoteright}Leary, Dianne P.} } @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 {13133, title = {Resource allocation for tracking multiple targets using particle filters}, journal = {The Eighth International Workshop on Visual Surveillance}, year = {2008}, month = {2008///}, abstract = {Particle filters have been very widely used to track targets in video sequences. However, they suffer from an exponential rise in the number of particles needed to jointly track multiple targets. On the other hand, using multiple independent filters to track in crowded scenes often leads to erroneous results. We present a new particle filtering framework which uses an intelligent resource allocation scheme allowing us to track a large number of targets using a small set of particles. First, targets with overlapping posterior distributions and similar appearance models are clustered into interaction groups and tracked jointly, but independent of other targets in the scene. Second, different number of particles are allocated to different groups based on the following observations. Groups with higher associations (quantifying spatial proximity and pairwise appearance similarity) are given more particles. Groups with larger number of targets are given a larger number of particles. Finally, groups with ineffective proposal distributions are assigned more particles. Our experiments demonstrate the effectiveness of this framework over the commonly used joint particle filter with Markov Chain Monte Carlo (MCMC) sampling.}, author = {Kembhavi,A. and Schwartz, W.R. and Davis, Larry S. and others} } @conference {16010, title = {The role of metacognition in robust AI systems}, booktitle = {AAAI-08 Workshop on Metareasoning,(Chicago, IL)}, year = {2008}, month = {2008///}, author = {Schmill,M. D and Oates,T. and Anderson,M. and Fults,S. and Josyula,D. and Perlis, Don and Wilson,S.} } @article {15965, title = {A self-help guide for autonomous systems}, journal = {AI Magazine}, volume = {29}, year = {2008}, month = {2008///}, pages = {67 - 67}, author = {Anderson,M. L and Fults,S. and Josyula,D. P and Oates,T. and Perlis, Don and Wilson,S. and Wright,D.} } @conference {13980, title = {Spherical Arrays Near Boundaries}, booktitle = {Hands-Free Speech Communication and Microphone Arrays, 2008. HSCMA 2008}, year = {2008}, month = {2008/05//}, pages = {1 - 1}, abstract = {Summary form only given. Solid spherical microphone arrays are beginning to be used for purposes such as beamforming, sound field capture and as audio cameras. They rely on the scattering of sound off their surface to achieve their purpose. This behavior is significantly affected in the presence of boundaries (floors, walls, ceilings), and the edges and corners they form. Algorithms designed for array analysis in a free field will work erroneously in this situation. We describe adaptation of the spherical microphone analysis algorithms to constructively use the scattering off the boundaries to significantly improve array performance. We also assess the influence of walls on beamforming algorithms for regular spherical arrays. Both synthetic and experimental results are presented.}, keywords = {analysis;audio, analysis;microphone, array, arrays;, arrays;sound, arrays;spherical, cameras;beamforming;solid, capture;spherical, field, microphone, spherical}, doi = {10.1109/HSCMA.2008.4538675}, author = {Duraiswami, Ramani and Gumerov, Nail A. and O{\textquoteright}Donovan,A.} } @article {13986, title = {Spherical microphone array based immersive audio scene rendering}, journal = {Proc. ICAD}, year = {2008}, month = {2008///}, abstract = {In many applications such as entertainment, education, mil-itary training, remote telepresence, surveillance, etc. it is necessary to capture an acoustic field and present it to listen- ers with a goal of creating the same acoustic perception for them as if they were actually present at the scene. Currently, there is much interest in the use of spherical microphone ar- rays for acoustic scene capture and reproduction. We de- scribe a 32-microphone spherical array based system im- plemented for spatial audio capture and reproduction. Our array embeds hardware that is traditionally external, such as preamplifiers, filters, digital-to-analog converters, and USB adaptor, resulting in a portable lightweight solution and re- quiring no hardware on the PC side whatsoever other than a high-speed USB port. We provide capability analysis of the array and describe software suite developed for the applica- tion. }, author = {O{\textquoteright}donovan,A.M. and Zotkin,Dmitry N and Duraiswami, Ramani} } @article {18484, title = {A spherical microphone array based system for immersive audio scene rendering}, volume = {UMIACS-TR-2008-09}, year = {2008}, month = {2008/03/25/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {For many applications it is necessary to capture an acoustic field and present it for human listeners, creating the same acoustic perception for them as if they were actually present in the scene. Possible applications of this technique include entertainment, education, military training, remote telepresence, surveillance, and others. Recently, there is much interest on the use of spherical microphone arrays in acoustic scene capture and reproduction application. We describe a 32-microphone spherical array based system implemented for spatial audio capture and reproduction. The array embeds hardware that is traditionally external, such as preamplifiers, filters, digital-to-analog converters, and USB interface adapter, resulting in a portable lightweight solution and requiring no hardware on PC side whatsoever other than a high-speed USB port. We provide capability analysis of the array and describe software suite developed for the application.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu//handle/1903/7556}, author = {O{\textquoteright}donovan,Adam and Zotkin,Dmitry N and Duraiswami, Ramani} } @article {15890, title = {Unlocking the Potential of the Spoken Word}, journal = {Science}, volume = {321}, year = {2008}, month = {2008///}, pages = {1787 - 1788}, doi = {10.1126/science.1157353}, url = {http://www.sciencemag.org/content/321/5897/1787.short}, author = {Oard, Douglas} } @article {15888, title = {User-assisted query translation for interactive cross-language information retrieval}, journal = {Information Processing \& Management}, volume = {44}, year = {2008}, month = {2008/01//}, pages = {181 - 211}, abstract = {Interactive Cross-Language Information Retrieval (CLIR), a process in which searcher and system collaborate to find documents that satisfy an information need regardless of the language in which those documents are written, calls for designs in which synergies between searcher and system can be leveraged so that the strengths of one can cover weaknesses of the other. This paper describes an approach that employs user-assisted query translation to help searchers better understand the system{\^a}{\texteuro}{\texttrademark}s operation. Supporting interaction and interface designs are introduced, and results from three user studies are presented. The results indicate that experienced searchers presented with this new system evolve new search strategies that make effective use of the new capabilities, that they achieve retrieval effectiveness comparable to results obtained using fully automatic techniques, and that reported satisfaction with support for cross-language searching increased. The paper concludes with a description of a freely available interactive CLIR system that incorporates lessons learned from this research.}, keywords = {Cross-language information retrieval, Machine translation, User studies}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2006.12.009}, url = {http://www.sciencedirect.com/science/article/pii/S0306457307000337}, author = {Oard, Douglas and He,Daqing and Wang,Jianqiang} } @article {14829, title = {Using specularities in comparing 3D models and 2D images}, journal = {Computer Vision and Image Understanding}, volume = {111}, year = {2008}, month = {2008/09//}, pages = {275 - 294}, abstract = {We aim to create systems that identify and locate objects by comparing known, 3D shapes to intensity images that they have produced. To do this we focus on verification methods that determine whether a known model in a specific pose is consistent with an image. We build on prior work that has done this successfully for Lambertian objects, to handle a much broader class of shiny objects that produce specular highlights. Our core contribution is a novel method for determining whether a known 3D shape is consistent with the 2D shape of a possible highlight found in an image. We do this using only a qualitative description of highlight formation that is consistent with most models of specular reflection, so no specific knowledge of an object{\textquoteright}s specular reflectance properties is needed. This allows us to treat non-Lambertian image effects as a positive source of information about object identity, rather than treating them as a potential source of noise. We then show how to integrate information about highlights into a system that also checks the consistency of Lambertian reflectance effects. Also, we show how to model Lambertian reflectance using a reference image, rather than albedos, which can be difficult to measure in shiny objects. We test each aspect of our approach using several different data sets. We demonstrate the potential value of our method of handling specular highlights by building a system that can locate shiny, transparent objects, such as glassware, on table tops. We demonstrate our hybrid methods on pottery, and our use of reference images with face recognition experiments.}, keywords = {illumination, Object recognition, Specularity}, isbn = {1077-3142}, doi = {10.1016/j.cviu.2007.12.004}, url = {http://www.sciencedirect.com/science/article/pii/S1077314207001713}, author = {Osadchy,Margarita and Jacobs, David W. and Ramamoorthi,Ravi and Tucker,David} } @conference {16064, title = {VAST 2008 Challenge: Introducing mini-challenges}, booktitle = {Visual Analytics Science and Technology, 2008. VAST {\textquoteright}08. IEEE Symposium on}, year = {2008}, month = {2008/10//}, pages = {195 - 196}, abstract = {Visual analytics experts realize that one effective way to push the field forward and to develop metrics for measuring the performance of various visual analytics components is to hold an annual competition. The VAST 2008 Challenge is the third year that such a competition was held in conjunction with the IEEE Visual Analytics Science and Technology (VAST) symposium. The authors restructured the contest format used in 2006 and 2007 to reduce the barriers to participation and offered four mini-challenges and a Grand Challenge. Mini Challenge participants were to use visual analytic tools to explore one of four heterogeneous data collections to analyze specific activities of a fictitious, controversial movement. Questions asked in the Grand Challenge required the participants to synthesize data from all four data sets. In this paper we give a brief overview of the data sets, the tasks, the participation, the judging, and the results.}, keywords = {2008, analytics;data, Challenge;heterogeneous, collections;visual, data, VAST, visualisation;}, doi = {10.1109/VAST.2008.4677383}, author = {Grinstein,G. and Plaisant, Catherine and Laskowski,S. and O{\textquoteright}Connell,T. and Scholtz,J. and Whiting,M.} } @article {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 {15831, title = {Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality}, journal = {PLoS Comput BiolPLoS Comput Biol}, volume = {4}, year = {2008}, month = {2008///}, pages = {e1000140 - e1000140}, abstract = {Analysis of protein interaction networks in the budding yeast Saccharomyces cerevisiae has revealed that a small number of proteins, the so-called hubs, interact with a disproportionately large number of other proteins. Furthermore, many hub proteins have been shown to be essential for survival of the cell{\textemdash}that is, in optimal conditions, yeast cannot grow and multiply without them. This relation between essentiality and the number of neighbors in the protein{\textendash}protein interaction network has been termed the centrality-lethality rule. However, why are such hubs essential? Jeong and colleagues [1] suggested that overrepresentation of essential proteins among high-degree nodes can be attributed to the central role that hubs play in mediating interactions among numerous, less connected proteins. Another view, proposed by He and Zhang, suggested that that the majority of proteins are essential due to their involvement in one or more essential protein{\textendash}protein interactions that are distributed uniformly at random along the network edges [2]. We find that none of the above reasons determines essentiality. Instead, the majority of hubs are essential due to their involvement in Essential Complex Biological Modules, a group of densely connected proteins with shared biological function that are enriched in essential proteins. This study sheds new light on the topological complexity of protein interaction networks.}, doi = {10.1371/journal.pcbi.1000140}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000140}, author = {Zotenko,Elena and Mestre,Julian and O{\textquoteright}Leary, Dianne P. and Przytycka,Teresa M.} } @inbook {15722, title = {Bridging the ROUGE/Human Evaluation Gap in Multi-Document Summarization}, booktitle = {Document Understanding Conference DUC 2007Document Understanding Conference DUC 2007}, year = {2007}, month = {2007/04/26/}, publisher = {HLT-NAACL}, organization = {HLT-NAACL}, address = {Rochester, NY}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @article {15837, title = {CLEF-2006 CL-SR at Maryland: English and Czech}, journal = {Evaluation of Multilingual and Multi-modal Information Retrieval}, year = {2007}, month = {2007///}, pages = {786 - 793}, author = {Wang,J. and Oard, Douglas} } @conference {16395, title = {Coevolution of Predators and Prey in a Spatial Model}, booktitle = {Genetic and Evolutionary Computation Conference (GECCO)}, year = {2007}, month = {2007///}, address = {London, England}, author = {Ottino-Lofler,J. and Rand, William and Wilensky,U.} } @article {14600, title = {COMPUTATIONAL BIOLOGY}, journal = {Nucleic acids research}, volume = {35}, year = {2007}, month = {2007///}, pages = {3163 - 3163}, author = {Leparc,GG and Mitra,RD and Vardhanabhuti,S. and Wang,J. and Hannenhalli, Sridhar and Smit,S. and Widmann,J. and Knight,R. and Wu,S. and Zhang,Y. and others} } @conference {15904, title = {Confidentiality-preserving rank-ordered search}, booktitle = {Proceedings of the 2007 ACM workshop on Storage security and survivability}, series = {StorageSS {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {7 - 12}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper introduces a new framework for confidentiality preserving rank-ordered search and retrieval over large document collections. The proposed framework not only protects document/query confidentiality against an outside intruder, but also prevents an untrusted data center from learning information about the query and the document collection. We present practical techniques for proper integration of relevance scoring methods and cryptographic techniques, such as order preserving encryption, to protect data collections and indices and provide efficient and accurate search capabilities to securely rank-order documents in response to a query. Experimental results on the W3C collection show that these techniques have comparable performance to conventional search systems designed for non-encrypted data in terms of search accuracy. The proposed methods thus form the first steps to bring together advanced information retrieval and secure search capabilities for a wide range of applications including managing data in government and business operations, enabling scholarly study of sensitive data, and facilitating the document discovery process in litigation.}, keywords = {encrypted domain search, Ranked retrieval, secure index}, isbn = {978-1-59593-891-6}, doi = {10.1145/1314313.1314316}, url = {http://doi.acm.org/10.1145/1314313.1314316}, author = {Swaminathan,Ashwin and Mao,Yinian and Su,Guan-Ming and Gou,Hongmei and Varna,Avinash L. and He,Shan and M. Wu and Oard, Douglas} } @article {19072, title = {Evolution of genes and genomes on the Drosophila phylogeny}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007}, pages = {203 - 218}, author = {Clark, A.G. and Eisen,M. B and Smith,D. R and Bergman, C.M. and Oliver, B. and Markow, T.A. and Kaufman, T.C. and Kellis, M. and Gelbart, W. and Iyer, V.N. and others} } @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 {15754, title = {Fast Robust Regression Algorithms for Problems with Toeplitz Structure}, journal = {Computational Statistics and Data Analysis}, volume = {52:2}, year = {2007}, month = {2007///}, pages = {1119 - 1131}, url = {doi:10.1016/j.csda.2007.05.008doi:10.1016/j.csda.2007.05.008}, author = {Mastronardi,Nicola and O{\textquoteright}Leary, Dianne P.} } @article {15279, title = {Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses}, journal = {Emerging Infectious DiseasesEmerg Infect Dis}, volume = {13}, year = {2007}, month = {2007/05//}, pages = {713 - 718}, abstract = {Although linked, these viruses are distinct from earlier outbreak strains., To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.}, isbn = {1080-6040}, doi = {10.3201/eid1305.070013}, author = {Salzberg,Steven L. and Kingsford, Carl and Cattoli,Giovanni and Spiro,David J. and Janies,Daniel A. and Aly,Mona Mehrez and Brown,Ian H. and Couacy-Hymann,Emmanuel and De Mia,Gian Mario and Dung,Do Huu and Guercio,Annalisa and Joannis,Tony and Ali,Ali Safar Maken and Osmani,Azizullah and Padalino,Iolanda and Saad,Magdi D. and Savi{\'c},Vladimir and Sengamalay,Naomi A. and Yingst,Samuel and Zaborsky,Jennifer and Zorman-Rojs,Olga and Ghedin,Elodie and Capua,Ilaria} } @conference {15986, title = {Hood College, Master of Business Administration, 2005 Hood College, Master of Science (Computer Science), 2001 Hood College, Bachelor of Science (Computer Science), 1998 Frederick Community College, Associate in Arts (Business Administration), 1993}, booktitle = {Proceedings of the Workshop on Metareasoning in Agent-Based Systems}, year = {2007}, month = {2007///}, author = {Anderson,M. L and Schmill,M. and Oates,T. and Perlis, Don and Josyula,D. and Wright,D. and Human,S. W.T.D.N and Metacognition,L. and Fults,S. and Josyula,D. P} } @conference {15902, title = {Improving text classification for oral history archives with temporal domain knowledge}, booktitle = {Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {623 - 630}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes two new techniques for increasing the accuracy oftopic label assignment to conversational speech from oral history interviews using supervised machine learning in conjunction with automatic speech recognition. The first, time-shifted classification, leverages local sequence information from the order in which the story is told. The second, temporal label weighting, takes the complementary perspective by using the position within an interview to bias label assignment probabilities. These methods, when used in combination, yield between 6\% and 15\% relative improvements in classification accuracy using a clipped R-precision measure that models the utility of label sets as segment summaries in interactive speech retrieval applications.}, keywords = {automatic topic classification, classifying with domain knowledge, spoken document classification}, isbn = {978-1-59593-597-7}, doi = {10.1145/1277741.1277848}, url = {http://doi.acm.org/10.1145/1277741.1277848}, author = {Olsson,J. Scott and Oard, Douglas} } @conference {13828, title = {Measuring variability in sentence ordering for news summarization}, booktitle = {Proceedings of the Eleventh European Workshop on Natural Language Generation}, series = {ENLG {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {81 - 88}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {The issue of sentence ordering is an important one for natural language tasks such as multi-document summarization, yet there has not been a quantitative exploration of the range of acceptable sentence orderings for short texts. We present results of a sentence reordering experiment with three experimental conditions. Our findings indicate a very high degree of variability in the orderings that the eighteen subjects produce. In addition, the variability of reorderings is significantly greater when the initial ordering seen by subjects is different from the original summary. We conclude that evaluation of sentence ordering should use multiple reference orderings. Our evaluation presents several metrics that might prove useful in assessing against multiple references. We conclude with a deeper set of questions: (a) what sorts of independent assessments of quality of the different reference orderings could be made and (b) whether a large enough test set would obviate the need for such independent means of quality assessment.}, url = {http://dl.acm.org/citation.cfm?id=1610163.1610177}, author = {Madnani,Nitin and Passonneau,Rebecca and Ayan,Necip Fazil and Conroy,John M. and Dorr, Bonnie J and Klavans,Judith L. and O{\textquoteright}Leary, Dianne P. and Schlesinger,Judith D.} } @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 {15771, title = {Modified Cholesky Algorithms: A Catalog with New Approaches}, journal = {Mathematical Programming}, year = {2007}, month = {2007///}, url = {doi:10.1007/s10107-007-0177-6doi:10.1007/s10107-007-0177-6}, author = {Fang,Hawren and O{\textquoteright}Leary, Dianne P.} } @conference {15997, title = {Ontologies for reasoning about failures in AI systems}, booktitle = {Proceedings from the Workshop on Metareasoning in Agent Based Systems at the Sixth International Joint Conference on Autonomous Agents and Multiagent Sytems}, year = {2007}, month = {2007///}, author = {Schmill,M. and Josyula,D. and Anderson,M. L and Wilson,S. and Oates,T. and Perlis, Don and Fults,S.} } @article {15790, title = {QCS: A system for querying, clustering and summarizing documents}, journal = {Information Processing \& Management}, volume = {43}, year = {2007}, month = {2007/11//}, pages = {1588 - 1605}, abstract = {Information retrieval systems consist of many complicated components. Research and development of such systems is often hampered by the difficulty in evaluating how each particular component would behave across multiple systems. We present a novel integrated information retrieval system{\textemdash}the Query, Cluster, Summarize (QCS) system{\textemdash}which is portable, modular, and permits experimentation with different instantiations of each of the constituent text analysis components. Most importantly, the combination of the three types of methods in the QCS design improves retrievals by providing users more focused information organized by topic.We demonstrate the improved performance by a series of experiments using standard test sets from the Document Understanding Conferences (DUC) as measured by the best known automatic metric for summarization system evaluation, ROUGE. Although the DUC data and evaluations were originally designed to test multidocument summarization, we developed a framework to extend it to the task of evaluation for each of the three components: query, clustering, and summarization. Under this framework, we then demonstrate that the QCS system (end-to-end) achieves performance as good as or better than the best summarization engines. Given a query, QCS retrieves relevant documents, separates the retrieved documents into topic clusters, and creates a single summary for each cluster. In the current implementation, Latent Semantic Indexing is used for retrieval, generalized spherical k-means is used for the document clustering, and a method coupling sentence {\textquotedblleft}trimming{\textquotedblright} and a hidden Markov model, followed by a pivoted QR decomposition, is used to create a single extract summary for each cluster. The user interface is designed to provide access to detailed information in a compact and useful format. Our system demonstrates the feasibility of assembling an effective IR system from existing software libraries, the usefulness of the modularity of the design, and the value of this particular combination of modules. }, keywords = {clustering, Information retrieval, latent semantic indexing, Sentence trimming, Summarization, TEXT PROCESSING}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2007.01.003}, url = {http://www.sciencedirect.com/science/article/pii/S0306457307000246}, author = {Dunlavy,Daniel M. and O{\textquoteright}Leary,Dianne P. and Conroy,John M. and Schlesinger,Judith D.} } @conference {13988, title = {Real Time Capture of Audio Images and their Use with Video}, booktitle = {Applications of Signal Processing to Audio and Acoustics, 2007 IEEE Workshop on}, year = {2007}, month = {2007/10//}, pages = {10 - 13}, 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 updated at a high frame rate to achieve a video stream if the data capture and intensity computations can be performed sufficiently quickly, there by creating a frame-rate audio camera. We describe how such a camera can be built and the processing done sufficiently quickly using graphics processors. The joint processing of captured frame-rate audio and video images enables applications such as visual identification of noise sources, beamforming and noise-suppression in video conferencing and others, provided it is possible to account 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 it is possible to perform such joint analysis. We provide several examples of real-time applications.}, doi = {10.1109/ASPAA.2007.4393037}, author = {O{\textquoteright}donovan,Adam and Duraiswami, Ramani and Gumerov, Nail A.} } @article {12008, title = {A roadmap to the integration of early visual modules}, journal = {International Journal of Computer Vision}, volume = {72}, year = {2007}, month = {2007///}, pages = {9 - 25}, author = {Ogale, A. S and Aloimonos, J.} } @conference {15105, title = {Round Complexity of Authenticated Broadcast with a Dishonest Majority}, booktitle = {Foundations of Computer Science, 2007. FOCS {\textquoteright}07. 48th Annual IEEE Symposium on}, year = {2007}, month = {2007/10//}, pages = {658 - 668}, abstract = {Broadcast among n parties in the presence of t ges n/3 malicious parties is possible only with some additional setup. The most common setup considered is the existence of a PKI and secure, digital signatures, where so-called authenticated broadcast is achievable for any t lt; n. It is known that t + 1 rounds are necessary and sufficient for deterministic protocols achieving authenticated broadcast. Recently, however, randomized protocols running in expected constant rounds have been shown for the case of t lt; n/2. It has remained open whether randomization can improve the round complexity when an honest majority is not present. We address this question and show upper/lower bounds on how much randomization can help: ldr For t les n/2 + k, we. show a randomized broadcast protocol that runs in expected O(k2) rounds. In particular, we obtain expected constant-round pivtocols for t = n/2 + O(1). ldr On the negative side, we show that even randomized protocols require Omega(2n/(n-t)) rounds. This in particular rules out expected constant-round protocols when the fraction of honest parties is sub-constant.}, keywords = {broadcast, complexity;cryptographic, complexity;deterministic, cryptography;, key, majority;randomized, PKI;authenticated, protocols;broadcasting;computational, protocols;digital, round, signatures;dishonest, signatures;public}, doi = {10.1109/FOCS.2007.44}, author = {Garay,J. A and Katz, Jonathan and Koo,Chiu-Yuen and Ostrovsky,R.} } @article {15841, title = {Searching spontaneous conversational speech}, journal = {ACM SIGIR Forum}, volume = {41}, year = {2007}, month = {2007/12/01/}, pages = {104 - 104}, isbn = {01635840}, doi = {10.1145/1328964.1328982}, url = {http://dl.acm.org/citation.cfm?id=1328982}, author = {Jong,Franciska De and Oard, Douglas and Ordelman,Roeland and Raaijmakers,Stephan} } @article {15777, title = {On Sensitivity of Gauss-Christoffel Quadrature}, journal = {Numerische Mathematik}, volume = {107}, year = {2007}, month = {2007///}, pages = {147 - 174}, abstract = {In numerical computations the question how much does a function change under perturbations of its arguments is of central importance. In this work, we investigate sensitivity of Gauss{\textendash}Christoffel quadrature with respect to small perturbations of the distribution function. In numerical quadrature, a definite integral is approximated by a finite sum of functional values evaluated at given quadrature nodes and multiplied by given weights. Consider a sufficiently smooth integrated function uncorrelated with the perturbation of the distribution function. Then it seems natural that given the same number of function evaluations, the difference between the quadrature approximations is of the same order as the difference between the (original and perturbed) approximated integrals. That is perhaps one of the reasons why, to our knowledge, the sensitivity question has not been formulated and addressed in the literature, though several other sensitivity problems, motivated, in particular, by computation of the quadrature nodes and weights from moments, have been thoroughly studied by many authors. We survey existing particular results and show that even a small perturbation of a distribution function can cause large differences in Gauss{\textendash}Christoffel quadrature estimates. We then discuss conditions under which the Gauss{\textendash}Christoffel quadrature is insensitive under perturbation of the distribution function, present illustrative examples, and relate our observations to known conjectures on some sensitivity problems.}, url = {doi:10.1007/s00211-007-0078-xdoi:10.1007/s00211-007-0078-x}, author = {O{\textquoteright}Leary, Dianne P. and Strako{\v s},Zden{\v e}k and Tich{\'y},Petr} } @conference {16426, title = {A spatial model of the red queen effect}, booktitle = {Proceedings of the 9th annual conference on Genetic and evolutionary computation}, series = {GECCO {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {490 - 491}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Van Valen first discovered the "Red Queen Effect" (RQE), where two species can dramatically co-evolve their phenotypes over time but never gain a relative advantage [2]. In the ideal version of the RQE, regardless of the actual values that the species evolve to obtain, they have not moved in relation to each other. Though previous models of the RQE exist, we developed an agent-based model (ABM) which has a base ontology more similar to real world coevolutionary systems than equation-based models (EBMs). For instance, this model contains spatial information and an individuallevel reproduction mechanism. Yet this model recreates traditional EBM results. For instance Dieckmann et al show that there are three possible outcomes of competitive coevolution: predator dominance, prey dominance and evolutionary cycling (RQE) [1]. By reconceptualizing this EBM using an ABM, we make it easier for students and researchers to understand, manipulate, and modify this model [4]. The model is written in the NetLogo agent-based modeling environment [3]. The model is initialized with 150 predator and 150 prey agents. Predator agents have a resistance level r and prey agents have a poison p. The agents are initially randomly distributed on a toroidal real-valued 35 by 35 grid. The initial resistance and poison values for the predators and prey are drawn from normal distributions with means {\textmu}r and {\textmu}p and a standard deviation of 1. During a model timestep, each agent moves one unit at a random heading. If at the end of its move a predator is within 1 unit of a prey, then it will challenge the prey. The predator will compare its resistance value to the prey{\textquoteright}s poison value and which ever agent has the larger value will win the challenge and the other agent will be killed. At the end of an agent{\textquoteright}s turn if the total number of agents is less than the maximum carrying capacity the agent will reproduce with a 50\% probability. The new agent{\textquoteright}s initial poison / resistance will be drawn from a normal distribution with the parent{\textquoteright}s poison / resistance as the mean value and a standard deviation of 1. Our goal was to investigate whether this ABMwould replicate the results of the EBM of [1]. Our parameter of interest was {\textmu}p; we held {\textmu}r constant at 25 and varied {\textmu}p from 0 to 50 at increments of 5. For each value we ran the model 10 times for 5000 timesteps. Figure 1 illustrates the final average values of both the resistance and the poison for the various initial values. If there are no predators or prey then a value of 0 is plotted for the respective final trait. In most cases, one species drives the other to extinction, and there is little change in the initial trait values. However when the value of {\textmu}p is similar to {\textmu}r then neither species is completely destroyed, but if there is any significant difference between {\textmu}r and {\textmu}p then one species will die off. The highest final trait values are found when {\textmu}p = {\textmu}r, in this case we see the results of the RQE since the final trait values are much higher than the initial values. These final values are more than 1.5 orders of magnitude larger than the initial values. This model reproduces classical models of the RQE, but has two different mobile species interacting on a spatial grid over time which is a closer representation of reality than traditional models. This closer representation makes ABMs excellent teaching and experimental tools because their basic assumptions can easily be manipulated and explored. Acknowledgments: We thank the National Science Foundation and NICO for supporting this research.}, keywords = {Agent-based modeling, coevolution, red queen effect, spatial modeling}, isbn = {978-1-59593-697-4}, doi = {10.1145/1276958.1277064}, url = {http://doi.acm.org/10.1145/1276958.1277064}, author = {Ottino-Loffler,Jules and Rand, William and Wilensky,Uri} } @article {15812, title = {Structural Footprinting in Protein Structure Comparison: The Impact of Structural Fragments}, journal = {BMC Structural Biology}, volume = {7}, year = {2007}, month = {2007///}, abstract = {Abstract Background One approach for speeding-up protein structure comparison is the projection approach, where a protein structure is mapped to a high-dimensional vector and structural similarity is approximated by distance between the corresponding vectors. Structural footprinting methods are projection methods that employ the same general technique to produce the mapping: first select a representative set of structural fragments as models and then map a protein structure to a vector in which each dimension corresponds to a particular model and "counts" the number of times the model appears in the structure. The main difference between any two structural footprinting methods is in the set of models they use; in fact a large number of methods can be generated by varying the type of structural fragments used and the amount of detail in their representation. How do these choices affect the ability of the method to detect various types of structural similarity? Results To answer this question we benchmarked three structural footprinting methods that vary significantly in their selection of models against the CATH database. In the first set of experiments we compared the methods{\textquoteright} ability to detect structural similarity characteristic of evolutionarily related structures, i.e., structures within the same CATH superfamily. In the second set of experiments we tested the methods{\textquoteright} agreement with the boundaries imposed by classification groups at the Class, Architecture, and Fold levels of the CATH hierarchy. Conclusion In both experiments we found that the method which uses secondary structure information has the best performance on average, but no one method performs consistently the best across all groups at a given classification level. We also found that combining the methods{\textquoteright} outputs significantly improves the performance. Moreover, our new techniques to measure and visualize the methods{\textquoteright} agreement with the CATH hierarchy, including the threshholded affinity graph, are useful beyond this work. In particular, they can be used to expose a similar composition of different classification groups in terms of structural fragments used by the method and thus provide an alternative demonstration of the continuous nature of the protein structure universe.}, url = {DOI:10.1186/1472-6807-7-53DOI:10.1186/1472-6807-7-53}, author = {Zotenko,Elena and Dogan,Rezarta Islamaj and Wilbur,W. John and O{\textquoteright}Leary, Dianne P. and Przytycka,Teresa M.} } @article {14893, title = {Surface Dependent Representations for Illumination Insensitive Image Comparison}, journal = {Pattern Analysis and Machine Intelligence, IEEE Transactions on}, volume = {29}, year = {2007}, month = {2007/01//}, pages = {98 - 111}, abstract = {We consider the problem of matching images to tell whether they come from the same scene viewed under different lighting conditions. We show that the surface characteristics determine the type of image comparison method that should be used. Previous work has shown the effectiveness of comparing the image gradient direction for surfaces with material properties that change rapidly in one direction. We show analytically that two other widely used methods, normalized correlation of small windows and comparison of multiscale oriented filters, essentially compute the same thing. Then, we show that for surfaces whose properties change more slowly, comparison of the output of whitening filters is most effective. This suggests that a combination of these strategies should be employed to compare general objects. We discuss indications that Gabor jets use such a mixed strategy effectively, and we propose a new mixed strategy. We validate our results on synthetic and real images}, keywords = {Automated;Reproducibility of Results;Sensitivity and Specificity;Subtraction Technique;, Computer-Assisted;Imaging, Gabor jets;Gaussian random surface;filter whitening;illumination;image comparison;image matching;lighting condition;multiscale oriented filter;surface dependent representation;image matching;image representation;Algorithms;Artificial Intelligence;Image En, Three-Dimensional;Information Storage and Retrieval;Lighting;Pattern Recognition}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2007.250602}, author = {Osadchy,M. and Jacobs, David W. and Lindenbaum,M.} } @article {16523, title = {Swarm Intelligence Systems Using Guided Self-Organization for Collective Problem Solving}, journal = {Advances in Complex Systems}, volume = {10}, year = {2007}, month = {2007///}, pages = {5 - 34}, author = {RodrIGuez,A. and Grushin,A. and Reggia, James A. and HAUPTMAN,AMI and SIPPER,M. and PAN,Z. and Reggia, James A. and GAO,D. and DARABOS,C. and GIACOBINI,M. and others} } @conference {15906, title = {Task-based interaction with an integrated multilingual, multimedia information system: a formative evaluation}, booktitle = {Proceedings of the 7th ACM/IEEE-CS joint conference on Digital libraries}, series = {JCDL {\textquoteright}07}, year = {2007}, month = {2007///}, pages = {117 - 126}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes a formative evaluation of an integrated multilingual, multimedia information system, a series of user studies designed to guide system development. The system includes automatic speech recognition for English, Chinese, and Arabic, automatic translation from Chinese and Arabic into English, and query-based and profile-based search options. The study design emphasizes repeated evaluation with the same (increasingly experienced) participants, exploration of alternative task designs, rich qualitative and quantitative data collection, and rapid analysis to provide the timely feedback needed to support iterative and responsive development. Results indicate that users presented with materials in a language that they do not know can generate remarkably useful work products, but that integration of transcription, translation, search and profile management poses challenges that would be less evident were each technology to be evaluated in isolation.}, keywords = {Cross-language information retrieval, multimedia, User studies}, isbn = {978-1-59593-644-8}, doi = {10.1145/1255175.1255199}, url = {http://doi.acm.org/10.1145/1255175.1255199}, author = {Zhang,Pengyi and Plettenberg,Lynne and Klavans,Judith L. and Oard, Douglas and Soergel,Dagobert} } @article {16322, title = {Techniques for Classifying Executions of Deployed Software to Support Software Engineering Tasks}, journal = {IEEE Transactions on Software Engineering}, volume = {33}, year = {2007}, month = {2007///}, pages = {287 - 304}, abstract = {There is an increasing interest in techniques that support analysis and measurement of fielded software systems. These techniques typically deploy numerous instrumented instances of a software system, collect execution data when the instances run in the field, and analyze the remotely collected data to better understand the system{\textquoteright}s in-the-field behavior. One common need for these techniques is the ability to distinguish execution outcomes (e.g., to collect only data corresponding to some behavior or to determine how often and under which condition a specific behavior occurs). Most current approaches, however, do not perform any kind of classification of remote executions and either focus on easily observable behaviors (e.g., crashes) or assume that outcomes{\textquoteright} classifications are externally provided (e.g., by the users). To address the limitations of existing approaches, we have developed three techniques for automatically classifying execution data as belonging to one of several classes. In this paper, we introduce our techniques and apply them to the binary classification of passing and failing behaviors. Our three techniques impose different overheads on program instances and, thus, each is appropriate for different application scenarios. We performed several empirical studies to evaluate and refine our techniques and to investigate the trade-offs among them. Our results show that 1) the first technique can build very accurate models, but requires a complete set of execution data; 2) the second technique produces slightly less accurate models, but needs only a small fraction of the total execution data; and 3) the third technique allows for even further cost reductions by building the models incrementally, but requires some sequential ordering of the software instances{\textquoteright} instrumentation.}, keywords = {execution classification, remote analysis/measurement.}, isbn = {0098-5589}, doi = {http://doi.ieeecomputersociety.org/10.1109/TSE.2007.1004}, author = {Haran,Murali and Karr,Alan and Last,Michael and Orso,Alessandro and Porter, Adam and Sanil,Ashish and Fouch?,Sandro} } @conference {16008, title = {Toward domain-neutral human-level metacognition}, booktitle = {AAAI Spring Symposium on Logical Formalizations of Commonsense Reasoning}, year = {2007}, month = {2007///}, author = {Anderson,M. L and Schmill,M. and Oates,T. and Perlis, Don and Josyula,D. and Wright,D. and Wilson,S.} } @article {15827, title = {Universal Duality in Conic Convex Optimization}, journal = {Mathematical Programming A}, volume = {109}, year = {2007}, month = {2007///}, pages = {69 - 88}, abstract = {Given a primal-dual pair of linear programs, it is well known that if their optimal values are viewed as lying on the extended real line, then the duality gap is zero, unless both problems are infeasible, in which case the optimal values are +$\infty$ and -$\infty$. In contrast, for optimization problems over nonpolyhedral convex cones, a nonzero duality gap can exist when either the primal or the dual is feasible.For a pair of dual conic convex programs, we provide simple conditions on the {\textquoteleft}{\textquoteleft}constraint matrices{\textquoteright}{\textquoteright} and cone under which the duality gap is zero for every choice of linear objective function and constraint right-hand side. We refer to this property as {\textquoteleft}{\textquoteleft}universal duality{\textquoteright}{\textquoteright}. Our conditions possess the following properties: (i) they are necessary and sufficient, in the sense that if (and only if) they do not hold, the duality gap is nonzero for some linear objective function and constraint right-hand side; (ii) they are metrically and topologically generic; and (iii) they can be verified by solving a single conic convex program. We relate to universal duality the fact that the feasible sets of a primal convex program and its dual cannot both be bounded, unless they are both empty. Finally we illustrate our theory on a class of semidefinite programs that appear in control theory applications. }, author = {Schurr,Simon P. and Tits,Andr{\'e} and O{\textquoteright}Leary, Dianne P.} } @conference {16074, title = {VAST 2007 Contest - Blue Iguanodon}, booktitle = {Visual Analytics Science and Technology, 2007. VAST 2007. IEEE Symposium on}, year = {2007}, month = {2007/11/30/1}, pages = {231 - 232}, abstract = {Visual analytics experts realize that one effective way to push the field forward and to develop metrics for measuring the performance of various visual analytics components is to hold an annual competition. The second visual analytics science and technology (VAST) contest was held in conjunction with the 2007 IEEE VAST symposium. In this contest participants were to use visual analytic tools to explore a large heterogeneous data collection to construct a scenario and find evidence buried in the data of illegal and terrorist activities that were occurring. A synthetic data set was made available as well as tasks. In this paper we describe some of the advances we have made from the first competition held in 2006.}, keywords = {activities;large, activities;visual, analytic, collection;terrorist, data, heterogeneous, illegal, interfaces;, tools;data, user, visualisation;graphical}, doi = {10.1109/VAST.2007.4389032}, author = {Grinstein,G. and Plaisant, Catherine and Laskowski,S. and O{\textquoteright}Connell,T. and Scholtz,J. and Whiting,M.} } @article {11970, title = {View-invariant modeling and recognition of human actions using grammars}, journal = {Dynamical Vision}, year = {2007}, month = {2007///}, pages = {115 - 126}, author = {Ogale, A. and Karapurkar, A. and Aloimonos, J.} } @article {12396, title = {Adding dense, weighted connections to wordnet}, journal = {Proceedings of the Third International WordNet Conference}, year = {2006}, month = {2006///}, pages = {29 - 36}, abstract = {WORDNET, a ubiquitous tool for natural language processing, suffers from sparsity of connectionsbetween its component concepts (synsets). Through the use of human annotators, a subset of the connections between 1000 hand-chosen synsets was assigned a value of {\textquotedblleft}evocation{\textquotedblright} representing how much the first concept brings to mind the second. These data, along with existing similarity measures, constitute the basis of a method for predicting evocation between previously unrated pairs. }, author = {Jordan Boyd-Graber and Fellbaum,C. and Osherson,D. and Schapire,R.} } @article {15712, title = {Algorithms for Structured Total Least Squares Problems with Applications to Blind Image Deblurring}, journal = {Journal of Research of the National Institute of Standards and Technology}, volume = {111}, year = {2006}, month = {2006///}, pages = {113 - 119}, abstract = {Mastronardi, Lemmerling, and van Huel presented an algorithm for solving a total least squares problem when the matrix and its perturbations are Toeplitz. A Toeplitz matrix is a special kind of matrix with small displacement rank. Here we generalize the fast algorithm to any matrix with small displacement rank. In particular, we show how to efficiently construct the generators whenever M has small displacement rank and show that in many important cases the Cholesky factorization of the matrix M M can also be determined fast. We further extend this problem to Tikhonov regularization of ill-posed problems and illustrate the use of the algorithm on an image deblurring problem.}, url = {http://nvl.nist.gov/pub/nistpubs/jres/111/2/V111.N02.A06.pdfhttp://nvl.nist.gov/pub/nistpubs/jres/111/2/V111.N02.A06.pdf}, author = {Kalsi,Anoop and O{\textquoteright}Leary, Dianne P.} } @conference {13723, title = {Annotation compatibility working group report}, booktitle = {Proceedings of the Workshop on Frontiers in Linguistically Annotated Corpora 2006}, series = {LAC {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {38 - 53}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This report explores the question of compatibility between annotation projects including translating annotation formalisms to each other or to common forms. Compatibility issues are crucial for systems that use the results of multiple annotation projects. We hope that this report will begin a concerted effort in the field to track the compatibility of annotation schemes for part of speech tagging, time annotation, treebanking, role labeling and other phenomena.}, isbn = {1-932432-78-7}, url = {http://dl.acm.org/citation.cfm?id=1641991.1641997}, author = {Meyers,A. and Fang,A. C. and Ferro,L. and K{\"u}bler,S. and Jia-Lin,T. and Palmer,M. and Poesio,M. and Dolbey,A. and Schuler,K. K. and Loper,E. and Zinsmeister,H. and Penn,G. and Xue,N. and Hinrichs,E. and Wiebe,J. and Pustejovsky,J. and Farwell,D. and Hajicova,E. and Dorr, Bonnie J and Hovy,E. and Onyshkevych,B. A. and Levin,L.} } @inbook {15719, title = {Back to Basics: CLASSY 2006}, booktitle = {DUC 06 Conference ProceedingsDUC 06 Conference Proceedings}, year = {2006}, month = {2006///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {The IDA/CCS summarization system, CLASSY, underwent significant change for this year{\textquoteright}sDUC. Two changes made processing simpler and faster: 1) we eliminated the use of a POS (part of speech) tagger for sentence splitting and to assist sentence trimming, and 2) we simplified the scoring of sentences for inclusion in the summary by introducing a new {\textquotedblleft}approximate oracle{\textquotedblright} score. An additional change introduced a modest amount of extra computation: we ordered sentences in the summary using a new Traveling Salesperson (TSP) formulation. These changes improved ROUGE scores on the DUC 2005 data from last year and gave strong performance in the DUC 2006 competition. }, url = {\tt http://duc.nist.gov/}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P. and Goldstein,Jade} } @article {14015, title = {Capture and rendering of spatial sound over headphones}, journal = {The Journal of the Acoustical Society of America}, volume = {120}, year = {2006}, month = {2006///}, pages = {3094 - 3094}, abstract = {A theory for capturing an audio scene and then rendering it remotely over headphones is developed. The method relies on capture of a sound field up to a certain order in terms of spherical wave functions. Then, the captured sound field is convolved with the head-related transfer function and rendered to provide presence in the auditory scene. The sound-field representation is then transmitted to a remote location for immediate rendering or stored for later use. A system that implements the capture using a spherical array is developed and tested. Head-related transfer functions are measured using the system described in [D.N. Zotkin et al., J. Acoustic. Soc. Am. (to appear)]. The sound renderer, coupled with the head tracker, reconstructs the acoustic field using individualized head-related transfer functions to preserve the perceptual spatial structure of the audio scene. [Work partially supported by VA.]}, url = {http://link.aip.org/link/?JAS/120/3094/4}, author = {Duraiswami, Ramani and Zotkin,Dmitry N and O{\textquoteright}donovan,Adam} } @article {17013, title = {Classifying science: Phenomena, data, theory, method, practice: Book Reviews}, journal = {J. Am. Soc. Inf. Sci. Technol.}, volume = {57}, year = {2006}, month = {2006/12//}, pages = {1977 - 1978}, abstract = {Due to e-mail{\textquoteright}s ubiquitous nature, millions of users are intimate with the technology; however, most users are only familiar with managing their own e-mail, which is an inherently different task from exploring an e-mail archive. Historians and social scientists believe that e-mail archives are important artifacts for understanding the individuals and communities they represent. To understand the conversations evidenced in an archive, context is needed. In this article, we present a new way to gain this necessary context: analyzing the temporal rhythms of social relationships. We provide methods for constructing meaningful rhythms from the e-mail headers by identifying relationships and interpreting their attributes. With these visualization techniques, e-mail archive explorers can uncover insights that may have been otherwise hidden in the archive. We apply our methods to an individual{\textquoteright}s 15-year e-mail archive, which consists of about 45,000 messages and over 4,000 relationships. {\textcopyright} 2006 Wiley Periodicals, Inc.}, keywords = {corpus_analysis, email, hci, project--email, text_analysis, Visualization}, isbn = {1532-2882}, url = {http://dx.doi.org/10.1002/asi.v57:14}, author = {Perer,Adam and Shneiderman, Ben and Oard, Douglas} } @inbook {15727, title = {CLASSYArabic and English Multi-Document Summarization}, booktitle = {Multi-Lingual Summarization Evaluation 2006Multi-Lingual Summarization Evaluation 2006}, year = {2006}, month = {2006///}, url = {http://www.isi.edu/ cyl/MTSE2006/MSE2006/papers/index.htmlhttp://www.isi.edu/ cyl/MTSE2006/MSE2006/papers/index.html}, author = {Conroy,John M. and O{\textquoteright}Leary, Dianne P. and Schlesinger,Judith D.} } @article {15864, title = {Clef-2005 cl-sr at maryland: Document and query expansion using side collections and thesauri}, journal = {Accessing Multilingual Information Repositories}, year = {2006}, month = {2006///}, pages = {800 - 809}, author = {Wang,J. and Oard, Douglas} } @conference {15905, title = {Combining bidirectional translation and synonymy for cross-language information retrieval}, booktitle = {Proceedings of the 29th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {202 - 209}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper introduces a general framework for the use of translation probabilities in cross-language information retrieval based on the notion that information retrieval fundamentally requires matching what the searcher means with what the author of a document meant. That perspective yields a computational formulation that provides a natural way of combining what have been known as query and document translation. Two well-recognized techniques are shown to be a special case of this model under restrictive assumptions. Cross-language search results are reported that are statistically indistinguishable from strong monolingual baselines for both French and Chinese documents.}, keywords = {cross-language IR, statistical translation}, isbn = {1-59593-369-7}, doi = {10.1145/1148170.1148208}, url = {http://doi.acm.org/10.1145/1148170.1148208}, author = {Wang,Jianqiang and Oard, Douglas} } @inbook {13751, title = {Cross-Language Access to Recorded Speech in the MALACH Project}, booktitle = {Text, Speech and DialogueText, Speech and Dialogue}, series = {Lecture Notes in Computer Science}, volume = {2448}, year = {2006}, month = {2006///}, pages = {197 - 212}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {The MALACH project seeks to help users find information in a vast multilingual collections of untranscribed oral history interviews. This paper introduces the goals of the project and focuses on supporting access by users who are unfamiliar with the interview language. It begins with a review of the state of the art in crosslanguage speech retrieval; approaches that will be investigated in the project are then described. Czech was selected as the first non-English language to be supported, so results of an initial experiment with Czech/English cross-language retrieval are reported.}, isbn = {978-3-540-44129-8}, url = {http://dx.doi.org/10.1007/3-540-46154-X_8}, author = {Oard, Douglas and Demner-Fushman,Dina and Haji{\v c},Jan and Ramabhadran,Bhuvana and Gustman,Samuel and Byrne,William and Soergel,Dagobert and Dorr, Bonnie J and Resnik, Philip and Picheny,Michael}, editor = {Sojka,Petr and Kopecek,Ivan and Pala,Karel} } @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.} } @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 {15744, title = {Efficient Circuits for Exact-Universal Computation with Qudits}, journal = {Quantum Information and Computation}, volume = {6}, year = {2006}, month = {2006///}, pages = {436 - 454}, author = {Brennen,Gavin K. and Bullock,Stephen S. and O{\textquoteright}Leary, Dianne P.} } @article {15932, title = {Enhancing reinforcement learning with metacognitive monitoring and control for improved perturbation tolerance}, journal = {Journal of Experimental and Theoretical Artificial Intelligence}, volume = {18}, year = {2006}, month = {2006///}, pages = {387 - 411}, author = {Anderson,M. L and Oates,T. and Chong,W. and Perlis, Don} } @conference {15852, title = {Evaluation of Multilingual and Multi-modal Information Retrieval-Seventh Workshop of the Cross-Language Evaluation Forum, CLEF 2006, Alicante, Spain, September 19-21, 2006, Revised Selected Papers}, booktitle = {Seventh Workshop of the Cross-Language Evaluation Forum, CLEF 2006}, year = {2006}, month = {2006///}, address = {Alicante, Spain}, author = {Peters,C. and Clough,P. and Gey,F. and Karlgren,J. and Magnini,B. and Oard, Douglas and De Rijke,M. and Stempfhuber,M.} } @conference {15887, title = {An exploratory study of the W3C mailing list test collection for retrieval of emails with pro/con arguments}, booktitle = {Proceedings of the Third Conference on Email and Anti-Spam, Mountain View, CA, July}, year = {2006}, month = {2006///}, author = {Wu,Y. and Oard, Douglas and Soboroff,I.} } @article {16006, title = {The metacognitive loop I: Enhancing reinforcement learning with metacognitive monitoring and control for improved perturbation tolerance}, journal = {Journal of Experimental \& Theoretical Artificial Intelligence}, volume = {18}, year = {2006}, month = {2006///}, pages = {387 - 411}, author = {Anderson,M. L and Oates,T. and Chong,W. and Perlis, Don} } @conference {15834, title = {Modeling identity in archival collections of email: A preliminary study}, booktitle = {Proceedings of the 2006 Conference on Email and Anti-Spam (CEAS 06)}, year = {2006}, month = {2006///}, pages = {95 - 103}, author = {Elsayed,T. and Oard, Douglas} } @article {13839, title = {Parallel syntactic annotation of multiple languages}, journal = {Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC2006). Genoa, Italy}, year = {2006}, month = {2006///}, abstract = {This paper describes an effort to investigate the incrementally deepening development of an interlingua notation, validated by humanannotation of texts in English plus six languages. We begin with deep syntactic annotation, and in this paper present a series of annotation manuals for six different languages at the deep-syntactic level of representation. Many syntactic differences between languages are removed in the proposed syntactic annotation, making them useful resources for multilingual NLP projects with semantic components. }, author = {Rambow,O. and Dorr, Bonnie J and Farwell,D. and Green,R. and Habash,N. and Helmreich,S. and Hovy,E. and Levin,L. and Miller,K.J. and Mitamura,T. and others} } @article {15785, title = {Parallelism for quantum computation with qudits}, journal = {Physical Review APhys. Rev. A}, volume = {74}, year = {2006}, month = {2006///}, pages = {032334 - 032334}, abstract = {Robust quantum computation with d-level quantum systems (qudits) poses two requirements: fast, parallel quantum gates and high-fidelity two-qudit gates. We first describe how to implement parallel single-qudit operations. It is by now well known that any single-qudit unitary can be decomposed into a sequence of Givens rotations on two-dimensional subspaces of the qudit state space. Using a coupling graph to represent physically allowed couplings between pairs of qudit states, we then show that the logical depth (time) of the parallel gate sequence is equal to the height of an associated tree. The implementation of a given unitary can then optimize the tradeoff between gate time and resources used. These ideas are illustrated for qudits encoded in the ground hyperfine states of the alkali-metal atoms 87Rb and 133Cs. Second, we provide a protocol for implementing parallelized nonlocal two-qudit gates using the assistance of entangled qubit pairs. Using known protocols for qubit entanglement purification, this offers the possibility of high-fidelity two-qudit gates.}, doi = {10.1103/PhysRevA.74.032334}, url = {http://link.aps.org/doi/10.1103/PhysRevA.74.032334}, author = {O{\textquoteright}Leary,Dianne P. and Brennen,Gavin K. and Bullock,Stephen S.} } @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 {15805, title = {Secondary Structure Spatial Conformation Footprint: A Novel Method for Fast Protein Structure Comparison and Classification}, journal = {BMC Structural Biology}, volume = {6}, year = {2006}, month = {2006///}, abstract = {Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance between projections, the success of any projection method depends on how well its mapping function is able to capture the salient features of protein structure. There is no agreement on what constitutes a good projection technique and the three currently known projection methods utilize very different approaches to the mapping construction, both in terms of what structural elements are included and how this information is integrated to produce a vector representation. Results In this paper we propose a novel projection method that uses secondary structure information to produce the mapping. First, a diverse set of spatial arrangements of triplets of secondary structure elements, a set of structural models, is automatically selected. Then, each protein structure is mapped into a high-dimensional vector of "counts" or footprint, where each count corresponds to the number of times a given structural model is observed in the structure, weighted by the precision with which the model is reproduced. We perform the first comprehensive evaluation of our method together with all other currently known projection methods. Conclusion The results of our evaluation suggest that the type of structural information used by a projection method affects the ability of the method to detect structural similarity. In particular, our method that uses the spatial conformations of triplets of secondary structure elements outperforms other methods in most of the tests.}, url = {DOI:10.1186/1472-6807-6-12DOI:10.1186/1472-6807-6-12}, author = {Zotenko,Elena and O{\textquoteright}Leary, Dianne P. and Przytycka,Teresa M.} } @conference {11979, title = {A sensory grammar for inferring behaviors in sensor networks}, booktitle = {Proceedings of the 5th international conference on Information processing in sensor networks}, series = {IPSN {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {251 - 259}, publisher = {ACM}, organization = {ACM}, address = {Nashville, Tennessee, USA}, abstract = {The ability of a sensor network to parse out observable activities into a set of distinguishable actions is a powerful feature that can potentially enable many applications of sensor networks to everyday life situations. In this paper we introduce a framework that uses a hierarchy of Probabilistic Context Free Grammars (PCFGs) to perform such parsing. The power of the framework comes from the hierarchical organization of grammars that allows the use of simple local sensor measurements for reasoning about more macroscopic behaviors. Our presentation describes how to use a set of phonemes to construct grammars and how to achieve distributed operation using a messaging model. The proposed framework is flexible. It can be mapped to a network hierarchy or can be applied sequentially and across the network to infer behaviors as they unfold in space and time. We demonstrate this functionality by inferring simple motion patterns using a sequence of simple direction vectors obtained from our camera sensor network testbed.}, keywords = {algorithms, behavior identification, human activity, human factors, pcfg, real-time and embedded systems, sensor grammars, sensor networks}, isbn = {1-59593-334-4}, doi = {10.1145/1127777.1127817}, author = {Lymberopoulos, Dimitrios and Ogale, Abhijit S. and Savvides, Andreas and Aloimonos, J.} } @inbook {15806, title = {Sentence Trimming and Selection: Mixing and Matching}, booktitle = {DUC 06 Conference Proceedings}, year = {2006}, month = {2006///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {We describe how components from two distinct multi-document summarization systems were combined. Twenty four possible combinations of components were considered. We observed some contrasts between conservative and aggressive sentence compression (i.e., trimming) in the context of multi-document summarization. }, url = {http://duc.nist.gov/}, author = {Zajic, David and Dorr, Bonnie J and Jimmy Lin and O{\textquoteright}Leary, Dianne P. and Conroy,John M. and Schlesinger,Judith D.} } @article {13864, title = {SParseval: Evaluation metrics for parsing speech}, journal = {Proc. LREC}, year = {2006}, month = {2006///}, abstract = {While both spoken and written language processing stand to benefit from parsing, the standard Parseval metrics (Black et al., 1991) andtheir canonical implementation (Sekine and Collins, 1997) are only useful for text. The Parseval metrics are undefined when the words input to the parser do not match the words in the gold standard parse tree exactly, and word errors are unavoidable with automatic speech recognition (ASR) systems. To fill this gap, we have developed a publicly available tool for scoring parses that implements a variety of metrics which can handle mismatches in words and segmentations, including: alignment-based bracket evaluation, alignment-based dependency evaluation, and a dependency evaluation that does not require alignment. We describe the different metrics, how to use the tool, and the outcome of an extensive set of experiments on the sensitivity of the metrics. }, author = {Roark,B. and Harper,M. and Charniak,E. and Dorr, Bonnie J and Johnson,M. and Kahn,J. and Liu,Y. and Ostendorf,M. and Hale,J. and Krasnyanskaya,A. and others} } @article {15810, title = {Stable Factorizations of Symmetric Tridiagonal and Triadic Matrices}, journal = {SIAM J. on Matrix Analysis and Applications}, volume = {28}, year = {2006}, month = {2006///}, pages = {576 - 595}, abstract = {We call a matrix triadic if it has no more than two nonzero off-diagonal elements in any column. A symmetric tridiagonal matrix is a special case. In this paper we consider $LXL^T$ factorizations of symmetric triadic matrices, where $L$ is unit lower triangular and $X$ is diagonal, block diagonal with $1\!\times\!1$ and $2\!\times\!2$ blocks, or the identity with $L$ lower triangular. We prove that with diagonal pivoting, the $LXL^T$ factorization of a symmetric triadic matrix is sparse, study some pivoting algorithms, discuss their growth factor and performance, analyze their stability, and develop perturbation bounds. These factorizations are useful in computing inertia, in solving linear systems of equations, and in determining modified Newton search directions.}, author = {Fang,Haw-ren and O{\textquoteright}Leary, Dianne P.} } @conference {15825, title = {Topic-focused multi-document summarization using an approximate oracle score}, booktitle = {Proceedings of the COLING/ACL on Main conference poster sessions}, series = {COLING-ACL {\textquoteright}06}, year = {2006}, month = {2006///}, pages = {152 - 159}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {We consider the problem of producing a multi-document summary given a collection of documents. Since most successful methods of multi-document summarization are still largely extractive, in this paper, we explore just how well an extractive method can perform. We introduce an "oracle" score, based on the probability distribution of unigrams in human summaries. We then demonstrate that with the oracle score, we can generate extracts which score, on average, better than the human summaries, when evaluated with ROUGE. In addition, we introduce an approximation to the oracle score which produces a system with the best known performance for the 2005 Document Understanding Conference (DUC) evaluation.}, url = {http://dl.acm.org/citation.cfm?id=1273073.1273093}, author = {Conroy,John M. and Schlesinger,Judith D. and O{\textquoteright}Leary, Dianne P.} } @article {17480, title = {Using rhythms of relationships to understand e-mail archives}, journal = {Journal of the American Society for Information Science and Technology}, volume = {57}, year = {2006}, month = {2006/12/01/}, pages = {1936 - 1948}, abstract = {Due to e-mail{\textquoteright}s ubiquitous nature, millions of users are intimate with the technology; however, most users are only familiar with managing their own e-mail, which is an inherently different task from exploring an e-mail archive. Historians and social scientists believe that e-mail archives are important artifacts for understanding the individuals and communities they represent. To understand the conversations evidenced in an archive, context is needed. In this article, we present a new way to gain this necessary context: analyzing the temporal rhythms of social relationships. We provide methods for constructing meaningful rhythms from the e-mail headers by identifying relationships and interpreting their attributes. With these visualization techniques, e-mail archive explorers can uncover insights that may have been otherwise hidden in the archive. We apply our methods to an individual{\textquoteright}s 15-year e-mail archive, which consists of about 45,000 messages and over 4,000 relationships.}, isbn = {1532-2890}, doi = {10.1002/asi.20387}, url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.20387/abstract}, author = {Perer,Adam and Shneiderman, Ben and Oard, Douglas} } @conference {16083, title = {VAST 2006 Contest - A Tale of Alderwood}, booktitle = {Visual Analytics Science And Technology, 2006 IEEE Symposium On}, year = {2006}, month = {2006/11/31/2}, pages = {215 - 216}, abstract = {Visual analytics experts realize that one effective way to push the field forward and to develop metrics for measuring the performance of various visual analytics components is to hold an annual competition. The first visual analytics science and technology (VAST) contest was held in conjunction with the 2006 IEEE VAST Symposium. The competition entailed the identification of possible political shenanigans in the fictitious town of Alderwood. A synthetic data set was made available as well as tasks. We summarize how we prepared and advertised the contest, developed some initial metrics for evaluation, and selected the winners. The winners were invited to participate at an additional live competition at the symposium to provide them with feedback from senior analysts}, keywords = {Alderwood;human, analysis;data, analytics, and, contest;data, information, interaction;sense, making;visual, Science, technology, visualisation;}, doi = {10.1109/VAST.2006.261420}, author = {Grinstein,G. and O{\textquoteright}Connell,T. and Laskowski,S. and Plaisant, Catherine and Scholtz,J. and Whiting,M.} } @conference {13481, title = {Visualization Support for Fusing Relational, Spatio-Temporal Data: Building Career Histories}, booktitle = {Information Fusion, 2006 9th International Conference on}, year = {2006}, month = {2006/07//}, pages = {1 - 7}, publisher = {IEEE}, organization = {IEEE}, abstract = {Many real-world domains resist analysis because they are best characterized by a variety of data types, including relational, spatial, and temporal components. Examples of such domains include disease outbreaks, criminal networks, and the World-Wide Web. We present two types of visualizations based on physical metaphors that facilitate fusion, analysis, and deep understanding of relational, spatio-temporal data. The first visualization is based on the metaphor of fluid flow through elastic pipes, and the second on wave propagation. We discuss both types of visualizations in the context of fusing information about the activities of scientists over time with the goal of constructing career histories}, isbn = {1-4244-0953-5, 0-9721844-6-5}, doi = {10.1109/ICIF.2006.301772}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4086058}, author = {Blythe,Jim and Patwardhan,Mithila and Oates,Tim and desJardins, Marie and Rheingans,Penny} } @conference {14325, title = {Are GSM phones THE solution for localization?}, booktitle = {Mobile Computing Systems and Applications, 2006. WMCSA{\textquoteright}06. Proceedings. 7th IEEE Workshop on}, year = {2005}, month = {2005///}, pages = {34 - 42}, author = {Varshavsky,A. and Chen,M.Y. and de Lara,E. and Jon Froehlich and Haehnel,D. and Hightower,J. and LaMarca,A. and Potter,F. and Sohn,T. and Tang,K. and others} } @article {15718, title = {Asymptotically Optimal Quantum Circuits for d-Level Systems}, journal = {Physical Review LettersPhys. Rev. Lett.}, volume = {94}, year = {2005}, month = {2005/06/14/}, pages = {230502 - 230502}, abstract = {Scalability of a quantum computation requires that the information be processed on multiple subsystems. However, it is unclear how the complexity of a quantum algorithm, quantified by the number of entangling gates, depends on the subsystem size. We examine the quantum circuit complexity for exactly universal computation on many d-level systems (qudits). Both a lower bound and a constructive upper bound on the number of two-qudit gates result, proving a sharp asymptotic of Θ(d2n) gates. This closes the complexity question for all d-level systems (d finite). The optimal asymptotic applies to systems with locality constraints, e.g., nearest neighbor interactions.}, doi = {10.1103/PhysRevLett.94.230502}, url = {http://link.aps.org/doi/10.1103/PhysRevLett.94.230502}, author = {Bullock,Stephen S. and O{\textquoteright}Leary,Dianne P. and Brennen,Gavin K.} } @article {15738, title = {Criteria for exact qudit universality}, journal = {Physical Review APhys. Rev. A}, volume = {71}, year = {2005}, month = {2005/05/16/}, pages = {052318 - 052318}, abstract = {We describe criteria for implementation of quantum computation in qudits. A qudit is a d-dimensional system whose Hilbert space is spanned by states |0⟩, |1⟩, {\textellipsis}, |d-1⟩. An important earlier work [ A. Muthukrishnan and C.R. Stroud, Jr. Phys. Rev. A 62 052309 (2000)] describes how to exactly simulate an arbitrary unitary on multiple qudits using a 2d-1 parameter family of single qudit and two qudit gates. That technique is based on the spectral decomposition of unitaries. Here we generalize this argument to show that exact universality follows given a discrete set of single qudit Hamiltonians and one two-qudit Hamiltonian. The technique is related to the QR-matrix decomposition of numerical linear algebra. We consider a generic physical system in which the single qudit Hamiltonians are a small collection of Hjkx=ℏΩ(|k⟩⟨j|+|j⟩⟨k|) and Hjky=ℏΩ(i|k⟩⟨j|-i|j⟩⟨k|). A coupling graph results taking nodes 0, {\textellipsis}, d-1 and edges j<->k iff Hjkx,y are allowed Hamiltonians. One qudit exact universality follows iff this graph is connected, and complete universality results if the two-qudit Hamiltonian H=ℏΩ|d-1,d-1⟩⟨d-1,d-1| is also allowed. We discuss implementation in the eight dimensional ground electronic states of 87Rb and construct an optimal gate sequence using Raman laser pulses.}, doi = {10.1103/PhysRevA.71.052318}, url = {http://link.aps.org/doi/10.1103/PhysRevA.71.052318}, author = {Brennen,Gavin K. and O{\textquoteright}Leary,Dianne P. and Bullock,Stephen S.} } @inbook {14211, title = {Detecting Independent 3D Movement}, booktitle = {Handbook of Geometric ComputingHandbook of Geometric Computing}, year = {2005}, month = {2005///}, pages = {383 - 401}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, isbn = {978-3-540-28247-1}, url = {http://dx.doi.org/10.1007/3-540-28247-5_12}, author = {Corrochano,Eduardo Bayro and Ogale, Abhijit S. and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {15869, title = {Dictionary-based cross-language retrieval}, journal = {Information Processing and Management}, volume = {41}, year = {2005}, month = {2005///}, pages = {523 - 547}, author = {Levow,G.A. and Oard, Douglas and Resnik, Philip} } @article {16689, title = {Dictionary-based techniques for cross-language information retrieval}, journal = {Information Processing \& Management}, volume = {41}, year = {2005}, month = {2005/05//}, pages = {523 - 547}, abstract = {Cross-language information retrieval (CLIR) systems allow users to find documents written in different languages from that of their query. Simple knowledge structures such as bilingual term lists have proven to be a remarkably useful basis for bridging that language gap. A broad array of dictionary-based techniques have demonstrated utility, but comparison across techniques has been difficult because evaluation results often span only a limited range of conditions. This article identifies the key issues in dictionary-based CLIR, develops unified frameworks for term selection and term translation that help to explain the relationships among existing techniques, and illustrates the effect of those techniques using four contrasting languages for systematic experiments with a uniform query translation architecture. Key results include identification of a previously unseen dependence of pre- and post-translation expansion on orthographic cognates and development of a query-specific measure for translation fanout that helps to explain the utility of structured query methods.}, keywords = {Cross-language information retrieval, Dictionary-based translation, Ranked retrieval}, isbn = {0306-4573}, doi = {10.1016/j.ipm.2004.06.012}, url = {http://www.sciencedirect.com/science/article/pii/S0306457304000810}, author = {Levow,Gina-Anne and Oard, Douglas and Resnik, Philip} } @article {15745, title = {Efficient iterative algorithms for the stochastic finite element method with application to acoustic scattering}, journal = {Computer Methods in Applied Mechanics and Engineering}, volume = {194}, year = {2005}, month = {2005/03/18/}, pages = {1037 - 1055}, abstract = {In this study, we describe the algebraic computations required to implement the stochastic finite element method for solving problems in which uncertainty is restricted to right-hand side data coming from forcing functions or boundary conditions. We show that the solution can be represented in a compact outer product form which leads to efficiencies in both work and storage, and we demonstrate that block iterative methods for algebraic systems with multiple right-hand sides can be used to advantage to compute this solution. We also show how to generate a variety of statistical quantities from the computed solution. Finally, we examine the behavior of these statistical quantities in one setting derived from a model of acoustic scattering.}, keywords = {01, 28, 60, finite element, multigrid, Multiple right-hand side, Scattering, Stochastic}, isbn = {0045-7825}, doi = {10.1016/j.cma.2004.06.028}, url = {http://www.sciencedirect.com/science/article/pii/S0045782504003123}, author = {Elman, Howard and Ernst, Oliver G. and O{\textquoteright}Leary,Dianne P. and Stewart, Michael} } @conference {14860, title = {On the equivalence of common approaches to lighting insensitive recognition}, booktitle = {Computer Vision, 2005. ICCV 2005. Tenth IEEE International Conference on}, volume = {2}, year = {2005}, month = {2005/10//}, pages = {1721 -1726 Vol. 2 - 1721 -1726 Vol. 2}, abstract = {Lighting variation is commonly handled by methods invariant to additive and multiplicative changes in image intensity. It has been demonstrated that comparing images using the direction of the gradient can produce broader insensitivity to changes in lighting conditions, even for 3D scenes. We analyze two common approaches to image comparison that are invariant, normalized correlation using small correlation windows, and comparison based on a large set of oriented difference of Gaussian filters. We show analytically that these methods calculate a monotonic (cosine) function of the gradient direction difference and hence are equivalent to the direction of gradient method. Our analysis is supported with experiments on both synthetic and real scenes}, keywords = {3D, conditions;lighting, cosine, difference;image, direction, filters;gradient, function;image, insensitive, intensity;lighting, recognition;image, recognition;lighting, scenes;Gaussian, segmentation;, variation;monotonic}, doi = {10.1109/ICCV.2005.179}, author = {Osadchy,M. and Jacobs, David W. and Lindenbaum,M.} } @article {14092, title = {The genome of the African trypanosome Trypanosoma brucei}, journal = {Science}, volume = {309}, year = {2005}, month = {2005///}, pages = {416 - 416}, author = {Berriman,M. and Ghedin,E. and Hertz-Fowler,C. and Blandin,G. and Renauld,H. and Bartholomeu,D. C and Lennard,N. J and Caler,E. and Hamlin,N. E and Haas,B. and others} } @article {19077, title = {The genome of the protist parasite Entamoeba histolytica}, journal = {Nature}, volume = {433}, year = {2005}, month = {2005}, pages = {865 - 868}, author = {Loftus,B. and Anderson,I. and Davies,R. and Alsmark,U. C.M and Samuelson,J. and Amedeo,P. and Roncaglia,P. and Berriman,M. and Hirt,R. P and Mann,B. J and others} } @article {14071, title = {The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease}, journal = {Science}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409.abstract}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {16291, title = {The Genome Sequence of Trypanosoma Cruzi, Etiologic Agent of Chagas Disease}, journal = {ScienceScience}, volume = {309}, year = {2005}, month = {2005/07/15/}, pages = {409 - 415}, abstract = {Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50\% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.1112631}, url = {http://www.sciencemag.org/content/309/5733/409}, author = {El-Sayed, Najib M. and Myler,Peter J. and Bartholomeu,Daniella C. and Nilsson,Daniel and Aggarwal,Gautam and Tran,Anh-Nhi and Ghedin,Elodie and Worthey,Elizabeth A. and Delcher,Arthur L. and Blandin,Ga{\"e}lle and Westenberger,Scott J. and Caler,Elisabet and Cerqueira,Gustavo C. and Branche,Carole and Haas,Brian and Anupama,Atashi and Arner,Erik and {\r A}slund,Lena and Attipoe,Philip and Bontempi,Esteban and Bringaud,Fr{\'e}d{\'e}ric and Burton,Peter and Cadag,Eithon and Campbell,David A. and Carrington,Mark and Crabtree,Jonathan and Darban,Hamid and da Silveira,Jose Franco and de Jong,Pieter and Edwards,Kimberly and Englund,Paul T. and Fazelina,Gholam and Feldblyum,Tamara and Ferella,Marcela and Frasch,Alberto Carlos and Gull,Keith and Horn,David and Hou,Lihua and Huang,Yiting and Kindlund,Ellen and Klingbeil,Michele and Kluge,Sindy and Koo,Hean and Lacerda,Daniela and Levin,Mariano J. and Lorenzi,Hernan and Louie,Tin and Machado,Carlos Renato and McCulloch,Richard and McKenna,Alan and Mizuno,Yumi and Mottram,Jeremy C. and Nelson,Siri and Ochaya,Stephen and Osoegawa,Kazutoyo and Pai,Grace and Parsons,Marilyn and Pentony,Martin and Pettersson,Ulf and Pop, Mihai and Ramirez,Jose Luis and Rinta,Joel and Robertson,Laura and Salzberg,Steven L. and Sanchez,Daniel O. and Seyler,Amber and Sharma,Reuben and Shetty,Jyoti and Simpson,Anjana J. and Sisk,Ellen and Tammi,Martti T. and Tarleton,Rick and Teixeira,Santuza and Van Aken,Susan and Vogt,Christy and Ward,Pauline N. and Wickstead,Bill and Wortman,Jennifer and White,Owen and Fraser,Claire M. and Stuart,Kenneth D. and Andersson,Bj{\"o}rn} } @article {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} } @article {15757, title = {HOPE: A Homotopy Optimization Method for Protein Structure Prediction}, journal = {Journal of Computational Biology}, volume = {12}, year = {2005}, month = {2005/12//}, pages = {1275 - 1288}, abstract = {We use a homotopy optimization method, HOPE, to minimize the potential energy associated with a protein model. The method uses the minimum energy conformation of one protein as a template to predict the lowest energy structure of a query sequence. This objective is achieved by following a path of conformations determined by a homotopy between the potential energy functions for the two proteins. Ensembles of solutions are produced by perturbing conformations along the path, increasing the likelihood of predicting correct structures. Successful results are presented for pairs of homologous proteins, where HOPE is compared to a variant of Newton{\textquoteright}s method and to simulated annealing.}, isbn = {1066-5277, 1557-8666}, doi = {10.1089/cmb.2005.12.1275}, url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2005.12.1275}, author = {Dunlavy,Daniel M. and O{\textquoteright}Leary, Dianne P. and Klimov,Dmitri and Thirumalai,D.} } @article {15155, title = {Identity-based zero-knowledge}, journal = {Security in Communication Networks}, year = {2005}, month = {2005///}, pages = {180 - 192}, abstract = {We introduce and define the notion of identity-based zero-knowledge, concentrating on the non-interactive setting. In this setting, our notion allows any prover to widely disseminate a proof of a statement while protecting the prover from plagiarism in the following sense: although proofs are transferable (i.e., publicly verifiable), they are also bound to the identity of the prover in a way which is recognizable to any verifier. Furthermore, an adversary is unable to change this identity (i.e., to claim the proof as his own, or to otherwise change the authorship), unless he could have proved the statement on his own.While we view the primary contribution of this work as a formal definition of the above notion, we also explore the relation of this notion to that of non-malleable (non-interactive) zero-knowledge. On the one hand, we show that these two notions are incomparable: that is, there are proof systems which are non-malleable but not identity-based, and vice versa. On the other hand, we show that a proof system of either type essentially implies a proof system of the other type. }, doi = {10.1007/978-3-540-30598-9_13}, author = {Katz, Jonathan and Ostrovsky,R. and Rabin,M.} } @article {14230, title = {Motion segmentation using occlusions}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {27}, year = {2005}, month = {2005/06//}, pages = {988 - 992}, abstract = {We examine the key role of occlusions in finding independently moving objects instantaneously in a video obtained by a moving camera with a restricted field of view. In this problem, the image motion is caused by the combined effect of camera motion (egomotion), structure (depth), and the independent motion of scene entities. For a camera with a restricted field of view undergoing a small motion between frames, there exists, in general, a set of 3D camera motions compatible with the observed flow field even if only a small amount of noise is present, leading to ambiguous 3D motion estimates. If separable sets of solutions exist, motion-based clustering can detect one category of moving objects. Even if a single inseparable set of solutions is found, we show that occlusion information can be used to find ordinal depth, which is critical in identifying a new class of moving objects. In order to find ordinal depth, occlusions must not only be known, but they must also be filled (grouped) with optical flow from neighboring regions. We present a novel algorithm for filling occlusions and deducing ordinal depth under general circumstances. Finally, we describe another category of moving objects which is detected using cardinal comparisons between structure from motion and structure estimates from another source (e.g., stereo).}, keywords = {3D motion estimation, algorithms, Artificial intelligence, CAMERAS, Computer vision, Filling, hidden feature removal, Image Enhancement, Image Interpretation, Computer-Assisted, image motion, Image motion analysis, Image segmentation, Layout, MOTION, Motion detection, Motion estimation, motion segmentation, Movement, Object detection, occlusion, occlusions, optical flow, ordinal depth, Pattern Recognition, Automated, Photography, Reproducibility of results, segmentation, Semiconductor device modeling, Sensitivity and Specificity, video analysis., Video Recording}, isbn = {0162-8828}, doi = {10.1109/TPAMI.2005.123}, author = {Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {14100, title = {Promoter architecture and response to a positive regulator of archaeal transcription}, journal = {Molecular Microbiology}, volume = {56}, year = {2005}, month = {2005/05/01/}, pages = {625 - 637}, abstract = {The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial-type effectors, especially activators, regulate a eukaryote-like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a {\textquoteleft}one-site{\textquoteright} minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.}, isbn = {1365-2958}, doi = {10.1111/j.1365-2958.2005.04563.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04563.x/abstract}, author = {Ouhammouch,Mohamed and Langham,Geoffrey E and Hausner,Winfried and Simpson,Anjana J. and El-Sayed, Najib M. and Geiduschek,E. Peter} } @article {15791, title = {QR Factorizations Using a Restricted Set of Rotations}, journal = {Electronic Transactions on Numerical Analysis}, volume = {21}, year = {2005}, month = {2005///}, pages = {20 - 27}, url = {http://etna.mcs.kent.edu/vol.21.2005/pp20-27.dir/pp20-27.pdfhttp://etna.mcs.kent.edu/vol.21.2005/pp20-27.dir/pp20-27.pdf}, author = {O{\textquoteright}Leary, Dianne P. and Bullock,Stephen S.} } @conference {11975, title = {Robust Contrast Invariant Stereo Correspondence}, booktitle = {Proceedings of the 2005 IEEE International Conference on Robotics and Automation, 2005. ICRA 2005}, year = {2005}, month = {2005/04/18/22}, pages = {819 - 824}, publisher = {IEEE}, organization = {IEEE}, abstract = {A stereo pair of cameras attached to a robot will inevitably yield images with different contrast. Even if we assume that the camera hardware is identical, due to slightly different points of view, the amount of light entering the two cameras is also different, causing dynamically adjusted internal parameters such as aperture, exposure and gain to be different. Due to the difficulty of obtaining and maintaining precise intensity or color calibration between the two cameras, contrast invariance becomes an extremely desirable property of stereo correspondence algorithms. The problem of achieving point correspondence between a stereo pair of images is often addressed by using the intensity or color differences as a local matching metric, which is sensitive to contrast changes. We present an algorithm for contrast invariant stereo matching which relies on multiple spatial frequency channels for local matching. A fast global framework uses the local matching to compute the correspondences and find the occlusions. We demonstrate that the use of multiple frequency channels allows the algorithm to yield good results even in the presence of significant amounts of noise.}, keywords = {Apertures, Calibration, CAMERAS, Computer science, contrast invariance, diffusion, Educational institutions, Frequency, gabor, Hardware, occlusions, Robot vision systems, Robotics and automation, Robustness, stereo}, isbn = {0-7803-8914-X}, doi = {10.1109/ROBOT.2005.1570218}, author = {Ogale, A. S and Aloimonos, J.} } @article {15088, title = {Secure remote authentication using biometric data}, journal = {Advances in Cryptology{\textendash}EUROCRYPT 2005}, year = {2005}, month = {2005///}, pages = {147 - 163}, abstract = {Biometric data offer a potential source of high-entropy, secret information that can be used in cryptographic protocols provided two issues are addressed: (1) biometric data are not uniformly distributed; and (2) they are not exactly reproducible. Recent work, most notably that of Dodis, Reyzin, and Smith, has shown how these obstacles may be overcome by allowing some auxiliary public information to be reliably sent from a server to the human user. Subsequent work of Boyen has shown how to extend these techniques, in the random oracle model, to enable unidirectional authentication from the user to the server without the assumption of a reliable communication channel.We show two efficient techniques enabling the use of biometric data to achieve mutual authentication or authenticated key exchange over a completely insecure (i.e., adversarially controlled) channel. In addition to achieving stronger security guarantees than the work of Boyen, we improve upon his solution in a number of other respects: we tolerate a broader class of errors and, in one case, improve upon the parameters of his solution and give a proof of security in the standard model. }, doi = {10.1007/11426639_9}, author = {Boyen,X. and Dodis,Y. and Katz, Jonathan and Ostrovsky,R. and Smith,A.} } @article {12057, title = {Shape and the stereo correspondence problem}, journal = {International Journal of Computer Vision}, volume = {65}, year = {2005}, month = {2005///}, pages = {147 - 162}, author = {Ogale, A. S and Aloimonos, J.} } @article {17841, title = {A simulation and data analysis system for large-scale, data-driven oil reservoir simulation studies}, journal = {Concurrency and Computation: Practice and Experience}, volume = {17}, year = {2005}, month = {2005///}, pages = {1441 - 1467}, author = {Kurc, T. and Catalyurek,U. and Zhang,X. and Saltz, J. and Martino,R. and Wheeler,M. and Peszy{\'n}ska,M. and Sussman, Alan and Hansen,C. and Sen,M. and others} } @article {13865, title = {Structural metadata and parsing speech}, year = {2005}, month = {2005///}, institution = {JHU Language Engineering Workshop}, author = {Harper,M. and Dorr, Bonnie J and Hale,J. and Roark,B. and Shafran,I. and Lease,M. and Liu,Y. and Snover,M. and Yung,L. and Krasnyanskaya,A. and others} } @inbook {14739, title = {Tagged Sets: A Secure and Transparent Coordination Medium}, booktitle = {Coordination Models and LanguagesCoordination Models and Languages}, series = {Lecture Notes in Computer Science}, volume = {3454}, year = {2005}, month = {2005///}, pages = {193 - 205}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {A simple and effective way of coordinating distributed, mobile, and parallel applications is to use a virtual shared memory (VSM), such as a Linda tuple-space. In this paper, we propose a new kind of VSM, called a tagged set . Each element in the VSM is a value with an associated tag, and values are read or removed from the VSM by matching the tag. Tagged sets exhibit three properties useful for VSMs: 1 Ease of use . A tagged value naturally corresponds to the notion that data has certain attributes, expressed by the tag, which can be used for later retrieval. 2 Flexibility . Tags are implemented as propositional logic formulae, and selection as logical implication, so the resulting system is quite powerful. Tagged sets naturally support a variety of applications, such as shared data repositories (e.g., for media or e-mail), message passing, and publish/subscribe algorithms; they are powerful enough to encode existing VSMs, such as Linda spaces. 3 Security . Our notion of tags naturally corresponds to keys, or capabilities: a user may not select data in the set unless she presents a legal key or keys. Normal tags correspond to symmetric keys, and we introduce asymmetric tags that correspond to public and private key pairs. Treating tags as keys permits users to easily specify protection criteria for data at a fine granularity. This paper motivates our approach, sketches its basic theory, and places it in the context of other data management strategies.}, isbn = {978-3-540-25630-4}, url = {http://dx.doi.org/10.1007/11417019_17}, author = {Oriol,Manuel and Hicks, Michael W.}, editor = {Jacquet,Jean-Marie and Picco,Gian} } @article {12932, title = {Temperature-Driven Campylobacter Seasonality in England and Wales}, journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.}, volume = {71}, year = {2005}, month = {2005/01/01/}, pages = {85 - 92}, abstract = {Campylobacter incidence in England and Wales between 1990 and 1999 was examined in conjunction with weather conditions. Over the 10-year interval, the average annual rate was determined to be 78.4 {\textpm} 15.0 cases per 100,000, with an upward trend. Rates were higher in males than in females, regardless of age, and highest in children less than 5 years old. Major regional differences were detected, with the highest rates in Wales and the southwest and the lowest in the southeast. The disease displayed a seasonal pattern, and increased campylobacter rates were found to be correlated with temperature. The most marked seasonal effect was observed for children under the age of 5. The seasonal pattern of campylobacter infections indicated a linkage with environmental factors rather than food sources. Therefore, public health interventions should not be restricted to food-borne approaches, and the epidemiology of the seasonal peak in human campylobacter infections may best be understood through studies in young children.}, isbn = {0099-2240, 1098-5336}, doi = {10.1128/AEM.71.1.85-92.2005}, url = {http://aem.asm.org/content/71/1/85}, author = {Louis,Val{\'e}rie R. and Gillespie,Iain A. and O{\textquoteright}Brien,Sarah J. and Russek-Cohen,Estelle and Pearson,Andrew D. and Rita R Colwell} } @article {15824, title = {Time reversal and n-qubit canonical decompositions}, journal = {Journal of Mathematical Physics}, volume = {46}, year = {2005}, month = {2005/05/17/}, pages = {062104-062104-19 - 062104-062104-19}, abstract = {On pure states of n quantum bits, the concurrence entanglement monotone returns the norm of the inner product of a pure state with its spin-flip. The monotone vanishes for n odd, but for n even there is an explicit formula for its value on mixed states, i.e., a closed-form expression computes the minimum over all ensemble decompositions of a given density. For n even a matrix decomposition ν = k1ak2 of the unitary group is explicitly computable and allows for study of the monotone{\textquoteright}s dynamics. The side factors k1 and k2 of this concurrence canonical decomposition (CCD) are concurrence symmetries, so the dynamics reduce to consideration of the a factor. This unitary a phases a basis of entangled states, and the concurrence dynamics of u are determined by these relative phases. In this work, we provide an explicit numerical algorithm computing ν = k1ak2 for n odd. Further, in the odd case we lift the monotone to a two-argument function. The concurrence capacity of ν according to the double argument lift may be nontrivial for n odd and reduces to the usual concurrence capacity in the literature for n even. The generalization may also be studied using the CCD, leading again to maximal capacity for most unitaries. The capacity of ν(x)I2 is at least that of ν, so odd-qubit capacities have implications for even-qubit entanglement. The generalizations require considering the spin-flip as a time reversal symmetry operator in Wigner{\textquoteright}s axiomatization, and the original Lie algebra homomorphism defining the CCD may be restated entirely in terms of this time reversal. The polar decomposition related to the CCD then writes any unitary evolution as the product of a time-symmetric and time-antisymmetric evolution with respect to the spin-flip. En route we observe a Kramers{\textquoteright} nondegeneracy: the existence of a nondegenerate eigenstate of any time reversal symmetric n-qubit Hamiltonian demands (i) n even and (ii) maximal concurrence of said eigenstate. We provide examples of how to apply this work to study the kinematics and dynamics of entanglement in spin chain Hamiltonians.}, isbn = {00222488}, doi = {doi:10.1063/1.1900293}, url = {http://jmp.aip.org/resource/1/jmapaq/v46/i6/p062104_s1}, author = {Bullock,Stephen S. and Brennen,Gavin K. and O{\textquoteright}Leary,Dianne P.} } @conference {14785, title = {Using Dynamic Tracing Sampling to Measure Long Running Programs}, booktitle = {Proceedings of the 2005 ACM/IEEE conference on Supercomputing}, series = {SC {\textquoteright}05}, year = {2005}, month = {2005///}, pages = {59{\textendash} - 59{\textendash}}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, abstract = {Detailed cache simulation can be useful to both system developers and application writers to understand an application{\textquoteright}s performance. However, measuring long running programs can be extremely slow. In this paper we present a technique to use dynamic sampling of trace snippets throughout an application{\textquoteright}s execution. We demonstrate that our approach improves accuracy compared to sampling a few timesteps at the beginning of execution by judiciously choosing the frequency, as well as the points in the control flow, at which samples are collected. Our approach is validated using the SIGMA tracing and simulation framework for the IBM Power family of processors.}, keywords = {data communications, design, experimentation, measurement, performance, tracing}, isbn = {1-59593-061-2}, doi = {http://dx.doi.org/10.1109/SC.2005.77}, url = {http://dx.doi.org/10.1109/SC.2005.77}, author = {Odom, Jeffrey and Hollingsworth, Jeffrey K and DeRose,Luiz and Ekanadham, Kattamuri and Sbaraglia, Simone} } @article {14263, title = {The Argus eye: a new imaging system designed to facilitate robotic tasks of motion}, journal = {IEEE Robotics \& Automation Magazine}, volume = {11}, year = {2004}, month = {2004/12//}, pages = {31 - 38}, abstract = {This article describes an imaging system that has been designed to facilitate robotic tasks of motion. The system consists of a number of cameras in a network, arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and, consequently, the estimation of shape models from the individual cameras. The reason is, inherent ambiguities of confusion between translation and rotation disappear. Pairs of cameras may also be arranged in multiple stereo configurations, which provide additional advantages for segmentation. Algorithms for the calibration of the system and the three-dimensional (3-D) motion estimation are provided.}, keywords = {Argus eye, Calibration, CAMERAS, computational geometry, Design automation, Eyes, image formation, imaging system, Information geometry, Layout, Motion estimation, multiple stereo configurations, panoramic robots, robot vision, Robot vision systems, robotic motion tasks, Robotics and automation, SHAPE, shape model estimation, system calibration}, isbn = {1070-9932}, doi = {10.1109/MRA.2004.1371606}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia} } @article {14167, title = {The Argus eye, a new tool for robotics}, journal = {IEEE Robotics and Automation Magazine}, volume = {11}, year = {2004}, month = {2004///}, pages = {31 - 38}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {13508, title = {Automatic recognition of spontaneous speech for access to multilingual oral history archives}, journal = {IEEE Transactions on Speech and Audio Processing, Special Issue on Spontaneous Speech Processing}, volume = {12}, year = {2004}, month = {2004/07//}, pages = {420 - 435}, abstract = {The MALACH project has the goal of developing the technologies needed to facilitate access to large collections of spontaneous speech. Its aim is to dramatically improve the state of the art in key Automatic Speech Recognition (ASR), Natural Language Processing (NLP) technologies for use in large-scale retrieval systems. The project leverages a unique collection of oral history interviews with survivors of the Holocaust that has been assembled and extensively annotated by the Survivors of the Shoah Visual History Foundation. This paper describes the collection, 116,000 hours of interviews in 32 languages, and the way in which system requirements have been discerned through user studies. It discusses ASR methods for very difficult speech (heavily accented, emotional, and elderly spontaneous speech), including transcription to create training data and methods for language modeling and speaker adaptation. Results are presented for for English and Czech. NLP results are presented for named entity tagging, topic segmentation, and supervised topic classification, and the architecture of an integrated search system that uses these results is described.}, author = {Byrne,W. and David Doermann and Franz,M. and Gustman,S. and Hajic,J. and Oard, Douglas and Picheny,M. and Psutka,J. and Ramabhadran,B.} } @conference {15901, title = {Building an information retrieval test collection for spontaneous conversational speech}, booktitle = {Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}04}, year = {2004}, month = {2004///}, pages = {41 - 48}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Test collections model use cases in ways that facilitate evaluation of information retrieval systems. This paper describes the use of search-guided relevance assessment to create a test collection for retrieval of spontaneous conversational speech. Approximately 10,000 thematically coherent segments were manually identified in 625 hours of oral history interviews with 246 individuals. Automatic speech recognition results, manually prepared summaries, controlled vocabulary indexing, and name authority control are available for every segment. Those features were leveraged by a team of four relevance assessors to identify topically relevant segments for 28 topics developed from actual user requests. Search-guided assessment yielded sufficient inter-annotator agreement to support formative evaluation during system development. Baseline results for ranked retrieval are presented to illustrate use of the collection.}, keywords = {assessment, Automatic speech recognition, oral history, search-guided relevance}, isbn = {1-58113-881-4}, doi = {10.1145/1008992.1009002}, url = {http://doi.acm.org/10.1145/1008992.1009002}, author = {Oard, Douglas and Soergel,Dagobert and David Doermann and Huang,Xiaoli and Murray,G. Craig and Wang,Jianqiang and Ramabhadran,Bhuvana and Franz,Martin and Gustman,Samuel and Mayfield,James and Kharevych,Liliya and Strassel,Stephanie} } @article {15345, title = {DNS of hypersonic turbulent boundary layers}, journal = {AIAA Paper}, volume = {2337}, year = {2004}, month = {2004///}, pages = {2004 - 2004}, author = {Martin, M.P and others} } @article {13771, title = {Extrinsic Evaluation of Automatic Metrics for Summarization}, year = {2004}, month = {2004/07/20/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This paper describes extrinsic-task evaluation of summarization. We show that it is possible to save time using summaries for relevance assessment without adversely impacting the degree of accuracy that would be possible with full documents. In addition, we demonstrate that the extrinsic task we have selected exhibits a high degree of interannotator agreement, i.e., consistent relevance decisions across subjects. We also conducted a composite experiment that better reflects the actual document selection process and found that using a surrogate improves the processing speed over reading the entire document. Finally, we have found a small yet statistically significant correlation between some of the intrinsic measures and a user{\textquoteright}s performance in an extrinsic task. The overall conclusion we can draw at this point is that ROUGE-1 does correlate with precision and to a somewhat lesser degree with accuracy, but that it remains to be investigated how stable these correlations are and how differences in ROUGE-1 translate into significant differences in human performance in an extrinsic task.}, keywords = {*ABSTRACTS, *ACCURACY, *DATA SUMMARIZATION, *DOCUMENT SUMMARIES, *DOCUMENTS, *READING MACHINES, *SOFTWARE METRICS, *STATISTICAL ANALYSIS, ABSTRACT SELECTION, ANNOTATIONS, Automation, COMPUTER PROGRAMMING AND SOFTWARE, COMPUTER SYSTEMS, CORRELATION TECHNIQUES, DATA PROCESSING, DOCUMENT SUMMARIES, EXTRINSIC TASKS, Information retrieval, INFORMATION SCIENCE, PERFORMANCE(HUMAN), PRECISION, RELEVANCY, ROUGE-1 COMPUTER PROGRAM, STATISTICS AND PROBABILITY, TEST AND EVALUATION}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA448065}, author = {Dorr, Bonnie J and Monz,Christof and Oard, Douglas and President,Stacy and Zajic, David and Schwartz,Richard} } @inbook {13787, title = {iCLEF 2003 at Maryland: Translation Selection and Document Selection}, booktitle = {Comparative Evaluation of Multilingual Information Access SystemsComparative Evaluation of Multilingual Information Access Systems}, series = {Lecture Notes in Computer Science}, volume = {3237}, year = {2004}, month = {2004///}, pages = {231 - 265}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {Maryland performed two sets of experiments for the 2003 Cross-Language Evaluation Forum{\textquoteright}s interactive track, one focused on interactive selection of appropriate translations for query terms, the second focused on interactive selection of relevant documents. Translation selection was supported using possible synonyms discovered through back translation and two techniques for generating KeyWord In Context (KWIC) examples of usage. The results indicate that searchers typically achieved a similar search effectiveness using fewer query iterations when interactive translation selection was available. For document selection, a complete extract of the first 40 words of each news story was compared to a compressed extract generated using an automated parse-and-trim approach that approximates one way in which people can produce headlines. The results indicate that compressed {\textquotedblleft}headlines{\textquotedblright} result in faster assessment, but with a 20\% relative reduction in the F α = 0.8 search effectiveness measure.}, isbn = {978-3-540-24017-4}, url = {http://dx.doi.org/10.1007/978-3-540-30222-3_42}, author = {Dorr, Bonnie J and He,Daqing and Luo,Jun and Oard, Douglas and Schwartz,Richard and Wang,Jianqiang and Zajic, David}, editor = {Peters,Carol and Gonzalo,Julio and Braschler,Martin and Kluck,Michael} } @article {15875, title = {iCLEF 2003 at Maryland: Translation selection and document selection}, journal = {Comparative Evaluation of Multilingual Information Access Systems}, year = {2004}, month = {2004///}, pages = {231 - 265}, author = {Dorr, Bonnie J and He,D. and Luo,J. and Oard, Douglas and Schwartz,R. and Wang,J. and Zajic, David} } @conference {15842, title = {iCLEF 2004 at Maryland: Summarization design for interactive cross-language question answering}, booktitle = {Proceeding of Cross Language Evaluation Forum (CLEF2004)}, year = {2004}, month = {2004///}, author = {He,D. and Wang,J. and Luo,J. and Oard, Douglas} } @article {15760, title = {Implementation of the regularized structured total least squares algorithms for blind image deblurring}, journal = {Linear Algebra and its Applications}, volume = {391}, year = {2004}, month = {2004/11/01/}, pages = {203 - 221}, abstract = {The structured total least squares (STLS) problem has been introduced to handle problems involving structured matrices corrupted by noise. Often the problem is ill-posed. Recently, regularization has been proposed in the STLS framework to solve ill-posed blind deconvolution problems encountered in image deblurring when both the image and the blurring function have uncertainty. The kernel of the regularized STLS (RSTLS) problem is a least squares problem involving Block{\textendash}Toeplitz{\textendash}Toeplitz{\textendash}Block matrices.In this paper an algorithm is described to solve this problem, based on a particular implementation of the generalized Schur Algorithm (GSA). It is shown that this new implementation improves the computational efficiency of the straightforward implementation of GSA from O(N2.5) to O(N2), where N is the number of pixels in the image. }, keywords = {Block Toeplitz matrix, Displacement rank, Generalized Schur algorithm, Image deblurring, Structured total least squares, Tikhonov regularization}, isbn = {0024-3795}, doi = {10.1016/j.laa.2004.07.006}, url = {http://www.sciencedirect.com/science/article/pii/S0024379504003362}, author = {Mastronardi,N. and Lemmerling,P. and Kalsi,A. and O{\textquoteright}Leary,D. P and Huffel,S. Van} } @conference {12034, title = {The influence of shape on image correspondence}, booktitle = {2nd International Symposium on 3D Data Processing, Visualization and Transmission, 2004. 3DPVT 2004. Proceedings}, year = {2004}, month = {2004/09/06/9}, pages = {945 - 952}, publisher = {IEEE}, organization = {IEEE}, abstract = {We examine the implications of shape on the process of finding dense correspondence and half-occlusions for a stereo pair of images. The desired property of the depth map is that it should be a piecewise continuous function which is consistent with the images and which has the minimum number of discontinuities. To zeroeth order, piecewise continuity becomes piecewise constancy. Using this approximation, we first discuss an approach for dealing with such a fronto-parallel shapeless world, and the problems involved therein. We then introduce horizontal and vertical slant to create a first order approximation to piecewise continuity. We highlight the fact that a horizontally slanted surface (ie. having depth variation in the direction of the separation of the two cameras) appears horizontally stretched in one image as compared to the other image. Thus, while corresponding two images, N pixels on a scanline in one image may correspond to a different number of pixels M in the other image, which has consequences with regard to sampling and occlusion detection. We also discuss the asymmetry between vertical and horizontal slant, and the central role of nonhorizontal edges in the context of vertical slant. Using experiments, we discuss cases where existing algorithms fail, and how the incorporation of new constraints provides correct results.}, keywords = {Automation, CAMERAS, Computational modeling, first order approximation, Geometrical optics, hidden feature removal, image sampling, Image segmentation, Layout, occlusion detection, piecewise continuous function, Pixel, SHAPE, Simulated annealing, stereo image processing, surface fitting}, isbn = {0-7695-2223-8}, doi = {10.1109/TDPVT.2004.1335418}, author = {Ogale, A. S and Aloimonos, J.} } @article {15850, title = {Interactive cross-language document selection}, journal = {information retrieval}, volume = {7}, year = {2004}, month = {2004///}, pages = {205 - 228}, author = {Oard, Douglas and Gonzalo,J. and Sanderson,M. and L{\'o}pez-Ostenero,F. and Wang,J.} } @article {13796, title = {Interlingual annotation of multilingual text corpora}, journal = {Proceedings of the North American Chapter of the Association for Computational Linguistics Workshop on Frontiers in Corpus Annotation}, year = {2004}, month = {2004///}, pages = {55 - 62}, abstract = {This paper describes a multi-site project toannotate six sizable bilingual parallel corpora for interlingual content. After presenting the background and objectives of the effort, we describe the data set that is being annotated, the interlingua representation language used, an interface environment that supports the an- notation task and the annotation process itself. We will then present a preliminary version of our evaluation methodology and conclude with a summary of the current status of the project along with a number of issues which have arisen. }, author = {Farwell,D. and Helmreich,S. and Dorr, Bonnie J and Habash,N. and Reeder,F. and Miller,K. and Levin,L. and Mitamura,T. and Hovy,E. and Rambow,O. and others} } @inbook {15766, title = {Left-Brain/Right-Brain Multi-Document Summarization}, booktitle = {DUC 04 Conference ProceedingsDUC 04 Conference Proceedings}, year = {2004}, month = {2004///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, url = {\tt http://duc.nist.gov/}, author = {Conroy,John M. and Schlesinger,Judith D. and Goldstein,Jade and O{\textquoteright}Leary, Dianne P.} } @article {15861, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, journal = {Computer Speech \& Language}, volume = {18}, year = {2004}, month = {2004/04//}, pages = {163 - 179}, abstract = {This paper describes the Mandarin{\^a}{\texteuro}{\textquotedblleft}English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English{\^a}{\texteuro}{\textquotedblleft}Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence, this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks {\^a}{\texteuro}{\textquotedblleft} multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {English{\^a}{\texteuro}{\textquotedblleft}Chinese cross-language spoken document retrieval, Multi-scale spoken document retrieval}, isbn = {0885-2308}, doi = {10.1016/j.csl.2003.09.003}, url = {http://www.sciencedirect.com/science/article/pii/S0885230803000524}, author = {Meng,Helen M. and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @article {16122, title = {Project portfolio earned value management using treemaps}, journal = {Proceedings of the Project Management Institute Research Conference}, year = {2004}, month = {2004///}, abstract = {Project portfolio management deals with organizing and managing a set of projects in anorganization. Each organization has its own way of managing the portfolio that meets its business goals. One of the main challenges is to track project performance across the entire portfolio in a timely and effective manner. It allows managers to diagnose performance trends and identify projects in need of attention, giving them the opportunity to take management action in a timely fashion. In this paper, we investigate the use of Earned Value Management (EVM) for tracking project performance across the portfolio, and explore the benefits of an interactive visualization technique called Treemaps to display project performance metrics for the entire portfolio on a single screen. }, author = {Cable,J. H and Ordonez,J. F and Chintalapani,G. and Plaisant, Catherine} } @article {15794, title = {Reconstructing Images of Bar Codes for Construction Site Object Recognition}, journal = {Automation in Construction (Elsevier)}, volume = {13}, year = {2004}, month = {2004///}, pages = {21 - 35}, author = {Gilsinn,David E. and Cheok,Geraldine S. and O{\textquoteright}Leary, Dianne P.} } @article {14253, title = {Robotics \& Automation Magazine Vol. 11}, journal = {IEEE Robotics \& Automation Magazine}, year = {2004}, month = {2004///}, pages = {132 - 132}, author = {Aliaga, D.G. and Allen,PK and Archibald,JK and Argyros,AA and Arkin,RC and Baker,C. and Baker, P. and Beard,RW and Bicchi,A. and Birgmajer,B. and others} } @article {15086, title = {Round-optimal secure two-party computation}, journal = {Advances in Cryptology{\textendash}CRYPTO 2004}, year = {2004}, month = {2004///}, pages = {3 - 34}, abstract = {We consider the central cryptographic task of secure two-party computation: two parties wish to compute some function of their private inputs (each receiving possibly different outputs) where security should hold with respect to arbitrarily-malicious behavior of either of the participants. Despite extensive research in this area, the exact round-complexity of this fundamental problem (i.e., the number of rounds required to compute an arbitrary poly-time functionality) was not previously known.Here, we establish the exact round complexity of secure two-party computation with respect to black-box proofs of security. We first show a lower bound establishing (unconditionally) that four rounds are not sufficient to securely compute the coin-tossing functionality for any super-logarithmic number of coins; this rules out 4-round protocols for other natural functionalities as well. Next, we construct protocols for securely computing any (randomized) functionality using only five rounds. Our protocols may be based either on certified trapdoor permutations or homomorphic encryption schemes satisfying certain additional properties. The former assumption is implied by, e.g., the RSA assumption for large public exponents, while the latter is implied by, e.g., the DDH assumption. Finally, we show how our protocols may be modified {\textendash} without increasing their round complexity and without requiring erasures {\textendash} to tolerate an adaptive malicious adversary. }, doi = {10.1007/978-3-540-28628-8_21}, author = {Katz, Jonathan and Ostrovsky,R.} } @article {13854, title = {Semantic annotation and lexico-syntactic paraphrase}, journal = {Proceedings of the 4th International Conference on Language Resources and Evaluation (LREC) Workshop on Building Lexical Resources from Semantically Annotated Corpora}, year = {2004}, month = {2004///}, pages = {47 - 52}, abstract = {The IAMTC project (Interlingual Annotation of Multilingual Translation Corpora) is developing an interlingual representation frameworkfor annotation of parallel corpora (English paired with Arabic, French, Hindi, Japanese, Korean, and Spanish) with deep-semantic representations. In particular, we are investigating meaning equivalent paraphrases involving conversives and non-literal language use, as well as extended paraphrases involving syntax, lexicon, and grammatical features. The interlingua representation has three levels of depth. Each level is characterized by the types of meaning equivalent paraphrases that receive identical representations at that level. }, author = {Dorr, Bonnie J and Green,R. and Levin,L. and Rambow,O. and Farwell,D. and Habash,N. and Helmreich,S. and Hovy,E. and Miller,K.J. and Mitamura,T. and others} } @article {13855, title = {Semantic Annotation for Interlingual Representation of Multilingual Texts}, journal = {Workshop Programme}, year = {2004}, month = {2004///}, pages = {19 - 19}, abstract = {This paper describes the annotation process being used in a multi-site project to create six sizable bilingual parallel corpora annotated with a consistent interlingua representation. After presenting the background and objectives of the effort, we describe the multilingual corpora and the three stages of interlingual representation being developed. We then focus on the annotation process itself, including an interface environment that supports the annotation task, and the methodology for evaluating the interlingua representation. Finally, we discuss some issues encountered during the annotation tasks. The resulting annotated multilingual corpora will be useful for a wide range of natural language processing research tasks, including machine translation, question answering, text summarization, and information extraction.}, author = {Mitamura,T. and Miller,K. and Dorr, Bonnie J and Farwell,D. and Habash,N. and Helmreich,S. and Hovy,E. and Levin,L. and Rambow,O. and Reeder,F. and others} } @article {17657, title = {SESSION 2: STREAMING}, journal = {Proceedings of the 14th International Workshop on Network and Operating Systems Support for Digital Audio and Video: NOSSDAV 2003: June 16-18, 2004, Cork, Ireland}, year = {2004}, month = {2004///}, pages = {3 - 3}, author = {Banerjee,S. and Lee,S. and Braud,R. and Bhattacharjee, Bobby and Srinivasan, Aravind and Chu,Y. and Zhang,H. and Sinha,R. and Papadopoulos,C. and Boustead,P. and others} } @conference {11951, title = {Stereo Correspondence with Slanted Surfaces: Critical Implications of Horizontal Slant}, booktitle = {Computer Vision and Pattern Recognition, IEEE Computer Society Conference on}, volume = {1}, year = {2004}, month = {2004///}, pages = {568 - 573}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, abstract = {We examine the stereo correspondence problem in the presence of slanted scene surfaces. In particular, we highlight a previously overlooked geometric fact: a horizontally slanted surface (i.e. having depth variation in the direction of the separation of the two cameras) will appear horizontally stretched in one image as compared to the other image. Thus, while corresponding two images, N pixels on a scanline in one image may correspond to a different number of pixels M in the other image. This leads to three important modifications to existing stereo algorithms: (a) due to unequal sampling, intensity matching metrics such as the popular Birchfield-Tomasi procedure must be modified, (b) unequal numbers of pixels in the two images must be allowed to correspond to each other, and (c) the uniqueness constraint, which is often used for detecting occlusions, must be changed to a 3D uniqueness constraint. This paper discusses these new constraints and provides a simple scanline based matching algorithm for illustration. We experimentally demonstrate test cases where existing algorithms fail, and how the incorporation of these new constraints provides correct results. Experimental comparisons of the scanline based algorithm with standard data sets are also provided.}, doi = {http://doi.ieeecomputersociety.org/10.1109/CVPR.2004.241}, author = {Ogale, Abhijit S. and Aloimonos, J.} } @conference {15877, title = {Transforming access to the spoken word}, booktitle = {Proceedings of the International Symposium on Large-scale Knowledge Resources}, year = {2004}, month = {2004///}, pages = {57 - 59}, author = {Oard, Douglas} } @article {14851, title = {Whitening for photometric comparison of smooth surfaces under varying illumination}, journal = {Computer Vision-ECCV 2004}, year = {2004}, month = {2004///}, pages = {217 - 228}, abstract = {We consider the problem of image comparison in order to match smooth surfaces under varying illumination. In a smooth surface nearby surface normals are highly correlated. We model such surfaces as Gaussian processes and derive the resulting statistical characterization of the corresponding images. Supported by this model, we treat the difference between two images, associated with the same surface and different lighting, as colored Gaussian noise, and use the whitening tool from signal detection theory to construct a measure of difference between such images. This also improves comparisons by accentuating the differences between images of different surfaces. At the same time, we prove that no linear filter, including ours, can produce lighting insensitive image comparisons. While our Gaussian assumption is a simplification, the resulting measure functions well for both synthetic and real smooth objects. Thus we improve upon methods for matching images of smooth objects, while providing insight into the performance of such methods. Much prior work has focused on image comparison methods appropriate for highly curved surfaces. We combine our method with one of these, and demonstrate high performance on rough and smooth objects.}, doi = {10.1007/978-3-540-24673-2_18}, author = {Osadchy,M. and Lindenbaum,M. and Jacobs, David W.} } @article {14578, title = {Whole-genome shotgun assembly and comparison of human genome assemblies}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, year = {2004}, month = {2004///}, pages = {1916 - 1916}, author = {Istrail,S. and Sutton,G. G and Florea,L. and Halpern,A. L and Mobarry,C. M and Lippert,R. and Walenz,B. and Shatkay,H. and Dew,I. and Miller,J. R and others} } @article {14066, title = {2003 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics October 19-22, 2003, New Paltz. NY}, journal = {2003 IEEE Workshop on Applications of Signal Processing to Audio and Acoustics: October 19-22, 2003, Mohonk Mountain House, New Paltz, NY, USA}, year = {2003}, month = {2003///}, pages = {238 - 238}, author = {Adams,N. and EssI,G. and Makino,S. and Martens,A.A.C.F.W.L. and Algazi,R. and Fellers,M. and Martin,R. and Avendano,C. and Fielder,L. and Mellody,M. and others} } @article {15721, title = {Blind Deconvolution Using a Regularized Structured Total Least Norm Approach}, journal = {SIAM J. on Matrix Analysis and Applications}, volume = {24}, year = {2003}, month = {2003///}, pages = {1018 - 1037}, url = {http://epubs.siam.org/sam-bin/dbq/article/39544http://epubs.siam.org/sam-bin/dbq/article/39544}, author = {Pruessner,Armin and O{\textquoteright}Leary, Dianne P.} } @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} } @inbook {15728, title = {Clustering and Summarizing Medline Abstracts}, booktitle = {BISTI 2003 Symposium on Digital Biology: The Emerging ParadigmBISTI 2003 Symposium on Digital Biology: The Emerging Paradigm}, year = {2003}, month = {2003///}, publisher = {U.S. National Institutes of Health Biomedical Information Science and Technology Initiative (BISTI)}, organization = {U.S. National Institutes of Health Biomedical Information Science and Technology Initiative (BISTI)}, author = {Dunlavy,Daniel M. and Conroy,John M. and O{\textquoteright}Leary,Timothy J and O{\textquoteright}Leary, Dianne P.} } @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.} } @article {14110, title = {Complete stagnation of}, journal = {Linear Algebra and its Applications}, volume = {367}, year = {2003}, month = {2003/07/01/}, pages = {165 - 183}, abstract = {We study problems for which the iterative method for solving linear systems of equations makes no progress in its initial iterations. Our tool for analysis is a nonlinear system of equations, the stagnation system, that characterizes this behavior. We focus on complete stagnation, for which there is no progress until the last iteration. We give necessary and sufficient conditions for complete stagnation of systems involving unitary matrices, and show that if a normal matrix completely stagnates then so does an entire family of nonnormal matrices with the same eigenvalues. Finally, we show that there are real matrices for which complete stagnation occurs for certain complex right-hand sides but not for real ones.}, keywords = {Convergence, GMRES, iterative methods, Stagnation}, isbn = {0024-3795}, doi = {16/S0024-3795(02)00612-2}, url = {http://www.sciencedirect.com/science/article/pii/S0024379502006122}, author = {Zavorin, Ilya and O{\textquoteright}Leary, Dianne P. and Elman, Howard} } @article {15730, title = {Complete stagnation of GMRES}, journal = {Linear Algebra and its Applications}, volume = {367}, year = {2003}, month = {2003/07/01/}, pages = {165 - 183}, abstract = {We study problems for which the iterative method gmres for solving linear systems of equations makes no progress in its initial iterations. Our tool for analysis is a nonlinear system of equations, the stagnation system, that characterizes this behavior. We focus on complete stagnation, for which there is no progress until the last iteration. We give necessary and sufficient conditions for complete stagnation of systems involving unitary matrices, and show that if a normal matrix completely stagnates then so does an entire family of nonnormal matrices with the same eigenvalues. Finally, we show that there are real matrices for which complete stagnation occurs for certain complex right-hand sides but not for real ones.}, keywords = {Convergence, GMRES, iterative methods, Stagnation}, isbn = {0024-3795}, doi = {10.1016/S0024-3795(02)00612-2}, url = {http://www.sciencedirect.com/science/article/pii/S0024379502006122}, author = {Zavorin, Ilya and O{\textquoteright}Leary,Dianne P. and Elman, Howard} } @article {13754, title = {Desparately seeking cebuano}, journal = {Third Conference on Human Language Technologies}, year = {2003}, month = {2003///}, abstract = {This paper describes an effort to rapidly de-velop language resources and component tech- nology to support searching Cebuano news sto- ries using English queries. Results from the first 60 hours of the exercise are presented. }, author = {Oard, Douglas and David Doermann and Dorr, Bonnie J and He,D. and Resnik, Philip and Weinberg, Amy and Byrne,W. and Khudanpur,S. and Yarowsky,D. and Leuski,A. and others} } @article {19078, title = {The dog genome: survey sequencing and comparative analysis}, journal = {Science}, volume = {301}, year = {2003}, month = {2003}, author = {Kirkness,E. F and Bafna,V. and Halpern,A. L and Levy,S. and Remington,K. and Rusch,D. B and Delcher,A. L and Pop, Mihai and Wang,W. and Fraser,C. M and others} } @article {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} } @conference {15840, title = {The effect of bilingual term list size on dictionary-based cross-language information retrieval}, booktitle = {Proceedings of the 36th Annual Hawaii International Conference on System Sciences, 2003}, year = {2003}, month = {2003/01/06/9}, publisher = {IEEE}, organization = {IEEE}, abstract = {Bilingual term lists are extensively used as a resource for dictionary-based cross-language information retrieval (CLIR), in which the goal is to find documents written in one natural language based on queries that are expressed in another. This paper identifies eight types of terms that affect retrieval effectiveness in CLIR applications through their coverage by general-purpose bilingual term lists, and reports results from an experimental evaluation of the coverage of 35 bilingual term lists in news retrieval application. Retrieval effectiveness was found to be strongly influenced by term list size for lists that contain between 3,000 and 30,000 unique terms per language. Supplemental techniques for named entity translation were found to be useful with even the largest lexicons. The contribution of named-entity translation was evaluated in a cross-language experiment involving English and Chinese. Smaller effects were observed from deficiencies in the coverage of domain-specific terminology when searching news stories.}, keywords = {bilingual term list, Chinese language, Computer science, Control systems, Cross-language information retrieval, data mining, Dictionaries, dictionary-based information retrieval, Educational institutions, English language, Frequency, Information retrieval, language translation, named-entity translation, natural languages, Surface morphology, Terminology}, isbn = {0-7695-1874-5}, doi = {10.1109/HICSS.2003.1174250}, author = {Demner-Fushman,D. and Oard, Douglas} } @conference {15143, title = {Forward secrecy in password-only key exchange protocols}, booktitle = {Proceedings of the 3rd international conference on Security in communication networks}, series = {SCN{\textquoteright}02}, year = {2003}, month = {2003///}, pages = {29 - 44}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, abstract = {Password-only authenticated key exchange (PAKE) protocols are designed to be secure even when users choose short, easily-guessed passwords. Security requires, in particular, that the protocol cannot be broken by an off-line dictionary attack in which an adversary enumerates all possible passwords in an attempt to determine the correct one based on previously-viewed transcripts. Recently, provably-secure protocols for PAKE were given in the idealized random oracle/ideal cipher models [2,8,19] and in the standard model based on general assumptions [11] or the DDH assumption [14]. The latter protocol (the KOY protocol) is currently the only known practical solution based on standard assumptions. However, only a proof of basic security for this protocol has appeared. In the basic setting the adversary is assumed not to corrupt clients (thereby learning their passwords) or servers (thereby modifying the value of stored passwords). Simplifying and unifying previous work, we present a natural definition of security which incorporates the more challenging requirement of forward secrecy. We then demonstrate via an explicit attack that the KOY protocol as originally presented is not secure under this definition. This provides the first natural example showing that forward secrecy is a strictly stronger requirement for PAKE protocols. Finally, we present a slight modification of the KOY protocol which prevents the attack and - as the main technical contribution of this paper - rigorously prove that the modified protocol achieves forward secrecy.}, isbn = {3-540-00420-3}, url = {http://dl.acm.org/citation.cfm?id=1766811.1766816}, author = {Katz, Jonathan and Ostrovsky,Rafail and Yung,Moti} } @article {17185, title = {HCIL Technical Report Listing (1993-2002)}, journal = {The craft of information visualization: readings and reflections}, volume = {27}, year = {2003}, month = {2003///}, pages = {393 - 393}, author = {Ceaparu,I. and Druin, Allison and Guimbretiere,F. and Manipulation,D. and Shneiderman, Ben and Westerlurid,B. and Keogh,E. and Hochheiser,H. and Shrieidemian,B. and Shneidemiari,B. and others} } @article {16301, title = {ICSE workshop on remote analysis and measurement of software systems (RAMSS)}, journal = {ACM SIGSOFT Software Engineering NotesSIGSOFT Softw. Eng. Notes}, volume = {28}, year = {2003}, month = {2003/11//}, pages = {10 - 10}, isbn = {01635948}, doi = {10.1145/966221.966232}, url = {http://dl.acm.org/citation.cfm?id=966232}, author = {Orso,Alessandro and Porter, Adam} } @article {12190, title = {The International Children{\textquoteright}s Digital Library}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {13928, title = {The International Children{\textquoteright}s Digital Library: Description and analysis of first use}, journal = {First Monday}, volume = {8}, year = {2003}, month = {2003///}, pages = {315 - 315}, author = {Druin, Allison and Bederson, Benjamin B. and Weeks,A. and Farber,A. and Grosjean,J. and Guha,M.L. and Hourcade,J. P and Lee,J. and Liao,S. and Reuter,K. and others} } @article {15769, title = {Machine and Human Performance for Single- and Multi-Document Summarization}, journal = {IEEE Intelligent Systems (special issue on Natural Language Processing)}, volume = {18}, year = {2003}, month = {2003///}, pages = {46 - 54}, url = {http://csdl.computer.org/comp/mags/ex/2003/01/x1toc.htmhttp://csdl.computer.org/comp/mags/ex/2003/01/x1toc.htm}, author = {Schlesinger,Judith D. and Conroy,John M. and Okurowski,Mary Ellen and O{\textquoteright}Leary, Dianne P.} } @article {15847, title = {Making miracles: Interactive translingual search for cebuano and hindi}, journal = {ACM Transactions on Asian Language Information Processing (TALIP)}, volume = {2}, year = {2003}, month = {2003///}, pages = {219 - 244}, author = {He,D. and Oard, Douglas and Wang,J. and Luo,J. and Demner-Fushman,D. and Darwish,K. and Resnik, Philip and Khudanpur,S. and Nossal,M. and Subotin,M. and others} } @conference {14235, title = {New eyes for robotics}, booktitle = {2003 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2003. (IROS 2003). Proceedings}, volume = {1}, year = {2003}, month = {2003/10/27/31}, pages = {1018- 1023 vol.1 - 1018- 1023 vol.1}, publisher = {IEEE}, organization = {IEEE}, abstract = {This paper describes an imaging system that has been designed to facilitate robotic tasks of motion. The system consists of a number of cameras in a network arranged so that they sample different parts of the visual sphere. This geometric configuration has provable advantages compared to small field of view cameras for the estimation of the system{\textquoteright}s own motion and consequently the estimation of shape models from the individual cameras. The reason is that inherent ambiguities of confusion between translation and rotation disappear. Pairs of cameras may also be arranged in multiple stereo configurations which provide additional advantages for segmentation. Algorithms for the calibration of the system and the 3D motion estimation are provided.}, keywords = {3D motion estimation, Argus eye, array signal processing, Birds, Calibration, CAMERAS, Control systems, Eyes, geometric configuration, imaging, imaging system, Layout, Motion estimation, multiple stereo configurations, Robot kinematics, robot vision, Robot vision systems, ROBOTICS, Robotics and automation, SHAPE, shape models}, isbn = {0-7803-7860-1}, doi = {10.1109/IROS.2003.1250761}, author = {Baker, P. and Ogale, A. S and Ferm{\"u}ller, Cornelia and Aloimonos, J.} } @article {13622, title = {Parsing and Tagging of Bilingual Dictionaries}, journal = {TALTraitement Automatique Des Langues}, volume = {44}, year = {2003}, month = {2003///}, pages = {125 - 150}, abstract = {Bilingual dictionaries hold great potential as a source of lexical resources for training and testing automated systems for optical character recognition, machine translation, and cross-language information retrieval. In this paper, we describe a system for extracting term lexicons from printed bilingual dictionaries. Our work was divided into three phases - dictionary segmentation, entry tagging, and generation. In segmentation, pages are divided into logical entries based on structural features learned from selected examples. The extracted entries are associated with functional labels and passed to a tagging module which associates linguistic labels with each word or phrase in the entry. The output of the system is a structure that represents the entries from the dictionary. We have used this approach to parse a variety of dictionaries with both Latin and non-Latin alphabets, and demonstrate the results of term lexicon generation for retrieval from a collection of French news stories using English queries.}, author = {Ma,Huanfeng and Karagol-Ayan,Burcu and David Doermann and Oard, Douglas and Wang,Jianqiang} } @inbook {15786, title = {Performance of a Three-Stage System for Multi-Document Summarization}, booktitle = {DUC 03 Conference ProceedingsDUC 03 Conference Proceedings}, year = {2003}, month = {2003///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, url = {http://duc.nist.gov/http://duc.nist.gov/}, author = {Dunlavy,Daniel M. and Conroy,John M. and Schlesinger,Judith D. and Goodman,Sarah A. and Okurowski,Mary Ellen and O{\textquoteright}Leary, Dianne P. and Halteren,Hans van} } @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} } @conference {15894, title = {Probabilistic structured query methods}, booktitle = {Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval}, series = {SIGIR {\textquoteright}03}, year = {2003}, month = {2003///}, pages = {338 - 344}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Structured methods for query term replacement rely on separate estimates of term tes of replacement probabilities. Statistically significantfrequency and document frequency to compute a weight for each query term. This paper reviews prior work on structured query techniques and introduces three new variants that leverage estima improvements in retrieval effectiveness are demonstrated for cross-language retrieval and for retrieval based on optical character recognition when replacement probabilities are used to estimate both term frequency and document frequency.}, keywords = {arabic, CLIR, OCR, structured queries, term replacement}, isbn = {1-58113-646-3}, doi = {10.1145/860435.860497}, url = {http://doi.acm.org/10.1145/860435.860497}, author = {Darwish,Kareem and Oard, Douglas} } @conference {15868, title = {Rapid-response machine translation for unexpected languages}, booktitle = {Proceedings of the MT Summit IX}, year = {2003}, month = {2003///}, author = {Oard, Douglas and Och,F.J.} } @conference {15140, title = {Round efficiency of multi-party computation with a dishonest majority}, booktitle = {Proceedings of the 22nd international conference on Theory and applications of cryptographic techniques}, series = {EUROCRYPT{\textquoteright}03}, year = {2003}, month = {2003///}, pages = {578 - 595}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {Berlin, Heidelberg}, abstract = {We consider the round complexity of multi-party computation in the presence of a static adversary who controls a majority of the parties. Here, n players wish to securely compute some functionality and up to n - 1 of these players may be arbitrarily malicious. Previous protocols for this setting (when a broadcast channel is available) require O(n) rounds. We present two protocols with improved round complexity: The first assumes only the existence of trapdoor permutations and dense cryptosystems, and achieves round complexity O(log n) based on a proof scheduling technique of Chor and Rabin [13]; the second requires a stronger hardness assumption (along with the non-black-box techniques of Barak [2]) and achieves O(1) round complexity.}, isbn = {3-540-14039-5}, url = {http://dl.acm.org/citation.cfm?id=1766171.1766222}, author = {Katz, Jonathan and Ostrovsky,Rafail and Smith,Adam} } @article {15803, title = {Scaling symmetric positive definite matrices to prescribed row sums}, journal = {Linear Algebra and its Applications}, volume = {370}, year = {2003}, month = {2003/09/01/}, pages = {185 - 191}, abstract = {We give a constructive proof of a theorem of Marshall and Olkin that any real symmetric positive definite matrix can be symmetrically scaled by a positive diagonal matrix to have arbitrary positive row sums. We give a slight extension of the result, showing that given a sign pattern, there is a unique diagonal scaling with that sign pattern, and we give upper and lower bounds on the entries of the scaling matrix.}, keywords = {Diagonal preconditioning, Homotopy, Matrix scaling, Positive definite matrices}, isbn = {0024-3795}, doi = {10.1016/S0024-3795(03)00387-2}, url = {http://www.sciencedirect.com/science/article/pii/S0024379503003872}, author = {O{\textquoteright}Leary,Dianne P.} } @article {15839, title = {Searching large collections of recorded speech: A preliminary study}, journal = {Proceedings of the American Society for Information Science and Technology}, volume = {40}, year = {2003}, month = {2003///}, pages = {330 - 339}, author = {Kim,J. and Oard, Douglas and Soergel,D.} } @conference {15846, title = {Searching recorded speech based on the temporal extent of topic labels}, booktitle = {AAAI Spring Symposium on Intelligent Multimedia Knowledge Management}, year = {2003}, month = {2003///}, abstract = {Recorded speech poses unusual challenges for the de- sign of interactive end-user search systems. Automatic speech recognition is sufficiently accurate to support the automated components of interactive search sys- tems in some applications, but finding useful recordings among those nominated by the system can be difficult because listening to audio is time consuming and be- cause recognition errors and speech disfluencies make it difficult to mitigate that effect by skimming automatic transcripts. Support for rapid browsing based on su- pervised learning for automatic classification has shown promise, however, and a segment-then-label framework has emerged as the dominant paradigm for applying that technique to news broadcasts. This paper argues for a more general framework, which we call an activation matrix, that provides a flexible representation for the mapping between labels and time. Three approaches to the generation of activation matrices are briefly de- scribed, with the main focus of the paper then being the use of activation matrices to support search and selec- tion in interactive systems.}, author = {Oard, Douglas and Leuski,A.} } @article {14104, title = {The sequence and analysis of Trypanosoma brucei chromosome II}, journal = {Nucleic acids research}, volume = {31}, year = {2003}, month = {2003///}, pages = {4856 - 4856}, author = {El-Sayed, Najib M. and Ghedin,E. and Song,J. and MacLeod,A. and Bringaud,F. and Larkin,C. and Wanless,D. and Peterson,J. and Hou,L. and Taylor,S. and others} } @article {15953, title = {Seven days in the life of a robotic agent}, journal = {Innovative Concepts for Agent-Based Systems}, year = {2003}, month = {2003///}, pages = {243 - 256}, author = {Chong,W. and O{\textquoteright}Donovan-Anderson,M. and Okamoto,Y. and Perlis, Don} } @article {15844, title = {The surprise language exercises}, journal = {ACM Transactions on Asian Language Information Processing}, volume = {2}, year = {2003}, month = {2003/06/01/}, pages = {79 - 84}, isbn = {15300226}, doi = {10.1145/974740.974741}, url = {http://dl.acm.org/citation.cfm?id=974741}, author = {Oard, Douglas} } @article {13657, title = {Tagging and Parsing of Bilingual Dictionary}, volume = {LAMP-TR-106,CFAR-TR-991,CS-TR-4529,UMIACS-TR-2003-97}, year = {2003}, month = {2003/09//}, institution = {University of Maryland, College Park}, abstract = {Bilingual dictionaries hold great potential as a source of lexical resources for training and testing automated systems for optical character recognition, machine translation, and cross-language information retrieval. In this paper, we describe a system for extracting term lexicons from printed bilingual dictionaries. Our work was divided into three phases - dictionary segmentation, entry tagging, and generation. In segmentation, pages are divided into logical entries based on structural features learned from selected examples. The extracted entries are associated with functional labels and passed to a tagging module which associates linguistic labels with each word or phrase in the entry. The output of the system is a structure that represents the entries from the dictionary. We have used this approach to parse a variety of dictionaries with both Latin and non-Latin alphabets, and demonstrate the results of term lexicon generation for retrieval from a collection of French news stories using English queries.}, author = {Ma,Huanfeng and Karagol-Ayan,Burcu and David Doermann and Oard, Douglas and Wang,Jianqiang} } @conference {14858, title = {Using specularities for recognition}, booktitle = {Computer Vision, 2003. Proceedings. Ninth IEEE International Conference on}, year = {2003}, month = {2003/10//}, pages = {1512 -1519 vol.2 - 1512 -1519 vol.2}, abstract = {Recognition systems have generally treated specular highlights as noise. We show how to use these highlights as a positive source of information that improves recognition of shiny objects. This also enables us to recognize very challenging shiny transparent objects, such as wine glasses. Specifically, we show how to find highlights that are consistent with a hypothesized pose of an object of known 3D shape. We do this using only a qualitative description of highlight formation that is consistent with most models of specular reflection, so no specific knowledge of an object{\textquoteright}s reflectance properties is needed. We first present a method that finds highlights produced by a dominant compact light source, whose position is roughly known. We then show how to estimate the lighting automatically for objects whose reflection is part specular and part Lambertian. We demonstrate this method for two classes of objects. First, we show that specular information alone can suffice to identify objects with no Lambertian reflectance, such as transparent wine glasses. Second, we use our complete system to recognize shiny objects, such as pottery.}, keywords = {3D, formation;object, glass;computer, image, information;specular, light, measurement;reflection;stereo, objects;specular, objects;wine, processing;, property;pottery;recognition, recognition;object, recognition;position, reflectance, reflection;compact, reflection;transparent, shape;Lambertian, source;highlight, systems;shiny, vision;lighting;object}, doi = {10.1109/ICCV.2003.1238669}, author = {Osadchy,M. and Jacobs, David W. and Ramamoorthi,R.} } @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 {13729, title = {Automatic transcription of Czech language oral history in the MALACH project: resources and initial experiments}, booktitle = {Proceedings of the The 5th International Conference on Text, Speech and Dialogue}, year = {2002}, month = {2002///}, pages = {57 - 64}, author = {Oard, Douglas and Demner-Fushman,D. and Hajic,J. and Ramabhadran,B. and Gustman,S. and Byrne,WJ and Soergel,D. and Dorr, Bonnie J and Resnik, Philip and Picheny,M.} } @article {19075, title = {Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440}, journal = {Environmental microbiology}, volume = {4}, year = {2002}, month = {2002}, pages = {799 - 808}, abstract = {Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85\% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.}, author = {Nelson,K. E and Weinel,C. and Paulsen,IT and Dodson,RJ and Hilbert,H. and Martins dos Santos,VAP and Fouts,DE and Gill,S. R and Pop, Mihai and Holmes,M. and others} } @article {13764, title = {Evaluating Arabic Retrieval from English or French Queries: The TREC-2001 Cross-Language Information Retrieval Track}, journal = {Proceedings of the Post Workshop of LREC}, year = {2002}, month = {2002///}, abstract = {The Cross-language information retrieval track at the 2001 Text Retrieval Conference (TREC-2001) produced the first large informationretrieval test collection for Arabic. The collection contains 383,872 Arabic news stories, 25 topic descriptions in Arabic, English and French from which queries can be formed, and manual (ground truth) relevance judgments for a useful subset of the topic-document combinations. This paper describes the way in which the collection was created, explains the evaluation measures that the collection is designed to support, and provides an overview of the results from the first set of experiments with the collection. The results make it possible to draw some inferences regarding the utility of the collection for post hoc evaluations. }, author = {Oard, Douglas and Gey,F.C. and Dorr, Bonnie J} } @conference {15881, title = {iCLEF 2001 at Maryland: comparing term-for-term gloss and MT}, booktitle = {Evaluation of Cross-Language Information Retrieval Systems}, year = {2002}, month = {2002///}, pages = {167 - 235}, author = {Wang,J. and Oard, Douglas} } @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 {17816, title = {Improving Performance of Agents by Activity Partitioning}, journal = {Technical Reports from UMIACS, UMIACS-TR-2002-96}, year = {2002}, month = {2002///}, abstract = {There is growing interest in software agents that provide a variety of services to humans, other agents, and third party software applications. Some of these agents are engaged in hundreds of activities at any given time point. In such cases, agents may try to examine a set A of activities and leverage commonalities between them in order to reduce their load. We call this activity merging. Unfortunately, in most application domains, activity merging turns out to be NP-complete. Thus, for each application domain, there is an integer k (which varies from domain to domain) such that activity merging can merge up to k activities while satisfying the application{\textquoteright}s performance expectations. In this paper, we consider the problem of what to do when the set of activities exceeds k. Our approach partitions A into disjoint sets A1 union A2 union ... union An such that each Ai contains at most k activities in it (thus the activities in each Ai can be merged using a merging algorithm). When creating such partitions, we would like to ensure that the activities inside each Ai share a lot of commonality, so that merging yields a lot of savings. In this paper, we propose two optimal algorithms (based on the A* algorithm and the branch and bound paradigm), as well as numerous greedy algorithms to solve the problem. We have implemented these algorithms and conducted detailed experiments. The results point out which algorithms are most appropriate for scaling agent performance.}, author = {Ozcan,F. and V.S. Subrahmanian} } @conference {13582, title = {Lexicon Acquisition from Bilingual Dictionaries}, booktitle = {SPIEPhotonic West Electronic Imaging Conference}, year = {2002}, month = {2002///}, pages = {37 - 48}, author = {David Doermann and Ma,H. and Karagol-Ayan,B. and Oard, Douglas} } @article {14152, title = {A multigrid method enhanced by Krylov subspace iteration for discrete Helmholtz equations}, journal = {SIAM Journal on scientific computing}, volume = {23}, year = {2002}, month = {2002///}, pages = {1291 - 1315}, author = {Elman, Howard and Ernst, O. G and O{\textquoteright}Leary, Dianne P. and others} } @proceedings {15793, title = {Reconstructing Images of Bar Codes for Construction Site Object Recognition}, year = {2002}, month = {2002/09//}, author = {Gilsinn,David E. and Cheok,Geraldine S. and O{\textquoteright}Leary, Dianne P.} } @conference {15897, title = {Supporting access to large digital oral history archives}, booktitle = {Proceedings of the 2nd ACM/IEEE-CS joint conference on Digital libraries}, series = {JCDL {\textquoteright}02}, year = {2002}, month = {2002///}, pages = {18 - 27}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {This paper describes our experience with the creation, indexing, and provision of access to a very large archive of videotaped oral histories - 116,000 hours of digitized interviews in 32 languages from 52,000 survivors, liberators, rescuers, and witnesses of the Nazi Holocaust. It goes on to identify a set of critical research issues that must be addressed if we are to provide full and detailed access to collections of this size: issues in user requirement studies, automatic speech recognition, automatic classification, segmentation, summarization, retrieval, and user interfaces. The paper ends by inviting others to discuss use of these materials in their own research.}, keywords = {cataloging, oral history, research agenda}, isbn = {1-58113-513-0}, doi = {10.1145/544220.544224}, url = {http://doi.acm.org/10.1145/544220.544224}, author = {Gustman,Samuel and Soergel,Dagobert and Oard, Douglas and Byrne,William and Picheny,Michael and Ramabhadran,Bhuvana and Greenberg,Douglas} } @conference {15893, title = {Term selection for searching printed Arabic}, 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 = {261 - 268}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {Since many Arabic documents are available only in print, automating retrieval from collections of scanned Arabic document images using Optical Character Recognition (OCR) is an interesting problem. Arabic combines rich morphology with a writing system that presents unique challenges to OCR systems. These factors must be considered when selecting terms for automatic indexing. In this paper, alternative choices of indexing terms are explored using both an existing electronic text collection and a newly developed collection built from images of actual printed Arabic documents. Character n-grams or lightly stemmed words were found to typically yield near-optimal retrieval effectiveness, and combining both types of terms resulted in robust performance across a broad range of conditions.}, keywords = {arabic, Information retrieval, OCR, term selection}, isbn = {1-58113-561-0}, doi = {10.1145/564376.564423}, url = {http://doi.acm.org/10.1145/564376.564423}, author = {Darwish,Kareem and Oard, Douglas} } @conference {15972, title = {Time-situated agency: Active logic and intention formation}, booktitle = {in: Workshop on Cognitive Agents, 25th German Conference on Artificial Intelligence}, year = {2002}, month = {2002///}, author = {Anderson,M. L and Josyula,D. P and Okamoto,Y. A and Perlis, Don} } @article {15884, title = {Translation-based indexing for cross-language retrieval}, journal = {Advances in Information Retrieval}, year = {2002}, month = {2002///}, pages = {425 - 447}, author = {Oard, Douglas and Ertunc,F.} } @inbook {15826, title = {Understanding Machine Performance in the Context of Human Performance for Multi-document Summarization}, booktitle = {DUC 02 Conference ProceedingsDUC 02 Conference Proceedings}, year = {2002}, month = {2002///}, publisher = {U.S. National Inst. of Standards and Technology}, organization = {U.S. National Inst. of Standards and Technology}, abstract = {We present a discussion of our summarization algorithm -- both single and multi-document -- along with a discussion of the evaluation experiments we have undertaken, what we have learned from them, and how we intend to utilize this information.}, url = {http://duc.nist.gov/http://duc.nist.gov/}, author = {Schlesinger,J.D. and Okurowski,M. E. and Conroy,J.M. and O{\textquoteright}Leary, Dianne P. and Taylor,A. and Hobbs,J. and Wilson,H. T.} } @article {15892, title = {The use of speech retrieval systems: a study design}, journal = {Information retrieval techniques for speech applications}, year = {2002}, month = {2002///}, pages = {86 - 93}, author = {Kim,J. and Oard, Douglas} } @conference {15955, title = {The use-mention distinction and its importance to HCI}, booktitle = {Proceedings of the Sixth Workshop on the Semantics and Pragmatics of Dialog}, year = {2002}, month = {2002///}, pages = {21 - 28}, author = {Anderson,M. L and Okamoto,Y. and Josyula,D. and Perlis, Don} } @article {13479, title = {Virtual Telescopes in Education}, journal = {Journal of Digital Information}, volume = {2}, year = {2002}, month = {2002///}, abstract = {Virtual Telescopes in Education is providing the services required to operate a virtual observatory comprising distributed telescopes, including an interactive, constraint-based scheduling service, data and resource archive, proposal preparation and review environment, and a VTIE Journal. A major goal of VTIE is to elicit from learners questions about the nature of celestial objects and the physical processes that give rise to the spectacular imagery that catches their imaginations. Generation of constrained science questions will assist learners in the science process. To achieve interoperability with other NSDL resources, our approach follows the Open Archives Initiative and the W3C Semantic Web activity.}, author = {Hoban,S. and desJardins, Marie and Farrell,N. and Rathod,P. and Sachs,J. and Sansare,S. and Yesha,Y. and Keating,J. and Busschots,B. and Means,J. and others} } @article {15872, title = {CLEF experiments at Maryland: Statistical stemming and backoff translation}, journal = {Cross-Language Information Retrieval and Evaluation}, year = {2001}, month = {2001///}, pages = {176 - 187}, author = {Oard, Douglas and Levow,G.A. and Cabezas,C.} } @article {15092, title = {Cryptographic counters and applications to electronic voting}, journal = {Advances in Cryptology{\textemdash}Eurocrypt 2001}, year = {2001}, month = {2001///}, pages = {78 - 92}, abstract = {We formalize the notion of a cryptographic counter, which allows a group of participants to increment and decrement a cryptographic representation of a (hidden) numerical value privately and robustly. The value of the counter can only be determined by a trusted authority (or group of authorities, which may include participants themselves), and participants cannot determine any information about the increment/decrement operations performed by other parties.Previous efficient implementations of such counters have relied on fully-homomorphic encryption schemes; this is a relatively strong requirement which not all encryption schemes satisfy. We provide an alternate approach, starting with any encryption scheme homomorphic over the additive group ℤ2 (i.e., 1-bit XOR). As our main result, we show a general and efficient reduction from any such encryption scheme to a general cryptographic counter. Our main reduction does not use additional assumptions, is efficient, and gives a novel implementation of a general counter. The result can also be viewed as an efficient construction of a general n-bit cryptographic counter from any 1-bit counter which has the additional property that counters can be added securely. As an example of the applicability of our construction, we present a cryptographic counter based on the quadratic residuosity assumption and use it to construct an efficient voting scheme which satisfies universal verifiability, privacy, and robustness. Work done while the author was at Telcordia Technologies. }, doi = {10.1007/3-540-44987-6_6}, author = {Katz, Jonathan and Myers,S. and Ostrovsky,R.} } @inbook {15072, title = {Efficient and Non-interactive Non-malleable Commitment}, booktitle = {Advances in Cryptology {\textemdash} EUROCRYPT 2001Advances in Cryptology {\textemdash} EUROCRYPT 2001}, series = {Lecture Notes in Computer Science}, volume = {2045}, year = {2001}, month = {2001///}, pages = {40 - 59}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {We present new constructions of non-malleable commitment schemes, in the public parameter model (where a trusted party makes parameters available to all parties), based on the discrete logarithm or RSA assumptions. The main features of our schemes are: they achieve near-optimal communication for arbitrarily-large messages and are non-interactive . Previous schemes either required (several rounds of) interaction or focused on achieving non-malleable commitment based on general assumptions and were thus efficient only when committing to a single bit. Although our main constructions are for the case of perfectly-hiding commitment, we also present a communication-efficient, non-interactive commitment scheme (based on general assumptions) that is perfectly binding.}, keywords = {Computer science}, isbn = {978-3-540-42070-5}, url = {http://www.springerlink.com/content/nhbj60a9da101w0r/abstract/}, author = {Di Crescenzo,Giovanni and Katz, Jonathan and Ostrovsky,Rafail and Smith,Adam}, editor = {Pfitzmann,Birgit} } @article {15093, title = {Efficient password-authenticated key exchange using human-memorable passwords}, journal = {Advances in Cryptology{\textemdash}EUROCRYPT 2001}, year = {2001}, month = {2001///}, pages = {475 - 494}, abstract = {There has been much interest in password-authenticated keyexchange protocols which remain secure even when users choose passwords from a very small space of possible passwords (say, a dictionary of English words). Under this assumption, one must be careful to design protocols which cannot be broken using off-line dictionary attacks in which an adversary enumerates all possible passwords in an attempt to determine the correct one. Many heuristic protocols have been proposed to solve this important problem. Only recently have formal validations of security (namely, proofs in the idealized random oracle and ideal cipher models) been given for specific constructions [3,10,22].Very recently, a construction based on general assumptions, secure in the standard model with human-memorable passwords, has been proposed by Goldreich and Lindell [17]. Their protocol requires no public parameters; unfortunately, it requires techniques from general multi-party computation which make it impractical. Thus, [17] only proves that solutions are possible {\textquotedblleft}in principal{\textquotedblright}. The main question left open by their work was finding an efficient solution to this fundamental problem. We showan efficient, 3-round, password-authenticated key exchange protocol with human-memorable passwords which is provably secure under the Decisional Diffie-Hellman assumption, yet requires only (roughly) 8 times more computation than {\textquotedblleft}standard{\textquotedblright} Diffie-Hellman key exchange [14] (which provides no authentication at all). We assume public parameters available to all parties. We stress that we work in the standard model only, and do not require a {\textquotedblleft}random oracle{\textquotedblright} assumption. }, doi = {10.1007/3-540-44987-6_29}, author = {Katz, Jonathan and Ostrovsky,R. and Yung,M.} } @conference {15949, title = {Handling uncertainty with active logic}, booktitle = {In Proceedings, AAAI Fall Symposium on Uncertainty in Computation}, year = {2001}, month = {2001///}, author = {Bhatia,M. and Chi,P. and Chong,W. and Josyula,D. P and Okamoto,Y. and Perlis, Don and Purang,K.} } @conference {16702, title = {Improved cross-language retrieval using backoff translation}, booktitle = {Proceedings of the first international conference on Human language technology research}, year = {2001}, month = {2001///}, pages = {1 - 3}, author = {Resnik, Philip and Oard, Douglas and Levow,G.} } @conference {15865, title = {Interactive cross-language information retrieval}, booktitle = {ACM SIGIR Forum}, volume = {35}, year = {2001}, month = {2001///}, pages = {1 - 3}, author = {Oard, Douglas} } @conference {15899, title = {Mandarin-English Information (MEI): investigating translingual speech retrieval}, booktitle = {Proceedings of the first international conference on Human language technology research}, series = {HLT {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {1 - 7}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper describes the Mandarin-English Information (MEI) project, where we investigated the problem of cross-language spoken document retrieval (CL-SDR), and developed one of the first English-Chinese CL-SDR systems. Our system accepts an entire English news story (text) as query, and retrieves relevant Chinese broadcast news stories (audio) from the document collection. Hence this is a cross-language and cross-media retrieval task. We applied a multi-scale approach to our problem, which unifies the use of phrases, words and subwords in retrieval. The English queries are translated into Chinese by means of a dictionary-based approach, where we have integrated phrase-based translation with word-by-word translation. Untranslatable named entities are transliterated by a novel subword translation technique. The multi-scale approach can be divided into three subtasks -- multi-scale query formulation, multi-scale audio indexing (by speech recognition) and multi-scale retrieval. Experimental results demonstrate that the use of phrase-based translation and subword translation gave performance gains, and multi-scale retrieval outperforms word-based retrieval.}, keywords = {cross-language, English-Chinese, spoken document retrieval}, doi = {10.3115/1072133.1072202}, url = {http://dx.doi.org/10.3115/1072133.1072202}, author = {Meng,Helen and Chen,Berlin and Khudanpur,Sanjeev and Levow,Gina-Anne and Lo,Wai-Kit and Oard, Douglas and Schone,Patrick and Tang,Karen and Wang,Hsin-Min and Wang,Jianqiang} } @conference {15859, title = {Modeling information content using observable behavior}, booktitle = {PROCEEDINGS OF THE ANNUAL MEETING-AMERICAN SOCIETY FOR INFORMATION SCIENCE}, volume = {38}, year = {2001}, month = {2001///}, pages = {481 - 488}, author = {Oard, Douglas and Kim,J.} } @conference {17824, title = {Optimal Agent Selection}, booktitle = {KI 2001: advances in artificial intelligence: Joint German/Austrian Conference on AI, Vienna, Austria, September 19-21, 2001: proceedings}, year = {2001}, month = {2001///}, pages = {2 - 2}, abstract = {The Internet contains a vast array of sources that provide identical or similar services. When an agent needs to solve a problem, it may split the problem into {\textquotedblleft}subproblems{\textquotedblright} and find an agent to solve each of the subproblems. Later, it may combine the results of these subproblems to solve the original problem. In this case, the agent is faced with the task of determining to which agents to assign the subproblems.We call this the agent selection problem (ASP for short). Solving ASP is complex because it must take into account several different parameters. For instance, different agents might take different amounts of time to process a request. Different agents might provide varying {\textquotedblleft}qualities{\textquotedblright} of answers. Network latencies associated with different agents might vary. In this paper, we first formalize the agent selection problem and show that it is NP-hard. We then propose a generic cost function that is general enough to take into account the costs of (i) network and server loads, (ii) source computations, and (iii) internal mediator costs. We then develop exact and heuristic based algorithms to solve the agent selection problem.}, author = {Ozcan,F. and V.S. Subrahmanian and Golubchik,L.} } @conference {17825, title = {Partitioning activities for agents}, booktitle = {INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE}, volume = {17}, year = {2001}, month = {2001///}, pages = {1218 - 1228}, abstract = {There are now numerous agent applications thattrack interests of thousands of users in situations where changes occur continuously. [Shim et al., 1994] suggested that such agents can be made effi- cient by merging commonalities in their activities. However, past algorithms cannot merge more than 10 or 20 concurrent activities. We develop tech- niques so that a large number of concurrent activ- ities (typically over 1000) can be partitioned into components (groups of activities) of small size (e.g. 10 to 50) so that each component{\textquoteright}s activities can be merged using previously developed algorithms (e.g. [Shim et al., 1994]). We first formalize the prob- lem and show that finding optimal partitions is NP- hard. We then develop three algorithms - Greedy, A -based and BAB (branch and bound). A -based and BAB are both guaranteed to compute optimal solutions. Greedy on the other hand uses heuris- tics and typically finds suboptimal solutions. We implemented all three algorithms. We experimen- tally show that the greedy algorithm finds partitions whose costs are at most 14\% worse than that found by A -based and BAB {\textemdash} however, Greedy is able to handle over thousand concurrent requests very fast while the other two methods are much slower and able to handle only 10-20 requests. Hence, Greedy appears to be the best. }, author = {Ozcan,F. and V.S. Subrahmanian} } @article {17827, title = {Probabilistic Temporal Databases, II: Calculus and Query Processing}, journal = {Technical Reports from UMIACS, UMIACS-TR-2001-79}, year = {2001}, month = {2001///}, abstract = {There is a vast class of applications in which we know that a certain event occurred, but do not know exactly when it occurred. However, as studied by Dyreson and Snodgrass \cite{ds98}, there are many natural scenarios where probability distributions exist and quantify this uncertainty. Dekhtyar et. al. extended Dyreson and Snodgrass{\textquoteright}s work and defined an extension of the relational algebra to handle such data. The first contribution of this paper is a declarative temporal probabilistic (TP for short) calculus which we show is equivalent in expressive power to the temporal probabilistic algebra of Dekhtyar et. al. Our second major contribution is a set of equivalence and containment results for the TP-algebra. Our third contribution is the development of cost models that may be used to estimate the cost of TP-algebra operations. Our fourth contribution is an experimental evaluation of the accuracy of our cost models and the use of the equivalence results as rewrite rules for optimizing queries by using an implementation of TP-databases on top of ODBC.}, author = {Dekhtyar,A. and Ozcan,F. and Ross,R. and V.S. Subrahmanian} } @conference {15898, title = {Rapidly retargetable interactive translingual retrieval}, booktitle = {Proceedings of the first international conference on Human language technology research}, series = {HLT {\textquoteright}01}, year = {2001}, month = {2001///}, pages = {1 - 5}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {This paper describes a system for rapidly retargetable interactive translingual retrieval. Basic functionality can be achieved for a new document language in a single day, and further improvements require only a relatively modest additional investment. We applied the techniques first to search Chinese collections using English queries, and have successfully added French, German, and Italian document collections. We achieve this capability through separation of language-dependent and language-independent components and through the application of asymmetric techniques that leverage an extensive English retrieval infrastructure.}, keywords = {cross-language, information, retrieval}, doi = {10.3115/1072133.1072212}, url = {http://dx.doi.org/10.3115/1072133.1072212}, author = {Levow,Gina-Anne and Oard, Douglas and Resnik, Philip} } @conference {15836, title = {Translation lexicon acquisition from bilingual dictionaries}, booktitle = {Proceedings of SPIE}, volume = {4670}, year = {2001}, month = {2001///}, pages = {37 - 37}, author = {David Doermann and Ma,H. and Karagol-Ayan,B. and Oard, Douglas} } @conference {15885, title = {User modeling for information access based on implicit feedback}, booktitle = {3rd Symposium of ISKO-France, Information Filtering and Automatic Summarisation in networds}, year = {2001}, month = {2001///}, author = {Kim,J. and Oard, Douglas and Romanik,K.} } @article {15709, title = {Adaptive Use of Iterative Methods in Predictor-Corrector Interior Point Methods for Linear Programming}, journal = {Numerical Algorithms}, volume = {25}, year = {2000}, month = {2000///}, pages = {387 - 406}, abstract = {In this work we devise efficient algorithms for finding the search directions for interior point methods applied to linear programming problems. There are two innovations. The first is the use of updating of preconditioners computed for previous barrier parameters. The second is an adaptive automated procedure for determining whether to use a direct or iterative solver, whether to reinitialize or update the preconditioner, and how many updates to apply. These decisions are based on predictions of the cost of using the different solvers to determine the next search direction, given costs in determining earlier directions. We summarize earlier results using a modified version of the OB1-R code of Lustig, Marsten, and Shanno, and we present results from a predictor{\textendash}corrector code PCx modified to use adaptive iteration. If a direct method is appropriate for the problem, then our procedure chooses it, but when an iterative procedure is helpful, substantial gains in efficiency can be obtained.}, author = {Wang,Weichung and O{\textquoteright}Leary, Dianne P.} } @article {15711, title = {Algorithm 805: computation and uses of the semidiscrete matrix decomposition}, journal = {ACM Trans. Math. Softw.}, volume = {26}, year = {2000}, month = {2000/09//}, pages = {415 - 435}, abstract = {We present algorithms for computing a semidiscrete approximation to a matrix in a weighted norm, with the Frobenius norm as a special case. The approximation is formed as a weighted sum of outer products of vectors whose elements are {\textpm}1 or 0, so the storage required by the approximation is quite small. We also present a related algorithm for approximation of a tensor. Applications of the algorithms are presented to data compression, filtering, and information retrieval; software is provided in C and in Matlab.}, keywords = {compression, latent semantic indexing, Matrix decomposition, semidiscrete decompositin, singular value decomposition}, isbn = {0098-3500}, doi = {10.1145/358407.358424}, url = {http://doi.acm.org/10.1145/358407.358424}, author = {Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P.} } @article {15724, title = {Chromosome Identification Using Hidden Markov Models: Comparison with Neural Networks, Singular Value Decomposition, Principal Components Analysis, and Fisher Discriminant Analysis}, journal = {Laboratory Investigation}, volume = {80}, year = {2000}, month = {2000/11/01/}, pages = {1629 - 1641}, abstract = {The analysis of G-banded chromosomes remains the most important tool available to the clinical cytogeneticist. The analysis is laborious when performed manually, and the utility of automated chromosome identification algorithms has been limited by the fact that classification accuracy of these methods seldom exceeds about 80\% in routine practice. In this study, we use four new approaches to automated chromosome identification {\textemdash} singular value decomposition (SVD), principal components analysis (PCA), Fisher discriminant analysis (FDA), and hidden Markov models (HMM) {\textemdash} to classify three well-known chromosome data sets (Philadelphia, Edinburgh, and Copenhagen), comparing these approaches with the use of neural networks (NN). We show that the HMM is a particularly robust approach to identification that attains classification accuracies of up to 97\% for normal chromosomes and retains classification accuracies of up to 95\% when chromosome telomeres are truncated or small portions of the chromosome are inverted. This represents a substantial improvement of the classification accuracy for normal chromosomes, and a doubling in classification accuracy for truncated chromosomes and those with inversions, as compared with NN-based methods. HMMs thus appear to be a promising approach for the automated identification of both normal and abnormal G-banded chromosomes.}, keywords = {addiction disorders, anxiety, depression, psychopharmacology, schizophrenia}, isbn = {0023-6837}, doi = {10.1038/labinvest.3780173}, url = {http://www.nature.com/labinvest/journal/v80/n11/full/3780173a.html}, author = {Conroy,John M. and Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P. and O{\textquoteright}Leary,Timothy J} } @conference {13893, title = {Designing StoryRooms: interactive storytelling spaces for children}, booktitle = {Proceedings of the 3rd conference on Designing interactive systems: processes, practices, methods, and techniques}, year = {2000}, month = {2000///}, pages = {95 - 104}, author = {Alborzi,H. and Druin, Allison and Montemayor,J. and Platner,M. and Porteous,J. and Sherman,L. and Boltman,A. and Tax{\'e}n,G. and Best,J. and Hammer,J. and others} } @conference {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 {18636, title = {Dynamic node management and measure estimation in a state-driven fault injector}, year = {2000}, month = {2000///}, pages = {248 - 261}, abstract = {Validation of distributed systems using fault injectionis difficult because of their inherent complexity, lack of a global clock, and lack of an easily accessible notion of a global state. To address these challenges, the Loki fault injector injects faults based on a partial view of the global state of a distributed system, and performs a post-runtime analysis using an off-line clock synchronization algorithm to determine whether the faults were properly injected. In this paper, we first describe an enhanced runtime architecture for the Loki fault injector and then present a new method for obtaining measures in Loki. The enhanced runtime allows dynamic entry and exit of nodes in the system. It also offers more efficient multicast of notification messages and more efficient communication between state machines on the same host, and is more scalable than the previous runtime. We then detail a new and flexible method for obtaining a wide range of performance and dependability measures in Loki. }, url = {https://www.perform.csl.illinois.edu/Papers/USAN_papers/00CHA01.pdf}, author = {Chandra,R. and Michel Cukier and Lefever,R. and Sanders,W. and others} } @article {18960, title = {The genome sequence of Drosophila melanogaster}, journal = {Science}, volume = {287}, year = {2000}, month = {2000///}, pages = {2185 - 2185}, abstract = {The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the \~{}120-megabase euchromatic portion of theDrosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes \~{}13,600 genes, somewhat fewer than the smaller Caenorhabditis elegansgenome, but with comparable functional diversity.}, isbn = {0036-8075, 1095-9203}, doi = {10.1126/science.287.5461.2185}, url = {http://www.sciencemag.org/content/287/5461/2185}, author = {Adams,M.D. and Celniker,S.E. and Holt,R.A. and Evans,C.A. and Gocayne,J.D. and Amanatides,P.G. and Scherer,S.E. and Li,P.W. and Hoskins,R.A. and Galle,R.F. and others} } @book {15819, title = {The Interface of Three Areas of Computer Science with the Mathematical Sciences}, year = {2000}, month = {2000///}, publisher = {National Academy Press}, organization = {National Academy Press}, address = {Washington, DC}, url = {http://www.nap.edu/books/NI000351/html/http://www.nap.edu/books/NI000351/html/}, author = {O{\textquoteright}Leary, Dianne P. and Weidman,Scott T.} } @article {15942, title = {Meta-reasoning for intelligent dialog repair}, year = {2000}, month = {2000///}, institution = {Technical report, University of Maryland}, abstract = {Under consideration for other conferences (specify)? We present a logical approach and implmentation of a real-time rational agent for dialogue management, which includes an ability to represent, reason about, and repair (both implicitly and explicitly) incoherence in dialogue. We exemplify a target problem of negative feedback in action directive subdialogues, with an ability to make reference resolution sensitive to dialogue context and like intentions. The resulting system is able to behave more sensibly in several situations than earlier dialogue management systems in these same conditions. Meta-reasoning for intelligent dialog repair We present a logical approach and implmentation of a real-time rational agent for dialogue management, which includes an ability to represent, reason about, and repair (both implicitly and explicitly) incoherence in dialogue. We exemplify a target problem of negative feedback in action directive subdialogues, with an ability to make reference resolution sensitive to dialogue context and like intentions. The resulting system is able to behave more sensibly in several situations than earlier dialogue management systems in these same conditions.}, author = {Purang,K. and Traum,D. and Purushothaman,D. and Chong,W. and Okamato,Y. and Perlis, Don} } @article {14652, title = {A Review of Current Routing Protocols for Ad Hoc}, journal = {IEEE Personal Communications}, volume = {29}, year = {2000}, month = {2000///}, pages = {156 - 71}, author = {Royer,E.M. and Toh,C.K. and Hicks, Michael W. and Kakkar,P. and Moore,J. T and Hicks, Michael W. and Moore,J. T and Alexander,D. S and Gunter,C. A and Nettles,S. and others} } @conference {15903, title = {Structured translation for cross-language information retrieval}, booktitle = {Proceedings of the 23rd annual international ACM SIGIR conference on Research and development in information retrieval}, series = {SIGIR {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {120 - 127}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {The paper introduces a query translation model that reflects the structure of the cross-language information retrieval task. The model is based on a structured bilingual dictionary in which the translations of each term are clustered into groups with distinct meanings. Query translation is modeled as a two-stage process, with the system first determining the intended meaning of a query term and then selecting translations appropriate to that meaning that might appear in the document collection. An implementation of structured translation based on automatic dictionary clustering is described and evaluated by using Chinese queries to retrieve English documents. Structured translation achieved an average precision that was statistically indistinguishable from Pirkola{\textquoteright}s technique for very short queries, but Pirkola{\textquoteright}s technique outperformed structured translation on long queries. The paper concludes with some observations on future work to improve retrieval effectiveness and on other potential uses of structured translation in interactive cross-language retrieval applications.}, isbn = {1-58113-226-3}, doi = {10.1145/345508.345562}, url = {http://doi.acm.org/10.1145/345508.345562}, author = {Sperer,Ruth and Oard, Douglas} } @article {15813, title = {Symbiosis between Linear Algebra and Optimization}, journal = {Journal of Computational and Applied Mathematics}, volume = {123}, year = {2000}, month = {2000///}, pages = {447 - 465}, abstract = {The efficiency and effectiveness of most optimization algorithms hinges on the numerical linearalgebra algorithms that they utilize. Effective linearalgebra is crucial to their success, and because of this, optimization applications have motivated fundamental advances in numerical linearalgebra. This essay will highlight contributions of numerical linearalgebra to optimization, as well as some optimization problems encountered within linearalgebra that contribute to a symbiotic relationship.}, author = {O{\textquoteright}Leary, Dianne P.} } @conference {18947, title = {Telicity as a cue to temporal and discourse structure in Chinese-English machine translation}, series = {NAACL-ANLP-Interlinguas {\textquoteright}00}, year = {2000}, month = {2000///}, pages = {34 - 41}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Machine translation between any two languages requires the generation of information that is implicit in the source language. In translating from Chinese to English, tense and other temporal information must be inferred from other grammatical and lexical cues. Moreover, Chinese multiple-clause sentences may contain inter-clausal relations (temporal or otherwise) that must be explicit in English (e.g., by means of a discourse marker). Perfective and imperfective grammatical aspect markers can provide cues to temporal structure, but such information is not present in every sentence. We report on a project to use the lexical aspect features of (a)telicity reflected in the Lexical Conceptual Structure of the input text to suggest tense and discourse structure in the English translation of a Chinese newspaper corpus.}, doi = {10.3115/1117554.1117559}, url = {http://dx.doi.org/10.3115/1117554.1117559}, author = {Olsen,Mari and Traum,David and Van Ess-Dykema,Carol and Weinberg, Amy and Dolan,Ron} } @article {15858, title = {Textual data mining to support science and technology management}, journal = {Journal of Intelligent Information Systems}, volume = {15}, year = {2000}, month = {2000///}, pages = {99 - 119}, author = {Losiewicz,P. and Oard, Douglas and Kostoff,R.N.} } @conference {13501, title = {ARobust Method for Unknown Forms Analysis}, booktitle = {ICDAR}, year = {1999}, month = {1999///}, pages = {531 - 534}, author = {Xingyuan,L. and David Doermann and Oh,W. and Gao,W.} } @article {16659, title = {The Bible as a parallel corpus: Annotating the {\textquoteleft}Book of 2000 Tongues{\textquoteright}}, journal = {Computers and the Humanities}, volume = {33}, year = {1999}, month = {1999///}, pages = {129 - 153}, author = {Resnik, Philip and Olsen,M.B. and Diab,M.} } @article {16694, title = {Creating a parallel corpus from the book of 2000 tongues}, journal = {Computers and the Humanities}, volume = {33}, year = {1999}, month = {1999///}, pages = {1 - 2}, author = {Resnik, Philip and Olsen,M.B. and Diab,M.} } @conference {13938, title = {Designing PETS: a personal electronic teller of stories}, booktitle = {Proceedings of the SIGCHI conference on Human factors in computing systems: the CHI is the limit}, series = {CHI {\textquoteright}99}, year = {1999}, month = {1999///}, pages = {326 - 329}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We have begun the development of a new robotic pet that cansupport children in the storytelling process. Children can build their own pet by snapping together the modular animal parts of the PETS robot. After their pet is built, children can tell stories using the My Pets software. These stories can then be acted out by their robotic pet. This video paper describes the motivation for this research and the design process of our intergenerational design team in building the first PETS prototypes. We will discuss our progress to date and our focus for the future. }, keywords = {children, cooperative inquiry, design techniques, educational applications, intergenerational design team, PETS, ROBOTICS}, isbn = {0-201-48559-1}, doi = {10.1145/302979.303103}, url = {http://doi.acm.org/10.1145/302979.303103}, author = {Druin, Allison and Montemayor,Jamie and Hendler,Jim and McAlister,Britt and Boltman,Angela and Fiterman,Eric and Plaisant,Aurelie and Kruskal,Alex and Olsen,Hanne and Revett,Isabella and Schwenn,Thomas Plaisant and Sumida,Lauren and Wagner,Rebecca} } @conference {15889, title = {Effects of term segmentation on Chinese/English cross-language information retrieval}, booktitle = {String Processing and Information Retrieval Symposium, 1999 and International Workshop on Groupware}, year = {1999}, month = {1999///}, pages = {149 - 157}, publisher = {IEEE}, organization = {IEEE}, abstract = {The majority of recent Cross-Language Information Retrieval (CLIR) research has focused on European languages. CLIR problems that involve East Asian languages such as Chinese introduce additional challenges, because written Chinese texts lack boundaries between terms. The paper examines three Chinese segmentation techniques in combination with two variants of dictionary-based Chinese to English query translation. The results indicate that failure to segment terms, particularly technical terms and names, can have a cascading effect that reduces retrieval effectiveness. Task-tuned segmentation algorithms and alternative term weighting strategies are suggested as productive directions for future work}, keywords = {alternative term weighting strategies, cascading effect, Chinese segmentation techniques, Chinese/English cross-language information retrieval, Chromium, CLIR problems, Cross-Language Information Retrieval research, data mining, Dictionaries, dictionary-based Chinese, East Asian languages, English query translation, European languages, future work, Information retrieval, language translation, linguistics, natural language processing, natural languages, productive directions, Reactive power, retrieval effectiveness, task-tuned segmentation algorithms, technical terms, term segmentation, text analysis, written Chinese texts}, isbn = {0-7695-0268-7}, doi = {10.1109/SPIRE.1999.796590}, author = {Oard, Douglas and Wang,Jianqiang} } @article {15747, title = {Eigenanalysis of Some Preconditioned Helmholtz Problems}, journal = {Numerische Mathematik}, volume = {83}, year = {1999}, month = {1999///}, pages = {231 - 257}, abstract = {In this work we calculate the eigenvalues obtained by preconditioning the discrete Helmholtz operator with Sommerfeld-like boundary conditions on a rectilinear domain, by a related operator with boundary conditions that permit the use of fast solvers. The main innovation is that the eigenvalues for two and three-dimensional domains can be calculated exactly by solving a set of one-dimensional eigenvalue problems. This permits analysis of quite large problems. For grids fine enough to resolve the solution for a given wave number, preconditioning using Neumann boundary conditions yields eigenvalues that are uniformly bounded, located in the first quadrant, and outside the unit circle. In contrast, Dirichlet boundary conditions yield eigenvalues that approach zero as the product of wave number with the mesh size is decreased. These eigenvalue properties yield the first insight into the behavior of iterative methods such as GMRES applied to these preconditioned problems.}, author = {Elman, Howard and O{\textquoteright}Leary, Dianne P.} } @article {16172, title = {The end of zero-hit queries: query previews for NASA{\textquoteright}s Global Change Master Directory}, journal = {International Journal on Digital Libraries}, volume = {2}, year = {1999}, month = {1999///}, pages = {79 - 90}, abstract = {The Human-Computer Interaction Laboratory (HCIL) of the University of Maryland and NASA have collaborated over three years to refine and apply user interface research concepts developed at HCIL in order to improve the usability of NASA data services. The research focused on dynamic query user interfaces, visualization, and overview + preview designs. An operational prototype, using query previews, was implemented with NASA{\textquoteright}s Global Change Master Directory (GCMD), a directory service for earth science datasets. Users can see the histogram of the data distribution over several attributes and choose among attribute values. A result bar shows the cardinality of the result set, thereby preventing users from submitting queries that would have zero hits. Our experience confirmed the importance of metadata accuracy and completeness. The query preview interfaces make visible the problems or gaps in the metadata that are undetectable with classic form fill-in interfaces. This could be seen as a problem, but we think that it will have a long-term beneficial effect on the quality of the metadata as data providers will be compelled to produce more complete and accurate metadata. The adaptation of the research prototype to the NASA data required revised data structures and algorithms.}, isbn = {1432-5012}, url = {http://dx.doi.org/10.1007/s007990050039}, author = {Greene,Stephan and Tanin,Egemen and Plaisant, Catherine and Shneiderman, Ben and Olsen,Lola and Major,Gene and Johns,Steve} } @article {12999, title = {Genes and other samples of DNA sequence data for phylogenetic inference}, journal = {The Biological Bulletin}, volume = {196}, year = {1999}, month = {1999/06//}, pages = {345 - 350}, author = {Cummings, Michael P. and Otto,S. P and Wakeley,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} } @inbook {15765, title = {Latent Semantic Indexing via a Semi-Discrete Matrix Decomposition}, booktitle = {The Mathematics of Information Coding, Extraction and DistributionThe Mathematics of Information Coding, Extraction and Distribution}, year = {1999}, month = {1999///}, pages = {73 - 80}, publisher = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, organization = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, address = {New York}, abstract = {With the electronic storage of documents comes the possibility of building search engines that can automatically choose documents relevant to a given set of topics. In information retrieval, we wish to match queries with relevant documents. Documents can be represented by the terms that appear within them, but literal matching of terms does not necessarily retrieve all relevant documents. There are a number of information retrieval systems based on inexact matches. Latent Semantic Indexing represents documents by approximations and tends to cluster documents on similar topics even if their term profiles are somewhat different. This approximate representation is usually accomplished using a low-rank singular value decomposition (SVD) approximation. In this paper, we use an alternate decomposition, the semi-discrete decomposition (SDD). For equal query times, the SDD does as well as the SVD and uses less than one-tenth the storage for the MEDLINE test set.}, author = {Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P.}, editor = {Cybenko,George and O{\textquoteright}Leary, Dianne P. and Rissanen,Jorma} } @article {15853, title = {Multilingual Information Discovery and AccesS (MIDAS): A Joint ACM DL{\textquoteright}99/ ACM SIGIR{\textquoteright}99 Workshop.}, journal = {D-Lib MagazineD-Lib Magazine}, volume = {5}, year = {1999}, month = {1999///}, pages = {1 - 12}, abstract = {Discusses a multidisciplinary workshop that addressed issues concerning internationally distributed information networks. Highlights include multilingual information access in media other than character-coded text; cross-language information retrieval and multilingual metadata; and evaluation of multilingual systems. (LRW)}, keywords = {Distributed computing, Electronic Media}, isbn = {ISSN-1082-9873}, url = {http://www.eric.ed.gov/ERICWebPortal/detail?accno=EJ601937}, author = {Oard, Douglas and Peters,Carol and Ruiz,Miguel and Frederking,Robert and Klavans,Judith and Sheridan,Paraic} } @article {13620, title = {Page Segmentation and Zone Classification: The State of the Art}, volume = {LAMP-TR-036,CAR-TR-927,CS-TR-4079}, year = {1999}, month = {1999/11//}, institution = {University of Maryland, College Park}, abstract = {Page segmentation and zone classification are key areas of research in document image processing, because they occupy an intermediate position between document preprocessing and higher-level document understanding such as logical page analysis and OCR. Such analysis of the page relies heavily on an appropriate document model and results in a representation of the physical structure of the document. The purpose of this review is to analyze progress made in page segmentation and zone classification and suggest what needs to be done to advance the field.}, author = {Okun,O. and David Doermann and Pietikainen,M.} } @article {16557, title = {Pathogenic mechanisms in ischemic damage: a computational study}, journal = {Computers in biology and medicine}, volume = {29}, year = {1999}, month = {1999///}, pages = {39 - 59}, author = {Ruppin,E. and Ofer,E. and Reggia, James A. and Revett,K.} } @article {16526, title = {Penumbral tissue damage following acute stroke: a computational investigation}, journal = {Progress in brain research}, volume = {121}, year = {1999}, month = {1999///}, pages = {243 - 260}, author = {Ruppin,E. and Revett,K. and Ofer,E. and Goodall,S. and Reggia, James A.} } @article {15787, title = {Pivoted Cauchy-Like Preconditioners for Regularized Solution of Ill-Posed Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {21}, year = {1999}, month = {1999///}, pages = {88 - 110}, url = {http://epubs.siam.org/sam-bin/dbq/article/30897http://epubs.siam.org/sam-bin/dbq/article/30897}, author = {Kilmer,Misha E. and O{\textquoteright}Leary, Dianne P.} } @article {18455, title = {A real-time audio{\textendash}video front-end for multimedia applications}, journal = {The Journal of the Acoustical Society of America}, volume = {106}, year = {1999}, month = {1999///}, pages = {2271 - 2271}, author = {Zotkin,Dmitry N and Duraiswami, Ramani and Hariatoglu,I. and Davis, Larry S. and Otsuka,T.} } @conference {17529, title = {Running EveryWare on the computational grid}, booktitle = {Proceedings of the 1999 ACM/IEEE conference on Supercomputing (CDROM)}, year = {1999}, month = {1999///}, pages = {6{\textendash}es - 6{\textendash}es}, author = {Wolski,R. and Brevik,J. and Krintz,C. and Obertelli,G. and Spring, Neil and Su,A.} } @article {16711, title = {Support for interactive document selection in cross-language information retrieval}, journal = {Information Processing \& Management}, volume = {35}, year = {1999}, month = {1999/05//}, pages = {363 - 379}, abstract = {As digital libraries grow to global scale, the provision of interactive access to content in many languages will become increasingly important. In systems that support query-based searching, the presence of multilingual content will affect both the search technology itself and the user interface components that support query formulation, document selection and query refinement. This article describes the interactions among these components and presents a practical way of evaluating the adequacy of the selection interface. A categorization-based model for the user{\textquoteright}s selection process is presented and an experimental methodology suitable for obtaining process centered results in this context is developed. The methodology is applied to assess the adequacy of a selection interface in which multiple candidate translations for a term can be simultaneously presented. The results indicate that the modeled selection process is somewhat less effective when users are presented with multi-translation glosses from Japanese to English rather than materials generated originally in English, but that users with access to the gloss translations substantially outperform a Naive Bayes classification algorithm.}, isbn = {0306-4573}, doi = {10.1016/S0306-4573(98)00066-1}, url = {http://www.sciencedirect.com/science/article/pii/S0306457398000661}, author = {Oard, Douglas and Resnik, Philip} } @article {13411, title = {A Survey of Research in Distributed, Continual Planning}, journal = {AI Magazine}, volume = {20}, year = {1999}, month = {1999/12/15/}, pages = {13 - 13}, isbn = {0738-4602}, doi = {10.1609/aimag.v20i4.1475}, url = {https://www.aaai.org/ojs/index.php/aimagazine/article/viewArticle/1475}, author = {desJardins, Marie and Durfee,Edmund H and Ortiz,Jr. and Wolverton,Michael J} } @article {15823, title = {Tikhonov Regularization and Total Least Squares}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {21}, year = {1999}, month = {1999///}, pages = {185 - 194}, abstract = {Discretizations of inverse problems lead to systems of linear equations with a highly ill-conditioned coefficient matrix, and in order to computestable solutions to these systems it is necessary to apply regularization methods. We show how Tikhonov{\textquoteright}s regularization method, which in its original formulation involves a least squares problem, can be recast in a total least squares formulation suited for problems in which both the coefficient matrix and the right-hand side are known only approximately. We analyze the regularizing properties of this method and demonstrate by a numerical example that, in certain cases with large perturbations, the new method is superior to standard regularization methods.}, keywords = {bidiagonalization, discrete ill-posed problems, regularization, total least squares}, doi = {10.1137/S0895479897326432}, url = {http://link.aip.org/link/?SML/21/185/1}, author = {Golub, Gene H. and Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.} } @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} } @article {17001, title = {Browsing Unix Directories With Dynamic Queries: An Evaluation of Three Information Display Techniques}, journal = {Technical Reports of the Computer Science Department}, year = {1998}, month = {1998/10/15/}, abstract = {We designed, implemented, and evaluated an innovative concept fordynamic queries which involves the direct manipulation of small databases. Our domain was directories in a Unix file system. Dynamic queries allow users to formulate queries and explore the databases with graphical widgets, such as sliders and buttons, without requiring them to have any knowledge about the underlying structure of the database query languages, or command language syntax. Three interfaces for presenting directories were developed and tested with eighteen subjects in a within-subject design. The results of the formative evaluation yielded some useful guidelines for software designers. (Also cross-referenced as CAR-TR-605) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/379}, author = {Liao,Holmes and Osada,Masakazu and Shneiderman, Ben} } @inbook {15729, title = {Commentary on Lanczos{\textquoteright}s {\textquoteleft}Analytical and Practical Curve Fitting of Equidistant Data{\textquoteright}}, booktitle = {Cornelius Lanczos Collected Published Papers with CommentariesCornelius Lanczos Collected Published Papers with Commentaries}, volume = {5}, year = {1998}, month = {1998///}, pages = {3-433 to 3-434 - 3-433 to 3-434}, publisher = {North Carolina State University Publishers}, organization = {North Carolina State University Publishers}, address = {Raleigh}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {al,William R. Davis et} } @article {13700, title = {A Comparative Study of Knowledge-Based Approaches for Cross-Language}, year = {1998}, month = {1998///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Cross-language retrieval systems seek to use queries in one natural language to guide theretrieval of documents that might be written in another. Acquisition and representation of translation knowledge plays a central role in this process. This paper explores the util- ity of two sources of manually encoded translation knowledge, bilingual dictionaries and translation lexicons, for cross-language retrieval. We have implemented six query trans- lation techniques that use bilingual dictionaries, one based on lexical-semantic analysis, and one based on direct use of the translation output from an existing machine transla- tion system; these are compared with a document translation technique that uses output from the same existing translation system. Average precision measures on portions of the TREC collection suggest that arbitrarily selecting a single translation from a bilingual dictionary is typically no less effective than using every translation in the dictionary, that query translation using an existing machine translation system can achieve some- what better effectiveness than simple dictionary-based techniques, and that performing document translation rather than query translation may result in further improvements in retrieval effectiveness under some conditions. }, author = {Oard, Douglas and Dorr, Bonnie J and Hackett,P. and Katsova,M.} } @article {15873, title = {A comparative study of query and document translation for cross-language information retrieval}, journal = {Machine Translation and the Information Soup}, year = {1998}, month = {1998///}, pages = {472 - 483}, author = {Oard, Douglas} } @article {17718, title = {On the convergence of a new Rayleigh quotient method with applications to large eigenproblems}, journal = {Electronic Transactions on Numerical Analysis}, volume = {7}, year = {1998}, month = {1998///}, pages = {182 - 189}, abstract = {In this paper we propose a variant of the Rayleigh quotient method to compute an eigenvalue and cor-responding eigenvectors of a matrix. It is based on the observation that eigenvectors of a matrix with eigenvalue zero are also singular vectors corresponding to zero singular values. Instead of computing eigenvector approximations by the inverse power method, we take them to be the singular vectors corresponding to the smallest singular value of the shifted matrix. If these singular vectors are computed exactly the method is quadratically convergent. However, ex- act singular vectors are not required for convergence, and the resulting method combined with Golub{\textendash}Kahan{\textendash}Krylov bidiagonalization looks promising for enhancement/refinement methods for large eigenvalue problems. }, author = {Oleary,D. P. and Stewart, G.W.} } @conference {17832, title = {Digital dynamic telepathology{\textendash}the Virtual Microscope.}, booktitle = {Proceedings of the AMIA Symposium}, year = {1998}, month = {1998///}, pages = {912 - 912}, author = {Afework,A. and Beynon,M. D and Bustamante,F. and Cho,S. and Demarzo,A. and Ferreira,R. and Miller,R. and Silberman,M. and Saltz, J. and Sussman, Alan and others} } @article {15746, title = {Efficient Iterative Solution of the Three-Dimensional Helmholtz Equation}, journal = {Journal of Computational Physics}, volume = {142}, year = {1998}, month = {1998/05/01/}, pages = {163 - 181}, abstract = {We examine preconditioners for the discrete indefinite Helmholtz equation on a three-dimensional box-shaped domain with Sommerfeld-like boundary conditions. The preconditioners are of two types. The first is derived by discretization of a related continuous operator that differs from the original only in its boundary conditions. The second is derived by a block Toeplitz approximation to the descretized problem. The resulting preconditioning matrices allow the use of fast transform methods and differ from the discrete Helmholtz operator by an operator of low rank. We present experimental results demonstrating that when these methods are combined with Krylov subspace iteration, convergence rates depend only mildly on both the wave number and discretization mesh size. In addition, the methods display high efficiencies in an implementation on an IBM SP-2 parallel computer.}, isbn = {0021-9991}, doi = {10.1006/jcph.1998.5939}, url = {http://www.sciencedirect.com/science/article/pii/S0021999198959393}, author = {Elman, Howard and O{\textquoteright}Leary, Dianne P.} } @inbook {13763, title = {Enhancing Automatic Acquisition of Thematic Structure in a Large-Scale Lexicon for Mandarin Chinese}, booktitle = {Machine Translation and the Information SoupMachine Translation and the Information Soup}, series = {Lecture Notes in Computer Science}, volume = {1529}, year = {1998}, month = {1998///}, pages = {41 - 50}, publisher = {Springer Berlin / Heidelberg}, organization = {Springer Berlin / Heidelberg}, abstract = {This paper describes a refinement to our procedure for porting lexical conceptual structure (LCS) into new languages. Specifically we describe a two-step process for creating candidate thematic grids for Mandarin Chinese verbs, using the English verb heading the VP in the subde_nitions to separate senses, and roughly parsing the verb complement structure to match thematic structure templates. We accomplished a substantial reduction in manual effort, without substantive loss. The procedure is part of a larger process of creating a usable lexicon for interlingual machine translation from a large on-line resource with both too much and too little information.}, isbn = {978-3-540-65259-5}, url = {http://dx.doi.org/10.1007/3-540-49478-2_4}, author = {Olsen,Mari and Dorr, Bonnie J and Thomas,Scott}, editor = {Farwell,David and Gerber,Laurie and Hovy,Eduard} } @conference {13765, title = {Evaluating Resources for Query Translation in Cross-Language Information Retrieval}, booktitle = {In Proceedings of the First International Conference on Language Resources and Evaluation}, year = {1998}, month = {1998///}, pages = {759 - 763}, abstract = {Our goal is to evaluate the utility of a lexical resource containing Lexical Conceptual Structures (LCS) for use in cross-language information retrieval. Our evaluation makes use of a combination of techniques from interlingual machine translation with conventional information retrieval techniques. Given a query in one language, we transform the query into the corresponding terms in a second language. Our focus is on the construction of disambiguated targetlanguage queries by using verb-based entries in our lexicon to construct Lexical Conceptual Structures. The main innovation of LCS-based query translation is that it provides a principled framework for controlling translation ambiguity in cross-language information retrieval applications. We evaluate this approach by comparing the resulting retrieval effectiveness with alternative techniques based that use offthe -shelf machine translation or translation knowledge extracted from machine readable dictionaries. We view this work as an important demonstration of techniques for evaluating the utility of alternative structures for multilingual lexicons in cross-language IR applications. In addition, this work provides a basis for measuring the extent to which disambiguation can enhance cross-language information retrieval effectiveness.}, author = {Dorr, Bonnie J and Oard, Douglas} } @article {14102, title = {Genetic nomenclature for Trypanosoma and Leishmania.}, journal = {Molecular and biochemical parasitology}, volume = {97}, year = {1998}, month = {1998///}, pages = {221 - 221}, author = {Clayton,C. and Adams,M. and Almeida,R. and Baltz,T. and Barrett,M. and Bastien,P. and Belli,S. and Beverley,S. and Biteau,N. and Blackwell,J. and others} } @article {15781, title = {Overcoming Instability In Computing The Fundamental Matrix For A Markov Chain}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {19}, year = {1998}, month = {1998///}, pages = {534 - 540}, abstract = {We present an algorithm for solving linear systems involving the probability or rate matrix for a Markov chain. It is based on a UL factorization but works only with a submatrix of the factor U. We demonstrate its utility on Erlang-B models as well as more complicated models of a telephone multiplexing system.}, keywords = {decision process, fundamental matrix, Markov chains}, doi = {10.1137/S0895479896301753}, url = {http://link.aip.org/link/?SML/19/534/1}, author = {Heyman,Daniel P. and O{\textquoteright}Leary, Dianne P.} } @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.} } @article {17951, title = {Salient Frame Detection for Molecular Dynamics Simulations}, journal = {Scientific Visualization: Interactions, Features, Metaphors}, volume = {2}, year = {1998}, month = {1998///}, pages = {160 - 175}, abstract = {Saliency-based analysis can be applied to time-varying 3D datasetsfor the purpose of summarization, abstraction, and motion analysis. As the sizes of time-varying datasets continue to grow, it becomes more and more difficult to comprehend vast amounts of data and information in a short period of time. Au- tomatically generated thumbnail images and previewing of time-varying datasets can help viewers explore and understand the datasets significantly faster as well as provide new insights. In this paper, we introduce a novel method for detect- ing salient frames for molecular dynamics simulations. Our method effectively detects crucial transitions in simulated mechanosensitive ion channel (MscS), in agreement with experimental data. }, author = {Kim,Y. and Patro,R. and Ip,C. Y and O{\textquoteright}Leary,D. P and Anishkin,A. and Sukharev,S. and Varshney, Amitabh} } @article {15705, title = {A semidiscrete matrix decomposition for latent semantic indexing information retrieval}, journal = {ACM Trans. Inf. Syst.}, volume = {16}, year = {1998}, month = {1998/10//}, pages = {322 - 346}, abstract = {The vast amount of textual information available today is useless unless it can be effectively and efficiently searched. The goal in information retrieval is to find documents that are relevant to a given user query. We can represent and document collection by a matrix whose (i, j) entry is nonzero only if the ith term appears in the jth document; thus each document corresponds to a columm vector. The query is also represented as a column vector whose ith term is nonzero only if the ith term appears in the query. We score each document for relevancy by taking its inner product with the query. The highest-scoring documents are considered the most relevant. Unfortunately, this method does not necessarily retrieve all relevant documents because it is based on literal term matching. Latent semantic indexing (LSI) replaces the document matrix with an approximation generated by the truncated singular-value decomposition (SVD). This method has been shown to overcome many difficulties associated with literal term matching. In this article we propose replacing the SVD with the semidiscrete decomposition (SDD). We will describe the SDD approximation, show how to compute it, and compare the SDD-based LSI method to the SVD-based LSI methods. We will show that SDD-based LSI does as well as SVD-based LSI in terms of document retrieval while requiring only one-twentieth the storage and one-half the time to compute each query. We will also show how to update the SDD approximation when documents are added or deleted from the document collection.}, keywords = {data mining, latent semantic indexing, semidiscrete decomposition, singular-value decomposition, text retrieval}, isbn = {1046-8188}, doi = {10.1145/291128.291131}, url = {http://doi.acm.org/10.1145/291128.291131}, author = {Kolda,Tamara G. and O{\textquoteright}Leary, Dianne P.} } @article {13717, title = {A Survey of Multilingual Text Retrieval}, year = {1998}, month = {1998/10/15/}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {This report reviews the present state of the artin selection of texts in one language based on queries in another, a problem we refer to as {\textquoteleft}{\textquoteleft}multilingual{\textquoteright}{\textquoteright} text retrieval. Present applications of multilingual text retrieval systems are limited by the cost and complexity of developing and using the multilingual thesauri on which they are based and by the level of user training that is required to achieve satisfactory search effectiveness. A general model for multilingual text retrieval is used to review the development of the field and to describe modern production and experimental systems. The report concludes with some observations on the present state of the art and an extensive bibliography of the technical literature on multilingual text retrieval. The research reported herein was supported, in part, by Army Research Office contract DAAL03-91-C-0034 through Battelle Corporation, NSF NYI IRI-9357731, Alfred P. Sloan Research Fellow Award BR3336, and a General Research Board Semester Award. (Also cross-referenced as UMIACS-TR-96-19) }, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/807}, author = {Oard, Douglas and Dorr, Bonnie J} } @article {15369, title = {2-D MOSFET modeling including surface effects and impact ionization by self-consistent solution of the Boltzmann, Poisson, and hole-continuity equations}, journal = {Electron Devices, IEEE Transactions on}, volume = {44}, year = {1997}, month = {1997/02//}, pages = {257 - 267}, abstract = {We present a new two-dimensional (2-D) MOSFET simulation method achieved by directly solving the Boltzmann transport equation for electrons, the hole-current continuity equation, and the Poisson equation self-consistently. The spherical harmonic method is used for the solution of the Boltzmann equation. The solution directly gives the electron distribution function, electrostatic potential, and the hole concentration for the entire 2-D MOSFET. Average quantities such as electron concentration and electron temperature are obtained directly from the integration of the distribution function. The collision integral is formulated to arbitrarily high spherical harmonic order, and new collision terms are included that incorporate effects of surface scattering and electron-hole pair recombination/generation. I-V characteristics, which agree with experiment, are calculated directly from the distribution function for an LDD submicron MOSFET. Electron-hole pair generation due to impact ionization is also included by direct application of the collision integral. The calculations are efficient enough for day-to-day engineering design on workstation-type computers}, keywords = {2D, characteristics;LDD, concentration;electron, concentration;hole-continuity, density;electron-hole, density;impact, device, distribution, effects;surface, equation;collision, equation;I-V, equation;MOSFET;electron, equations;impact, equations;semiconductor, function;electron, generation;electron-hole, harmonic, integral;electron, ionisation;integral, ionization;self-consistent, method;Boltzmann, method;surface, modeling;Boltzmann, models;surface, MOSFET, MOSFET;Poisson, pair, potential;hole, recombination;electrostatic, recombination;hole, scattering;, scattering;two-dimensional, simulation, solution;spherical, submicron, temperature;electron-hole, transport}, isbn = {0018-9383}, doi = {10.1109/16.557713}, author = {Liang,Wenchao and Goldsman,N. and Mayergoyz, Issak D and Oldiges,P.J.} } @conference {15870, title = {Adaptive filtering of multilingual document streams}, booktitle = {Fifth RIAO Conference on Computer Assisted Information Searching on the Internet, June}, year = {1997}, month = {1997///}, author = {Oard, Douglas} } @article {13726, title = {Aspectual Modifications to a LCS Database for NLP Applications}, year = {1997}, month = {1997///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {Verbal and compositional lexical aspect provide the underlying temporal structure ofevents. Knowledge of lexical aspect, e.g., (a)telicity, is therefore required for interpret- ing event sequences in discourse (Dowty, 1986: Moens and Steedman, 1988; Passoneau, 1988), interfacing to temporal databases (Androutsopoulos, 1996), processing temporal modifiers (Antonisse, 1994), describing allowable alternations and their semantic effects (Resnik, 1996; Tenny, 1994), and selecting tense and lexical items for natural language generation ((Dorr and Olsen, 1996; Klavans and Chodorow, 1992), cf. (Slobin and Bo- caz, 1988)). We show that it is possible to represent lexical aspect{\textemdash}both verbal and compositional{\textemdash}on a large scale, using Lexical Conceptual Structure (LCS) representa- tions of verbs in the classes cataloged by Levin (1993). We show how proper consideration of these universal pieces of verb meaning may be used to refine lexical representations and derive a range of meanings from combinations of LCS representations. A single al- gorithm may therefore be used to determine lexical aspect classes and features at both verbal and sentence levels. Finally, we illustrate how knowledge of lexical aspect facili- tates the interpretation of events in NLP applications. }, author = {Dorr, Bonnie J and Olsen,M.B.} } @conference {13753, title = {Deriving verbal and compositional lexical aspect for NLP applications}, booktitle = {Proceedings of the 35th Annual Meeting of the Association for Computational Linguistics and Eighth Conference of the European Chapter of the Association for Computational Linguistics}, series = {ACL {\textquoteright}98}, year = {1997}, month = {1997///}, pages = {151 - 158}, publisher = {Association for Computational Linguistics}, organization = {Association for Computational Linguistics}, address = {Stroudsburg, PA, USA}, abstract = {Verbal and compositional lexical aspect provide the underlying temporal structure of events. Knowledge of lexical aspect, e.g., (a)telicity, is therefore required for interpreting event sequences in discourse (Dowty, 1986; Moens and Steedman, 1988; Passoneau, 1988), interfacing to temporal databases (Androutsopoulos, 1996), processing temporal modifiers (Antonisse, 1994), describing allowable alternations and their semantic effects (Resnik, 1996; Tenny, 1994), and selecting tense and lexical items for natural language generation ((Dorr and Olsen, 1996; Klavans and Chodorow, 1992), cf. (Slobin and Bocaz, 1988)). We show that it is possible to represent lexical aspect---both verbal and compositional---on a large scale, using Lexical Conceptual Structure (LCS) representations of verbs in the classes cataloged by Levin (1993). We show how proper consideration of these universal pieces of verb meaning may be used to refine lexical representations and derive a range of meanings from combinations of LCS representations. A single algorithm may therefore be used to determine lexical aspect classes and features at both verbal and sentence levels. Finally, we illustrate how knowledge of lexical aspect facilitates the interpretation of events in NLP applications.}, doi = {10.3115/976909.979637}, url = {http://dx.doi.org/10.3115/976909.979637}, author = {Dorr, Bonnie J and Olsen,Mari Broman} } @article {14473, title = {Effective redundant constraints for online scheduling}, journal = {PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE}, year = {1997}, month = {1997///}, pages = {302 - 307}, abstract = {The use of heuristics as a means to improve constraint solverperformance has been researched widely. However, most work has been on problem-independent heuristics (e.g., vari- able and value ordering), and has focused on offline prob- lems (e.g., one-shot constraint satisfaction). In this paper, we present an online scheduling problem for which we are developing a real-time scheduling algorithm. While we can and do use generic heuristics in the scheduler, here we fo- cus on the use of domain-specific redundant constraints to ef- fectively approximate optimal offline solutions. We present a taxonomy of redundant domain constraints, and examine their impact on the effectiveness of the scheduler. We also describe several techniques for generating redundant con- straints, which can be applied to a large class of job shop scheduling problems. }, author = {Getoor, Lise and Ottosson,G. and Fromherz,M. and Carlson,B.} } @article {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 {16706, title = {Implicit object constructions and the (in) transitivity continuum}, journal = {33rd Proceedings of the Chicago Linguistic Society}, year = {1997}, month = {1997///}, pages = {327 - 336}, author = {Olsen,M.B. and Resnik, Philip} } @inbook {15795, title = {Regularization algorithms based on total least squares}, booktitle = {Recent advances in total least squares techniques and errors-in-variables modeling (Leuven, 1996)Recent advances in total least squares techniques and errors-in-variables modeling (Leuven, 1996)}, year = {1997}, month = {1997///}, pages = {127 - 137}, publisher = {SIAM}, organization = {SIAM}, address = {Philadelphia, PA}, author = {Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.} } @article {15796, title = {Regularization by Truncated Total Least Squares}, journal = {SIAM Journal on Scientific Computing}, volume = {18}, year = {1997}, month = {1997///}, pages = {1223 - 1241}, abstract = {The total least squares (TLS) method is a successful method for noise reduction in linear least squares problems in a number of applications. The TLS method is suited to problems in which both the coefficient matrix and the right-hand side are not precisely known. This paper focuses on the use of TLS for solving problems with very ill-conditioned coefficient matrices whose singular values decay gradually (so-called discrete ill-posed problems), where some regularization is necessary to stabilize the computed solution. We filter the solution by truncating the small singular values of the TLS matrix. We express our results in terms of the singular value decomposition (SVD) of the coefficient matrix rather than the augmented matrix. This leads to insight into the filtering properties of the truncated TLS method as compared to regularized least squares solutions. In addition, we propose and test an iterative algorithm based on Lanczos bidiagonalization for computing truncated TLS solutions.}, keywords = {bidiagonalization, discrete ill-posed problems, regularization, total least squares}, doi = {10.1137/S1064827594263837}, url = {http://link.aip.org/link/?SCE/18/1223/1}, author = {Fierro,R. D. and Golub, G. H and Hansen,P. C. and O{\textquoteright}Leary, Dianne P.} } @article {15900, title = {Serving Users in Many Languages: Cross-Language Information Retrievalfor Digital Libraries}, year = {1997}, month = {1997///}, institution = {Corporation for National Research Initiatives}, author = {Oard, Douglas} } @article {15871, title = {The state of the art in text filtering}, journal = {User Modeling and User-Adapted Interaction}, volume = {7}, year = {1997}, month = {1997///}, pages = {141 - 178}, author = {Oard, Douglas} } @article {13878, title = {Toward Compact Monotonically Compositional Interlingua Using Lexical Aspect}, year = {1997}, month = {1997/12//}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {We describe a theoretical investigation into the semantic space described by our interlingua (IL), which currently has 191 main verb classes divided into 434 subclasses. represented by 237 distinct Lexical Conceptual Structures (LCSs). Using the model of aspect in Olsen (1994b, 1997a) monotonic aspectual composition we have identified 71 aspectually basic subclasses that are associated with one or more of 68 aspectually non-basic classes via some lexical ("type-shifting") rule (Bresnan 1982, Pinker 1984, Levin and Rappaport Hovav 1995). This allows us to refine the IL and address certain computational and theoretical issues at the same time. From a linguistic viewpoint, the expected benefits include a refinement of the aspectual model in (Olsen :1994b, 1997a) (which provides necessary but not sufficient conditions for aspectual composition), and a refinement of the verb classifications in (Levin 1993); we also expect our approach to eventually produce a systematic definition (in terms of LCSs and compositional operations) of the precise meaning components responsible for Levin{\textquoteright}s classification. Computationally, the lexicon is made more compact.}, keywords = {*LEXICOGRAPHY, *SEMANTICS, COMPOSITION(PROPERTY), linguistics, MODELS, STRUCTURES, THEORY, Vocabulary}, url = {http://stinet.dtic.mil/oai/oai?\&verb=getRecord\&metadataPrefix=html\&identifier=ADA458248}, author = {Dorr, Bonnie J and Olsen,Mari B and Thomas,Scott C} } @article {13891, title = {Using WordNet to Posit Hierarchical Structure in Levin{\textquoteright}s Verb Classes}, year = {1997}, month = {1997///}, institution = {Instititue for Advanced Computer Studies, Univ of Maryland, College Park}, abstract = {In this paper we report on experiments using WordNet synset tags to evaluate the seman-tic properties of the verb classes cataloged by Levin 1993. This paper represents ongoing research begun at the University of Pennsylvania (Rosenzweig et al. 1997, Palmer et al. 1997) and the University of Maryland (Dorr and Jones 1996b, 1996d, 1996e). Using WordNet sense tags to constrain the intersection of Levin classes, we avoid spurious class intersections introduced by homonymy and polysemy (run a bath, run a mile). By adding class intersections based on a single shared sense-tagged word, we minimize the impact of the non-exhaustiveness of Levin{\textquoteright}s database (Dorr and Olsen 1996, Dorr to appear). By examining the syntactic properties of the intersective classes, we provide a clearer picture of the relationship between WordNet/EuroWordNet and the LCS interlingua for machine translation and other NLP applications. }, author = {Olsen,M.B. and Dorr, Bonnie J and Clark,D.J.} } @article {15697, title = {A Block-GTH Algorithm for Finding the Stationary Vector of a Markov Chain}, journal = {SIAM Journal on Matrix Applications}, volume = {17}, year = {1996}, month = {1996///}, pages = {470 - 488}, url = {http://epubs.siam.org/sam-bin/dbq/article/26253http://epubs.siam.org/sam-bin/dbq/article/26253}, author = {O{\textquoteright}Leary, Dianne P. and Wu,Yuan-Jye Jason} } @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.} } @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 {13832, title = {Multilingual generation: The role of telicity in lexical choice and syntactic realization}, journal = {Machine Translation}, volume = {11}, year = {1996}, month = {1996///}, pages = {37 - 74}, abstract = {Multilingual generation in machine translation (MT) requires a knowledge organization that facilitates the task of lexical choice, i.e. selection of lexical units to be used in the generation of a target-language sentence. This paper investigates the extent to which lexicalization patterns involving the lexical aspect feature [+telic] may be used for translating events and states among languages. Telicity has been correlated syntactically with both transitivity and unaccusativity, and semantically with Talmy{\textquoteright}s {\textquoteleft}path{\textquoteright} of a motion event, the representation of which characterizes languages parametrically.}, isbn = {0922-6567}, url = {http://dx.doi.org/10.1007/BF00349353}, author = {Dorr, Bonnie J and Olsen,Mari Broman} } @conference {13769, title = {Experimental investigation of high performance cognitive and interactive text filtering}, booktitle = {, IEEE International Conference on Systems, Man and Cybernetics, 1995. Intelligent Systems for the 21st Century}, volume = {5}, year = {1995}, month = {1995/10/22/25}, pages = {4398-4403 vol.5 - 4398-4403 vol.5}, publisher = {IEEE}, organization = {IEEE}, abstract = {Text filtering has become increasingly important as the volume of networked information has exploded in recent years. This paper reviews recent progress in that field and reports on the development of a testbed for experimental investigation of cognitive and interactive text selection based on a history of user evaluations. An interactive filtering system model is presented and a new cognitive filtering technique which the authors call the Gaussian User Model is described. Because development of analytic measures of text selection effectiveness has proven intractable, the authors have modified the Cornell SMART text retrieval system to create a flexible text filtering testbed for experimental determination of filtering effectiveness. The paper concludes with a description of the design of this testbed system}, keywords = {Cause effect analysis, Computer science, Contracts, Cornell SMART text retrieval system, Educational institutions, Gaussian User Model, high performance cognitive interactive text filtering, History, Information filtering, Information filters, Information retrieval, information retrieval system evaluation, Libraries, Matched filters, online front-ends, Query processing, System testing, text selection effectiveness, user evaluations, User interfaces, user modelling}, isbn = {0-7803-2559-1}, doi = {10.1109/ICSMC.1995.538486}, author = {Oard, Douglas and DeClaris,N. and Dorr, Bonnie J and Faloutsos,C. and Marchionini,G.} } @article {13018, title = {Sampling properties of DNA sequence data in phylogenetic analysis}, journal = {Mol Biol Evol}, volume = {12}, year = {1995}, month = {1995/09//}, pages = {814 - 822}, abstract = {We inferred phylogenetic trees from individual genes and random samples of nucleotides from the mitochondrial genomes of 10 vertebrates and compared the results to those obtained by analyzing the whole genomes. Individual genes are poor samples in that they infrequently lead to the whole-genome tree. A large number of nucleotide sites is needed to exactly determine the whole-genome tree. A relatively small number of sites, however, often results in a tree close to the whole-genome tree. We found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome. Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies.}, author = {Cummings, Michael P. and Otto,S. P and Wakeley,J.} } @inbook {15821, title = {The SVD in Image Restoration}, booktitle = {SVD and Signal Processing III: Algorithms, Architectures, and ApplicationsSVD and Signal Processing III: Algorithms, Architectures, and Applications}, year = {1995}, month = {1995///}, pages = {315 - 322}, publisher = {Elsevier}, organization = {Elsevier}, address = {New York}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Moonen,Marc and DeMoor,Bart} } @inbook {15829, title = {What is Fundamental for Markov Chains: First Passage Times, Fundamental Matrices, and Group Generalized Inverses}, booktitle = {Proceedings of the Second International Workshop on Markov ChainsProceedings of the Second International Workshop on Markov Chains}, year = {1995}, month = {1995///}, pages = {151 - 161}, publisher = {Kluwer Academic Publishers}, organization = {Kluwer Academic Publishers}, author = {Heyman,D. P. and O{\textquoteright}Leary, Dianne P.}, editor = {Stewart,W.} } @article {15830, title = {Why Broyden{\textquoteright}s Nonsymmetric Method Terminates on Linear Equations}, journal = {SIAM Journal on Optimization}, volume = {5}, year = {1995}, month = {1995///}, pages = {231 - 235}, author = {O{\textquoteright}Leary, Dianne P.} } @conference {13837, title = {On automatic filtering of multilingual texts}, booktitle = {, 1994 IEEE International Conference on Systems, Man, and Cybernetics, 1994. {\textquoteright}Humans, Information and Technology{\textquoteright}}, volume = {2}, year = {1994}, month = {1994/10/02/5}, pages = {1645-1650 vol.2 - 1645-1650 vol.2}, publisher = {IEEE}, organization = {IEEE}, abstract = {An emerging requirement to sift through the increasing flood of text information has led to the rapid development of information filtering technology in the past five years. This study introduces novel approaches for filtering texts regardless of their source language. We begin with a brief description of related developments in text filtering and multilingual information retrieval. We then present three alternative approaches to selecting texts from a multilingual information stream which represent a logical evolution from existing techniques in related disciplines. Finally, a practical automated performance evaluation technique is proposed}, keywords = {automated performance evaluation, Business communication, Computer science, Discussion forums, Displays, Educational institutions, Floods, Government, Information filtering, Information filters, Information retrieval, multilingual information retrieval, multilingual text filtering, natural languages, performance evaluation}, isbn = {0-7803-2129-4}, doi = {10.1109/ICSMC.1994.400083}, author = {Oard, Douglas and DeClaris,N. and Dorr, Bonnie J and Faloutsos,C.} } @article {15732, title = {Confidence Intervals for Discrete Approximations to Ill-Posed Problems}, journal = {The Journal of Computational and Graphical Statistics}, volume = {3}, year = {1994}, month = {1994///}, pages = {67 - 96}, author = {Rust,Bert W. and O{\textquoteright}Leary, Dianne P.} } @article {15820, title = {The linear algebra of block quasi-newton algorithms}, journal = {Linear Algebra and its Applications}, volume = {212{\textendash}213}, year = {1994}, month = {1994/11/15/}, pages = {153 - 168}, abstract = {The quasi-Newton family of algorithms for minimizing functions and solving systems of nonlinear equations has achieved a great deal of computational success and forms the core of many software libraries for solving these problems. In this work we extend the theory of the quasi-Newton algorithms to the block case, in which we minimize a collection of functions having a common Hessian matrix, or we solve a collection of nonlinear equations having a common Jacobian matrix. This paper focuses on the linear algebra: update formulas, positive definiteness, least-change secant properties, relation to block conjugate gradient algorithms, finite termination for quadratic function minimization or solving linear systems, and the use of the quasi-Newton matrices as preconditioners.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(94)90401-4}, url = {http://www.sciencedirect.com/science/article/pii/0024379594904014}, author = {O{\textquoteright}Leary, Dianne P. and Yeremin,A.} } @article {15782, title = {Parallel Computing: Emerging from a Time Warp}, journal = {IEEE Computational Science \& Engineering}, volume = {1}, year = {1994}, month = {1994///}, pages = {1,15 - 1,15}, author = {O{\textquoteright}Leary, Dianne P.} } @proceedings {15797, title = {Regularization by Truncated Total Least Squares}, year = {1994}, month = {1994///}, pages = {250 - 254}, publisher = {SIAM Press}, address = {Philadelphia}, author = {Fierro,Richardo and Golub, Gene H. and Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.}, editor = {Lewis,J.G.} } @inbook {15798, title = {Regularization of Ill-Posed Problems in Image Restoration}, booktitle = {Proceedings of the Fifth SIAM Conference on Applied Linear AlgebraProceedings of the Fifth SIAM Conference on Applied Linear Algebra}, year = {1994}, month = {1994///}, pages = {102 - 105}, publisher = {SIAM Press}, organization = {SIAM Press}, address = {Philadelphia}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Lewis,J.G.} } @inbook {15809, title = {Some Themes in Gene H.Golub{\textquoteright}s Work on Iterative Methods}, booktitle = {Recent Advances in Iterative MethodsRecent Advances in Iterative Methods}, volume = {60}, year = {1994}, month = {1994///}, pages = {1 - 11}, publisher = {Springer-Verlag IMA Volumes in Mathematics and Its Applications}, organization = {Springer-Verlag IMA Volumes in Mathematics and Its Applications}, address = {New York}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Golub, Gene H. and Greenbaum,Anne and Luskin,Mitchell} } @article {12183, title = {Space variant image processing}, journal = {International Journal of Computer Vision}, volume = {13}, year = {1994}, month = {1994///}, pages = {71 - 90}, author = {Wallace,R.S. and Ong,P.W. and Bederson, Benjamin B. and Schwartz,E.L.} } @article {15828, title = {URV ESPRIT for tracking time-varying signals}, journal = {Signal Processing, IEEE Transactions on}, volume = {42}, year = {1994}, month = {1994/12//}, pages = {3441 - 3448}, abstract = {ESPRIT is an algorithm for determining the fixed directions of arrival of a set of narrowband signals at an array of sensors. Unfortunately, its computational burden makes it unsuitable for real time processing of signals with time-varying directions of arrival. The authors develop a new implementation of ESPRIT that has potential for real time processing. It is based on a rank-revealing URV decomposition, rather than the eigendecomposition or singular value decomposition used in previous ESPRIT algorithms. The authors demonstrate its performance on simulated data representing both constant and time-varying signals. They find that the URV-based ESPRIT algorithm is effective for estimating time-varying directions-of-arrival at considerable computational savings over the SVD-based algorithm}, keywords = {arrival;narrowband, decomposition;real, directions, ESPRIT;fixed, estimation;real-time, of, processing;time-varying, signals;performance;rank-revealing, signals;tracking;direction-of-arrival, systems;time-varying, systems;tracking;, TIME, URV}, isbn = {1053-587X}, doi = {10.1109/78.340778}, author = {Liu,K. J.R and O{\textquoteright}Leary, Dianne P. and Stewart, G.W. and Wu,Y.-J.J.} } @conference {15713, title = {An adaptive ESPRIT based on URV decomposition}, booktitle = {Acoustics, Speech, and Signal Processing, 1993. ICASSP-93., 1993 IEEE International Conference on}, volume = {4}, year = {1993}, month = {1993/04//}, pages = {37 -40 vol.4 - 37 -40 vol.4}, abstract = {ESPRIT is an algorithm for determining the fixed directions of arrival of a set of narrowband signals at an array of sensors. Its computational burden makes it unsuitable for real-time processing of signals with time-varying directions of arrival. The authors develop a new implementation of ESPRIT that has potential for real-time processing. It is based on a rank-revealing URV decomposition, rather than the eigendecomposition or singular value decomposition (SVD) used in previous ESPRIT algorithms. Its performance is demonstrated on simulated data representing both constant and time-varying signals. It is shown that the URV-based ESPRIT algorithm is effective for estimating time-varying directions-of-arrival at considerable computational savings over the SVD-based algorithm.<>}, keywords = {algorithm;array, complexity;parameter, decomposition;real-time, ESPRIT, estimation;real-time, filters;array, of, processing;adaptive, processing;computational, savings;performance;rank-revealing, sensors;computational, signal, systems;, systems;time-varying, URV, URV-based}, doi = {10.1109/ICASSP.1993.319588}, author = {Liu,K. J.R and O{\textquoteright}Leary, Dianne P. and Stewart, G.W. and Wu,Y.-J.J.} } @article {16956, title = {Alpha Slider: Searching Textual Lists with Sliders}, journal = {Institute for Systems Research Technical Reports}, year = {1993}, month = {1993///}, abstract = {AlphaSlider is a query interface that uses a direct manipulation slider to select words, phrases, or names from an existing list. This paper introduces a prototype of AlphaSlider, describes the design issues, reports on an experimental evaluation, and offers directions for further research. The experiment tested 24 subjects selecting items from lists of 40, 80, 160, and 320 entries. Mean selection times only doubled with the 8-fold increase in list length. Users quickly accommodated to this selection method.}, keywords = {direct manipulation, Human-computer interaction, keyboard data entry, sliders, Systems Integration, touchscreen}, url = {http://drum.lib.umd.edu/handle/1903/5397}, author = {Osada,M. and Liao,Holmes and Shneiderman, Ben} } @article {16957, title = {Alphaslider: Development and Evaluation of Text Retrieval Methods Using Sliders}, journal = {Ninth Symposium on Human Interface}, year = {1993}, month = {1993///}, pages = {91 - 94}, abstract = {AlphaSlider is a query interface that uses a direct manipulation slider to select words, phrases, or names from an existing list. This paper introduces a prototype of AlphaSlider, describes the design issues, reports on an experimental evaluation, and offers directions for further research. The experiment tested 24 subjects selecting items from lists of 40, 80, 160, and 320 entries. Mean selection times only doubled with the 8-fold increase in list length. Users quickly accommodated to this selection method.}, author = {Osada,M. and Liao,H. and Shneiderman, Ben} } @conference {17000, title = {Browsing Unix directories with dynamic queries: An analytical and experimental evaluation}, booktitle = {Proc. Ninth Japanese Symp. Human Interface}, year = {1993}, month = {1993///}, pages = {95 - 98}, abstract = {We designed, implemented, and evaluated an innovative concept for dynamic queries which involves the direct manipulation of small databases. Our domain was directories in a Unix file system. Dynamic queries allow users to formulate queries and explore the databases with graphical widgets, such as sliders and buttons, without requiring them to have any knowledge about the underlying structure of the database query languages, or command language syntax. Three interfaces for presenting directories were developed and tested with eighteen subjects in a within-subject design. The results of the formative evaluation yielded some useful guidelines for software designers.}, author = {Liao,H. and Osada,M. and Shneiderman, Ben} } @inbook {15764, title = {Iterative Methods for Finding the Stationary Vector for Markov Chains}, booktitle = {Linear Algebra, Markov Chains, and Queuing ModelsLinear Algebra, Markov Chains, and Queuing Models}, volume = {48}, year = {1993}, month = {1993///}, pages = {125 - 136}, publisher = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, organization = {Springer-Verlag IMA Volumes in Math. and Its Applics.}, address = {New York}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Meyer,Carl and Plemmons,Robert} } @article {15702, title = {A Krylov multisplitting algorithm for solving linear systems of equations}, journal = {Linear Algebra and its Applications}, volume = {194}, year = {1993}, month = {1993/11/15/}, pages = {9 - 29}, abstract = {We consider the practical implementation of Krylov subspace methods (conjugate gradients, Gmres, etc.) for parallel computers in the case where the preconditioning matrix arises from a multisplitting. We show that the algorithm can be efficiently implemented by dividing the work into tasks that generate search directions and a single task that minimizes over the resulting subspace. Each task is assigned to a subset of processors. It is not necessary for the minimization task to send frequent information to the direction generating tasks, and this leads to high utilization with a minimum of synchronization. We study the convergence properties of various forms of the algorithm and present results of numerical examples on a sequential computer.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(93)90110-A}, url = {http://www.sciencedirect.com/science/article/pii/002437959390110A}, author = {Huang,Chiou-Ming and O{\textquoteright}Leary, Dianne P.} } @article {15822, title = {The Use of the L-Curve in the Regularization of Discrete Ill-Posed Problems}, journal = {SIAM Journal on Scientific Computing}, volume = {14}, year = {1993}, month = {1993///}, pages = {1487 - 1503}, abstract = {Regularization algorithms are often used to produce reasonable solutions to ill-posed problems. The L-curve is a plot{\textemdash}for all valid regularization parameters{\textemdash}of the size of the regularized solution versus the size of the corresponding residual. Two main results are established. First a unifying characterization of various regularization methods is given and it is shown that the measurement of {\textquotedblleft}size{\textquotedblright} is dependent on the particular regularization method chosen. For example, the 2-norm is appropriate for Tikhonov regularization, but a 1-norm in the coordinate system of the singular value decomposition (SVD) is relevant to truncated SVD regularization. Second, a new method is proposed for choosing the regularization parameter based on the L-curve, and it is shown how this method can be implemented efficiently. The method is compared to generalized cross validation and this new method is shown to be more robust in the presence of correlated errors.}, keywords = {discrepancy principle, generalized cross validation, ill-posed problems, L-curve, parameter choice, regularization}, doi = {10.1137/0914086}, url = {http://link.aip.org/link/?SCE/14/1487/1}, author = {Hansen,Per Christian and O{\textquoteright}Leary, Dianne P.} } @article {15737, title = {Constrained Matrix Sylvester Equations}, journal = {SIAM Journal on Matrix Analysis and Applications}, volume = {13}, year = {1992}, month = {1992///}, pages = {1 - 9}, abstract = {The problem of finding matrices $L$ and $T$ satisfying $TA - FT = LC$ and $TB = 0$ is considered. Existence conditions for the solution are established and an algorithm for computing the solution is derived. Conditions under which the matrix $[C^T ,T^T ]$ is full rank are also discussed. The problem arises in control theory in the design of reduced-order observers that achieve loop transfer recovery.}, keywords = {loop transfer recovery, matrix Liapunov equation, Sylvester operator}, doi = {10.1137/0613002}, url = {http://link.aip.org/link/?SML/13/1/1}, author = {Barlow,Jewel B. and Monahemi,Moghen M. and O{\textquoteright}Leary, Dianne P.} } @article {15818, title = {The Design of Reduced Order Observers with Precise Loop Transfer Recovery}, journal = {AIAA Journal of Guidance, Control, and Dynamics}, volume = {15}, year = {1992}, month = {1992///}, pages = {1320 - 1326}, author = {Monahemi,Moghen M. and Barlow,Jewel B. and O{\textquoteright}Leary, Dianne P.} } @book {16924, title = {A formative evaluation of three interfaces for browsing directories using dynamic queries}, year = {1992}, month = {1992///}, publisher = {University of Maryland, Center for Automation Research, Computer Vision Laboratory}, organization = {University of Maryland, Center for Automation Research, Computer Vision Laboratory}, author = {Liao,H.S. and Osada,M. and Shneiderman, Ben} } @inbook {15779, title = {On the Precise Loop Transfer Recovery and Transmission Zeroes}, booktitle = {First IEEE Conference on Control ApplicationsFirst IEEE Conference on Control Applications}, year = {1992}, month = {1992/09//}, address = {Dayton, Ohio}, author = {Monahemi,M. and Barlow,J. and O{\textquoteright}Leary, Dianne P.} } @conference {15789, title = {Preconditioning parallel multisplittings for solving linear systems of equations}, booktitle = {Proceedings of the 6th international conference on Supercomputing}, series = {ICS {\textquoteright}92}, year = {1992}, month = {1992///}, pages = {478 - 484}, publisher = {ACM}, organization = {ACM}, address = {New York, NY, USA}, abstract = {We consider the practical implementation of Krylov subspace methods (conjugate gradients, GMRES, etc.) for parallel computers in the case where the preconditioning matrix is a multisplitting. The algorithm can be efficiently implemented by dividing the work into tasks that generate search directions and a single task that minimizes over the resulting subspace. Each task is assigned to a subset of processors. It is not necessary for the minimization task to send information to the direction generating tasks, and this leads to high utilization with a minimum of synchronization. We study the convergence properties of various forms of the algorithm.}, isbn = {0-89791-485-6}, doi = {10.1145/143369.143454}, url = {http://doi.acm.org/10.1145/143369.143454}, author = {Huang,Chiou-Ming and O{\textquoteright}Leary, Dianne P.} } @inbook {15736, title = {Considerations on Loop Transfer Recovery for Non-minimum Phase Plants}, booktitle = {Proceedings of the AIAA Aircraft Design Systems and Operations MeetingProceedings of the AIAA Aircraft Design Systems and Operations Meeting}, volume = {AIAA-91-3086}, year = {1991}, month = {1991/09//}, address = {Baltimore}, author = {Monahemi,M. and Barlow,J. and O{\textquoteright}Leary, Dianne P.} } @inbook {15817, title = {The Design of Reduced Order Luenberger Observers with Precise LTR}, booktitle = {Proceedings of the AIAA Meeting on Guidance, Navigation and ControlProceedings of the AIAA Meeting on Guidance, Navigation and Control}, volume = {AIAA-91-2731}, year = {1991}, month = {1991/08//}, address = {New Orleans}, abstract = {This work concerns the design of reduced-order observers for controllable, observable, and regular systems in which the number of measurements is more than the number of controls. It uses eigenstructure assignment whereas other approaches use Kalman filter (LQG/LTR) methods. The advantages of this approach are: (1) precise LTR rather than approximate LTR, (2) no restriction to minimum phase systems, (3) finite observer gain rather than asymptotic observer gain, and (4) simpler and more efficient numerical calculation. Case studies are presented illustrating these features in aircraft control applications.}, author = {Monahemi,M. and Barlow,J. and O{\textquoteright}Leary, Dianne P.} } @article {15833, title = {Yet another polynomial preconditioner for the conjugate gradient algorithm}, journal = {Linear Algebra and its Applications}, volume = {154{\textendash}156}, year = {1991}, month = {1991/08//}, pages = {377 - 388}, abstract = {Polynomial preconditioning is a useful tool in the effective use of the conjugate gradient algorithm on special architectures such as message-passing parallel computers, machines with hierarchical memory, vector processors, and machines with very limited memory. In this work we investigate the use of a new adaptive algorithm which uses the polynomial preconditioner based on the residual polynomial from k steps of the conjugate gradient algorithm.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(91)90385-A}, url = {http://www.sciencedirect.com/science/article/pii/002437959190385A}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15776, title = {On bounds for scaled projections and pseudoinverses}, journal = {Linear Algebra and its Applications}, volume = {132}, year = {1990}, month = {1990/04/15/}, pages = {115 - 117}, abstract = {Let X be a matrix of full column rank, and let D be a positive definite diagonal matrix. In a recent paper, Stewart considered the weighted pseudoinverse X{\textdagger}D = (XTDX)-1XTD and the associated oblique projection PD = XX{\textdagger}D, and gave bounds, independent of D, for the norms of these matrices. In this note, we answer a question he raised by showing that the bounds are computable.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(90)90056-I}, url = {http://www.sciencedirect.com/science/article/pii/002437959090056I}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15731, title = {Computing the eigenvalues and eigenvectors of symmetric arrowhead matrices}, journal = {Journal of Computational Physics}, volume = {90}, year = {1990}, month = {1990/10//}, pages = {497 - 505}, isbn = {0021-9991}, doi = {10.1016/0021-9991(90)90177-3}, url = {http://www.sciencedirect.com/science/article/pii/0021999190901773}, author = {O{\textquoteright}Leary, Dianne P. and Stewart, G.W.} } @article {16639, title = {Connectionist models and information retrieval}, journal = {Annual review of information science and technology}, volume = {25}, year = {1990}, month = {1990///}, pages = {209 - 262}, author = {Doszkocs,T. E and Reggia, James A. and others} } @article {15784, title = {Parallel QR factorization by householder and modified Gram-Schmidt algorithms}, journal = {Parallel Computing}, volume = {16}, year = {1990}, month = {1990/11//}, pages = {99 - 112}, abstract = {In this paper, the parallel implementation of two algorithms for forming a QR factorization of a matrix is studied. We propose parallel algorithms for the modified Gram-Schmidt and the Householder algorithms on message passing systems in which the matrix is distributed by blocks or rows. The models that predict performance of the algorithms are validated by experimental results on several parallel machines.}, keywords = {Gram-Schmidt algorithm, Householder algorithm, Message passing systems, QR factorization}, isbn = {0167-8191}, doi = {10.1016/0167-8191(90)90163-4}, url = {http://www.sciencedirect.com/science/article/pii/0167819190901634}, author = {O{\textquoteright}Leary, Dianne P. and Whitman,Peter} } @article {15801, title = {Robust Regression Computation Using Iteratively Reweighted Least Squares}, journal = {SIAM Journal of Matrix Analysis and Applications}, volume = {11}, year = {1990}, month = {1990///}, pages = {466 - 480}, author = {O{\textquoteright}Leary, Dianne P.} } @inbook {15743, title = {Domino: A Transportable System for Parallel Processing}, booktitle = {Parallel Processing and Medium-Scale Multiprocessors (Proceedings of a 1986 Conference)Parallel Processing and Medium-Scale Multiprocessors (Proceedings of a 1986 Conference)}, year = {1989}, month = {1989///}, pages = {25 - 34}, publisher = {SIAM Press}, organization = {SIAM Press}, address = {Philadelphia}, author = {O{\textquoteright}Leary, Dianne P. and Stewart, G.W. and Geijn,Robert van de}, editor = {Wouk,Arthur} } @article {15808, title = {Some History of the Conjugate Gradient and Lanczos Algorithms: 1948{\textendash}1976}, journal = {SIAM Review}, volume = {31}, year = {1989}, month = {1989///}, pages = {50 - 102}, abstract = {This paper gives some of the history of the conjugate gradient and Lanczos algorithms and an annotated bibliography for the period 1948-1976}, keywords = {Conjugate gradient algorithm, Lanczos algorithm, variable metric algorithms}, doi = {10.1137/1031003}, url = {http://link.aip.org/link/?SIR/31/50/1}, author = {Golub, Gene H. and O{\textquoteright}Leary, Dianne P.} } @article {17354, title = {Selection devices for user of an electronic encyclopedia: An empirical comparison of four possibilities}, journal = {Information Processing \& Management}, volume = {24}, year = {1988}, month = {1988///}, pages = {665 - 680}, abstract = {This study measured the speed, error rates, and subjective evaluation of arrow-jump keys, a jump-mouse, number keys, and a touch screen in an interactive encyclopedia. A summary of previous studies comparing selection devices and strategies is presented to provide the background for this study. We found the touch screen to be the fastest in time, the least accurate but the overall favorite of the participants. The results are discussed and improvements are suggested accordingly.}, isbn = {0306-4573}, doi = {10.1016/0306-4573(88)90004-0}, url = {http://www.sciencedirect.com/science/article/pii/0306457388900040}, author = {Ostroff,Daniel and Shneiderman, Ben} } @article {15807, title = {Some algorithms for approximating convolutions}, journal = {Computer Vision, Graphics, and Image Processing}, volume = {41}, year = {1988}, month = {1988/03//}, pages = {333 - 345}, abstract = {This paper presents some algorithms for approximating two-dimensional convolution operators of size n {\texttimes} n, n odd, by a product, or sum of products, of 3 {\texttimes} 3 convolutions. Inaccuracies resulting from the approximation as well as from fixed point computation are discussed and examples are given.}, isbn = {0734-189X}, doi = {10.1016/0734-189X(88)90107-7}, url = {http://www.sciencedirect.com/science/article/pii/0734189X88901077}, author = {O{\textquoteright}Leary, Dianne P.} } @inbook {15755, title = {Fine and Medium Grained Parallel Algorithms for Matrix QR Factorization}, booktitle = {Algorithms and Applications on Vector and Parallel ComputersAlgorithms and Applications on Vector and Parallel Computers}, year = {1987}, month = {1987///}, pages = {347 - 349}, publisher = {Elsevier Science Publishers B.V. (North Holland)}, organization = {Elsevier Science Publishers B.V. (North Holland)}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Riele,H.J.J. te and Dekker,Th.J. and Vorst,H.A. van der} } @article {15756, title = {From Determinacy to Systaltic Arrays}, journal = {Computers, IEEE Transactions on}, volume = {C-36}, year = {1987}, month = {1987/11//}, pages = {1355 - 1359}, abstract = {In this paper we extend a model of Karp and Miller for parallel computation. We show that the extended model is deterministic, in the sense that under different scheduling regimes each process in the computation consumes the same input and generates the same output. Moreover, if the computation halts, the final state is independent of scheduling. The model is applied to the generation of precedence graphs, from which lower time bounds may be deduced, and to the synchronization of systolic arrays by local rather than global control.}, isbn = {0018-9340}, doi = {10.1109/TC.1987.5009475}, author = {O{\textquoteright}Leary, Dianne P. and Stewart, G.W.} } @article {15703, title = {A note on the capacitance matrix algorithm, substructuring, and mixed or neumann boundary conditions}, journal = {Applied Numerical Mathematics}, volume = {3}, year = {1987}, month = {1987/08//}, pages = {339 - 345}, abstract = {We develop in this work variants of the capacitance matrix algorithm which can be used to solve discretizations of elliptic partial differential equations when either the original system of equations or one which arises from substructuring has a rank-deficient matrix.}, isbn = {0168-9274}, doi = {10.1016/0168-9274(87)90038-9}, url = {http://www.sciencedirect.com/science/article/pii/0168927487900389}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15783, title = {Parallel implementation of the block conjugate gradient algorithm}, journal = {Parallel Computing}, volume = {5}, year = {1987}, month = {1987/07//}, pages = {127 - 139}, abstract = {The conjugate gradient algorithm is well-suited for vector computation but, because of its many synchronization points and relatively short message packets, is more difficult to implement for parallel computation. In this work we introduce a parallel implementation of the block conjugate gradient alhorithm. In this algorithm, we carry a block of vectors along at each iteration, reducing the number of iterations and increasing the length of each message. On machines with relatively costly message passing, this algorithm is a significant improvement over the standard conjugate gradient algorithm.}, keywords = {Conjugate gradient algorithm, message passing architectures, parallel implementation}, isbn = {0167-8191}, doi = {10.1016/0167-8191(87)90013-5}, url = {http://www.sciencedirect.com/science/article/pii/0167819187900135}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15814, title = {Systolic Arrays for Matrix Transpose and Other Reorderings}, journal = {Computers, IEEE Transactions on}, volume = {C-36}, year = {1987}, month = {1987/01//}, pages = {117 - 122}, abstract = {In this correspondence, a systolic array is described for computing the transpose of an n {\~A}— n matrix in time 3n - 1 using n2 switching processors and n2 bit buffers. A one-dimensional implementation is also described. Arrays are also given to take a matrix in by rows and put it out by diagonals, and vice versa.}, isbn = {0018-9340}, doi = {10.1109/TC.1987.5009457}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15717, title = {Assignment and scheduling in parallel matrix factorization}, journal = {Linear Algebra and its Applications}, volume = {77}, year = {1986}, month = {1986/05//}, pages = {275 - 299}, abstract = {We consider the problem of factoring a dense n{\texttimes}n matrix on a network consisting of P MIMD processors, with no shared memory, when the network is smaller than the number of elements in the matrix (P\<n2). The specific example analyzed is a computational network that arises in computing the LU, QR, or Cholesky factorizations. We prove that if the nodes of the network are evenly distributed among processors and if computations are scheduled by a round-robin or a least-recently-executed scheduling algorithm, then optimal order of speedup is achieved. However, such speedup is not necessarily achieved for other scheduling algorithms or if the computation for the nodes is inappropriately split across processors, and we give examples of these phenomena. Lower bounds on execution time for the algorithm are established for two important node-assignment strategies.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(86)90172-2}, url = {http://www.sciencedirect.com/science/article/pii/0024379586901722}, author = {O{\textquoteright}Leary, Dianne P. and Stewart, G.W.} } @article {15733, title = {Confidence Intervals for Inequality-Constrained Least Squares Problems, with Applications to Ill-Posed Problems}, journal = {SIAM Journal on Scientific and Statistical Computing}, volume = {7}, year = {1986}, month = {1986///}, pages = {473 - 489}, abstract = {Computing confidence intervals for functions b(x) wT"x,where Kx y + e and e is a normallydistributed error vector, is a standard problem in multivariate statistics. In this work, we develop an algorithm for solving this problem if additional information, x->0, is given. Applications to estimating solutions to integral equations of the first kind are given. }, author = {O{\textquoteright}Leary, Dianne P. and Rust,B. W.} } @article {16967, title = {An experimental comparison of a mouse and arrow-jump keys for an interactive encyclopedia}, journal = {International Journal of Man-Machine Studies}, volume = {24}, year = {1986}, month = {1986/01//}, pages = {29 - 45}, abstract = {This paper reports on an experiment which was conducted to examine relative merits of using a mouse or arrow-jump keys to select text in an interactive encyclopedia. Timed path traversais were performed by subjects using each device, and were followed by subjective questions. Personality and background of the subjects were recorded to see if those attributes would affect device preference and performance. The arrow-jump keys were found to have the quickest traversal times for paths with either short or long target distances. The subjective responses indicated that the arrow-jump method was overwhelmingly preferred over the mouse method. Personality type was not found to play a critical role.}, isbn = {0020-7373}, doi = {10.1016/S0020-7373(86)80038-4}, url = {http://www.sciencedirect.com/science/article/pii/S0020737386800384}, author = {Ewing,John and Mehrabanzad,Simin and Sheck,Scott and Ostroff,Dan and Shneiderman, Ben} } @article {15739, title = {Data-flow algorithms for parallel matrix computation}, journal = {Communications of the ACM}, volume = {28}, year = {1985}, month = {1985/08//}, pages = {840 - 853}, abstract = {In this article we develop some algorithms and tools for solving matrix problems on parallel processing computers. Operations are synchronized through data-flow alone, which makes global synchronization unnecessary and enables the algorithms to be implemented on machines with very simple operating systems and communication protocols. As examples, we present algorithms that form the main modules for solving Liapounov matrix equations. We compare this approach to wave front array processors and systolic arrays, and note its advantages in handling missized problems, in evaluating variations of algorithms or architectures, in moving algorithms from system to system, and in debugging parallel algorithms on sequential machines.}, isbn = {0001-0782}, doi = {10.1145/4021.4025}, url = {http://doi.acm.org/10.1145/4021.4025}, author = {O{\textquoteright}Leary, Dianne P. and Stewart, G.W.} } @article {14928, title = {A High-Level Interactive System for Designing VLSI Signal Processors}, volume = {ISR-TR-1985-7}, year = {1985}, month = {1985///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {This paper describes a high-level interactive system that can be used to generate VLSI designs for various operations in signal processing such as filtering, convolution and computing the discrete Fourier transform. The overall process is fully automated and requires that the user specifies only a few parameters such as operation, precision, size and architecture type. The built-in architectures are new digit-on-line bit-serial architectures that are based on recently derived fast algorithms for the above operations. The basic elements are compact and have a very small gate delay. We feel that our system will offer a flexible and easy to use tool that can produce practical designs which are easy to test, efficient and fast.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/4383}, author = {Owens,R. M. and JaJa, Joseph F.} } @article {15773, title = {Multi-splittings of Matrices and Parallel Solution of Linear Systems}, journal = {SIAM Journal on Algebraic and Discrete Methods}, volume = {6}, year = {1985}, month = {1985///}, pages = {630 - 640}, author = {O{\textquoteright}Leary, Dianne P. and White,R. E.} } @article {15046, title = {VLSI Architectures Based on the Small N Algorithms}, volume = {ISR-TR-1985-8}, year = {1985}, month = {1985///}, institution = {Institute for Systems Research, University of Maryland, College Park}, abstract = {Digital convolution and the discrete Fourier transform are basic operations whose computational requirements are of great importance in many applications. In this paper, we propose new types of VLSI architectures which are shown to be quite suitable to handle these operations. These architectures will result in fully pipelined bit-serial arrays which require no control units. Some preliminary implementations indicate a substantial speed-up gain over other existing designs.}, keywords = {Technical Report}, url = {http://drum.lib.umd.edu/handle/1903/4384}, author = {JaJa, Joseph F. and Owens,R. M.} } @article {15780, title = {Ordering Schemes for Parallel Processing of Certain Mesh Problems}, journal = {SIAM Journal on Scientific and Statistical Computing}, volume = {5}, year = {1984}, month = {1984///}, pages = {620 - 632}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15715, title = {Analysis of Relaxation Processes: the Two Node, Two Label Case}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {SMC-13}, year = {1983}, month = {1983///}, pages = {618 - 623}, author = {O{\textquoteright}Leary, Dianne P. and Peleg,Shmuel} } @article {15742, title = {Digital Image Compression by Outer Product Expansion}, journal = {Communications, IEEE Transactions on}, volume = {31}, year = {1983}, month = {1983/03//}, pages = {441 - 444}, abstract = {We approximate a digital image as a sum of outer products dxyTwheredis a real number but the vectorsxandyhave elements +1, -1, or 0 only. The expansion gives a least squares approximation. Work is proportional to the number of pixels; reconstruction involves only additions.}, keywords = {approximation;, coding;, image, Least-squares, Transform}, isbn = {0090-6778}, doi = {10.1109/TCOM.1983.1095823}, author = {O{\textquoteright}Leary, Dianne P. and Peleg,S.} } @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} } @article {15699, title = {A Discrete Newton Algorithm for Minimizing a Function of Many Variables}, journal = {Mathematical Programming}, volume = {23}, year = {1982}, month = {1982///}, pages = {20 - 33}, abstract = {A Newton-like method is presented for minimizing a function of n variables. It uses only function and gradient values and is a variant of the discrete Newton algorithm. This variant requires fewer operations than the standard method when n > 39, and storage is proportional to n rather than n.}, author = {O{\textquoteright}Leary, Dianne P.} } @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 {15710, title = {Algorithm 572: Solution of the Helmholtz Equation for the Dirichlet Problem on General Bounded Three-Dimensional Regions [D3]}, journal = {ACM Transactions on Mathematical Software}, volume = {7}, year = {1981}, month = {1981/06//}, pages = {239 - 246}, isbn = {0098-3500}, doi = {10.1145/355945.355954}, url = {http://doi.acm.org/10.1145/355945.355954}, author = {O{\textquoteright}Leary, Dianne P. and Widlund,Olof} } @article {15696, title = {A Bidiagonalization-Regularization Procedure for Large Scale Discretizations of Ill-Posed Problems}, journal = {SIAM Journal on Scientific and Statistical Computing}, volume = {2}, year = {1981}, month = {1981///}, pages = {474 - 489}, abstract = {In this paper, we consider ill-posed problems which discretize to linear least squares problems with matrices $K$ of high dimensions. The algorithm proposed uses $K$ only as an operator and does not need to explicitly store or modify it. A method related to one of Lanczos is used to project the problem onto a subspace for which $K$ is bidiagonal. It is then an easy matter to solve the projected problem by standard regularization techniques. These ideas are illustrated with some integral equations of the first kind with convolution kernels, and sample numerical results are given.}, keywords = {first kind integral equation, ill-posed problems, Lanczos algorithm, regularization}, doi = {10.1137/0902037}, url = {http://link.aip.org/link/?SCE/2/474/1}, author = {O{\textquoteright}Leary, Dianne P. and Simmons,John A.} } @article {15725, title = {Classification of Gynecologic Flow Cytometry Data: A Comparison of Methods}, journal = {Journal of Analytical and Quantitative Cytology}, volume = {3}, year = {1981}, month = {1981///}, pages = {135 - 142}, author = {O{\textquoteright}Leary,Timothy J and O{\textquoteright}Leary, Dianne P. and Habbersett,Mary C. and Herman,Chester J.} } @article {15816, title = {The block conjugate gradient algorithm and related methods}, journal = {Linear Algebra and its Applications}, volume = {29}, year = {1980}, month = {1980/02//}, pages = {293 - 322}, abstract = {The development of the Lanczos algorithm for finding eigenvalues of large sparse symmetric matrices was followed by that of block forms of the algorithm. In this paper, similar extensions are carried out for a relative of the Lanczos method, the conjugate gradient algorithm. The resulting block algorithms are useful for simultaneously solving multiple linear systems or for solving a single linear system in which the matrix has several separated eigenvalues or is not easily accessed on a computer. We develop a block biconjugate gradient algorithm for general matrices, and develop block conjugate gradient, minimum residual, and minimum error algorithms for symmetric semidefinite matrices. Bounds on the rate of convergence of the block conjugate gradient algorithm are presented, and issues related to computational implementation are discussed. Variants of the block conjugate gradient algorithm applicable to symmetric indefinite matrices are also developed.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(80)90247-5}, url = {http://www.sciencedirect.com/science/article/pii/0024379580902475}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15749, title = {Estimating Matrix Condition Numbers}, journal = {SIAM Journal on Scientific and Statistical Computing}, volume = {1}, year = {1980}, month = {1980///}, pages = {205 - 209}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15700, title = {A generalized conjugate gradient algorithm for solving a class of quadratic programming problems}, journal = {Linear Algebra and its Applications}, volume = {34}, year = {1980}, month = {1980/12//}, pages = {371 - 399}, abstract = {In this paper we apply matrix splitting techniques and a conjugate gradient algorithm to the problem of minimizing a convex quadratic form subject to upper and lower bounds on the variables. This method exploits sparsity structure in the matrix of the quadratic form. Choices of the splitting operator are discussed, and convergence results are established. We present the results of numerical experiments showing the effectiveness of the algorithm on free boundary problems for elliptic partial differential equations, and we give comparisons with other algorithms.}, isbn = {0024-3795}, doi = {10.1016/0024-3795(80)90173-1}, url = {http://www.sciencedirect.com/science/article/pii/0024379580901731}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15723, title = {Capacitance Matrix Methods for the Helmholtz Equation on General Three Dimensional Regions}, journal = {Mathematics of Computation}, volume = {33}, year = {1979}, month = {1979///}, pages = {849 - 879}, author = {O{\textquoteright}Leary, Dianne P. and Widlund,Olof} } @article {15734, title = {Conjugate Gradient Algorithms in the Solution of Optimization Problems for Nonlinear Elliptic Partial Differential Equations}, journal = {Computing}, volume = {22}, year = {1979}, month = {1979///}, pages = {59 - 77}, abstract = {Several variants of the conjugate gradient algorithm are discussed with emphasis on determining the parameters without performing line searches and on using splitting techniques to accelerate convergence. The splittings used here are related to the nonlinear SSOR algorithm. The behavior of the methods is illustrated on a discretization of a nonlinear elliptic partial differential boundary value problem, the minimal surface equation. A conjugate gradient algorithm with splittings is also developed for constrained minimization with upper and lower bounds on the variables, and the method is applied to the obstacle problem for the minimal surface equation.}, author = {O{\textquoteright}Leary, Dianne P.} } @article {15750, title = {Estimating the Largest Eigenvalue of a Positive Definite Matrix}, journal = {Mathematics of Computation}, volume = {33}, year = {1979}, month = {1979///}, pages = {1289 - 1292}, author = {O{\textquoteright}Leary, Dianne P. and Stewart, G.W. and Vandergraft,James S.} } @inbook {15767, title = {Linear programming Problems Arising from Partial Differential Equations}, booktitle = {Sparse Matrix Proceedings 1978Sparse Matrix Proceedings 1978}, year = {1979}, month = {1979///}, pages = {25 - 40}, publisher = {SIAM Press}, organization = {SIAM Press}, address = {Philadelphia}, author = {O{\textquoteright}Leary, Dianne P.}, editor = {Duff,Iain S. and Stewart, G.W.} } @article {15748, title = {Elastoplastic torsion by quadratic programming}, journal = {Computer Methods in Applied Mechanics and Engineering}, volume = {16}, year = {1978}, month = {1978/12//}, pages = {361 - 368}, abstract = {A finite element scheme (together with a conjugate gradient algorithm) is demonstrated to be a very effective method for analyzing general elastoplastic torsion of prismatic bars posed as quadratic programming problems. Solutions for bars with elliptical and Sokolovsky{\textquoteright}s oval cross-sections are presented. The solutions for the elliptical bars agree with the existing elastic and limit plastic solutions at the two extremes of the elastic-plastic range. The algorithm also reproduces accurately the Sokolovsky solution and extends it beyond its limitations.}, isbn = {0045-7825}, doi = {10.1016/0045-7825(78)90107-X}, url = {http://www.sciencedirect.com/science/article/pii/004578257890107X}, author = {O{\textquoteright}Leary, Dianne P. and Yang,Wei H.} } @article {15775, title = {Numerical Solution of Nonlinear Elliptic Partial Differential Equations by a Generalized Conjugate Gradient Method}, journal = {Computing}, volume = {19}, year = {1978}, month = {1978///}, pages = {321 - 339}, abstract = {We have studied previously a generalized conjugate gradient method for solving sparse positive-definite systems of linear equations arising from the discretization of elliptic partial-differential boundary-value problems. Here, extensions to the nonlinear case are considered. We split the original discretized operator into the sum of two operators, one of which corresponds to a more easily solvable system of equations, and accelerate the associated iteration based on this splitting by (nonlinear) conjugate gradients. The behavior of the method is illustrated for the minimal surface equation with splittings corresponding to nonlinear SSOR, to approximate factorization of the Jacobian matrix, and to elliptic operators suitable for use with fast direct methods. The results of numerical experiments are given as well for a mildy nonlinear example, for which, in the corresponding linear case, the finite termination property of the conjugate gradient algorithm is crucial.}, author = {Concus,Paul and Golub, Gene H. and O{\textquoteright}Leary, Dianne P.} } @inbook {15701, title = {A Generalized Conjugate Gradient Method for the Numerical Solution of Elliptic Partial Differential Equations}, booktitle = {Sparse Matrix ComputationsSparse Matrix Computations}, year = {1976}, month = {1976///}, pages = {309 - 332}, publisher = {Academic Press}, organization = {Academic Press}, address = {New York}, abstract = {We consider a generalized conjugate gradient method for solvingsparse, symmetric, positive-definite systems of linear equations, principally those arising from the discretization of boundary value problems for elliptic partial differential equations. The method is based on splitting off from the original coefficient matrix a symmetric, positive-definiteonethat corresponds to a more easily solvable system of equations, and then accelerating the associated iteration using conjugate gradients. Optimality and convergence properties are presented, and the relation to other methods is discussed. Several splittings for which the method seems particularly effective are also discussed, and for some, numerical examples are given }, author = {Concus,Paul and Golub, Gene H. and O{\textquoteright}Leary, Dianne P.}, editor = {Bunch,James R. and Rose,Donald J.} }